#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
RTF1	23168	broad.mit.edu	37	15	41763442	41763442	+	Silent	SNP	G	G	A			TCGA-06-0167-01A-01D-1491-08	TCGA-06-0167-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d530c696-235d-4a41-944d-e7f7ae21aa17	74292da7-2a53-455d-8d33-438db411fa67	g.chr15:41763442G>A	ENST00000389629.4	+	8	1110	c.1098G>A	c.(1096-1098)cgG>cgA	p.R366R		NM_015138.4	NP_055953.3	Q92541	RTF1_HUMAN	Rtf1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)	366	Plus3. {ECO:0000255|PROSITE- ProRule:PRU00693}.				DNA-templated transcription, initiation (GO:0006352)|endodermal cell fate commitment (GO:0001711)|histone H3-K4 trimethylation (GO:0080182)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|single-stranded DNA binding (GO:0003697)	p.R241R(1)		central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(1)	18		all_cancers(109;1.79e-19)|all_epithelial(112;8.18e-17)|Lung NSC(122;3.16e-11)|all_lung(180;8.14e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;1.15e-16)|GBM - Glioblastoma multiforme(113;1.81e-06)|BRCA - Breast invasive adenocarcinoma(123;0.119)		GATTATCACGGCATAAGCTAG	0.458																																						uc001zny.3																			1	Substitution - coding silent(1)	p.R241R(1)	kidney(1)	central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(1)	18						c.(1096-1098)cgG>cgA		Homo sapiens Rtf1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae) (RTF1), mRNA.							164.0	155.0	158.0					15																	41763442		2203	4300	6503	SO:0001819	synonymous_variant	23168				histone modification|regulation of transcription, DNA-dependent|transcription initiation, DNA-dependent	nucleoplasm	protein binding|single-stranded DNA binding	g.chr15:41763442G>A	D87440	CCDS32200.2	15q14	2004-03-03	2005-07-20	2005-07-20	ENSG00000137815	ENSG00000137815			28996	protein-coding gene	gene with protein product		611633	"""KIAA0252"""	KIAA0252		15632063	Standard	NM_015138		Approved		uc001zny.3	Q92541	OTTHUMG00000133744	ENST00000389629.4:c.1098G>A	15.37:g.41763442G>A							p.R366R	NM_015138	NP_055953	Q92541	RTF1_HUMAN		OV - Ovarian serous cystadenocarcinoma(18;1.15e-16)|GBM - Glioblastoma multiforme(113;1.81e-06)|BRCA - Breast invasive adenocarcinoma(123;0.119)	7	1110	+		all_cancers(109;1.79e-19)|all_epithelial(112;8.18e-17)|Lung NSC(122;3.16e-11)|all_lung(180;8.14e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)	366			Plus3.		Q96BX6	Silent	SNP	ENST00000389629.4	37	c.1098G>A	CCDS32200.2																																																																																				0.458	RTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258111.1	NM_015138	
MRPL10	124995	broad.mit.edu	37	17	45905957	45905957	+	Silent	SNP	C	C	T			TCGA-06-0167-01A-01D-1491-08	TCGA-06-0167-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d530c696-235d-4a41-944d-e7f7ae21aa17	74292da7-2a53-455d-8d33-438db411fa67	g.chr17:45905957C>T	ENST00000351111.2	-	2	137	c.132G>A	c.