#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_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_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	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_Description	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_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_AccessionNumbers	i_HGNC_CCDS IDs	i_HGNC_CCDSIDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_DateModified	i_HGNC_DateNameChanged	i_HGNC_DateSymbolChanged	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_EnsemblGeneID	i_HGNC_EnsemblIDsuppliedbyEnsembl	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_Genefamilydescription	i_HGNC_HGNC ID	i_HGNC_HGNCID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_LocusGroup	i_HGNC_LocusType	i_HGNC_Name Synonyms	i_HGNC_NameSynonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_OMIMIDsuppliedbyNCBI	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_PreviousNames	i_HGNC_PreviousSymbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_PubmedIDs	i_HGNC_Record Type	i_HGNC_RecordType	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_RefSeqsuppliedbyNCBI	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UCSCIDsuppliedbyUCSC	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_UniProtIDsuppliedbyUniProt	i_HGNC_VEGA IDs	i_HGNC_VEGAIDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	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_Region	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_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_folddegenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_hg18_pos1coor	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_init_n_lod	i_init_t_lod	i_n_alt_count	i_n_alt_count_full	i_n_ref_count	i_n_ref_count_full	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_lod_fstar	i_t_lod_fstar_full	i_t_ref_count_full	i_tumor_f_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	tumor_f
CDH6	1004	broad.mit.edu	37	5	31317540	31317540	+	Missense_Mutation	SNP	C	C	T	rs202247793		TCGA-VD-A8KF-01A-11D-A39W-08	TCGA-VD-A8KF-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3c90a47-1079-4c13-b7f6-fbf3e05322e6	5f953c98-fc2c-4be3-a94c-ce5ce67df7e7	g.chr5:31317540C>T	ENST00000265071.2	+	10	1836	c.1571C>T	c.(1570-1572)tCg>tTg	p.S524L	CDH6_ENST00000514738.1_Missense_Mutation_p.S469L	NM_004932.3	NP_004923.1	P55285	CADH6_HUMAN	cadherin 6, type 2, K-cadherin (fetal kidney)	524	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)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(42)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						CACCAATTTTCGTTTTCCTTG	0.403																																						ENST00000265071.2											0			NS(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(42)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						c.(1570-1572)tCg>tTg	cadherin 6, type 2, K-cadherin (fetal kidney)						94.0	90.0	91.0					5																	31317540		2203	4300	6503	SO:0001583	missense	1004			adherens junction organization|cell junction assembly|homophilic cell adhesion	cytoplasm|integral to membrane|nucleus|plasma membrane	calcium ion binding	g.chr5:31317540C>T	D31784	D31784	CCDS3894.1	CCDS3894.1	5p13.3	2010-01-26			2010-01-26			ENSG00000113361	ENSG00000113361	ENSG00000113361	ENSG00000113361		"""Cadherins / Major cadherins"""	"""Cadherins / Major cadherins"""	1765	1765	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product	"""K-Cadherin"""	"""K-Cadherin"""	603007	603007						7743525, 10191097	7743525, 10191097	Standard	Standard	NM_004932	NM_004932		Approved		uc003jhe.2	uc003jhe.2	P55285	P55285	OTTHUMG00000090673	OTTHUMG00000090673	ENST00000265071.2:c.1571C>T	5.37:g.31317540C>T	ENSP00000265071:p.Ser524Leu		CDH6_ENST00000514738.1_Missense_Mutation_p.S469L	p.S524L	NM_004932.3	NP_004923.1	P55285	CADH6_HUMAN			10	1836	+			524	Cadherin 5.	A8K5H5|Q9BWS0	Missense_Mutation	SNP	ENST00000265071.2	37	c.1571C>T	CCDS3894.1	.	.	.	.	.	.	.	.	.	.	C	11.03	1.518873	0.27211	.	.	ENSG00000113361	ENST00000514738;ENST00000265071	T;T	0.54071	0.59;0.59	4.75	4.75	0.60458	4.75	4.75	0.60458	Cadherin (4);Cadherin-like (1);	0.365840	0.29300	N	0.012543	T	0.48241	0.1489	L	0.49126	1.545	0.49051	D	0.999747	B;B	0.30114	0.269;0.01	B;B	0.26094	0.066;0.008	T	0.43734	-0.9373	10	0.29301	T	0.29	.	18.3208	0.90238	0.0:1.0:0.0:0.0	.	524;524	P55285;P55285-2	CADH6_HUMAN;.	L	469;524	ENSP00000424843:S469L;ENSP00000265071:S524L	ENSP00000265071:S524L	S	+	2	0	0	CDH6	31353297	31353297	0.994000	0.37717	0.871000	0.34182	0.358000	0.29455	3.601000	0.54059	2.621000	0.88768	0.650000	0.86243	TCG		0.403	CDH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207355.2		-31.476309	3	3	128	128	NM_004932		4	7.340452	7.340452	152	0.025641	0	0	0	1	0	4	152	0.025641
