#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
IGHV1OR16-3	28313	broad.mit.edu	37	16	32070612	32070612	+	RNA	SNP	A	A	C	rs368458790		TCGA-ET-A4KN-01A-11D-A257-08	TCGA-ET-A4KN-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	178d0486-cb0d-4979-8bdf-bb3fe99149bd	e3d4072c-07ef-4978-a687-43828578a9b3	g.chr16:32070612A>C	ENST00000566806.1	-	0	499																											GGTCTCCTGCAAGGCTTCTGG	0.552																																						ENST00000566806.1																			0																																																			0							g.chr16:32070612A>C																													16.37:g.32070612A>C														0	499	-									RNA	SNP	ENST00000566806.1	37																																																																																						0.552	RP11-1166P10.6-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000432459.1			5	69	0	0	0	1	0	5	69				
PRC1	9055	broad.mit.edu	37	15	91517940	91517940	+	Nonsense_Mutation	SNP	G	G	A	rs549267890		TCGA-ET-A4KN-01A-11D-A257-08	TCGA-ET-A4KN-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	178d0486-cb0d-4979-8bdf-bb3fe99149bd	e3d4072c-07ef-4978-a687-43828578a9b3	g.chr15:91517940G>A	ENST00000361188.5	-	10	2436	c.1225C>T	c.(1225-1227)Cga>Tga	p.R409*	PRC1_ENST00000394249.3_Nonsense_Mutation_p.R409*|PRC1_ENST00000442656.2_Nonsense_Mutation_p.R368*|PRC1_ENST00000361919.3_Nonsense_Mutation_p.R409*|Y_RNA_ENST00000363272.1_RNA|PRC1-AS1_ENST00000554388.1_RNA|PRC1-AS1_ENST00000556200.1_RNA					protein regulator of cytokinesis 1											endometrium(1)|kidney(2)|large_intestine(7)|lung(9)|ovary(3)|prostate(1)|skin(2)	25	Lung NSC(78;0.0987)|all_lung(78;0.175)					AATTCAATTCGTGCCTTCAAC	0.413																																						ENST00000361188.5																			0				endometrium(1)|kidney(2)|large_intestine(7)|lung(9)|ovary(3)|prostate(1)|skin(2)	25						c.(1225-1227)Cga>Tga		protein regulator of cytokinesis 1							343.0	308.0	320.0					15																	91517940		2198	4298	6496	SO:0001587	stop_gained	9055				cytokinesis|mitotic spindle elongation	cytoplasm|nucleus|spindle microtubule|spindle pole	protein binding	g.chr15:91517940G>A	AF044588	CCDS32334.1, CCDS45352.1, CCDS45353.1, CCDS45353.2	15q26.1	2013-05-29		2006-07-07	ENSG00000198901	ENSG00000198901			9341	protein-coding gene	gene with protein product	"""anaphase spindle elongation 1 homolog (S. cerevisiae)"""	603484				9885575	Standard	NM_003981		Approved	ASE1	uc002bqm.4	O43663	OTTHUMG00000171685	ENST00000361188.5:c.1225C>T	15.37:g.91517940G>A	ENSP00000354679:p.Arg409*					PRC1_ENST00000361919.3_Nonsense_Mutation_p.R409*|PRC1_ENST00000442656.2_Nonsense_Mutation_p.R368*|PRC1_ENST00000394249.3_Nonsense_Mutation_p.R409*|PRC1-AS1_ENST00000554388.1_RNA	p.R409*			O43663	PRC1_HUMAN			10	2436	-	Lung NSC(78;0.0987)|all_lung(78;0.175)		409			Spectrin-fold.			Nonsense_Mutation	SNP	ENST00000361188.5	37	c.1225C>T	CCDS45352.1	.	.	.	.	.	.	.	.	.	.	G	47	13.332810	0.99735	.	.	ENSG00000198901	ENST00000394249;ENST00000361919;ENST00000361188;ENST00000555455;ENST00000442656	.	.	.	5.54	3.56	0.40772	.	0.570075	0.19903	N	0.103471	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13470	T	0.59	.	14.4014	0.67050	0.0:0.0:0.5522:0.4478	.	.	.	.	X	409;409;409;12;368	.	ENSP00000354679:R409X	R	-	1	2	PRC1	89318944	0.010000	0.17322	0.547000	0.28179	0.946000	0.59487	0.995000	0.29706	1.523000	0.49018	0.650000	0.86243	CGA		0.413	PRC1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414760.1	NM_003981		9	199	0	0	0	1	0	9	199				
BOD1L1	259282	broad.mit.edu	37	4	13597501	13597501	+	Missense_Mutation	SNP	C	C	T			TCGA-ET-A4KN-01A-11D-A257-08	TCGA-ET-A4KN-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	178d0486-cb0d-4979-8bdf-bb3fe99149bd	e3d4072c-07ef-4978-a687-43828578a9b3	g.chr4:13597501C>T	ENST00000040738.5	-	12	8222	c.8087G>A	c.(8086-8088)gGa>gAa	p.G2696E		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	2696						nucleus (GO:0005634)	DNA binding (GO:0003677)										ACTTGGCTTTCCCCCACACAG	0.378																																						ENST00000040738.5																			0											c.(8086-8088)gGa>gAa		biorientation of chromosomes in cell division 1-like 1							179.0	185.0	183.0					4																	13597501		2203	4300	6503	SO:0001583	missense	259282						DNA binding	g.chr4:13597501C>T	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"""family with sequence similarity 44, member A"", ""biorientation of chromosomes in cell division 1-like"""	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.8087G>A	4.37:g.13597501C>T	ENSP00000040738:p.Gly2696Glu						p.G2696E	NM_148894.2	NP_683692.2	Q8NFC6	BOD1L_HUMAN			12	8222	-			2696					Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	37	c.8087G>A	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	C	0.015	-1.570811	0.00895	.	.	ENSG00000038219	ENST00000040738	T	0.05786	3.39	4.84	-4.41	0.03590	.	1.173830	0.06193	N	0.681784	T	0.03695	0.0105	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45116	-0.9283	10	0.27082	T	0.32	-0.0285	13.0357	0.58870	0.0:0.2371:0.0:0.7629	.	2696	Q8NFC6	BOD1L_HUMAN	E	2696	ENSP00000040738:G2696E	ENSP00000040738:G2696E	G	-	2	0	BOD1L	13206599	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.715000	0.04997	-0.924000	0.03780	-0.355000	0.07637	GGA		0.378	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		16	123	0	0	0	1	0	16	123				
