#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
TTLL8	164714	broad.mit.edu	37	22	50472804	50472804	+	Missense_Mutation	SNP	C	C	T			TCGA-EM-A4FK-01A-11D-A257-08	TCGA-EM-A4FK-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04e58e29-933d-4488-91a8-06a5ee8f408d	db575be4-4c41-4cf6-8883-b31b1377db2c	g.chr22:50472804C>T	ENST00000266182.6	-	9	1008	c.1009G>A	c.(1009-1011)Gcc>Acc	p.A337T	TTLL8_ENST00000440475.1_Missense_Mutation_p.A321T			A6PVC2	TTLL8_HUMAN	tubulin tyrosine ligase-like family, member 8	357	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cilium assembly (GO:0042384)|protein polyglycylation (GO:0018094)	axoneme (GO:0005930)|cilium (GO:0005929)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	protein-glycine ligase activity (GO:0070735)|protein-glycine ligase activity, initiating (GO:0070736)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|ovary(4)	12		all_cancers(38;3.44e-07)|all_epithelial(38;2.44e-06)|all_lung(38;0.00141)|Breast(42;0.00519)|Lung NSC(38;0.0199)|Ovarian(80;0.142)|Lung SC(80;0.162)		READ - Rectum adenocarcinoma(2;0.000882)|Colorectal(2;0.00311)|BRCA - Breast invasive adenocarcinoma(115;0.226)		CGGGACTTGGCCGCGGGCTTT	0.592																																						ENST00000266182.6																			0				NS(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|ovary(4)	12						c.(1009-1011)Gcc>Acc		tubulin tyrosine ligase-like family, member 8							39.0	43.0	42.0					22																	50472804		1909	4105	6014	SO:0001583	missense	164714							g.chr22:50472804C>T			22q13.33	2013-02-14			ENSG00000138892	ENSG00000138892		"""Tubulin tyrosine ligase-like family"""	34000	protein-coding gene	gene with protein product						15890843	Standard	XM_003403745		Approved			A6PVC2	OTTHUMG00000150241	ENST00000266182.6:c.1009G>A	22.37:g.50472804C>T	ENSP00000266182:p.Ala337Thr					TTLL8_ENST00000440475.1_Missense_Mutation_p.A321T	p.A337T						READ - Rectum adenocarcinoma(2;0.000882)|Colorectal(2;0.00311)|BRCA - Breast invasive adenocarcinoma(115;0.226)	9	1008	-		all_cancers(38;3.44e-07)|all_epithelial(38;2.44e-06)|all_lung(38;0.00141)|Breast(42;0.00519)|Lung NSC(38;0.0199)|Ovarian(80;0.142)|Lung SC(80;0.162)						B5MDV0	Missense_Mutation	SNP	ENST00000266182.6	37	c.1009G>A		.	.	.	.	.	.	.	.	.	.	C	18.82	3.705389	0.68615	.	.	ENSG00000138892	ENST00000266182;ENST00000440475;ENST00000433387	T;T;T	0.42900	3.26;0.96;0.96	4.48	4.48	0.54585	.	0.129159	0.52532	D	0.000074	T	0.66208	0.2766	M	0.82132	2.575	0.41865	D	0.990244	D	0.89917	1.0	D	0.72338	0.977	T	0.73069	-0.4099	10	0.72032	D	0.01	.	16.2818	0.82694	0.0:1.0:0.0:0.0	.	337	B5MDV0	.	T	337;321;357	ENSP00000266182:A337T;ENSP00000387509:A321T;ENSP00000392252:A357T	ENSP00000266182:A337T	A	-	1	0	TTLL8	48814931	1.000000	0.71417	0.923000	0.36655	0.294000	0.27393	5.385000	0.66231	2.194000	0.70268	0.462000	0.41574	GCC		0.592	TTLL8-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_001080447		3	30	0	0	0	1	0	3	30				
SH3RF2	153769	broad.mit.edu	37	5	145439568	145439568	+	Silent	SNP	C	C	T	rs142262740	byFrequency	TCGA-EM-A4FK-01A-11D-A257-08	TCGA-EM-A4FK-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04e58e29-933d-4488-91a8-06a5ee8f408d	db575be4-4c41-4cf6-8883-b31b1377db2c	g.chr5:145439568C>T	ENST00000511217.1	+	8	1747	c.1695C>T	c.(1693-1695)gcC>gcT	p.A565A	SH3RF2_ENST00000359120.4_Silent_p.A565A|SH3RF2_ENST00000511705.1_3'UTR			Q8TEC5	SH3R2_HUMAN	SH3 domain containing ring finger 2	565					negative regulation of phosphatase activity (GO:0010923)|protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|phosphatase binding (GO:0019902)|protein phosphatase 1 binding (GO:0008157)|protein phosphatase inhibitor activity (GO:0004864)|zinc ion binding (GO:0008270)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(9)|ovary(1)|prostate(1)|skin(2)|stomach(1)	22			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CCCCCTCAGCCGTGGTGGTGG	0.672													C|||	2	0.000399361	0.0	0.0	5008	,	,		15485	0.001		0.0	False		,,,				2504	0.001					ENST00000511217.1																			0				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(9)|ovary(1)|prostate(1)|skin(2)|stomach(1)	22						c.