KIAA2013	90231	broad.mit.edu	37	1	11983371	11983371	+	Silent	SNP	C	C	A			TCGA-VD-A8KF-01A-11D-A39W-08	TCGA-VD-A8KF-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3c90a47-1079-4c13-b7f6-fbf3e05322e6	5f953c98-fc2c-4be3-a94c-ce5ce67df7e7	g.chr1:11983371C>A	ENST00000376572.3	-	2	1394	c.1209G>T	c.(1207-1209)ggG>ggT	p.G403G	KIAA2013_ENST00000376576.3_Silent_p.G403G	NM_138346.2	NP_612355.1	Q8IYS2	K2013_HUMAN	KIAA2013	403						integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	7	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00149)|all_lung(284;0.00189)|Breast(348;0.00586)|Colorectal(325;0.0062)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0556)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.88e-06)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		TGGTGGCGTGCCCGCTGAAGC	0.647																																						ENST00000376572.3											0			endometrium(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	7						c.(1207-1209)ggG>ggT	KIAA2013						52.0	43.0	46.0					1																	11983371		2203	4300	6503	SO:0001819	synonymous_variant	90231				integral to membrane		g.chr1:11983371C>A	AB095933	AB095933	CCDS141.1	CCDS141.1	1p36.22	2011-02-09			2011-02-09			ENSG00000116685	ENSG00000116685	ENSG00000116685	ENSG00000116685				28513	28513	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product										12477932	12477932	Standard	Standard	NM_138346	NM_138346		Approved	MGC33867, RP5-1077B9.1	uc001atk.3	uc001atk.3	Q8IYS2	Q8IYS2	OTTHUMG00000002391	OTTHUMG00000002391	ENST00000376572.3:c.1209G>T	1.37:g.11983371C>A			KIAA2013_ENST00000376576.3_Silent_p.G403G	p.G403G	NM_138346.2	NP_612355.1	Q8IYS2	K2013_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.88e-06)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)	2	1394	-	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00149)|all_lung(284;0.00189)|Breast(348;0.00586)|Colorectal(325;0.0062)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0556)|Ovarian(437;0.0731)	403		Q5JXC1|Q8IVF8|Q8NDI7|Q9BSY1	Silent	SNP	ENST00000376572.3	37	c.1209G>T	CCDS141.1																																																																																									0.647	KIAA2013-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006858.1		2.904502	-19	-19	32	32	NM_138346		3	7.192323	7.192323	25	0.107143	1	0	0.115264	1	0.115264	3	25	0.107143
GNA11	2767	broad.mit.edu	37	19	3118942	3118942	+	Missense_Mutation	SNP	A	A	T			TCGA-VD-A8KF-01A-11D-A39W-08	TCGA-VD-A8KF-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3c90a47-1079-4c13-b7f6-fbf3e05322e6	5f953c98-fc2c-4be3-a94c-ce5ce67df7e7	g.chr19:3118942A>T	ENST00000078429.4	+	5	868	c.626A>T	c.(625-627)cAg>cTg	p.Q209L	AC005262.3_ENST00000587701.1_RNA|AC005262.2_ENST00000585980.1_RNA|GNA11_ENST00000586180.1_3'UTR	NM_002067.2	NP_002058.2	P29992	GNA11_HUMAN	guanine nucleotide binding protein (G protein), alpha 11 (Gq class)	209					action potential (GO:0001508)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|cellular response to pH (GO:0071467)|developmental pigmentation (GO:0048066)|heart development (GO:0007507)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|platelet activation (GO:0030168)|regulation of melanocyte differentiation (GO:0045634)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)|type 2A serotonin receptor binding (GO:0031826)	p.Q209L(80)|p.Q209P(2)		endometrium(2)|eye(132)|kidney(1)|large_intestine(2)|lung(1)|meninges(5)|ovary(1)|prostate(1)|skin(16)	161		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.79e-05)|OV - Ovarian serous cystadenocarcinoma(105;2.68e-113)|Epithelial(107;1.22e-111)|all cancers(105;5.78e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00141)|STAD - Stomach adenocarcinoma(1328;0.181)		GTGGGGGGCCAGCGGTCGGAG	0.612			Mis		uveal melanoma																																	ENST00000078429.4		Dom	yes		19	19p13.3	2767	"""guanine nucleotide binding protein (G protein), alpha 11 (Gq class)"""		E	82	Substitution - Missense(82)	eye(69)|skin(8)|meninges(5)	endometrium(2)|eye(132)|kidney(1)|large_intestine(2)|lung(1)|meninges(5)|ovary(1)|prostate(1)|skin(16)	161						c.