MMP2	4313	broad.mit.edu	37	16	55516924	55516924	+	Missense_Mutation	SNP	C	C	G			TCGA-ET-A4KN-01A-11D-A257-08	TCGA-ET-A4KN-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	178d0486-cb0d-4979-8bdf-bb3fe99149bd	e3d4072c-07ef-4978-a687-43828578a9b3	g.chr16:55516924C>G	ENST00000219070.4	+	2	766	c.257C>G	c.(256-258)aCa>aGa	p.T86R	MMP2_ENST00000570308.1_Missense_Mutation_p.T10R|MMP2_ENST00000437642.2_Missense_Mutation_p.T36R|MMP2_ENST00000543485.1_Missense_Mutation_p.T10R	NM_004530.4	NP_004521.1	P08253	MMP2_HUMAN	matrix metallopeptidase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)	86					angiogenesis (GO:0001525)|blood vessel maturation (GO:0001955)|bone trabecula formation (GO:0060346)|cellular protein metabolic process (GO:0044267)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|intramembranous ossification (GO:0001957)|positive regulation of innate immune response (GO:0045089)|proteolysis (GO:0006508)|response to hypoxia (GO:0001666)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|sarcomere (GO:0030017)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|liver(2)|lung(23)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	58		Renal(780;0.00183)|Breast(268;0.00354)|Hepatocellular(780;0.00826)|all_neural(199;0.0189)		UCEC - Uterine corpus endometrioid carcinoma (183;0.0185)|all cancers(182;7.16e-45)|Epithelial(162;5.26e-37)|GBM - Glioblastoma multiforme(240;9e-08)|Kidney(780;0.00227)|BRCA - Breast invasive adenocarcinoma(181;0.00786)	Captopril(DB01197)|Marimastat(DB00786)	CTGCCCCAGACAGGTGATCTT	0.532																																						ENST00000219070.4																			0				NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|liver(2)|lung(23)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	58						c.(256-258)aCa>aGa		matrix metallopeptidase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)	Marimastat(DB00786)|Sulindac(DB00605)						126.0	118.0	121.0					16																	55516924		2198	4300	6498	SO:0001583	missense	0				angiogenesis|collagen catabolic process|proteolysis	extracellular space|membrane|nucleus|proteinaceous extracellular matrix	metalloendopeptidase activity|protein binding|zinc ion binding	g.chr16:55516924C>G		CCDS10752.1, CCDS45487.1	16q13-q21	2008-02-05	2005-08-08		ENSG00000087245	ENSG00000087245	3.4.24.24		7166	protein-coding gene	gene with protein product		120360	"""matrix metalloproteinase 2 (gelatinase A, 72kD gelatinase, 72kD type IV collagenase)"", ""matrix metalloproteinase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)"""	CLG4, CLG4A			Standard	NM_004530		Approved	TBE-1	uc002ehz.4	P08253	OTTHUMG00000133202	ENST00000219070.4:c.257C>G	16.37:g.55516924C>G	ENSP00000219070:p.Thr86Arg					MMP2_ENST00000437642.2_Missense_Mutation_p.T36R|MMP2_ENST00000543485.1_Missense_Mutation_p.T10R|MMP2_ENST00000570308.1_Missense_Mutation_p.T10R	p.T86R	NM_004530.4	NP_004521.1	P08253	MMP2_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (183;0.0185)|all cancers(182;7.16e-45)|Epithelial(162;5.26e-37)|GBM - Glioblastoma multiforme(240;9e-08)|Kidney(780;0.00227)|BRCA - Breast invasive adenocarcinoma(181;0.00786)	2	766	+		Renal(780;0.00183)|Breast(268;0.00354)|Hepatocellular(780;0.00826)|all_neural(199;0.0189)	86					B2R6U1|B4DWH3|E9PE45|Q9UCJ8	Missense_Mutation	SNP	ENST00000219070.4	37	c.257C>G	CCDS10752.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.714076	0.89112	.	.	ENSG00000087245	ENST00000219070;ENST00000543485;ENST00000437642	T;T;T	0.55588	0.51;0.51;0.51	5.05	5.05	0.67936	Peptidoglycan binding-like (2);Metallopeptidase, catalytic domain (1);	0.050205	0.85682	D	0.000000	T	0.81531	0.4842	H	0.95679	3.705	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.87679	0.2546	10	0.87932	D	0	.	18.4152	0.90567	0.0:1.0:0.0:0.0	.	36;86	E9PE45;P08253	.;MMP2_HUMAN	R	86;10;36	ENSP00000219070:T86R;ENSP00000444143:T10R;ENSP00000394237:T36R	ENSP00000219070:T86R	T	+	2	0	MMP2	54074425	1.000000	0.71417	0.998000	0.56505	0.912000	0.54170	7.818000	0.86416	2.354000	0.79902	0.460000	0.39030	ACA		0.532	MMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256913.3			12	81	0	0	0	1	0	12	81				
ITGA7	3679	broad.mit.edu	37	12	56091578	56091578	+	Missense_Mutation	SNP	T	T	G			TCGA-ET-A4KN-01A-11D-A257-08	TCGA-ET-A4KN-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	178d0486-cb0d-4979-8bdf-bb3fe99149bd	e3d4072c-07ef-4978-a687-43828578a9b3	g.chr12:56091578T>G	ENST00000555728.1	-	10	1470	c.1442A>C	c.(1441-1443)aAg>aCg	p.K481T	ITGA7_ENST00000553804.1_Missense_Mutation_p.K441T|ITGA7_ENST00000257880.7_Missense_Mutation_p.K481T|ITGA7_ENST00000452168.2_Missense_Mutation_p.K344T|ITGA7_ENST00000394230.2_Missense_Mutation_p.K441T|ITGA7_ENST00000394229.2_Missense_Mutation_p.K437T|ITGA7_ENST00000347027.6_Missense_Mutation_p.K437T|ITGA7_ENST00000257879.6_Missense_Mutation_p.K437T			Q13683	ITA7_HUMAN	integrin, alpha 7	481					blood vessel morphogenesis (GO:0048514)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|regulation of cell shape (GO:0008360)|skeletal muscle tissue development (GO:0007519)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|integrin alpha7-beta1 complex (GO:0034677)|muscle tendon junction (GO:0005927)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(16)|ovary(2)|prostate(2)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						GCCGAAGCTCTTGATGCCCAC	0.622																																						ENST00000257880.7																			0				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(16)|ovary(2)|prostate(2)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						c.(1441-1443)aAg>aCg		integrin, alpha 7							97.0	97.0	97.0					12																	56091578		2203	4300	6503	SO:0001583	missense	3679				cell-matrix adhesion|integrin-mediated signaling pathway|muscle organ development|regulation of cell shape	integrin complex	receptor activity	g.chr12:56091578T>G		CCDS8888.1, CCDS44914.1, CCDS55832.1	12q13	2014-09-17				ENSG00000135424		"""Integrins"""	6143	protein-coding gene	gene with protein product		600536				7607681	Standard	NM_002206		Approved		uc001shh.3	Q13683		ENST00000555728.1:c.1442A>C	12.37:g.56091578T>G	ENSP00000452387:p.Lys481Thr					ITGA7_ENST00000553804.1_Missense_Mutation_p.K441T|ITGA7_ENST00000394230.2_Missense_Mutation_p.K441T|ITGA7_ENST00000394229.2_Missense_Mutation_p.K437T|ITGA7_ENST00000347027.6_Missense_Mutation_p.K437T|ITGA7_ENST00000257879.6_Missense_Mutation_p.K437T|ITGA7_ENST00000452168.2_Missense_Mutation_p.K344T|ITGA7_ENST00000555728.1_Missense_Mutation_p.K481T	p.K481T			Q13683	ITA7_HUMAN			10	1661	-			481					B4E3U0|C9JMD3|C9JMZ6|O43197|Q86W93|Q9NY89|Q9UET0|Q9UEV2	Missense_Mutation	SNP	ENST00000555728.1	37	c.1442A>C		.	