(1693-1695)gcC>gcT		SH3 domain containing ring finger 2							62.0	58.0	59.0					5																	145439568		2203	4300	6503	SO:0001819	synonymous_variant	153769						ligase activity|protein phosphatase 1 binding|zinc ion binding	g.chr5:145439568C>T	AL833297	CCDS4280.1	5q32	2013-01-09	2011-11-04	2011-11-04	ENSG00000156463	ENSG00000156463		"""RING-type (C3HC4) zinc fingers"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	26299	protein-coding gene	gene with protein product	"""heart protein phosphatase 1-binding protein"", ""POSH-eliminating RING protein"""	613377	"""protein phosphatase 1, regulatory subunit 39"""	PPP1R39		22128169	Standard	NM_152550		Approved	FLJ23654, RNF158, Hepp1, POSHER	uc003lnt.3	Q8TEC5	OTTHUMG00000129685	ENST00000511217.1:c.1695C>T	5.37:g.145439568C>T						SH3RF2_ENST00000359120.4_Silent_p.A565A|SH3RF2_ENST00000511705.1_3'UTR	p.A565A			Q8TEC5	SH3R2_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		8	1747	+			565					A8K961|Q08AM9|Q6GMR9|Q8N5S8|Q96LP8	Silent	SNP	ENST00000511217.1	37	c.1695C>T	CCDS4280.1																																																																																				0.672	SH3RF2-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372804.1	NM_152550		4	70	0	0	0	1	0	4	70				
TNXB	7148	broad.mit.edu	37	6	32015643	32015643	+	Missense_Mutation	SNP	C	C	T			TCGA-EM-A4FK-01A-11D-A257-08	TCGA-EM-A4FK-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04e58e29-933d-4488-91a8-06a5ee8f408d	db575be4-4c41-4cf6-8883-b31b1377db2c	g.chr6:32015643C>T	ENST00000375244.3	-	30	10393	c.10192G>A	c.(10192-10194)Gtg>Atg	p.V3398M	TNXB_ENST00000375247.2_Missense_Mutation_p.V3396M|TNXB_ENST00000451343.1_5'Flank			P22105	TENX_HUMAN	tenascin XB	3443	Fibronectin type-III 25. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						ACCGGCACCACCTGGAGCCGA	0.612																																						ENST00000375244.3																			0				endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						c.(10192-10194)Gtg>Atg		tenascin XB							31.0	38.0	36.0					6																	32015643		1428	2650	4078	SO:0001583	missense	7148				actin cytoskeleton organization|cell adhesion|collagen metabolic process|elastic fiber assembly|signal transduction	extracellular space|intracellular|proteinaceous extracellular matrix	heparin binding|integrin binding	g.chr6:32015643C>T	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.10192G>A	6.37:g.32015643C>T	ENSP00000364393:p.Val3398Met					TNXB_ENST00000375247.2_Missense_Mutation_p.V3396M	p.V3398M			P22105	TENX_HUMAN			30	10393	-			3443					P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	37	c.10192G>A		.	.	.	.	.	.	.	.	.	.	C	7.008	0.556275	0.13436	.	.	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.57907	0.37;0.37	4.76	1.99	0.26369	.	0.921592	0.08990	N	0.864568	T	0.27063	0.0663	L	0.50333	1.59	0.09310	N	1	B	0.21520	0.057	B	0.27380	0.079	T	0.40079	-0.9582	10	0.46703	T	0.11	.	7.8756	0.29592	0.0:0.7316:0.0:0.2684	.	3396	P22105-3	.	M	3398;3396	ENSP00000364393:V3398M;ENSP00000364396:V3396M	ENSP00000364393:V3398M	V	-	1	0	TNXB	32123621	0.053000	0.20554	0.005000	0.12908	0.005000	0.04900	0.587000	0.23909	0.219000	0.20840	0.591000	0.81541	GTG		0.612	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		10	14	0	0	0	1	0	10	14				
BAGE2	85319	broad.mit.edu	37	21	11058353	11058353	+	RNA	SNP	T	T	C	rs79433933		TCGA-EM-A4FK-01A-11D-A257-08	TCGA-EM-A4FK-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04e58e29-933d-4488-91a8-06a5ee8f408d	db575be4-4c41-4cf6-8883-b31b1377db2c	g.chr21:11058353T>C	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2							extracellular region (GO:0005576)								Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		GAAATCTCTTTATAAAACCTT	0.343																																						ENST00000470054.1																			0													B melanoma antigen family, member 2							20.0	18.0	19.0					21																	11058353		692	1589	2281			85319							g.chr21:11058353T>C	AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172			15723	protein-coding gene	gene with protein product	"""cancer/testis antigen family 2, member 2"""					12461691	Standard	NM_182482		Approved	CT2.2		Q86Y30	OTTHUMG00000074128		21.37:g.11058353T>C												Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)	0	324	-								A8K925|Q08ER0	RNA	SNP	ENST00000470054.1	37																																																																																						0.343	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	NM_182482		7	81	0	0	0	1	0	7	81				