(625-627)cAg>cTg	guanine nucleotide binding protein (G protein), alpha 11 (Gq class)						104.0	89.0	94.0					19																	3118942		2203	4300	6503	SO:0001583	missense	2767			activation of phospholipase C activity by dopamine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|platelet activation|protein ADP-ribosylation|regulation of action potential	cytoplasm|heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity	g.chr19:3118942A>T	AF493900	AF493900	CCDS12103.1	CCDS12103.1	19p13.3	2014-02-04			2014-02-04			ENSG00000088256	ENSG00000088256	ENSG00000088256	ENSG00000088256				4379	4379	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			139313	139313	"""hypocalciuric hypercalcemia 2"""	HHC2	"""hypocalciuric hypercalcemia 2"""	HHC2		1302014, 23802516	1302014, 23802516	Standard	Standard	NM_002067	NM_002067		Approved	FBH, FBH2, FHH2	uc002lxd.3	uc002lxd.3	P29992	P29992	OTTHUMG00000180631	OTTHUMG00000180631	ENST00000078429.4:c.626A>T	19.37:g.3118942A>T	ENSP00000078429:p.Gln209Leu		AC005262.3_ENST00000587701.1_RNA|GNA11_ENST00000586180.1_3'UTR	p.Q209L	NM_002067.2	NP_002058.2	P29992	GNA11_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (162;6.79e-05)|OV - Ovarian serous cystadenocarcinoma(105;2.68e-113)|Epithelial(107;1.22e-111)|all cancers(105;5.78e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00141)|STAD - Stomach adenocarcinoma(1328;0.181)	5	868	+		Hepatocellular(1079;0.137)	209		O15109|Q14350|Q6IB00	Missense_Mutation	SNP	ENST00000078429.4	37	c.626A>T	CCDS12103.1	.	.	.	.	.	.	.	.	.	.	.	15.05	2.718086	0.48622	.	.	ENSG00000088256	ENST00000078429	D	0.91237	-2.81	3.26	3.26	0.37387	3.26	3.26	0.37387	.	0.000000	0.64402	U	0.000006	D	0.96950	0.9004	H	0.99357	4.53	0.80722	D	1	D	0.59767	0.986	D	0.68483	0.958	D	0.96823	0.9605	10	0.87932	D	0	.	10.7338	0.46113	1.0:0.0:0.0:0.0	.	209	P29992	GNA11_HUMAN	L	209	ENSP00000078429:Q209L	ENSP00000078429:Q209L	Q	+	2	0	0	GNA11	3069942	3069942	1.000000	0.71417	0.438000	0.26821	0.027000	0.11550	9.104000	0.94239	1.256000	0.44068	0.379000	0.24179	CAG		0.612	GNA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452261.2		53.474156	-13	-13	68	68	NM_002067		17	53.480694	53.480694	16	0.515152	0	0	0	1	0	17	16	0.515152
ATAD3A	55210	broad.mit.edu	37	1	1463226	1463226	+	Missense_Mutation	SNP	G	G	A			TCGA-VD-A8KF-01A-11D-A39W-08	TCGA-VD-A8KF-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3c90a47-1079-4c13-b7f6-fbf3e05322e6	5f953c98-fc2c-4be3-a94c-ce5ce67df7e7	g.chr1:1463226G>A	ENST00000378755.5	+	14	1727	c.1633G>A	c.(1633-1635)Gcc>Acc	p.A545T	ATAD3A_ENST00000536055.1_Missense_Mutation_p.A418T|ATAD3A_ENST00000378756.3_Missense_Mutation_p.A497T	NM_018188.3	NP_060658.3	Q9NVI7	ATD3A_HUMAN	ATPase family, AAA domain containing 3A	545					cell growth (GO:0016049)|negative regulation of apoptotic process (GO:0043066)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)			endometrium(4)|kidney(6)|large_intestine(1)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	20	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.12e-36)|OV - Ovarian serous cystadenocarcinoma(86;2.18e-22)|Colorectal(212;0.000164)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00233)|BRCA - Breast invasive adenocarcinoma(365;0.00469)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0347)|Lung(427;0.147)		TCTTAAGCCGGCCACAGAAGG	0.582																																						ENST00000378755.5											0			endometrium(4)|kidney(6)|large_intestine(1)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	20						c.(1633-1635)Gcc>Acc	ATPase family, AAA domain containing 3A						93.0	100.0	98.0					1																	1463226		2203	4300	6503	SO:0001583	missense	55210					ATP binding|nucleoside-triphosphatase activity|protein binding	g.chr1:1463226G>A	AK025865	AK025865	CCDS31.1, CCDS53259.1, CCDS53260.1	CCDS31.1, CCDS53259.1, CCDS53260.1	1p36.33	2010-04-21		2007-02-08	2010-04-21		2007-02-08	ENSG00000197785	ENSG00000197785	ENSG00000197785	ENSG00000197785		"""ATPases / AAA-type"""	"""ATPases / AAA-type"""	25567	25567	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			612316	612316						12477932	12477932	Standard	Standard	NM_018188	NM_018188		Approved	FLJ10709	uc001afz.2	uc001afz.2	Q9NVI7	Q9NVI7	OTTHUMG00000000575	OTTHUMG00000000575	ENST00000378755.5:c.1633G>A	1.37:g.1463226G>A	ENSP00000368030:p.Ala545Thr		ATAD3A_ENST00000536055.1_Missense_Mutation_p.A418T|ATAD3A_ENST00000378756.3_Missense_Mutation_p.A497T	p.A545T	NM_018188.3	NP_060658.3	Q9NVI7	ATD3A_HUMAN		Epithelial(90;1.12e-36)|OV - Ovarian serous cystadenocarcinoma(86;2.18e-22)|Colorectal(212;0.000164)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00233)|BRCA - Breast invasive adenocarcinoma(365;0.00469)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0347)|Lung(427;0.147)	14	1727	+	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)	545		B3KPB3|D2K8Q1|G3V1I6|Q5SV23|Q8N275|Q96A50	Missense_Mutation	SNP	ENST00000378755.5	37	c.1633G>A	CCDS31.