.	.	.	.	.	.	.	.	.	T	8.202	0.798338	0.16397	.	.	ENSG00000135424	ENST00000553804;ENST00000257879;ENST00000347027;ENST00000452168;ENST00000257880;ENST00000394230;ENST00000394229;ENST00000353687;ENST00000555728	T;T;T;T;T;T;T;T	0.70986	-0.53;-0.53;-0.53;-0.53;-0.53;-0.53;-0.53;-0.53	4.28	-1.67	0.08238	.	0.494083	0.19772	N	0.106405	T	0.45458	0.1343	N	0.16130	0.375	0.38961	D	0.958542	B;B;B;B	0.18461	0.028;0.003;0.011;0.018	B;B;B;B	0.18871	0.023;0.007;0.023;0.021	T	0.09037	-1.0693	10	0.48119	T	0.1	.	4.6958	0.12802	0.0:0.3193:0.1599:0.5208	.	344;481;441;500	Q13683-13;Q13683;Q13683-3;Q4LE35	.;ITA7_HUMAN;.;.	T	441;437;437;344;481;441;437;481;481	ENSP00000452120:K441T;ENSP00000257879:K437T;ENSP00000343009:K437T;ENSP00000393844:K344T;ENSP00000257880:K481T;ENSP00000377777:K441T;ENSP00000377776:K437T;ENSP00000452387:K481T	ENSP00000257879:K437T	K	-	2	0	ITGA7	54377845	0.000000	0.05858	0.982000	0.44146	0.579000	0.36224	-1.670000	0.01956	-0.114000	0.11936	-0.366000	0.07423	AAG		0.622	ITGA7-014	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000410138.1	NM_002206		7	121	0	0	0	1	0	7	121				
CHEK2	11200	broad.mit.edu	37	22	29091841	29091841	+	Silent	SNP	G	G	A	rs146546850	byFrequency	TCGA-ET-A4KN-01A-11D-A257-08	TCGA-ET-A4KN-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	178d0486-cb0d-4979-8bdf-bb3fe99149bd	e3d4072c-07ef-4978-a687-43828578a9b3	g.chr22:29091841G>A	ENST00000405598.1	-	12	1307	c.1116C>T	c.(1114-1116)tcC>tcT	p.S372S	CHEK2_ENST00000348295.3_Silent_p.S343S|CHEK2_ENST00000382578.1_Silent_p.S281S|CHEK2_ENST00000403642.1_Silent_p.S281S|CHEK2_ENST00000544772.1_Silent_p.S151S|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000382580.2_Silent_p.S415S|CHEK2_ENST00000328354.6_Silent_p.S372S|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000402731.1_Silent_p.S343S|CHEK2_ENST00000404276.1_Silent_p.S372S|CHEK2_ENST00000464581.1_5'Flank			O96017	CHK2_HUMAN	checkpoint kinase 2	372	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|T-loop/activation segment.				cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)	p.S372S(8)		central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						CCAAAATCTTGGAGTGCCCAA	0.413			F			breast		Direct reversal of damage;Other conserved DNA damage response genes																														ENST00000544772.1			yes	Rec		familial breast cancer	22	22q12.1	11200	F	CHK2 checkpoint homolog (S. pombe)			E		breast			8	Substitution - coding silent(8)	p.S372S(8)	kidney(4)|prostate(2)|endometrium(1)|central_nervous_system(1)	central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						c.(451-453)tcC>tcT	Direct reversal of damage;Other conserved DNA damage response genes	checkpoint kinase 2							43.0	44.0	44.0					22																	29091841		2203	4300	6503	SO:0001819	synonymous_variant	11200				cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity	g.chr22:29091841G>A	AF086904	CCDS13843.1, CCDS13844.1, CCDS33629.1	22q12.1	2014-09-17	2011-11-11	2001-09-27	ENSG00000183765	ENSG00000183765			16627	protein-coding gene	gene with protein product		604373	"""CHK2 (checkpoint, S.pombe) homolog"", ""CHK2 checkpoint homolog (S. pombe)"""	RAD53		9836640, 10097108	Standard	NM_001257387		Approved	CDS1, CHK2, HuCds1, PP1425, bA444G7	uc003adt.1	O96017	OTTHUMG00000151023	ENST00000405598.1:c.1116C>T	22.37:g.29091841G>A						CHEK2_ENST00000328354.6_Silent_p.S372S|CHEK2_ENST00000405598.1_Silent_p.S372S|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000404276.1_Silent_p.S372S|CHEK2_ENST00000402731.1_Silent_p.S343S|CHEK2_ENST00000382580.2_Silent_p.S415S|CHEK2_ENST00000403642.1_Silent_p.S281S|CHEK2_ENST00000382578.1_Silent_p.S281S|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000348295.3_Silent_p.S343S	p.S151S	NM_001257387.1	NP_001244316.1	O96017	CHK2_HUMAN			12	1889	-			372			FHA.		A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Silent	SNP	ENST00000405598.1	37	c.453C>T	CCDS13843.1	.	.	.	.	.	.	.	.	.	.	G	5.792	0.330417	0.10956	.	.	ENSG00000183765	ENST00000434810	.	.	.	5.89	-2.11	0.07187	.	.	.	.	.	T	0.42154	0.1190	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33854	-0.9852	4	.	.	.	-7.6356	3.2532	0.06822	0.327:0.1103:0.4613:0.1014	.	.	.	.	L	116	.	.	P	-	2	0	CHEK2	27421841	0.997000	0.39634	0.996000	0.52242	0.470000	0.32858	0.318000	0.19504	-0.075000	0.12798	-0.907000	0.02831	CCA		0.413	CHEK2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321150.1	NM_001005735		4	46	0	0	0	1	0	4	46				
CDIP1	29965	broad.mit.edu	37	16	4563025	4563025	+	Silent	SNP	G	G	A			TCGA-ET-A4KN-01A-11D-A257-08	TCGA-ET-A4KN-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	178d0486-cb0d-4979-8bdf-bb3fe99149bd	e3d4072c-07ef-4978-a687-43828578a9b3	g.chr16:4563025G>A	ENST00000399599.3	-	4	830	c.282C>T	c.(280-282)taC>taT	p.Y94Y	CDIP1_ENST00000567695.1_Silent_p.Y94Y|CDIP1_ENST00000563507.1_Intron|CDIP1_ENST00000562334.1_Intron|CDIP1_ENST00000563332.2_Silent_p.Y94Y|CDIP1_ENST00000564828.1_Intron			Q9H305	CDIP1_HUMAN	cell death-inducing p53 target 1	94	Pro-rich.				apoptotic process (GO:0006915)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	nucleus (GO:0005634)											CTGGGGGGTAGTAGCCCATGG	0.657																																						ENST00000399599.3																			0											c.(280-282)taC>taT		cell death-inducing p53 target 1							10.0	11.0	10.0					16																	4563025		1844	4053	5897	SO:0001819	synonymous_variant	29965							g.chr16:4563025G>A	AF131218	CCDS42114.1, CCDS58419.1, CCDS58420.1	16p13.3	2012-11-14	2012-11-14	2012-11-14	ENSG00000089486	ENSG00000089486			13234	protein-coding gene	gene with protein product	"""cell death involved p53-target"", ""lipopolysaccharide-induced TNF factor-like"""	610503	"""chromosome 16 open reading frame 5"""	C16orf5		10570909, 17599062	Standard	NM_013399		Approved	CDIP, LITAFL	uc002cww.3	Q9H305	OTTHUMG00000177172	ENST00000399599.3:c.282C>T	16.37:g.4563025G>A						CDIP1_ENST00000564828.1_Intron|CDIP1_ENST00000562334.1_Intron|CDIP1_ENST00000567695.1_Silent_p.Y94Y|CDIP1_ENST00000563507.1_Intron|CDIP1_ENST00000563332.2_Silent_p.Y94Y	p.Y94Y							4	830	-								A8K7M1|B4DFU1|B4DY75|D3DUD6|Q96ID8|Q9H0Q4|Q9P112	Silent	SNP	ENST00000399599.3	37	c.282C>T	CCDS42114.1																																																																																				0.657	CDIP1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435718.2	NM_013399		3	3	0	0	0	1	0	3	3				