UNC79	57578	broad.mit.edu	37	14	94067104	94067104	+	Missense_Mutation	SNP	C	C	T			TCGA-EM-A4FK-01A-11D-A257-08	TCGA-EM-A4FK-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04e58e29-933d-4488-91a8-06a5ee8f408d	db575be4-4c41-4cf6-8883-b31b1377db2c	g.chr14:94067104C>T	ENST00000393151.2	+	25	3562	c.3562C>T	c.(3562-3564)Cct>Tct	p.P1188S	UNC79_ENST00000555664.1_Missense_Mutation_p.P1188S|UNC79_ENST00000256339.4_Missense_Mutation_p.P1011S|UNC79_ENST00000553484.1_Missense_Mutation_p.P1188S			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	1188					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						CAAGGAATTTCCTTTTCCTAC	0.403																																						ENST00000553484.1																			0				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						c.(3562-3564)Cct>Tct		unc-79 homolog (C. elegans)							84.0	81.0	82.0					14																	94067104		2203	4300	6503	SO:0001583	missense	57578					integral to membrane		g.chr14:94067104C>T	AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"""KIAA1409"""	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.3562C>T	14.37:g.94067104C>T	ENSP00000376858:p.Pro1188Ser					UNC79_ENST00000555664.1_Missense_Mutation_p.P1188S|UNC79_ENST00000393151.2_Missense_Mutation_p.P1188S|UNC79_ENST00000256339.4_Missense_Mutation_p.P1011S	p.P1188S			Q9P2D8	UNC79_HUMAN			25	3716	+			1188					B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	37	c.3562C>T		.	.	.	.	.	.	.	.	.	.	C	15.39	2.820897	0.50633	.	.	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.18174	2.23;2.23;2.23;2.23	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.22551	0.0544	N	0.05078	-0.115	0.58432	D	0.999997	D	0.71674	0.998	D	0.80764	0.994	T	0.28681	-1.0036	10	0.12766	T	0.61	-14.614	20.6593	0.99626	0.0:1.0:0.0:0.0	.	1188	C9JQL1	.	S	1011;1188;1188;1188;1188	ENSP00000256339:P1011S;ENSP00000450868:P1188S;ENSP00000451360:P1188S;ENSP00000376858:P1188S	ENSP00000256339:P1011S	P	+	1	0	KIAA1409	93136857	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.885000	0.99019	0.655000	0.94253	CCT		0.403	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395		7	15	0	0	0	1	0	7	15				
NRAS	4893	broad.mit.edu	37	1	115256529	115256529	+	Missense_Mutation	SNP	T	T	C	rs11554290	byFrequency	TCGA-EM-A4FK-01A-11D-A257-08	TCGA-EM-A4FK-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04e58e29-933d-4488-91a8-06a5ee8f408d	db575be4-4c41-4cf6-8883-b31b1377db2c	g.chr1:115256529T>C	ENST00000369535.4	-	3	435	c.182A>G	c.(181-183)cAa>cGa	p.Q61R		NM_002524.4	NP_002515.1	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	61			Q -> K (in CMNS and NCMS; somatic mutation). {ECO:0000269|PubMed:23392294}.|Q -> R (in CMNS, NCMS and KNEN; also found in lung carcinoma cell and melanoma; dbSNP:rs11554290). {ECO:0000269|PubMed:18633438, ECO:0000269|PubMed:22499344, ECO:0000269|PubMed:23392294, ECO:0000269|PubMed:3276402}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of skeletal muscle tissue development (GO:0048642)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|small GTPase mediated signal transduction (GO:0007264)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.Q61R(817)|p.Q61L(175)|p.Q61P(23)|p.Q61K(1)		NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		GTACTCTTCTTGTCCAGCTGT	0.458	Q61L(C3A_LIVER)|Q61L(HEPG2_LIVER)|Q61L(HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(IPC298_SKIN)|Q61L(KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(MELJUSO_SKIN)|Q61L(MHHES1_BONE)|Q61L(MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61P(TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(HT1197_URINARY_TRACT)|Q61R(KMS27_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(KU1919_URINARY_TRACT)|Q61R(NCIH2347_LUNG)|Q61R(ONS76_CENTRAL_NERVOUS_SYSTEM)|Q61R(SKMEL2_SKIN)|Q61R(SW1271_LUNG)|Q61R(TT2609C02_THYROID)	50	Mis		"""melanoma, MM, AML, thyroid"""				Noonan syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)																												ENST00000369535.4	Q61L(C3A_LIVER)|Q61L(HEPG2_LIVER)|Q61L(HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(IPC298_SKIN)|Q61L(KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(MELJUSO_SKIN)|Q61L(MHHES1_BONE)|Q61L(MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61P(TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(HT1197_URINARY_TRACT)|Q61R(KMS27_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(KU1919_URINARY_TRACT)|Q61R(NCIH2347_LUNG)|Q61R(ONS76_CENTRAL_NERVOUS_SYSTEM)|Q61R(SKMEL2_SKIN)|Q61R(SW1271_LUNG)|Q61R(TT2609C02_THYROID)	50		Dom	yes		1	1p13.2	4893	Mis	neuroblastoma RAS viral (v-ras) oncogene homolog			"""L, E"""			"""melanoma, MM, AML, thyroid"""		1016	Substitution - Missense(1016)	p.Q61R(817)|p.Q61L(175)|p.Q61P(23)|p.Q61K(1)	skin(466)|thyroid(279)|haematopoietic_and_lymphoid_tissue(124)|NS(50)|large_intestine(27)|lung(17)|urinary_tract(11)|adrenal_gland(7)|liver(7)|breast(7)|soft_tissue(4)|testis(3)|endometrium(3)|ovary(3)|central_nervous_system(2)|pancreas(2)|eye(1)|prostate(1)|meninges(1)|autonomic_ganglia(1)	NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085						c.