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	16.34|16.34	3.095164|3.095164	0.56075|0.56075	.|.	.|.	ENSG00000197785|ENSG00000197785	ENST00000378756;ENST00000378755;ENST00000378759;ENST00000536055;ENST00000400830|ENST00000339113	D;D;D|.	0.94650|.	-3.24;-3.11;-3.48|.	4.15|4.15	4.15|4.15	0.48705|0.48705	4.15|4.15	4.15|4.15	0.48705|0.48705	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.74366|0.74366	0.3707|0.3707	M|M	0.76002|0.76002	2.32|2.32	0.80722|0.80722	D|D	1|1	B;B|.	0.32731|.	0.382;0.382|.	B;B|.	0.35607|.	0.15;0.206|.	T|T	0.76318|0.76318	-0.3003|-0.3003	10|5	0.38643|.	T|.	0.18|.	.|.	15.6717|15.6717	0.77283|0.77283	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	497;545|.	D2K8Q1;Q9NVI7|.	.;ATD3A_HUMAN|.	T|D	497;545;174;418;160|482	ENSP00000368031:A497T;ENSP00000368030:A545T;ENSP00000439290:A418T|.	ENSP00000368030:A545T|.	A|G	+|+	1|2	0|0	0|0	ATAD3A|ATAD3A	1453089|1453089	1453089|1453089	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.939000|0.939000	0.58152|0.58152	9.465000|9.465000	0.97660|0.97660	2.157000|2.157000	0.67596|0.67596	0.556000|0.556000	0.70494|0.70494	GCC|GGC		0.582	ATAD3A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000001365.1		-3.917653	-16	-16	75	75	NM_018188		3	6.479106	6.479106	48	0.058824	0	0	0	1	0	3	48	0.058824
PCDH9	5101	broad.mit.edu	37	13	67800083	67800083	+	Silent	SNP	G	G	A			TCGA-VD-A8KF-01A-11D-A39W-08	TCGA-VD-A8KF-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3c90a47-1079-4c13-b7f6-fbf3e05322e6	5f953c98-fc2c-4be3-a94c-ce5ce67df7e7	g.chr13:67800083G>A	ENST00000377865.2	-	1	2624	c.2490C>T	c.(2488-2490)atC>atT	p.I830I	PCDH9_ENST00000544246.1_Silent_p.I830I|PCDH9_ENST00000328454.5_Silent_p.I830I|PCDH9_ENST00000377861.3_Silent_p.I830I|PCDH9_ENST00000456367.1_Silent_p.I830I			Q9HC56	PCDH9_HUMAN	protocadherin 9	830					forebrain development (GO:0030900)|homophilic cell adhesion (GO:0007156)	cell-cell contact zone (GO:0044291)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(33)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	103		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)		CGGTGACGAAGATCACAACAA	0.507																																						ENST00000544246.1											0			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(33)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	103						c.(2488-2490)atC>atT	protocadherin 9						200.0	176.0	184.0					13																	67800083		2203	4300	6503	SO:0001819	synonymous_variant	5101			homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	g.chr13:67800083G>A	AF169692	AF169692	CCDS9443.1, CCDS9444.1	CCDS9443.1, CCDS9444.1	13q21.32	2010-02-22			2010-02-22			ENSG00000184226	ENSG00000184226	ENSG00000184226	ENSG00000184226		"""Cadherins / Protocadherins : Non-clustered"""	"""Cadherins / Protocadherins : Non-clustered"""	8661	8661	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			603581	603581						9787079	9787079	Standard	Standard	NM_020403	NM_020403		Approved		uc001vik.3	uc001vik.3	Q9HC56	Q9HC56	OTTHUMG00000017040	OTTHUMG00000017040	ENST00000377865.2:c.2490C>T	13.37:g.67800083G>A			PCDH9_ENST00000456367.1_Silent_p.I830I|PCDH9_ENST00000377865.2_Silent_p.I830I|PCDH9_ENST00000377861.3_Silent_p.I830I|PCDH9_ENST00000328454.5_Silent_p.I830I	p.I830I	NM_203487.2	NP_982354.1	Q9HC56	PCDH9_HUMAN		GBM - Glioblastoma multiforme(99;0.00819)	2	3181	-		Hepatocellular(98;0.0906)|Breast(118;0.107)	830		A2A6U1|Q5VT83|Q7Z3U0|Q8N3K7	Silent	SNP	ENST00000377865.2	37	c.2490C>T	CCDS9444.1																																																																																									0.507	PCDH9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276387.1		163.400063	-13	-13	90	90	NM_203487		52	163.419333	163.419333	49	0.514851	0	0	0	1	0	52	49	0.514851