(130-132)cgG>cgA	p.R44R	MRPL10_ENST00000414011.1_Silent_p.R54R|MRPL10_ENST00000290208.7_Silent_p.R54R	NM_145255.3	NP_660298.2	Q7Z7H8	RM10_HUMAN	mitochondrial ribosomal protein L10	44					ribosome biogenesis (GO:0042254)|translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrion (GO:0005739)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(3)|large_intestine(1)|lung(3)|ovary(1)	8						TCAGCTTCTGCCGCTGAAAGT	0.597																																						uc002ily.3																			0				endometrium(3)|large_intestine(1)|lung(3)|ovary(1)	8						c.(160-162)cgG>cgA		Homo sapiens mitochondrial ribosomal protein L10 (MRPL10), nuclear gene encoding mitochondrial protein, transcript variant 2, mRNA.							54.0	50.0	51.0					17																	45905957		2203	4300	6503	SO:0001819	synonymous_variant	124995				ribosome biogenesis|translation	mitochondrial large ribosomal subunit	structural constituent of ribosome	g.chr17:45905957C>T	AB051618	CCDS11516.1, CCDS11517.1	17q21.3	2012-09-13			ENSG00000159111	ENSG00000159111		"""Mitochondrial ribosomal proteins / large subunits"""	14055	protein-coding gene	gene with protein product	"""39S ribosomal protein L10, mitochondrial"""	611825				11551941	Standard	NM_148887		Approved	RPML8, MRP-L8, L10MT, MRP-L10, MRPL8, MGC17973	uc002ily.3	Q7Z7H8	OTTHUMG00000156302	ENST00000351111.2:c.132G>A	17.37:g.45905957C>T						MRPL10_uc002ilz.3_Silent_p.R44R|MRPL10_uc010wky.2_Silent_p.R5R	p.R54R	NM_148887	NP_683685	Q7Z7H8	RM10_HUMAN			2	260	-			44					A6NGJ4|Q96B80|Q96Q55	Silent	SNP	ENST00000351111.2	37	c.162G>A	CCDS11516.1																																																																																				0.597	MRPL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343764.1	NM_145255	
ITGB2	3689	broad.mit.edu	37	21	46326937	46326937	+	Missense_Mutation	SNP	G	G	A	rs201354221		TCGA-06-0167-01A-01D-1491-08	TCGA-06-0167-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d530c696-235d-4a41-944d-e7f7ae21aa17	74292da7-2a53-455d-8d33-438db411fa67	g.chr21:46326937G>A	ENST00000397850.2	-	5	673	c.221C>T	c.(220-222)gCg>gTg	p.A74V	ITGB2_ENST00000397857.1_Missense_Mutation_p.A74V|ITGB2_ENST00000397854.3_Missense_Mutation_p.A74V|ITGB2_ENST00000397852.1_Missense_Mutation_p.A74V|ITGB2_ENST00000302347.5_Missense_Mutation_p.A74V|ITGB2_ENST00000523126.1_5'Flank|ITGB2_ENST00000355153.4_Missense_Mutation_p.A74V			P05107	ITB2_HUMAN	integrin, beta 2 (complement component 3 receptor 3 and 4 subunit)	74					apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|neutrophil chemotaxis (GO:0030593)|receptor clustering (GO:0043113)|regulation of cell shape (GO:0008360)|regulation of immune response (GO:0050776)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|vesicle (GO:0031982)	cell adhesion molecule binding (GO:0050839)|glycoprotein binding (GO:0001948)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(4)|skin(3)	35				Colorectal(79;0.0669)	Simvastatin(DB00641)	GTCGTCAGCCGCACAGCCCCT	0.617													G|||	1	0.000199681	0.0008	0.0	5008	,	,		16070	0.0		0.0	False		,,,				2504	0.0					uc002zgd.2																			0				breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(4)|skin(3)	35						c.(220-222)gCg>gTg		Homo sapiens integrin, beta 2 (complement component 3 receptor 3 and 4 subunit) (ITGB2), transcript variant 2, mRNA.	