GLI2	2736	broad.mit.edu	37	2	121729541	121729541	+	Missense_Mutation	SNP	G	G	A	rs370677655		TCGA-ET-A4KN-01A-11D-A257-08	TCGA-ET-A4KN-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	178d0486-cb0d-4979-8bdf-bb3fe99149bd	e3d4072c-07ef-4978-a687-43828578a9b3	g.chr2:121729541G>A	ENST00000452319.1	+	8	1144	c.1084G>A	c.(1084-1086)Gtc>Atc	p.V362I	GLI2_ENST00000314490.11_Missense_Mutation_p.V34I|GLI2_ENST00000361492.4_Missense_Mutation_p.V362I|GLI2_ENST00000435313.2_3'UTR					GLI family zinc finger 2											NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(24)|ovary(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(3;0.0496)	Prostate(154;0.0623)				TGAGTCGGCCGTCAGCAGCAC	0.592																																						ENST00000452319.1																			0				NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(24)|ovary(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						c.(1084-1086)Gtc>Atc		GLI family zinc finger 2		G	ILE/VAL	0,4406		0,0,2203	64.0	58.0	60.0		1084	4.8	0.9	2		60	1,8599	1.2+/-3.3	0,1,4299	no	missense	GLI2	NM_005270.4	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	362/1587	121729541	1,13005	2203	4300	6503	SO:0001583	missense	2736				axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr2:121729541G>A		CCDS33283.1	2q14	2013-01-25	2009-03-05		ENSG00000074047	ENSG00000074047		"""Zinc fingers, C2H2-type"""	4318	protein-coding gene	gene with protein product	"""tax-responsive element-2 holding protein"", ""tax helper protein 1"", ""tax helper protein 2"""	165230	"""GLI-Kruppel family member GLI2"", ""glioma-associated oncogene family zinc finger 2"""			2850480, 9557682	Standard	NM_005270		Approved	THP2, HPE9, THP1	uc010flp.3	P10070	OTTHUMG00000153741	ENST00000452319.1:c.1084G>A	2.37:g.121729541G>A	ENSP00000390436:p.Val362Ile					GLI2_ENST00000314490.11_Missense_Mutation_p.V34I|GLI2_ENST00000361492.4_Missense_Mutation_p.V362I|GLI2_ENST00000435313.2_3'UTR	p.V362I			P10070	GLI2_HUMAN			8	1144	+	Renal(3;0.0496)	Prostate(154;0.0623)	362						Missense_Mutation	SNP	ENST00000452319.1	37	c.1084G>A	CCDS33283.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.158123	0.78114	0.0	1.16E-4	ENSG00000074047	ENST00000452319;ENST00000361492;ENST00000314490	T;T;T	0.18810	2.19;2.19;2.19	4.81	4.81	0.61882	.	0.000000	0.85682	D	0.000000	T	0.49372	0.1553	M	0.79475	2.455	0.58432	D	0.999994	P;D;D;D;D	0.89917	0.835;0.999;0.999;0.999;1.0	B;D;D;D;D	0.81914	0.137;0.979;0.991;0.948;0.995	T	0.53920	-0.8370	10	0.66056	D	0.02	.	18.0581	0.89369	0.0:0.0:1.0:0.0	.	362;362;34;34;34	P10070;Q0VGA0;P10070-2;P10070-4;P10070-3	GLI2_HUMAN;.;.;.;.	I	362;362;34	ENSP00000390436:V362I;ENSP00000354586:V362I;ENSP00000312694:V34I	ENSP00000312694:V34I	V	+	1	0	GLI2	121446011	1.000000	0.71417	0.947000	0.38551	0.161000	0.22273	9.652000	0.98499	2.498000	0.84270	0.561000	0.74099	GTC		0.592	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270		12	47	0	0	0	1	0	12	47				
MON2	23041	broad.mit.edu	37	12	62986421	62986421	+	Silent	SNP	C	C	T			TCGA-ET-A4KN-01A-11D-A257-08	TCGA-ET-A4KN-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	178d0486-cb0d-4979-8bdf-bb3fe99149bd	e3d4072c-07ef-4978-a687-43828578a9b3	g.chr12:62986421C>T	ENST00000393632.2	+	35	5437	c.5046C>T	c.(5044-5046)tgC>tgT	p.C1682C	MON2_ENST00000551397.1_Silent_p.C56C|MON2_ENST00000552738.1_Silent_p.C1653C|MON2_ENST00000393629.2_Silent_p.C1676C|MON2_ENST00000546600.1_3'UTR|MON2_ENST00000393630.3_Silent_p.C1683C	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	1682					actin cytoskeleton organization (GO:0030036)|Golgi to endosome transport (GO:0006895)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(15)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	57			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		TAGTAGAATGCATCACCTGTT	0.393																																						ENST00000393630.3																			0				NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(15)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	57						c.(5047-5049)tgC>tgT		MON2 homolog (S. cerevisiae)							131.0	119.0	123.0					12																	62986421		2203	4300	6503	SO:0001819	synonymous_variant	23041				Golgi to endosome transport|protein transport	cytoplasm	ARF guanyl-nucleotide exchange factor activity|binding	g.chr12:62986421C>T		CCDS31849.1, CCDS61175.1, CCDS61177.1, CCDS61178.1	12q14.1	2014-08-12	2006-04-04		ENSG00000061987	ENSG00000061987			29177	protein-coding gene	gene with protein product			"""MON2 homolog (yeast)"""			16301316, 24285343	Standard	NM_015026		Approved	KIAA1040	uc001sre.3	Q7Z3U7	OTTHUMG00000169992	ENST00000393632.2:c.5046C>T	12.37:g.62986421C>T						MON2_ENST00000546600.1_3'UTR|MON2_ENST00000393632.2_Silent_p.C1682C|MON2_ENST00000551397.1_Silent_p.C56C|MON2_ENST00000393629.2_Silent_p.C1676C|MON2_ENST00000552738.1_Silent_p.C1653C	p.C1683C	NM_001278470.1|NM_001278472.1	NP_001265399.1|NP_001265401.1	Q7Z3U7	MON2_HUMAN	BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)	36	5440	+			1683					A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Silent	SNP	ENST00000393632.2	37	c.5049C>T	CCDS31849.1																																																																																				0.393	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406767.3	NM_015026		22	43	0	0	0	1	0	22	43				