(181-183)cAa>cGa		neuroblastoma RAS viral (v-ras) oncogene homolog							180.0	156.0	164.0					1																	115256529		2203	4300	6503	SO:0001583	missense	4893	Noonan syndrome	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	activation of MAPKK activity|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	Golgi membrane|plasma membrane	GTP binding|GTPase activity	g.chr1:115256529T>C	BC005219	CCDS877.1	1p13.2	2014-09-17			ENSG00000213281	ENSG00000213281			7989	protein-coding gene	gene with protein product		164790					Standard	NM_002524		Approved	N-ras	uc009wgu.3	P01111	OTTHUMG00000012059	ENST00000369535.4:c.182A>G	1.37:g.115256529T>C	ENSP00000358548:p.Gln61Arg	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)					p.Q61R	NM_002524.4	NP_002515.1	P01111	RASN_HUMAN		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)	3	435	-	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)	61		Q -> K (in neuroblastoma cell).|Q -> R (in lung carcinoma cell and melanoma; dbSNP:rs11554290).			Q14971|Q15104|Q15282	Missense_Mutation	SNP	ENST00000369535.4	37	c.182A>G	CCDS877.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.004139	0.74932	.	.	ENSG00000213281	ENST00000369535	D	0.83673	-1.75	5.08	5.08	0.68730	Small GTP-binding protein domain (1);	0.000000	0.53938	U	0.000043	D	0.86489	0.5945	M	0.92604	3.325	0.80722	D	1	B	0.28512	0.214	B	0.39590	0.304	D	0.88255	0.2919	10	0.66056	D	0.02	.	15.0132	0.71565	0.0:0.0:0.0:1.0	rs11554290;rs11554290	61	P01111	RASN_HUMAN	R	61	ENSP00000358548:Q61R	ENSP00000358548:Q61R	Q	-	2	0	NRAS	115058052	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.761000	0.85260	2.120000	0.65058	0.533000	0.62120	CAA		0.458	NRAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033395.2	NM_002524		66	107	0	0	0	1	0	66	107				
ANKRD11	29123	broad.mit.edu	37	16	89345698	89345698	+	Missense_Mutation	SNP	T	T	C			TCGA-EM-A4FK-01A-11D-A257-08	TCGA-EM-A4FK-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04e58e29-933d-4488-91a8-06a5ee8f408d	db575be4-4c41-4cf6-8883-b31b1377db2c	g.chr16:89345698T>C	ENST00000301030.4	-	9	7712	c.7252A>G	c.(7252-7254)Atc>Gtc	p.I2418V	ANKRD11_ENST00000378330.2_Missense_Mutation_p.I2418V	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	2418					bone development (GO:0060348)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|odontogenesis of dentin-containing tooth (GO:0042475)|skeletal system morphogenesis (GO:0048705)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		GCGTCCACGATGGCGGCCAGC	0.617																																						ENST00000301030.4																			0				breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83						c.(7252-7254)Atc>Gtc		ankyrin repeat domain 11							25.0	23.0	24.0					16																	89345698		2198	4299	6497	SO:0001583	missense	29123					nucleus		g.chr16:89345698T>C	AY373756	CCDS32513.1	16q24.3	2013-01-10				ENSG00000167522		"""Ankyrin repeat domain containing"""	21316	protein-coding gene	gene with protein product		611192				11483580	Standard	NM_001256182		Approved	LZ16, T13	uc002fnc.2	Q6UB99		ENST00000301030.4:c.7252A>G	16.37:g.89345698T>C	ENSP00000301030:p.Ile2418Val					ANKRD11_ENST00000378330.2_Missense_Mutation_p.I2418V	p.I2418V	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)	9	7712	-		all_hematologic(23;0.00824)|Colorectal(91;0.0475)	2418					Q6NTG1|Q6QMF8	Missense_Mutation	SNP	ENST00000301030.4	37	c.7252A>G	CCDS32513.1	.	.	.	.	.	.	.	.	.	.	t	10.16	1.274966	0.23307	.	.	ENSG00000167522	ENST00000301030;ENST00000378330	T;T	0.42513	0.97;0.97	4.96	4.96	0.65561	.	0.259771	0.30492	N	0.009519	T	0.38241	0.1033	L	0.50333	1.59	0.80722	D	1	B	0.29188	0.236	B	0.26416	0.069	T	0.21008	-1.0258	10	0.37606	T	0.19	.	14.6349	0.68682	0.0:0.0:0.0:1.0	.	2418	Q6UB99	ANR11_HUMAN	V	2418	ENSP00000301030:I2418V;ENSP00000367581:I2418V	ENSP00000301030:I2418V	I	-	1	0	ANKRD11	87873199	1.000000	0.71417	1.000000	0.80357	0.518000	0.34316	3.767000	0.55288	1.865000	0.54081	0.157000	0.16456	ATC		0.617	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275		7	17	0	0	0	1	0	7	17				