Simvastatin(DB00641)						93.0	87.0	89.0					21																	46326937		2203	4300	6503	SO:0001583	missense	3689				apoptosis|blood coagulation|cell-cell signaling|cell-matrix adhesion|inflammatory response|integrin-mediated signaling pathway|leukocyte cell-cell adhesion|multicellular organismal development|neutrophil chemotaxis|regulation of cell shape|regulation of immune response|regulation of peptidyl-tyrosine phosphorylation	integrin complex	glycoprotein binding|protein kinase binding|receptor activity	g.chr21:46326937G>A	AK222505	CCDS13716.1	21q22.3	2014-09-17	2006-03-02		ENSG00000160255	ENSG00000160255		"""CD molecules"", ""Complement system"", ""Integrins"""	6155	protein-coding gene	gene with protein product		600065	"""integrin, beta 2 (antigen CD18 (p95), lymphocyte function-associated antigen 1; macrophage antigen 1 (mac-1) beta subunit)"""	CD18, MFI7			Standard	NM_000211		Approved	LFA-1, MAC-1	uc002zgf.3	P05107	OTTHUMG00000090257	ENST00000397850.2:c.221C>T	21.37:g.46326937G>A	ENSP00000380948:p.Ala74Val					ITGB2_uc002zgf.3_Missense_Mutation_p.A74V|ITGB2_uc011afl.1_5'UTR|ITGB2_uc010gpw.2_Missense_Mutation_p.A74V|ITGB2_uc002zgg.2_Missense_Mutation_p.A74V	p.A74V	NM_001127491	NP_001120963	P05107	ITB2_HUMAN		Colorectal(79;0.0669)	2	265	-			74					B3KTS8|D3DSM1|Q16418|Q53HS5|Q9UD72	Missense_Mutation	SNP	ENST00000397850.2	37	c.221C>T	CCDS13716.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	7.738	0.700591	0.15106	.	.	ENSG00000160255	ENST00000397852;ENST00000397857;ENST00000397854;ENST00000355153;ENST00000397850;ENST00000302347;ENST00000545414;ENST00000320216;ENST00000523663;ENST00000522931;ENST00000517563;ENST00000522688;ENST00000524251	D;D;D;D;D;D;D;D;D;D;D;D	0.92805	-3.11;-3.11;-3.11;-3.11;-3.11;-3.11;-3.11;-3.11;-3.11;-3.11;-3.11;-3.11	4.66	-4.16	0.03869	Integrin beta subunit, N-terminal (2);	.	.	.	.	D	0.86908	0.6046	M	0.70595	2.14	0.09310	N	1	B;B	0.19445	0.036;0.024	B;B	0.11329	0.003;0.006	T	0.73148	-0.4074	9	0.42905	T	0.14	.	1.2441	0.01969	0.2322:0.1111:0.2097:0.447	.	74;74	A8MYE6;P05107	.;ITB2_HUMAN	V	74;74;74;74;74;74;74;65;74;74;74;5;5	ENSP00000380950:A74V;ENSP00000380955:A74V;ENSP00000380952:A74V;ENSP00000347279:A74V;ENSP00000380948:A74V;ENSP00000303242:A74V;ENSP00000317697:A65V;ENSP00000428503:A74V;ENSP00000428979:A74V;ENSP00000428413:A74V;ENSP00000428125:A5V;ENSP00000430901:A5V	ENSP00000303242:A74V	A	-	2	0	ITGB2	45151365	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.385000	0.07379	-0.662000	0.05338	-0.416000	0.06073	GCG		0.617	ITGB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206566.2	NM_000211	
NPNT	255743	broad.mit.edu	37	4	106888371	106888371	+	Missense_Mutation	SNP	G	G	A	rs146652028		TCGA-06-0167-01A-01D-1491-08	TCGA-06-0167-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d530c696-235d-4a41-944d-e7f7ae21aa17	74292da7-2a53-455d-8d33-438db411fa67	g.chr4:106888371G>A	ENST00000379987.2	+	11	1588	c.1372G>A	c.