ADD2	119	broad.mit.edu	37	2	70900084	70900084	+	Missense_Mutation	SNP	G	G	A			TCGA-ET-A4KN-01A-11D-A257-08	TCGA-ET-A4KN-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	178d0486-cb0d-4979-8bdf-bb3fe99149bd	e3d4072c-07ef-4978-a687-43828578a9b3	g.chr2:70900084G>A	ENST00000264436.4	-	15	2240	c.1796C>T	c.(1795-1797)gCt>gTt	p.A599V	ADD2_ENST00000355733.3_Missense_Mutation_p.L628F|ADD2_ENST00000407644.2_Missense_Mutation_p.A599V	NM_001617.3	NP_001608.1	P35612	ADDB_HUMAN	adducin 2 (beta)	599					actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|barbed-end actin filament capping (GO:0051016)|hemopoiesis (GO:0030097)|positive regulation of protein binding (GO:0032092)|protein complex assembly (GO:0006461)	cytoplasmic membrane-bounded vesicle (GO:0016023)|F-actin capping protein complex (GO:0008290)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|spectrin binding (GO:0030507)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(11)|lung(13)|ovary(3)|pancreas(1)|skin(2)	36						CACTGGAGAAGCAGGTGCAGA	0.512																																						ENST00000264436.3																			0				autonomic_ganglia(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(11)|lung(13)|ovary(3)|pancreas(1)|skin(2)	36						c.(1795-1797)gCt>gTt		adducin 2 (beta)							38.0	37.0	37.0					2																	70900084		2203	4300	6503	SO:0001583	missense	119				actin filament bundle assembly|barbed-end actin filament capping|positive regulation of protein binding	cytoplasm|F-actin capping protein complex|plasma membrane	actin filament binding|calmodulin binding|metal ion binding|protein heterodimerization activity|protein homodimerization activity|spectrin binding	g.chr2:70900084G>A	X58199	CCDS1906.1, CCDS1909.1, CCDS46318.1, CCDS54365.1	2p13.3	2008-02-05			ENSG00000075340	ENSG00000075340			244	protein-coding gene	gene with protein product		102681				1840603	Standard	NM_001617		Approved	ADDB	uc021vjc.1	P35612	OTTHUMG00000129710	ENST00000264436.4:c.1796C>T	2.37:g.70900084G>A	ENSP00000264436:p.Ala599Val					ADD2_ENST00000407644.2_Missense_Mutation_p.A599V|ADD2_ENST00000355733.3_Missense_Mutation_p.L628F	p.A599V	NM_001617.3	NP_001608.1	P35612	ADDB_HUMAN			15	2240	-			599					A8K4P2|B4DM17|D6W5G7|D6W5G8|Q13482|Q16412|Q59G82|Q5U5P4|Q6P0P2|Q6PGQ4|Q7Z688|Q7Z689|Q7Z690|Q7Z691	Missense_Mutation	SNP	ENST00000264436.4	37	c.1796C>T	CCDS1906.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.29|13.29	2.191944|2.191944	0.38707|0.38707	.|.	.|.	ENSG00000075340|ENSG00000075340	ENST00000264436;ENST00000407644;ENST00000456320|ENST00000355733	T;T|T	0.14893|0.08896	2.47;2.47|3.04	5.97|5.97	5.97|5.97	0.96955|0.96955	.|.	0.292022|.	0.31872|.	N|.	0.006939|.	T|T	0.12561|0.12561	0.0305|0.0305	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	B;B|B	0.06786|0.27791	0.0;0.001|0.189	B;B|B	0.06405|0.31686	0.002;0.001|0.134	T|T	0.02081|0.02081	-1.1217|-1.1217	9|8	0.25106|0.72032	T|D	0.35|0.01	-3.9928|-3.9928	17.9218|17.9218	0.88969|0.88969	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	599;599|628	Q05DK5;P35612|P35612-3	.;ADDB_HUMAN|.	V|F	599;599;351|628	ENSP00000264436:A599V;ENSP00000384677:A599V|ENSP00000347972:L628F	ENSP00000264436:A599V|ENSP00000347972:L628F	A|L	-|-	2|1	0|0	ADD2|ADD2	70753592|70753592	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.514000|0.514000	0.34195|0.34195	3.745000|3.745000	0.55119|0.55119	2.837000|2.837000	0.97791|0.97791	0.655000|0.655000	0.94253|0.94253	GCT|CTT		0.512	ADD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251918.4	NM_001617		6	29	0	0	0	1	0	6	29				
C10orf54	64115	broad.mit.edu	37	10	73521443	73521443	+	Silent	SNP	G	G	A			TCGA-ET-A4KN-01A-11D-A257-08	TCGA-ET-A4KN-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	178d0486-cb0d-4979-8bdf-bb3fe99149bd	e3d4072c-07ef-4978-a687-43828578a9b3	g.chr10:73521443G>A	ENST00000394957.3	-	2	481	c.423C>T	c.(421-423)agC>agT	p.S141S	C10orf54_ENST00000481568.2_5'UTR|CDH23_ENST00000224721.6_Intron	NM_022153.1	NP_071436.1	Q9H7M9	GI24_HUMAN	chromosome 10 open reading frame 54	141	Ig-like.				BMP signaling pathway (GO:0030509)|negative regulation of CD4-positive, alpha-beta T cell proliferation (GO:2000562)|negative regulation of T cell cytokine production (GO:0002725)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of stem cell differentiation (GO:2000738)|stem cell differentiation (GO:0048863)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|endometrium(1)|lung(1)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	9						AGTAGAGGCCGCTATCCAGCA	0.642																																						ENST00000394957.3																			0				breast(1)|central_nervous_system(2)|endometrium(1)|lung(1)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	9						c.(421-423)agC>agT		chromosome 10 open reading frame 54							59.0	54.0	56.0					10																	73521443		2203	4300	6503	SO:0001819	synonymous_variant	64115					integral to membrane	receptor activity	g.chr10:73521443G>A	AF193048	CCDS31218.1	10q22.1	2013-11-28			ENSG00000107738	ENSG00000107738		"""Immunoglobulin superfamily / V-set domain containing"""	30085	protein-coding gene	gene with protein product	"""stress induced secreted protein 1"""	615608				12975309	Standard	NM_022153		Approved	SISP1, GI24, B7-H5, B7H5	uc001jsd.3	Q9H7M9	OTTHUMG00000018426	ENST00000394957.3:c.423C>T	10.37:g.73521443G>A						C10orf54_ENST00000481568.1_5'UTR|CDH23_ENST00000224721.6_Intron	p.S141S	NM_022153.1	NP_071436.1	Q9H7M9	GI24_HUMAN			2	481	-			141			Ig-like.		A1L0X9|A4ZYV1|A8MVH5|Q6UXF3|Q8WUG3|Q8WYZ8	Silent	SNP	ENST00000394957.3	37	c.423C>T	CCDS31218.1																																																																																				0.642	C10orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048548.1	NM_022153		3	38	0	0	0	1	0	3	38				