FRG1B	284802	broad.mit.edu	37	20	29625891	29625891	+	Silent	SNP	C	C	G			TCGA-EM-A4FK-01A-11D-A257-08	TCGA-EM-A4FK-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04e58e29-933d-4488-91a8-06a5ee8f408d	db575be4-4c41-4cf6-8883-b31b1377db2c	g.chr20:29625891C>G	ENST00000278882.3	+	5	515	c.135C>G	c.(133-135)ggC>ggG	p.G45G	FRG1B_ENST00000358464.4_Silent_p.G45G|FRG1B_ENST00000439954.2_Silent_p.G50G			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	45										endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						TGAAATCTGGCTATGGAAAAT	0.343																																						ENST00000278882.3																			0				endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						c.(133-135)ggC>ggG																																						SO:0001819	synonymous_variant	0							g.chr20:29625891C>G			20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531			15792	other	unknown			"""chromosome 20 open reading frame 80"""	C20orf80			Standard	NR_003579		Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.135C>G	20.37:g.29625891C>G						FRG1B_ENST00000358464.4_Silent_p.G45G|FRG1B_ENST00000439954.2_Silent_p.G50G	p.G45G							5	515	+								C4AME5	Silent	SNP	ENST00000278882.3	37	c.135C>G																																																																																					0.343	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078494.2	NR_003579		5	93	0	0	0	1	0	5	93				
DCHS1	8642	broad.mit.edu	37	11	6653563	6653563	+	Silent	SNP	T	T	G			TCGA-EM-A4FK-01A-11D-A257-08	TCGA-EM-A4FK-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04e58e29-933d-4488-91a8-06a5ee8f408d	db575be4-4c41-4cf6-8883-b31b1377db2c	g.chr11:6653563T>G	ENST00000299441.3	-	6	3591	c.3180A>C	c.(3178-3180)ctA>ctC	p.L1060L	RP11-732A19.6_ENST00000526633.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	1060	Cadherin 10. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CCTCACGGTCTAGTGCTGCCC	0.592																																						ENST00000299441.3																			0				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103						c.(3178-3180)ctA>ctC		dachsous cadherin-related 1							98.0	83.0	88.0					11																	6653563		2201	4296	6497	SO:0001819	synonymous_variant	8642				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	g.chr11:6653563T>G	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"""Cadherins / Cadherin-related"""	13681	protein-coding gene	gene with protein product	"""cadherin-related family member 6"""	603057	"""protocadherin 16"", ""dachsous 1 (Drosophila)"""	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.3180A>C	11.37:g.6653563T>G						RP11-732A19.6_ENST00000526633.1_RNA	p.L1060L	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)	6	3591	-		Medulloblastoma(188;0.00263)|all_neural(188;0.026)	1060			Cadherin 10.		O15098	Silent	SNP	ENST00000299441.3	37	c.3180A>C	CCDS7771.1																																																																																				0.592	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		18	29	0	0	0	1	0	18	29				
KRTAP4-11	653240	broad.mit.edu	37	17	39274364	39274364	+	Missense_Mutation	SNP	T	T	G	rs425784		TCGA-EM-A4FK-01A-11D-A257-08	TCGA-EM-A4FK-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04e58e29-933d-4488-91a8-06a5ee8f408d	db575be4-4c41-4cf6-8883-b31b1377db2c	g.chr17:39274364T>G	ENST00000391413.2	-	1	242	c.204A>C	c.(202-204)agA>agC	p.R68S		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	68	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].		Missing (in allele KAP4.14). {ECO:0000269|PubMed:15955084}.			keratin filament (GO:0045095)				endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			AGATGCAGCATCTGGGGCGGC	0.667																																						ENST00000391413.2																			0				endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33						c.(202-204)agA>agC		keratin associated protein 4-11							8.0	12.0	11.0					17																	39274364		676	1581	2257	SO:0001583	missense	653240					keratin filament		g.chr17:39274364T>G	AC025904	CCDS45675.1	17q21.2	2013-06-25			ENSG00000212721	ENSG00000212721		"""Keratin associated proteins"""	18911	protein-coding gene	gene with protein product			"""keratin associated protein 4-14"""	KRTAP4-14			Standard	NM_033059		Approved	KAP4.11, KAP4.14	uc002hvz.3	Q9BYQ6	OTTHUMG00000133586	ENST00000391413.2:c.204A>C	17.37:g.39274364T>G	ENSP00000375232:p.Arg68Ser						p.R68S	NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	STAD - Stomach adenocarcinoma(17;0.000371)		1	242	-		Breast(137;0.000496)	68		Missing (in allele KAP4.14).	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].		A0AUY2	Missense_Mutation	SNP	ENST00000391413.2	37	c.204A>C	CCDS45675.1	.	.	.	.	.	.	.	.	.	.	.	0.572	-0.840659	0.02692	.	.	ENSG00000212721	ENST00000391413	T	0.01139	5.28	3.77	-0.689	0.11313	.	91.536500	0.00963	N	0.003131	T	0.00271	0.0008	N	0.00022	-2.74	0.09310	N	0.999996	B	0.02656	0.0	B	0.01281	0.0	T	0.53429	-0.8440	10	0.02654	T	1	.	0.7939	0.01062	0.2891:0.1622:0.3809:0.1678	rs425784	68	Q9BYQ6	KR411_HUMAN	S	68	ENSP00000375232:R68S	ENSP00000375232:R68S	R	-	3	2	KRTAP4-11	36527890	0.005000	0.15991	0.041000	0.18516	0.133000	0.20885	-0.083000	0.11286	-0.156000	0.11079	-0.875000	0.02981	AGA		0.667	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1			8	64	0	0	0	1	0	8	64				