(1372-1374)Gcc>Acc	p.A458T	NPNT_ENST00000514622.1_Missense_Mutation_p.A429T|NPNT_ENST00000305572.8_Missense_Mutation_p.A429T|NPNT_ENST00000427316.2_Missense_Mutation_p.A488T|NPNT_ENST00000453617.2_Missense_Mutation_p.A475T|NPNT_ENST00000506666.1_Missense_Mutation_p.A459T	NM_001033047.2	NP_001028219.1	Q6UXI9	NPNT_HUMAN	nephronectin	458	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cellular response to tumor necrosis factor (GO:0071356)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|pilomotor reflex (GO:0097195)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|ureteric bud development (GO:0001657)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integrin alpha8-beta1 complex (GO:0034678)|proteinaceous extracellular matrix (GO:0005578)|smooth muscle contractile fiber (GO:0030485)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)	p.A458T(1)		kidney(5)|large_intestine(2)|lung(10)|prostate(2)|skin(1)|urinary_tract(1)	21		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.41e-07)		AGTGTCGGCAGCCAAAGCCCC	0.552																																						uc011cfd.2																			1	Substitution - Missense(1)	p.A458T(1)	skin(1)	kidney(5)|large_intestine(2)|lung(10)|prostate(2)|skin(1)|urinary_tract(1)	21						c.(1462-1464)Gcc>Acc		Homo sapiens nephronectin (NPNT), transcript variant 3, mRNA.							39.0	41.0	41.0					4																	106888371		2203	4300	6503	SO:0001583	missense	255743				cell differentiation	membrane	calcium ion binding	g.chr4:106888371G>A		CCDS34046.1, CCDS54784.1, CCDS54785.1, CCDS54786.1, CCDS54787.1	4q25	2005-10-07							27405	protein-coding gene	gene with protein product		610306				15754038	Standard	NM_001033047		Approved	EGFL6L, POEM	uc011cfd.2	Q6UXI9		ENST00000379987.2:c.1372G>A	4.37:g.106888371G>A	ENSP00000369323:p.Ala458Thr					NPNT_uc011cfc.2_Missense_Mutation_p.A475T|NPNT_uc011cfe.2_Missense_Mutation_p.A459T|NPNT_uc003hya.3_Missense_Mutation_p.A458T|NPNT_uc011cff.2_Missense_Mutation_p.A429T	p.A488T	NM_001184691	NP_001171620	Q6UXI9	NPNT_HUMAN		OV - Ovarian serous cystadenocarcinoma(123;5.41e-07)	11	1675	+		Hepatocellular(203;0.217)	458			MAM.		A6NFT9|A8K1W4|B4DIT4|B4DYK3|B4E2H7|B4E3H2|D6RCA1|E9PCK8|E9PCQ1|E9PE64|E9PF04	Missense_Mutation	SNP	ENST00000379987.2	37	c.1462G>A	CCDS34046.1	.	.	.	.	.	.	.	.	.	.	G	15.88	2.964801	0.53507	.	.	ENSG00000168743	ENST00000379987;ENST00000453617;ENST00000427316;ENST00000514622;ENST00000305572;ENST00000506666;ENST00000503451	T;T;T;T;T;T;T	0.01947	4.54;4.54;4.54;4.54;4.54;4.54;4.54	4.65	2.73	0.32206	Concanavalin A-like lectin/glucanase (1);MAM domain (2);	0.234443	0.43260	D	0.000591	T	0.01489	0.0048	N	0.02916	-0.46	0.29088	N	0.882299	B;P;P;P;B;P	0.47484	0.002;0.801;0.896;0.896;0.001;0.822	B;B;P;P;B;P	0.47744	0.004;0.315;0.556;0.556;0.003;0.556	T	0.50759	-0.8790	10	0.31617	T	0.26	.	7.6705	0.28455	0.106:0.4094:0.4846:0.0	.	429;459;488;475;429;458	E9PF04;E9PE64;E9PCQ1;E9PCK8;Q6UXI9-2;Q6UXI9	.;.;.;.;.;NPNT_HUMAN	T	458;475;488;429;429;459;505	ENSP00000369323:A458T;ENSP00000402884:A475T;ENSP00000389252:A488T;ENSP00000422044:A429T;ENSP00000302557:A429T;ENSP00000422474:A459T;ENSP00000426146:A505T	ENSP00000302557:A429T	A	+	1	0	NPNT	107107820	0.790000	0.28787	0.826000	0.32828	0.551000	0.35334	1.440000	0.35024	1.079000	0.41038	0.650000	0.86243	GCC		0.552	NPNT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364083.1	NM_198278	