LRRC15	131578	broad.mit.edu	37	3	194081424	194081424	+	Missense_Mutation	SNP	G	G	T			TCGA-VD-A8KF-01A-11D-A39W-08	TCGA-VD-A8KF-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3c90a47-1079-4c13-b7f6-fbf3e05322e6	5f953c98-fc2c-4be3-a94c-ce5ce67df7e7	g.chr3:194081424G>T	ENST00000347624.3	-	2	434	c.349C>A	c.(349-351)Ccc>Acc	p.P117T	LRRC15_ENST00000428839.1_Missense_Mutation_p.P123T|LRRC15_ENST00000439944.2_Missense_Mutation_p.P123T	NM_130830.4	NP_570843.2	Q8TF66	LRC15_HUMAN	leucine rich repeat containing 15	117					negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|positive regulation of cell migration (GO:0030335)|receptor-mediated virion attachment to host cell (GO:0046813)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	collagen binding (GO:0005518)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)			biliary_tract(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(20)|ovary(4)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.94e-05)		AGGCCGATGGGCAGAACCTGC	0.602																																						ENST00000347624.3											0			biliary_tract(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(20)|ovary(4)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						c.(349-351)Ccc>Acc	leucine rich repeat containing 15						53.0	56.0	55.0					3																	194081424		2203	4300	6503	SO:0001583	missense	131578				integral to membrane		g.chr3:194081424G>T	AB071037	AB071037	CCDS3306.1, CCDS46984.1	CCDS3306.1, CCDS46984.1	3q29	2008-02-05			2008-02-05			ENSG00000172061	ENSG00000172061	ENSG00000172061	ENSG00000172061				20818	20818	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product										12923058	12923058	Standard	Standard	NM_001135057	NM_001135057		Approved	LIB	uc003ftu.3	uc003ftu.3	Q8TF66	Q8TF66	OTTHUMG00000156048	OTTHUMG00000156048	ENST00000347624.3:c.349C>A	3.37:g.194081424G>T	ENSP00000306276:p.Pro117Thr		LRRC15_ENST00000428839.1_Missense_Mutation_p.P123T|LRRC15_ENST00000439944.2_Missense_Mutation_p.P123T	p.P117T	NM_130830.4	NP_570843.2	Q8TF66	LRC15_HUMAN	OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.94e-05)	2	434	-	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		117		Q495Q6|Q7RTN7	Missense_Mutation	SNP	ENST00000347624.3	37	c.349C>A	CCDS3306.1	.	.	.	.	.	.	.	.	.	.	G	19.64	3.866379	0.72065	.	.	ENSG00000172061	ENST00000347624;ENST00000439944;ENST00000428839	T;T;T	0.59224	0.28;3.06;3.06	4.8	4.8	0.61643	4.8	4.8	0.61643	.	0.085123	0.50627	D	0.000109	T	0.78097	0.4230	M	0.81614	2.55	0.54753	D	0.999982	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.984	T	0.80612	-0.1305	10	0.59425	D	0.04	.	18.7514	0.91818	0.0:0.0:1.0:0.0	.	117;123	Q8TF66;Q8TF66-2	LRC15_HUMAN;.	T	117;123;123	ENSP00000306276:P117T;ENSP00000389128:P123T;ENSP00000413707:P123T	ENSP00000306276:P117T	P	-	1	0	0	LRRC15	195562719	195562719	1.000000	0.71417	0.997000	0.53966	0.852000	0.48524	5.249000	0.65427	2.602000	0.87976	0.462000	0.41574	CCC		0.602	LRRC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342858.2		65.988172	-14	-14	49	49			19	68.036559	68.036559	1	0.950000	1	0	5.3912e-06	1	6.16138e-06	19	1	0.95
ZFC3H1	196441	broad.mit.edu	37	12	72057131	72057131	+	Nonsense_Mutation	SNP	G	G	T			TCGA-VD-A8KF-01A-11D-A39W-08	TCGA-VD-A8KF-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3c90a47-1079-4c13-b7f6-fbf3e05322e6	5f953c98-fc2c-4be3-a94c-ce5ce67df7e7	g.chr12:72057131G>T	ENST00000378743.3	-	1	618	c.260C>A	c.(259-261)tCa>tAa	p.S87*	ZFC3H1_ENST00000548100.1_Nonsense_Mutation_p.S87*|ZFC3H1_ENST00000552037.1_Nonsense_Mutation_p.S87*|THAP2_ENST00000547843.1_5'Flank|ZFC3H1_ENST00000549407.1_5'UTR|THAP2_ENST00000308086.2_5'UTR	NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing	87	Ser-rich.				RNA processing (GO:0006396)	extracellular space (GO:0005615)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						CCGCGAGCGTGAGAAATTCCT	0.657											OREG0021993	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000378743.3											0			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						c.(259-261)tCa>tAa	zinc finger, C3H1-type containing						59.0	66.0	64.0					12																	72057131		1969	4152	6121	SO:0001587	stop_gained	196441			RNA processing	intracellular	metal ion binding	g.chr12:72057131G>T	AB011118	AB011118	CCDS41813.1	CCDS41813.1	12q21.1	2013-01-25	2008-10-01	2008-10-01	2013-01-25	2008-10-01	2008-10-01		ENSG00000133858		ENSG00000133858		"""Zinc finger, C3H1-type containing"""	"""Zinc finger, C3H1-type containing"""	28328	28328	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product					"""proline/serine-rich coiled-coil 2"", ""coiled-coil domain containing 131"""	PSRC2, CCDC131	"""proline/serine-rich coiled-coil 2"", ""coiled-coil domain containing 131"""	PSRC2, CCDC131		9628581	9628581	Standard	Standard	NM_144982	NM_144982		Approved	MGC23401, KIAA0546	uc001swo.2	uc001swo.2	O60293	O60293	OTTHUMG00000169545	OTTHUMG00000169545	ENST00000378743.3:c.260C>A	12.37:g.72057131G>T	ENSP00000368017:p.Ser87*	1134	ZFC3H1_ENST00000552037.1_Nonsense_Mutation_p.S87*|ZFC3H1_ENST00000548100.1_Nonsense_Mutation_p.S87*|ZFC3H1_ENST00000549407.1_5'UTR|THAP2_ENST00000308086.2_5'UTR	p.S87*	NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN			1	618	-			87	Ser-rich.	Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	Nonsense_Mutation	SNP	ENST00000378743.3	37	c.260C>A	CCDS41813.1	.	.	.	.	.	.	.	.	.	.	G	39	7.359003	0.98235	.	.	ENSG00000133858	ENST00000378743;ENST00000548100;ENST00000552037	.	.	.	4.09	3.18	0.36537	4.09	3.18	0.36537	.	0.118844	0.34362	N	0.004034	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.5178	0.56042	0.0:0.168:0.832:0.0	.	.	.	.	X	87	.	ENSP00000368017:S87X	S	-	2	0	0	ZFC3H1	70343398	70343398	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.122000	0.50446	1.048000	0.40298	0.455000	0.32223	TCA		0.657	ZFC3H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404751.1		122.463607	-10	-10	102	102	NM_144982		41	122.657448	122.657448	50	0.450549	1	0	3.4345e-17	1	4.57933e-17	41	50	0.450549
MRPS18C	51023	broad.mit.edu	37	4	84377254	84377254	+	Silent	SNP	C	C	T	rs141532727	byFrequency	TCGA-VD-A8KF-01A-11D-A39W-08	TCGA-VD-A8KF-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3c90a47-1079-4c13-b7f6-fbf3e05322e6	5f953c98-fc2c-4be3-a94c-ce5ce67df7e7	g.chr4:84377254C>T	ENST00000295491.4	+	1	137	c.24C>T	c.(22-24)tgC>tgT	p.C8C	MRPS18C_ENST00000507349.1_Silent_p.C8C|HELQ_ENST00000510985.1_5'Flank|MRPS18C_ENST00000507019.1_Silent_p.C8C|HELQ_ENST00000440639.2_5'Flank|HELQ_ENST00000295488.3_5'Flank	NM_016067.2	NP_057151.1	Q9Y3D5	RT18C_HUMAN	mitochondrial ribosomal protein S18C	8					translation (GO:0006412)	mitochondrial small ribosomal subunit (GO:0005763)	structural constituent of ribosome (GO:0003735)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)	5		Hepatocellular(203;0.114)				TTGCTGTTTGCGGTGGTCTAG	0.552																																						ENST00000295491.4											0			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)	5						c.(22-24)tgC>tgT	mitochondrial ribosomal protein S18C	C		4,4402	8.1+/-20.4	0,4,2199	190.0	195.0	193.0		24	-0.0	0.0	4	dbSNP_134	193	0,8600		0,0,4300	no	coding-synonymous	MRPS18C	NM_016067.2		0,4,6499	TT,TC,CC		0.0,0.0908,0.0308		8/143	84377254	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	51023			translation	mitochondrial small ribosomal subunit	structural constituent of ribosome	g.chr4:84377254C>T			CCDS3604.1, CCDS75159.1	CCDS3604.1, CCDS75159.1	4q21.21-q21.23	2012-09-13			2012-09-13			ENSG00000163319	ENSG00000163319	ENSG00000163319	ENSG00000163319		"""Mitochondrial ribosomal proteins / small subunits"""	"""Mitochondrial ribosomal proteins / small subunits"""	16633	16633	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			611983	611983						11279123, 10810093	11279123, 10810093	Standard	Standard	XM_005263043	XM_005263043		Approved	MRPS18-1, CGI-134, FLJ11146, FLJ22967	uc003hor.4	uc003hor.4	Q9Y3D5	Q9Y3D5	OTTHUMG00000130430	OTTHUMG00000130430	ENST00000295491.4:c.24C>T	4.37:g.84377254C>T			MRPS18C_ENST00000507349.1_Silent_p.C8C|MRPS18C_ENST00000507019.1_Silent_p.C8C	p.C8C	NM_016067.2	NP_057151.1	Q9Y3D5	RT18C_HUMAN			1	137	+		Hepatocellular(203;0.114)	8			Silent	SNP	ENST00000295491.4	37	c.24C>T	CCDS3604.1	.	.	.	.	.	.	.	.	.	.	C	5.334	0.246952	0.10130	9.08E-4	0.0	ENSG00000163319	ENST00000509970	.	.	.	4.72	-0.0422	0.13864	4.72	-0.0422	0.13864	.	.	.	.	.	T	0.23451	0.0567	.	.	.	0.19775	N	0.999951	.	.	.	.	.	.	T	0.25537	-1.0129	4	.	.	.	0.0289	4.1526	0.10245	0.0:0.4496:0.1685:0.3819	.	.	.	.	W	7	.	.	R	+	1	2	2	MRPS18C	84596278	84596278	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.225000	0.02956	0.037000	0.15575	-0.137000	0.14449	CGG		0.552	MRPS18C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252820.2		-35.147103	-38	-38	178	178			4	7.209012	7.209012	164	0.023810	0	0	0	1	0	4	164	0.02381
SAMD15	161394	broad.mit.edu	37	14	77857522	77857522	+	Missense_Mutation	SNP	C	C	A			TCGA-VD-A8KF-01A-11D-A39W-08	TCGA-VD-A8KF-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3c90a47-1079-4c13-b7f6-fbf3e05322e6	5f953c98-fc2c-4be3-a94c-ce5ce67df7e7	g.chr14:77857522C>A	ENST00000216471.4	+	3	2246	c.1960C>A	c.(1960-1962)Cag>Aag	p.Q654K	SAMD15_ENST00000533095.2_Missense_Mutation_p.Q68K	NM_001010860.1	NP_001010860.1	Q9P1V8	SAM15_HUMAN	sterile alpha motif domain containing 15	654										breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						AGCAGGATTACAGGATTATGC	0.388																																						ENST00000216471.4											0			breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						c.