PKN2	5586	broad.mit.edu	37	1	89273120	89273120	+	Missense_Mutation	SNP	A	A	G			TCGA-EM-A4FK-01A-11D-A257-08	TCGA-EM-A4FK-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04e58e29-933d-4488-91a8-06a5ee8f408d	db575be4-4c41-4cf6-8883-b31b1377db2c	g.chr1:89273120A>G	ENST00000370521.3	+	13	2287	c.1928A>G	c.(1927-1929)gAc>gGc	p.D643G	PKN2_ENST00000370505.3_Missense_Mutation_p.D486G|PKN2_ENST00000544045.1_Missense_Mutation_p.D317G|PKN2_ENST00000370513.5_Missense_Mutation_p.D595G	NM_006256.2	NP_006247.1	Q16513	PKN2_HUMAN	protein kinase N2	643					apical junction assembly (GO:0043297)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|epithelial cell migration (GO:0010631)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic cell cycle (GO:0045931)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	apical junction complex (GO:0043296)|centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium (GO:0030027)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(3)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(1)	33		Lung NSC(277;0.123)		all cancers(265;0.0136)|Epithelial(280;0.0301)		GAACTTGAGGACAGAAGGTAA	0.333																																						ENST00000370521.3																			0				breast(2)|endometrium(3)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(1)	33						c.(1927-1929)gAc>gGc		protein kinase N2							101.0	96.0	97.0					1																	89273120		1828	4079	5907	SO:0001583	missense	5586				signal transduction	cytoplasm	ATP binding|histone deacetylase binding|protein kinase C activity	g.chr1:89273120A>G	U33052	CCDS714.1	1p22	2014-04-23	2004-07-01	2004-07-01	ENSG00000065243	ENSG00000065243			9406	protein-coding gene	gene with protein product	"""cardiolipin-activated protein kinase Pak2"""	602549	"""protein kinase C-like 2"""	PRKCL2		7988719, 7851406	Standard	NM_006256		Approved	PRK2, Pak-2, STK7	uc001dmn.3	Q16513	OTTHUMG00000010074	ENST00000370521.3:c.1928A>G	1.37:g.89273120A>G	ENSP00000359552:p.Asp643Gly					PKN2_ENST00000370513.5_Missense_Mutation_p.D595G|PKN2_ENST00000544045.1_Missense_Mutation_p.D317G|PKN2_ENST00000370505.3_Missense_Mutation_p.D486G	p.D643G	NM_006256.2	NP_006247.1	Q16513	PKN2_HUMAN		all cancers(265;0.0136)|Epithelial(280;0.0301)	13	2287	+		Lung NSC(277;0.123)	643					B4DQ21|B4DTP5|B4DVG1|D3DT24|Q08AF4|Q9H1W4	Missense_Mutation	SNP	ENST00000370521.3	37	c.1928A>G	CCDS714.1	.	.	.	.	.	.	.	.	.	.	A	4.173	0.030685	0.08101	.	.	ENSG00000065243	ENST00000370521;ENST00000370505;ENST00000370513;ENST00000544045	T;T;T;T	0.69435	-0.39;-0.39;-0.4;-0.39	5.97	5.97	0.96955	Protein kinase-like domain (1);	0.141093	0.31323	U	0.007847	T	0.44829	0.1312	L	0.44542	1.39	0.46725	D	0.99917	B;B;B	0.24258	0.0;0.1;0.1	B;B;B	0.18561	0.002;0.022;0.022	T	0.43163	-0.9408	10	0.22706	T	0.39	.	16.4534	0.84003	1.0:0.0:0.0:0.0	.	627;595;643	B4DTP5;E7ESL7;Q16513	.;.;PKN2_HUMAN	G	643;486;595;317	ENSP00000359552:D643G;ENSP00000359536:D486G;ENSP00000359544:D595G;ENSP00000439643:D317G	ENSP00000359536:D486G	D	+	2	0	PKN2	89045708	0.999000	0.42202	0.990000	0.47175	0.228000	0.25075	3.579000	0.53900	2.285000	0.76669	0.477000	0.44152	GAC		0.333	PKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027828.3	NM_006256		5	89	0	0	0	1	0	5	89				