SEC24B	10427	broad.mit.edu	37	4	110437770	110437770	+	Silent	SNP	C	C	T			TCGA-06-0167-01A-01D-1491-08	TCGA-06-0167-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d530c696-235d-4a41-944d-e7f7ae21aa17	74292da7-2a53-455d-8d33-438db411fa67	g.chr4:110437770C>T	ENST00000265175.5	+	11	2155	c.2100C>T	c.(2098-2100)tgC>tgT	p.C700C	SEC24B_ENST00000504968.2_Silent_p.C730C|SEC24B_ENST00000399100.2_Silent_p.C665C	NM_006323.2	NP_006314.2	O95487	SC24B_HUMAN	SEC24 family member B	700					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|aorta morphogenesis (GO:0035909)|auditory receptor cell stereocilium organization (GO:0060088)|cellular protein metabolic process (GO:0044267)|cochlear nucleus development (GO:0021747)|COPII vesicle coating (GO:0048208)|coronary artery morphogenesis (GO:0060982)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|lung lobe morphogenesis (GO:0060463)|membrane organization (GO:0061024)|neural tube closure (GO:0001843)|outflow tract morphogenesis (GO:0003151)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|pulmonary artery morphogenesis (GO:0061156)|regulation of cargo loading into COPII-coated vesicle (GO:1901301)|regulation of establishment of planar polarity involved in neural tube closure (GO:0090178)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|membrane (GO:0016020)	transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.03e-05)		CAATTTTGTGCCAGTCACTCC	0.318																																						uc003hzk.3																			0				breast(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						c.(2098-2100)tgC>tgT		Homo sapiens SEC24 family, member B (S. cerevisiae) (SEC24B), transcript variant 1, mRNA.							86.0	76.0	79.0					4																	110437770		1827	4095	5922	SO:0001819	synonymous_variant	10427				COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|Golgi membrane|perinuclear region of cytoplasm	protein binding|transporter activity|zinc ion binding	g.chr4:110437770C>T	AJ131245	CCDS43260.1, CCDS47124.1, CCDS75179.1	4q25	2013-10-21	2013-10-21		ENSG00000138802	ENSG00000138802			10704	protein-coding gene	gene with protein product		607184	"""SEC24 (S. cerevisiae) related gene family, member B"", ""SEC24 family, member B (S. cerevisiae)"""			10075675, 10329445	Standard	XM_005262688		Approved		uc003hzk.3	O95487	OTTHUMG00000161372	ENST00000265175.5:c.2100C>T	4.37:g.110437770C>T						SEC24B_uc003hzl.3_Silent_p.C665C|SEC24B_uc011cfp.2_Silent_p.C730C|SEC24B_uc011cfq.2_Silent_p.C699C|SEC24B_uc011cfr.2_Silent_p.C664C	p.C700C	NM_006323	NP_006314	O95487	SC24B_HUMAN		OV - Ovarian serous cystadenocarcinoma(123;3.03e-05)	10	2155	+		Hepatocellular(203;0.217)	700					B7ZKM8|B7ZKN4|Q0VG08	Silent	SNP	ENST00000265175.5	37	c.2100C>T	CCDS47124.1																																																																																				0.318	SEC24B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364693.2		