(1960-1962)Cag>Aag	sterile alpha motif domain containing 15						82.0	82.0	82.0					14																	77857522		2203	4300	6503	SO:0001583	missense	161394						g.chr14:77857522C>A	AK093282	AK093282	CCDS32126.1	CCDS32126.1	14q24.3	2013-01-10	2010-10-20	2010-10-20	2013-01-10	2010-10-20	2010-10-20	ENSG00000100583	ENSG00000100583	ENSG00000100583	ENSG00000100583		"""Sterile alpha motif (SAM) domain containing"""	"""Sterile alpha motif (SAM) domain containing"""	18631	18631	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product					"""family with sequence similarity 15, member A"", ""chromosome 14 open reading frame 174"""	FAM15A, C14orf174	"""family with sequence similarity 15, member A"", ""chromosome 14 open reading frame 174"""	FAM15A, C14orf174				Standard	Standard	XM_006720069	XM_006720069		Approved	FLJ35963	uc001xtq.1	uc001xtq.1	Q9P1V8	Q9P1V8			ENST00000216471.4:c.1960C>A	14.37:g.77857522C>A	ENSP00000216471:p.Gln654Lys		SAMD15_ENST00000533095.2_Missense_Mutation_p.Q68K	p.Q654K	NM_001010860.1	NP_001010860.1	Q9P1V8	SAM15_HUMAN			3	2246	+			654		Q2M3P3	Missense_Mutation	SNP	ENST00000216471.4	37	c.1960C>A	CCDS32126.1	.	.	.	.	.	.	.	.	.	.	C	12.29	1.892353	0.33442	.	.	ENSG00000100583	ENST00000533095;ENST00000216471	T	0.19250	2.16	5.64	-3.32	0.04973	5.64	-3.32	0.04973	.	.	.	.	.	T	0.14830	0.0358	L	0.36672	1.1	0.09310	N	1	P	0.44734	0.842	B	0.35114	0.196	T	0.25745	-1.0123	9	0.59425	D	0.04	-5.6079	14.7721	0.69688	0.0:0.291:0.6408:0.0682	.	654	Q9P1V8	SAM15_HUMAN	K	68;654	ENSP00000216471:Q654K	ENSP00000216471:Q654K	Q	+	1	0	0	SAMD15	76927275	76927275	0.947000	0.32204	0.928000	0.36995	0.702000	0.40608	-0.176000	0.09811	-0.206000	0.10203	-0.182000	0.12963	CAG		0.388	SAMD15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394587.2		77.801269	-18	-18	47	47	NM_001010860		24	77.820117	77.820117	22	0.521739	1	0	9.57634e-11	1	1.17863e-10	24	22	0.521739
LGALS9	3965	broad.mit.edu	37	17	25974373	25974373	+	Missense_Mutation	SNP	G	G	A	rs149003631		TCGA-VD-A8KF-01A-11D-A39W-08	TCGA-VD-A8KF-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3c90a47-1079-4c13-b7f6-fbf3e05322e6	5f953c98-fc2c-4be3-a94c-ce5ce67df7e7	g.chr17:25974373G>A	ENST00000395473.2	+	10	2304	c.836G>A	c.(835-837)cGc>cAc	p.R279H	LGALS9_ENST00000413914.2_Intron|LGALS9_ENST00000310394.5_Missense_Mutation_p.R235H|LGALS9_ENST00000313648.6_Intron|LGALS9_ENST00000302228.5_Missense_Mutation_p.R247H	NM_009587.2	NP_033665.1	O00182	LEG9_HUMAN	lectin, galactoside-binding, soluble, 9	279	Galectin 2. {ECO:0000255|PROSITE- ProRule:PRU00639}.				positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)|galactose binding (GO:0005534)|signal transducer activity (GO:0004871)			endometrium(3)|large_intestine(2)|lung(12)|skin(1)	18	Lung NSC(42;0.0103)		BRCA - Breast invasive adenocarcinoma(3;0.0141)	UCEC - Uterine corpus endometrioid carcinoma (53;0.155)		GCTGTGGTCCGCAACACCCAG	0.587																																					Melanoma(106;677 1527 28724 29571 46552)|Ovarian(193;263 2088 2118 29005 43023)	ENST00000395473.2											0			endometrium(3)|large_intestine(2)|lung(12)|skin(1)	18						c.(835-837)cGc>cAc	lectin, galactoside-binding, soluble, 9	G	HIS/ARG,HIS/ARG	0,4406		0,0,2203	92.0	87.0	88.0		740,836	3.4	1.0	17	dbSNP_134	88	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	LGALS9	NM_002308.3,NM_009587.2	29,29	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging,probably-damaging	247/324,279/356	25974373	2,13004	2203	4300	6503	SO:0001583	missense	3965			positive regulation of I-kappaB kinase/NF-kappaB cascade	cytoplasm|extracellular region	galactose binding|signal transducer activity	g.chr17:25974373G>A	AB006782	AB006782	CCDS11222.1, CCDS32592.1	CCDS11222.1, CCDS32592.1	17q11.2	2013-03-28	2008-07-25		2013-03-28	2008-07-25		ENSG00000168961	ENSG00000168961	ENSG00000168961	ENSG00000168961		"""Lectins, galactoside-binding"""	"""Lectins, galactoside-binding"""	6570	6570	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product	"""galectin 9"""	"""galectin 9"""	601879	601879						9045665	9045665	Standard	Standard	NM_009587	NM_009587		Approved	LGALS9A	uc002gzp.3	uc002gzp.3	O00182	O00182	OTTHUMG00000179831	OTTHUMG00000179831	ENST00000395473.2:c.836G>A	17.37:g.25974373G>A	ENSP00000378856:p.Arg279His		LGALS9_ENST00000413914.2_Intron|LGALS9_ENST00000313648.6_Intron|LGALS9_ENST00000310394.5_Missense_Mutation_p.R235H|LGALS9_ENST00000302228.5_Missense_Mutation_p.R247H	p.R279H	NM_009587.2	NP_033665.1	O00182	LEG9_HUMAN	BRCA - Breast invasive adenocarcinoma(3;0.0141)	UCEC - Uterine corpus endometrioid carcinoma (53;0.155)	10	2304	+	Lung NSC(42;0.0103)		279	Galectin 2.	A7VJG6|O14532|O75028|Q3B8N1|Q53FQ0|Q9NQ58	Missense_Mutation	SNP	ENST00000395473.2	37	c.836G>A	CCDS11222.