CDKN1A	1026	broad.mit.edu	37	6	36651904	36651904	+	Missense_Mutation	SNP	G	G	C	rs143419412	byFrequency	TCGA-ET-A4KN-01A-11D-A257-08	TCGA-ET-A4KN-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	178d0486-cb0d-4979-8bdf-bb3fe99149bd	e3d4072c-07ef-4978-a687-43828578a9b3	g.chr6:36651904G>C	ENST00000405375.1	+	2	261	c.26G>C	c.(25-27)cGt>cCt	p.R9P	CDKN1A_ENST00000244741.5_Missense_Mutation_p.R9P|CDKN1A_ENST00000373711.2_Missense_Mutation_p.R9P|CDKN1A_ENST00000448526.2_Missense_Mutation_p.R43P|CDKN1A_ENST00000478800.1_3'UTR	NM_001220778.1	NP_001207707.1	P38936	CDN1A_HUMAN	cyclin-dependent kinase inhibitor 1A (p21, Cip1)	9					cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to extracellular stimulus (GO:0031668)|cellular response to ionizing radiation (GO:0071479)|cellular senescence (GO:0090398)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle (GO:0000278)|mitotic cell cycle arrest (GO:0071850)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of gene expression (GO:0010629)|negative regulation of phosphorylation (GO:0042326)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ regeneration (GO:0031100)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of programmed cell death (GO:0043068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of DNA biosynthetic process (GO:2000278)|regulation of protein import into nucleus, translocation (GO:0033158)|response to arsenic-containing substance (GO:0046685)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to hyperoxia (GO:0055093)|response to organonitrogen compound (GO:0010243)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|stress-induced premature senescence (GO:0090400)	cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCNA-p21 complex (GO:0070557)	cyclin-dependent protein kinase activating kinase activity (GO:0019912)|cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|urinary_tract(5)	15						GGGGATGTCCGTCAGAACCCA	0.632																																						ENST00000405375.1																			0				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|urinary_tract(5)	15						c.(25-27)cGt>cCt		cyclin-dependent kinase inhibitor 1A (p21, Cip1)							28.0	29.0	29.0					6																	36651904		2203	4300	6503	SO:0001583	missense	1026				cell cycle arrest|cellular response to extracellular stimulus|cellular response to ionizing radiation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|induction of apoptosis by intracellular signals|negative regulation of cell growth|negative regulation of cell proliferation|positive regulation of fibroblast proliferation|positive regulation of reactive oxygen species metabolic process|Ras protein signal transduction|S phase of mitotic cell cycle|stress-induced premature senescence	cyclin-dependent protein kinase holoenzyme complex|cytosol|nucleoplasm|PCNA-p21 complex	cyclin-dependent protein kinase activating kinase activity|cyclin-dependent protein kinase inhibitor activity|metal ion binding	g.chr6:36651904G>C	U03106	CCDS4824.1	6p21.1	2009-01-21			ENSG00000124762	ENSG00000124762			1784	protein-coding gene	gene with protein product		116899		CDKN1			Standard	NM_000389		Approved	P21, CIP1, WAF1, SDI1, CAP20, p21CIP1, p21Cip1/Waf1	uc021yzb.1	P38936	OTTHUMG00000014603	ENST00000405375.1:c.26G>C	6.37:g.36651904G>C	ENSP00000384849:p.Arg9Pro					CDKN1A_ENST00000244741.5_Missense_Mutation_p.R9P|CDKN1A_ENST00000448526.2_Missense_Mutation_p.R43P|CDKN1A_ENST00000478800.1_3'UTR|CDKN1A_ENST00000373711.2_Missense_Mutation_p.R9P	p.R9P	NM_001220778.1	NP_001207707.1	P38936	CDN1A_HUMAN			2	261	+			9					Q14010|Q6FI05|Q9BUT4	Missense_Mutation	SNP	ENST00000405375.1	37	c.26G>C	CCDS4824.1	.	.	.	.	.	.	.	.	.	.	G	12.03	1.816583	0.32145	.	.	ENSG00000124762	ENST00000448526;ENST00000244741;ENST00000405375;ENST00000373711	D;D;D;D	0.82081	-1.54;-1.57;-1.57;-1.57	5.06	-0.214	0.13161	.	0.538000	0.17088	N	0.187482	T	0.55386	0.1917	L	0.54323	1.7	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.08055	0.003;0.003;0.003	T	0.48948	-0.8989	10	0.46703	T	0.11	-0.2002	1.9604	0.03385	0.1877:0.3482:0.3256:0.1385	.	43;9;9	B4DQP9;P38936;Q96LE1	.;CDN1A_HUMAN;.	P	43;9;9;9	ENSP00000409259:R43P;ENSP00000244741:R9P;ENSP00000384849:R9P;ENSP00000362815:R9P	ENSP00000244741:R9P	R	+	2	0	CDKN1A	36759882	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.184000	0.09698	-0.252000	0.09528	0.561000	0.74099	CGT		0.632	CDKN1A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040354.1	NM_078467		7	32	0	0	0	1	0	7	32				
MED11	400569	broad.mit.edu	37	17	4634849	4634849	+	Missense_Mutation	SNP	G	G	A			TCGA-ET-A4KN-01A-11D-A257-08	TCGA-ET-A4KN-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	178d0486-cb0d-4979-8bdf-bb3fe99149bd	e3d4072c-07ef-4978-a687-43828578a9b3	g.chr17:4634849G>A	ENST00000293777.5	+	1	121	c.65G>A	c.(64-66)gGc>gAc	p.G22D	MED11_ENST00000573708.1_Missense_Mutation_p.G22D|CXCL16_ENST00000576153.1_5'Flank|RP11-314A20.5_ENST00000570493.2_RNA|MED11_ENST00000575284.1_Missense_Mutation_p.G22D	NM_001001683.2	NP_001001683.1	Q9P086	MED11_HUMAN	mediator complex subunit 11	22						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			lung(2)|ovary(2)	4						CGGGAAATCGGCGCCATCCTT	0.577											OREG0024104	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000293777.5																			0				lung(2)|ovary(2)	4						c.(64-66)gGc>gAc		mediator complex subunit 11							94.0	75.0	82.0					17																	4634849		2203	4300	6503	SO:0001583	missense	400569				regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex	protein binding	g.chr17:4634849G>A	AF161414	CCDS32533.1	17p13.2	2007-07-30	2007-07-30			ENSG00000161920			32687	protein-coding gene	gene with protein product		612383	"""mediator of RNA polymerase II transcription, subunit 11 homolog (S. cerevisiae)"""			15175163, 12584197	Standard	NM_001001683		Approved	HSPC296, MGC88387	uc002fyp.3	Q9P086		ENST00000293777.5:c.65G>A	17.37:g.4634849G>A	ENSP00000293777:p.Gly22Asp		OREG0024104	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	620	MED11_ENST00000575284.1_Missense_Mutation_p.G22D|MED11_ENST00000573708.1_Missense_Mutation_p.G22D	p.G22D	NM_001001683.2	NP_001001683.1	Q9P086	MED11_HUMAN			1	121	+			22					Q6NS89	Missense_Mutation	SNP	ENST00000293777.5	37	c.65G>A	CCDS32533.