C6orf203	51250	broad.mit.edu	37	6	107372330	107372330	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0167-01A-01D-1491-08	TCGA-06-0167-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d530c696-235d-4a41-944d-e7f7ae21aa17	74292da7-2a53-455d-8d33-438db411fa67	g.chr6:107372330C>T	ENST00000405204.2	+	4	1220	c.613C>T	c.(613-615)Cgg>Tgg	p.R205W	C6orf203_ENST00000443043.1_Missense_Mutation_p.R210W|C6orf203_ENST00000311381.5_Missense_Mutation_p.R205W	NM_001142468.1	NP_001135940.1	Q9P0P8	CF203_HUMAN	chromosome 6 open reading frame 203	205						mitochondrion (GO:0005739)				large_intestine(4)|lung(2)|prostate(1)|urinary_tract(1)	8	Breast(9;0.00124)|all_epithelial(6;0.0729)	all_cancers(87;0.00461)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|Colorectal(196;0.171)|all_epithelial(87;0.23)	BRCA - Breast invasive adenocarcinoma(8;0.000395)|all cancers(7;0.00065)|Epithelial(6;0.000834)|OV - Ovarian serous cystadenocarcinoma(5;0.244)	BRCA - Breast invasive adenocarcinoma(108;0.117)		GACAGTTATGCGGATTCTCTT	0.383																																						uc011eaj.2																			0				large_intestine(4)|lung(2)|prostate(1)|urinary_tract(1)	8						c.(628-630)Cgg>Tgg		Homo sapiens chromosome 6 open reading frame 203 (C6orf203), transcript variant 3, mRNA.							105.0	111.0	109.0					6																	107372330		2203	4300	6503	SO:0001583	missense	51250							g.chr6:107372330C>T	AF151064	CCDS5058.1	6q21	2012-02-22			ENSG00000130349	ENSG00000130349			17971	protein-coding gene	gene with protein product						11042152, 11707072	Standard	XM_005267008		Approved	HSPC230, PRED31	uc003prq.3	Q9P0P8	OTTHUMG00000015307	ENST00000405204.2:c.613C>T	6.37:g.107372330C>T	ENSP00000384867:p.Arg205Trp					C6orf203_uc003prq.3_Missense_Mutation_p.R205W|C6orf203_uc010kde.3_Missense_Mutation_p.R205W	p.R210W	NM_001142470	NP_057571	Q9P0P8	CF203_HUMAN	BRCA - Breast invasive adenocarcinoma(8;0.000395)|all cancers(7;0.00065)|Epithelial(6;0.000834)|OV - Ovarian serous cystadenocarcinoma(5;0.244)	BRCA - Breast invasive adenocarcinoma(108;0.117)	4	1303	+	Breast(9;0.00124)|all_epithelial(6;0.0729)	all_cancers(87;0.00461)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|Colorectal(196;0.171)|all_epithelial(87;0.23)	205					B3KRG9	Missense_Mutation	SNP	ENST00000405204.2	37	c.628C>T	CCDS5058.1	.	.	.	.	.	.	.	.	.	.	C	19.26	3.793326	0.70452	.	.	ENSG00000130349	ENST00000443043;ENST00000405204;ENST00000311381	T;T;T	0.33216	1.42;1.42;1.42	5.93	1.67	0.24075	.	0.000000	0.64402	D	0.000001	T	0.44030	0.1274	M	0.70275	2.135	0.58432	D	0.999996	D	0.89917	1.0	D	0.72625	0.978	T	0.56697	-0.7936	10	0.87932	D	0	-9.6707	17.0298	0.86458	0.6997:0.3002:0.0:0.0	.	205	Q9P0P8	CF203_HUMAN	W	210;205;205	ENSP00000390153:R210W;ENSP00000384867:R205W;ENSP00000310951:R205W	ENSP00000310951:R205W	R	+	1	2	C6orf203	107479023	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	0.522000	0.22909	0.284000	0.22305	0.655000	0.94253	CGG		0.383	C6orf203-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041684.1	NM_016487	