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.268327	0.80469	0.0	2.33E-4	ENSG00000168961	ENST00000395473;ENST00000302228;ENST00000310394	T;T;T	0.14144	2.53;2.53;2.53	4.36	3.38	0.38709	4.36	3.38	0.38709	Concanavalin A-like lectin/glucanase (1);Galectin, carbohydrate recognition domain (4);Concanavalin A-like lectin/glucanase, subgroup (1);	0.000000	0.85682	D	0.000000	T	0.48786	0.1519	H	0.97131	3.945	0.80722	D	1	D;D;D	0.89917	1.0;0.993;0.996	D;P;P	0.75484	0.986;0.878;0.894	T	0.63102	-0.6712	10	0.72032	D	0.01	.	11.312	0.49368	0.0:0.0:0.8163:0.1837	.	190;247;279	B4DJD7;Q3B8N1;O00182	.;.;LEG9_HUMAN	H	279;247;235	ENSP00000378856:R279H;ENSP00000306228:R247H;ENSP00000312259:R235H	ENSP00000306228:R247H	R	+	2	0	0	LGALS9	22998500	22998500	0.998000	0.40836	1.000000	0.80357	0.880000	0.50808	5.359000	0.66074	1.036000	0.39998	0.467000	0.42956	CGC		0.587	LGALS9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255583.1		-4.517596	-21	-21	78	78	NM_009587		3	6.42779	6.427790	50	0.056604	0	0	0	1	0	3	50	0.056604
FAM86HP	729375	broad.mit.edu	37	3	129823181	129823181	+	RNA	DEL	A	A	-			TCGA-VD-A8KF-01A-11D-A39W-08	TCGA-VD-A8KF-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3c90a47-1079-4c13-b7f6-fbf3e05322e6	5f953c98-fc2c-4be3-a94c-ce5ce67df7e7	g.chr3:129823181delA	ENST00000500074.2	-	0	257									family with sequence similarity 86, member H, pseudogene																		CAGCAATCAGAAAACAAGTGG	0.522																																						ENST00000500074.2											0																																																0						g.chr3:129823181delA					3q22.1	2011-07-01			2011-07-01			ENSG00000253540	ENSG00000253540	ENSG00000253540	ENSG00000253540				42359	42359	pseudogene	pseudogene	pseudogene	pseudogene												Standard	Standard	NR_024252	NR_024252		Approved		uc011ble.1	uc011ble.1			OTTHUMG00000159796	OTTHUMG00000159796		3.37:g.129823181delA											0	257	-						RNA	DEL	ENST00000500074.2	37																																																																																											0.522	FAM86HP-002	PUTATIVE	basic	processed_transcript	pseudogene	OTTHUMT00000358348.1	.	.	-1	-1	4	4			2			4	0.33						2	4	0.33
ITGB4	3691	broad.mit.edu	37	17	73749891	73749891	+	Frame_Shift_Del	DEL	T	T	-			TCGA-VD-A8KF-01A-11D-A39W-08	TCGA-VD-A8KF-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3c90a47-1079-4c13-b7f6-fbf3e05322e6	5f953c98-fc2c-4be3-a94c-ce5ce67df7e7	g.chr17:73749891delT	ENST00000200181.3	+	33	4341	c.4154delT	c.(4153-4155)ctgfs	p.L1385fs	ITGB4_ENST00000339591.3_Intron|ITGB4_ENST00000579662.1_Intron|GALK1_ENST00000225614.2_Intron|ITGB4_ENST00000449880.2_Intron|ITGB4_ENST00000450894.3_Intron	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	1385					amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			GAGCTGGACCTGCGGCGCGTC	0.776																																						ENST00000200181.3											0			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43						c.(4153-4155)ctgfs	integrin, beta 4						8.0	10.0	9.0					17																	73749891		2169	4252	6421	SO:0001589	frameshift_variant	3691			cell communication|cell motility|cell-matrix adhesion|hemidesmosome assembly|integrin-mediated signaling pathway|multicellular organismal development|response to wounding	cell leading edge|cell surface|hemidesmosome|integrin complex	protein binding|receptor activity	g.chr17:73749891delT			CCDS11727.1, CCDS32736.1, CCDS58599.1	CCDS11727.1, CCDS32736.1, CCDS58599.1	17q25.1	2013-09-19			2013-09-19			ENSG00000132470	ENSG00000132470	ENSG00000132470	ENSG00000132470		"""CD molecules"", ""Integrins"", ""Fibronectin type III domain containing"""	"""CD molecules"", ""Integrins"", ""Fibronectin type III domain containing"""	6158	6158	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			147557	147557						2070796	2070796	Standard	Standard	XM_005257309	XM_005257309		Approved	CD104	uc002jpg.3	uc002jpg.3	P16144	P16144	OTTHUMG00000179814	OTTHUMG00000179814	ENST00000200181.3:c.4154delT	17.37:g.73749891delT	ENSP00000200181:p.Leu1385fs		ITGB4_ENST00000579662.1_Intron|ITGB4_ENST00000450894.3_Intron|ITGB4_ENST00000449880.2_Intron|ITGB4_ENST00000339591.3_Intron|GALK1_ENST00000225614.2_Intron	p.L1385fs	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)		33	4341	+	all_cancers(13;1.5e-07)		1385		A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Frame_Shift_Del	DEL	ENST00000200181.3	37	c.4154delT	CCDS11727.1																																																																																									0.776	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1	.	.	-1	-1	7	7			2			4	0.33						2	4	0.33