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.009514	0.75046	.	.	ENSG00000161920	ENST00000293777	.	.	.	5.06	5.06	0.68205	.	0.066615	0.56097	D	0.000030	T	0.31702	0.0805	N	0.08118	0	0.43242	D	0.995152	B	0.26195	0.144	B	0.23852	0.049	T	0.15263	-1.0443	9	0.39692	T	0.17	-25.2285	11.6077	0.51041	0.0:0.1796:0.8204:0.0	.	22	Q9P086	MED11_HUMAN	D	22	.	ENSP00000293777:G22D	G	+	2	0	MED11	4581598	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.826000	0.62715	2.630000	0.89119	0.655000	0.94253	GGC		0.577	MED11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439574.1	NM_001001683		10	37	0	0	0	1	0	10	37				
CHEK2	11200	broad.mit.edu	37	22	29091840	29091840	+	Missense_Mutation	SNP	T	T	C	rs142470496	byFrequency	TCGA-ET-A4KN-01A-11D-A257-08	TCGA-ET-A4KN-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	178d0486-cb0d-4979-8bdf-bb3fe99149bd	e3d4072c-07ef-4978-a687-43828578a9b3	g.chr22:29091840T>C	ENST00000405598.1	-	12	1308	c.1117A>G	c.(1117-1119)Aag>Gag	p.K373E	CHEK2_ENST00000348295.3_Missense_Mutation_p.K344E|CHEK2_ENST00000382578.1_Missense_Mutation_p.K282E|CHEK2_ENST00000403642.1_Missense_Mutation_p.K282E|CHEK2_ENST00000544772.1_Missense_Mutation_p.K152E|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000382580.2_Missense_Mutation_p.K416E|CHEK2_ENST00000328354.6_Missense_Mutation_p.K373E|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000402731.1_Missense_Mutation_p.K344E|CHEK2_ENST00000404276.1_Missense_Mutation_p.K373E|CHEK2_ENST00000464581.1_5'Flank			O96017	CHK2_HUMAN	checkpoint kinase 2	373	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|T-loop/activation segment.				cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)	p.K373E(9)		central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						CCCAAAATCTTGGAGTGCCCA	0.418			F			breast		Direct reversal of damage;Other conserved DNA damage response genes																														ENST00000544772.1			yes	Rec		familial breast cancer	22	22q12.1	11200	F	CHK2 checkpoint homolog (S. pombe)			E		breast			9	Substitution - Missense(9)	p.K373E(9)	kidney(4)|prostate(2)|endometrium(1)|stomach(1)|central_nervous_system(1)	central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						c.(454-456)Aag>Gag	Direct reversal of damage;Other conserved DNA damage response genes	checkpoint kinase 2																																				SO:0001583	missense	11200				cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity	g.chr22:29091840T>C	AF086904	CCDS13843.1, CCDS13844.1, CCDS33629.1	22q12.1	2014-09-17	2011-11-11	2001-09-27	ENSG00000183765	ENSG00000183765			16627	protein-coding gene	gene with protein product		604373	"""CHK2 (checkpoint, S.pombe) homolog"", ""CHK2 checkpoint homolog (S. pombe)"""	RAD53		9836640, 10097108	Standard	NM_001257387		Approved	CDS1, CHK2, HuCds1, PP1425, bA444G7	uc003adt.1	O96017	OTTHUMG00000151023	ENST00000405598.1:c.1117A>G	22.37:g.29091840T>C	ENSP00000386087:p.Lys373Glu					CHEK2_ENST00000328354.6_Missense_Mutation_p.K373E|CHEK2_ENST00000405598.1_Missense_Mutation_p.K373E|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000404276.1_Missense_Mutation_p.K373E|CHEK2_ENST00000402731.1_Missense_Mutation_p.K344E|CHEK2_ENST00000382580.2_Missense_Mutation_p.K416E|CHEK2_ENST00000403642.1_Missense_Mutation_p.K282E|CHEK2_ENST00000382578.1_Missense_Mutation_p.K282E|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000348295.3_Missense_Mutation_p.K344E	p.K152E	NM_001257387.1	NP_001244316.1	O96017	CHK2_HUMAN			12	1890	-			373			FHA.		A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Missense_Mutation	SNP	ENST00000405598.1	37	c.454A>G	CCDS13843.1	.	.	.	.	.	.	.	.	.	.	T	19.06	3.754336	0.69648	.	.	ENSG00000183765	ENST00000348295;ENST00000382578;ENST00000544772;ENST00000328354;ENST00000404276;ENST00000405598;ENST00000382580;ENST00000403642;ENST00000402731	T;T;T;T;T;T;T;T;T	0.54071	0.9;0.59;0.59;0.59;0.59;0.59;0.59;0.59;0.9	5.89	5.89	0.94794	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.043710	0.85682	D	0.000000	T	0.56292	0.1975	N	0.11756	0.17	0.80722	D	1	D;D;D;D;D;D	0.76494	0.996;0.999;0.998;0.998;0.993;0.991	P;D;D;D;D;P	0.74674	0.905;0.984;0.943;0.969;0.923;0.896	T	0.64769	-0.6329	10	0.87932	D	0	-1.7726	15.4726	0.75453	0.0:0.0:0.0:1.0	.	282;152;373;344;373;416	O96017-4;Q9HBS5;A8JZZ5;O96017-12;O96017;O96017-9	.;.;.;.;CHK2_HUMAN;.	E	344;282;152;373;373;373;416;282;344	ENSP00000329012:K344E;ENSP00000372021:K282E;ENSP00000442458:K152E;ENSP00000329178:K373E;ENSP00000385747:K373E;ENSP00000386087:K373E;ENSP00000372023:K416E;ENSP00000384919:K282E;ENSP00000384835:K344E	ENSP00000329178:K373E	K	-	1	0	CHEK2	27421840	1.000000	0.71417	1.000000	0.80357	0.479000	0.33129	4.270000	0.58896	2.248000	0.74166	0.528000	0.53228	AAG		0.418	CHEK2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321150.1	NM_001005735		4	47	0	0	0	1	0	4	47				