MSL3	10943	broad.mit.edu	37	X	11790350	11790350	+	Missense_Mutation	SNP	G	G	A	rs140880282		TCGA-06-0167-01A-01D-1491-08	TCGA-06-0167-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d530c696-235d-4a41-944d-e7f7ae21aa17	74292da7-2a53-455d-8d33-438db411fa67	g.chrX:11790350G>A	ENST00000312196.4	+	11	1462	c.1357G>A	c.(1357-1359)Gca>Aca	p.A453T	MSL3_ENST00000398527.2_Missense_Mutation_p.A441T|MSL3_ENST00000380693.3_Missense_Mutation_p.A287T|MSL3_ENST00000361672.2_Missense_Mutation_p.A304T	NM_078629.3	NP_523353.2	Q8N5Y2	MS3L1_HUMAN	male-specific lethal 3 homolog (Drosophila)	453	MRG. {ECO:0000255|PROSITE- ProRule:PRU00972}.				chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|multicellular organismal development (GO:0007275)|transcription from RNA polymerase II promoter (GO:0006366)	MSL complex (GO:0072487)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(3)|cervix(1)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|urinary_tract(1)	19						CATTTATGGGGCACAACATTT	0.463																																						uc004cuw.3																			0				breast(1)|central_nervous_system(3)|cervix(1)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|urinary_tract(1)	19						c.(1357-1359)Gca>Aca		Homo sapiens male-specific lethal 3 homolog (Drosophila) (MSL3), transcript variant 1, mRNA.		G	THR/ALA,THR/ALA,THR/ALA	0,3835		0,0,1632,571	109.0	98.0	102.0		1321,859,1357	3.4	1.0	X	dbSNP_134	102	1,6727		0,1,2427,1872	no	missense,missense,missense	MSL3	NM_001193270.1,NM_006800.3,NM_078629.3	58,58,58	0,1,4059,2443	AA,AG,GG,G		0.0149,0.0,0.0095	benign,benign,benign	441/510,287/356,453/522	11790350	1,10562	2203	4300	6503	SO:0001583	missense	10943				histone H4-K16 acetylation|multicellular organismal development|transcription from RNA polymerase II promoter	MSL complex	DNA binding|methylated histone residue binding|sequence-specific DNA binding transcription factor activity	g.chrX:11790350G>A	AF117065	CCDS14147.1, CCDS14148.1, CCDS14149.1, CCDS55369.1, CCDS65213.1	Xp22.3	2008-10-29	2008-10-29	2008-10-29	ENSG00000005302	ENSG00000005302			7370	protein-coding gene	gene with protein product		300609	"""male-specific lethal-3 (Drosophila)-like 1"", ""male-specific lethal 3-like 1 (Drosophila)"""	MSL3L1		10395802, 10908644	Standard	NM_078628		Approved		uc004cuw.3	Q8N5Y2	OTTHUMG00000021132	ENST00000312196.4:c.1357G>A	X.37:g.11790350G>A	ENSP00000312244:p.Ala453Thr					MSL3_uc011mig.2_Missense_Mutation_p.A304T|MSL3_uc011mih.2_Missense_Mutation_p.A441T|MSL3_uc004cuy.3_Missense_Mutation_p.A287T	p.A453T	NM_078629	NP_006791	Q8N5Y2	MS3L1_HUMAN			10	1462	+			453					A6NCU2|A6NHW8|A8K165|B4DUV8|B7Z227|Q9UG70|Q9Y5Z8	Missense_Mutation	SNP	ENST00000312196.4	37	c.1357G>A	CCDS14147.1	.	.	.	.	.	.	.	.	.	.	G	15.50	2.852122	0.51270	0.0	1.49E-4	ENSG00000005302	ENST00000312196;ENST00000361672;ENST00000398527;ENST00000380693	T;T;T;T	0.13538	2.58;2.58;2.58;2.58	4.39	3.43	0.39272	.	0.224065	0.39341	N	0.001393	T	0.22742	0.0549	M	0.89968	3.075	0.49213	D	0.999768	B;B;B;P	0.36683	0.166;0.336;0.137;0.565	B;B;B;B	0.35550	0.094;0.104;0.057;0.205	T	0.04400	-1.0954	10	0.72032	D	0.01	.	9.6977	0.40167	0.0:0.0:0.3362:0.6638	.	441;304;394;453	B4DUV8;B7Z227;Q8N5Y2-2;Q8N5Y2	.;.;.;MS3L1_HUMAN	T	453;304;441;287	ENSP00000312244:A453T;ENSP00000354562:A304T;ENSP00000381538:A441T;ENSP00000370069:A287T	ENSP00000312244:A453T	A	+	1	0	MSL3	11700271	1.000000	0.71417	0.998000	0.56505	0.333000	0.28666	4.730000	0.62015	0.717000	0.32145	0.529000	0.55759	GCA		0.463	MSL3-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055757.1	NM_006800	