BAGE2	85319	broad.mit.edu	37	21	11098827	11098827	+	RNA	SNP	C	C	T	rs79274499	byFrequency	TCGA-EM-A4FK-01A-11D-A257-08	TCGA-EM-A4FK-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04e58e29-933d-4488-91a8-06a5ee8f408d	db575be4-4c41-4cf6-8883-b31b1377db2c	g.chr21:11098827C>T	ENST00000470054.1	-	0	98							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2							extracellular region (GO:0005576)								Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		ccatccagagcgagacgagcc	0.637																																						ENST00000470054.1																			0													B melanoma antigen family, member 2							18.0	29.0	26.0					21																	11098827		691	1591	2282			85319							g.chr21:11098827C>T	AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172			15723	protein-coding gene	gene with protein product	"""cancer/testis antigen family 2, member 2"""					12461691	Standard	NM_182482		Approved	CT2.2		Q86Y30	OTTHUMG00000074128		21.37:g.11098827C>T												Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)	0	98	-								A8K925|Q08ER0	RNA	SNP	ENST00000470054.1	37																																																																																						0.637	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	NM_182482		12	32	0	0	0	1	0	12	32				
HMCN1	83872	broad.mit.edu	37	1	185834992	185834992	+	Silent	SNP	T	T	C			TCGA-EM-A4FK-01A-11D-A257-08	TCGA-EM-A4FK-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04e58e29-933d-4488-91a8-06a5ee8f408d	db575be4-4c41-4cf6-8883-b31b1377db2c	g.chr1:185834992T>C	ENST00000271588.4	+	4	847	c.618T>C	c.(616-618)aaT>aaC	p.N206N	HMCN1_ENST00000367492.2_Silent_p.N206N	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	206	VWFA.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						AACAAGTTAATGAGGTCAGTT	0.353																																						ENST00000271588.4																			0				NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						c.(616-618)aaT>aaC		hemicentin 1							74.0	76.0	75.0					1																	185834992		2203	4300	6503	SO:0001819	synonymous_variant	83872				response to stimulus|visual perception	basement membrane	calcium ion binding	g.chr1:185834992T>C	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.618T>C	1.37:g.185834992T>C						HMCN1_ENST00000367492.2_Silent_p.N206N	p.N206N	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN			4	847	+			206			VWFA.		A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	37	c.618T>C	CCDS30956.1																																																																																				0.353	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		10	19	0	0	0	1	0	10	19				
RBM12	10137	broad.mit.edu	37	20	34241438	34241438	+	Missense_Mutation	SNP	G	G	A			TCGA-EM-A4FK-01A-11D-A257-08	TCGA-EM-A4FK-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04e58e29-933d-4488-91a8-06a5ee8f408d	db575be4-4c41-4cf6-8883-b31b1377db2c	g.chr20:34241438G>A	ENST00000374114.3	-	3	2070	c.1807C>T	c.(1807-1809)Cgc>Tgc	p.R603C	CPNE1_ENST00000397445.1_Intron|CPNE1_ENST00000397446.1_Intron|CPNE1_ENST00000317619.3_Intron|RBM12_ENST00000359646.1_Missense_Mutation_p.R603C|RP1-309K20.6_ENST00000541176.2_Intron|CPNE1_ENST00000352393.4_Intron|RBM12_ENST00000374104.3_Missense_Mutation_p.R603C|CPNE1_ENST00000317677.5_Intron|CPNE1_ENST00000397442.1_Intron|CPNE1_ENST00000397443.1_Intron	NM_001198838.1|NM_001198840.1|NM_006047.5	NP_001185767.1|NP_001185769.1|NP_006038.2	Q9NTZ6	RBM12_HUMAN	RNA binding motif protein 12	603						nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(7)|kidney(1)|large_intestine(3)|lung(14)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36	Lung NSC(9;0.00608)|all_lung(11;0.00918)		BRCA - Breast invasive adenocarcinoma(18;0.00953)			CGGTGTAAGCGTTCAGACTTA	0.398																																						ENST00000374114.3																			0				breast(3)|endometrium(7)|kidney(1)|large_intestine(3)|lung(14)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						c.(1807-1809)Cgc>Tgc		RNA binding motif protein 12							183.0	175.0	178.0					20																	34241438		2203	4300	6503	SO:0001583	missense	10137					nucleus	nucleotide binding|protein binding|RNA binding	g.chr20:34241438G>A	AJ289772	CCDS13261.1	20q11.21	2013-02-12			ENSG00000244462	ENSG00000244462		"""RNA binding motif (RRM) containing"""	9898	protein-coding gene	gene with protein product		607179				11435693	Standard	NM_006047		Approved	HRIHFB2091, KIAA0765, SWAN	uc021wcq.1	Q9NTZ6	OTTHUMG00000032350	ENST00000374114.3:c.1807C>T	20.37:g.34241438G>A	ENSP00000363228:p.Arg603Cys					CPNE1_ENST00000352393.4_Intron|CPNE1_ENST00000397445.1_Intron|CPNE1_ENST00000317677.5_Intron|RBM12_ENST00000374104.3_Missense_Mutation_p.R603C|CPNE1_ENST00000317619.3_Intron|RBM12_ENST00000359646.1_Missense_Mutation_p.R603C|CPNE1_ENST00000397446.1_Intron|CPNE1_ENST00000397442.1_Intron|CPNE1_ENST00000397443.1_Intron	p.R603C	NM_001198838.1|NM_001198840.1|NM_006047.5	NP_001185767.1|NP_001185769.1|NP_006038.2	Q9NTZ6	RBM12_HUMAN	BRCA - Breast invasive adenocarcinoma(18;0.00953)		3	2070	-	Lung NSC(9;0.00608)|all_lung(11;0.00918)		603					B3KRU2|E1P5R6|O94865|Q8N3B1|Q9H196	Missense_Mutation	SNP	ENST00000374114.3	37	c.1807C>T	CCDS13261.1	.	.	.	.	.	.	.	.	.	.	G	13.55	2.271231	0.40194	.	.	ENSG00000244462	ENST00000374114;ENST00000359646;ENST00000374104;ENST00000349942	T;T;T	0.17528	2.27;2.27;2.27	5.1	3.18	0.36537	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.071171	0.56097	D	0.000034	T	0.18718	0.0449	L	0.56769	1.78	0.80722	D	1	B	0.06786	0.001	B	0.12837	0.008	T	0.04347	-1.0958	10	0.87932	D	0	1.8231	11.2924	0.49258	0.1452:0.0:0.8548:0.0	.	603	Q9NTZ6	RBM12_HUMAN	C	603;603;603;402	ENSP00000363228:R603C;ENSP00000352668:R603C;ENSP00000363217:R603C	ENSP00000339879:R402C	R	-	1	0	RBM12	33704852	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.735000	0.62051	0.747000	0.32809	-0.251000	0.11542	CGC		0.398	RBM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078894.1	NM_006047		54	95	0	0	0	1	0	54	95				
PAPSS1	9061	broad.mit.edu	37	4	108641276	108641280	+	Splice_Site	DEL	CCAGT	CCAGT	-			TCGA-EM-A4FK-01A-11D-A257-08	TCGA-EM-A4FK-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04e58e29-933d-4488-91a8-06a5ee8f408d	db575be4-4c41-4cf6-8883-b31b1377db2c	g.chr4:108641276_108641280delCCAGT	ENST00000265174.4	-	1	328_332	c.56_60delACTGG	c.(55-60)aactgg>a	p.NW19fs	PAPSS1_ENST00000511304.1_5'UTR	NM_005443.4	NP_005434.4	O43252	PAPS1_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase 1	19					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sulfate assimilation (GO:0000103)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	adenylylsulfate kinase activity (GO:0004020)|ATP binding (GO:0005524)|nucleotidyltransferase activity (GO:0016779)|sulfate adenylyltransferase (ATP) activity (GO:0004781)			NS(1)|endometrium(2)|kidney(5)|large_intestine(2)|lung(5)|ovary(1)	16		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.49e-05)		CCCAGCTTACCCAGTTCTGCGCGTT	0.673																																						ENST00000265174.4																			0				NS(1)|endometrium(2)|kidney(5)|large_intestine(2)|lung(5)|ovary(1)	16						c.e1+1		3'-phosphoadenosine 5'-phosphosulfate synthase 1																																				SO:0001630	splice_region_variant	9061				3'-phosphoadenosine 5'-phosphosulfate biosynthetic process|skeletal system development|sulfate assimilation|xenobiotic metabolic process	cytosol	adenylylsulfate kinase activity|ATP binding|sulfate adenylyltransferase (ATP) activity	g.chr4:108641276_108641280delCCAGT	Y10387	CCDS3676.1	4q24	2012-07-13			ENSG00000138801	ENSG00000138801	2.7.7.4, 2.7.1.25		8603	protein-coding gene	gene with protein product		603262				9576487, 9771708	Standard	NM_005443		Approved	ATPSK1, PAPSS	uc003hyk.3	O43252	OTTHUMG00000131210	ENST00000265174.4:c.60+1ACTGG>-	4.37:g.108641276_108641280delCCAGT						PAPSS1_ENST00000511304.1_5'UTR	p.NW19_splice	NM_005443.4	NP_005434.4	O43252	PAPS1_HUMAN		OV - Ovarian serous cystadenocarcinoma(123;5.49e-05)	1	328_332	-		Hepatocellular(203;0.217)	19					O43841|O75332|Q96FB1|Q96TF4|Q9P1P9|Q9UE98	Splice_Site	DEL	ENST00000265174.4	37	c.60_splice	CCDS3676.1																																																																																				0.673	PAPSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253946.2		Frame_Shift_Del	12	36						12	36	---	---	---	---
OTX2-AS1	100309464	broad.mit.edu	37	14	57509058	57509064	+	RNA	DEL	TCCAAGC	TCCAAGC	-	rs369895963	byFrequency	TCGA-EM-A4FK-01A-11D-A257-08	TCGA-EM-A4FK-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04e58e29-933d-4488-91a8-06a5ee8f408d	db575be4-4c41-4cf6-8883-b31b1377db2c	g.chr14:57509058_57509064delTCCAAGC	ENST00000554725.1	+	0	344									OTX2 antisense RNA 1 (head to head)																		CCAGAAGCCTTCCAAGCTCCAAGCCCT	0.483														289	0.0577077	0.0681	0.0548	5008	,	,		16601	0.003		0.1352	False		,,,				2504	0.0225					ENST00000554725.1																			0																																																			0							g.chr14:57509058_57509064delTCCAAGC	BC041486		14q22.3	2012-10-19	2012-10-17		ENSG00000248550	ENSG00000248550		"""Long non-coding RNAs"", ""-"""	43906	non-coding RNA	RNA, long non-coding			"""OTX2 antisense RNA 1 (non-protein coding)"", ""OTX2 antisense RNA 1"""			15703187	Standard	NR_029385		Approved	OTX2OS1	uc001xcr.3		OTTHUMG00000171304		14.37:g.57509065_57509071delTCCAAGC														0	344	+									RNA	DEL	ENST00000554725.1	37																																																																																						0.483	OTX2-AS1-002	KNOWN	basic	antisense	antisense	OTTHUMT00000412895.1	NR_029385		5	8						5	8	---	---	---	---