PTK2B	2185	broad.mit.edu	37	8	27291612	27291612	+	Missense_Mutation	SNP	G	G	A			TCGA-ET-A4KN-01A-11D-A257-08	TCGA-ET-A4KN-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	178d0486-cb0d-4979-8bdf-bb3fe99149bd	e3d4072c-07ef-4978-a687-43828578a9b3	g.chr8:27291612G>A	ENST00000397501.1	+	17	1916	c.1108G>A	c.(1108-1110)Ggt>Agt	p.G370S	PTK2B_ENST00000420218.2_Missense_Mutation_p.G370S|PTK2B_ENST00000338238.4_Missense_Mutation_p.G370S|PTK2B_ENST00000346049.5_Missense_Mutation_p.G370S|PTK2B_ENST00000397497.4_Missense_Mutation_p.G116S|PTK2B_ENST00000544172.1_Missense_Mutation_p.G370S|PTK2B_ENST00000517339.1_Missense_Mutation_p.G370S	NM_173174.2	NP_775266.1	Q14289	FAK2_HUMAN	protein tyrosine kinase 2 beta	370					activation of Janus kinase activity (GO:0042976)|activation of Rac GTPase activity (GO:0032863)|apoptotic process (GO:0006915)|blood vessel endothelial cell migration (GO:0043534)|bone resorption (GO:0045453)|cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|cellular response to retinoic acid (GO:0071300)|chemokine-mediated signaling pathway (GO:0070098)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|glial cell proliferation (GO:0014009)|integrin-mediated signaling pathway (GO:0007229)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term synaptic potentiation (GO:0060291)|MAPK cascade (GO:0000165)|marginal zone B cell differentiation (GO:0002315)|negative regulation of apoptotic process (GO:0043066)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cell proliferation (GO:0008285)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of potassium ion transport (GO:0043267)|neuron projection development (GO:0031175)|oocyte maturation (GO:0001556)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of B cell chemotaxis (GO:2000538)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell adhesion (GO:0030155)|regulation of cell shape (GO:0008360)|regulation of establishment of cell polarity (GO:2000114)|regulation of inositol trisphosphate biosynthetic process (GO:0032960)|regulation of macrophage chemotaxis (GO:0010758)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000058)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|response to calcium ion (GO:0051592)|response to cAMP (GO:0051591)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to hormone (GO:0009725)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|response to lithium ion (GO:0010226)|response to mechanical stimulus (GO:0009612)|response to osmotic stress (GO:0006970)|response to stress (GO:0006950)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|sprouting angiogenesis (GO:0002040)|stress fiber assembly (GO:0043149)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	apical dendrite (GO:0097440)|axon (GO:0030424)|cell body (GO:0044297)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane raft (GO:0045121)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|signal transducer activity (GO:0004871)			breast(2)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(17)|ovary(4)|skin(12)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Ovarian(32;2.72e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|Epithelial(17;6.61e-10)|BRCA - Breast invasive adenocarcinoma(99;0.226)|Colorectal(74;0.229)	Leflunomide(DB01097)	CTTCCTAGATGGTGAGAAGCG	0.582																																						ENST00000397501.1																			0				breast(2)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(17)|ovary(4)|skin(12)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	47						c.(1108-1110)Ggt>Agt		protein tyrosine kinase 2 beta							124.0	116.0	119.0					8																	27291612		2203	4300	6503	SO:0001583	missense	2185				apoptosis|bone resorption|positive regulation of cell proliferation|signal complex assembly	cytosol	ATP binding|non-membrane spanning protein tyrosine kinase activity|signal transducer activity	g.chr8:27291612G>A	U33284	CCDS6057.1, CCDS6058.1	8p21.1	2013-02-18	2013-02-18		ENSG00000120899	ENSG00000120899			9612	protein-coding gene	gene with protein product		601212	"""protein tyrosine kinase 2 beta"", ""PTK2B protein tyrosine kinase 2 beta"""	FAK2		7544443, 7499242	Standard	NM_173174		Approved	CAKB, PYK2, RAFTK, PTK, CADTK	uc003xfp.2	Q14289	OTTHUMG00000102082	ENST00000397501.1:c.1108G>A	8.37:g.27291612G>A	ENSP00000380638:p.Gly370Ser					PTK2B_ENST00000544172.1_Missense_Mutation_p.G370S|PTK2B_ENST00000397497.4_Missense_Mutation_p.G116S|PTK2B_ENST00000338238.4_Missense_Mutation_p.G370S|PTK2B_ENST00000346049.5_Missense_Mutation_p.G370S|PTK2B_ENST00000517339.1_Missense_Mutation_p.G370S|PTK2B_ENST00000420218.2_Missense_Mutation_p.G370S	p.G370S	NM_173174.2	NP_775266.1	Q14289	FAK2_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|Epithelial(17;6.61e-10)|BRCA - Breast invasive adenocarcinoma(99;0.226)|Colorectal(74;0.229)	17	1916	+		Ovarian(32;2.72e-05)	370					D3DST0|Q13475|Q14290|Q16709|Q6PID4	Missense_Mutation	SNP	ENST00000397501.1	37	c.1108G>A	CCDS6057.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.28|15.28	2.785508|2.785508	0.49997|0.49997	.|.	.|.	ENSG00000120899|ENSG00000120899	ENST00000397501;ENST00000539100;ENST00000338238;ENST00000544172;ENST00000346049;ENST00000420218;ENST00000517339;ENST00000397497|ENST00000519512	T;T;T;T;T;T;T|.	0.74526|.	-0.85;-0.8;-0.85;-0.85;-0.8;-0.8;-0.81|.	5.22|5.22	5.22|5.22	0.72569|0.72569	.|.	0.447714|.	0.26262|.	N|.	0.025394|.	T|.	0.48909|.	0.1526|.	L|L	0.36672|0.36672	1.1|1.1	0.35223|0.35223	D|D	0.776227|0.776227	B;B;B;B|.	0.13145|.	0.004;0.001;0.007;0.003|.	B;B;B;B|.	0.17098|.	0.005;0.003;0.011;0.017|.	T|.	0.57183|.	-0.7855|.	10|.	0.32370|.	T|.	0.25|.	.|.	9.8231|9.8231	0.40894|0.40894	0.0939:0.0:0.9061:0.0|0.0939:0.0:0.9061:0.0	.|.	375;116;370;370|.	Q59GM4;E9PBI4;Q14289-2;Q14289|.	.;.;.;FAK2_HUMAN|.	S|X	370;375;370;370;370;370;370;116|130	ENSP00000380638:G370S;ENSP00000342242:G370S;ENSP00000440926:G370S;ENSP00000332816:G370S;ENSP00000391995:G370S;ENSP00000427931:G370S;ENSP00000380634:G116S|.	ENSP00000342242:G370S|.	G|W	+|+	1|2	0|0	PTK2B|PTK2B	27347529|27347529	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.806000|0.806000	0.45545|0.45545	2.182000|2.182000	0.42556|0.42556	2.414000|2.414000	0.81942|0.81942	0.655000|0.655000	0.94253|0.94253	GGT|TGG		0.582	PTK2B-009	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219916.1	NM_004103		22	89	0	0	0	1	0	22	89				
GPSM1	26086	broad.mit.edu	37	9	139235482	139235482	+	Intron	DEL	C	C	-	rs374298038|rs145729152	byFrequency	TCGA-ET-A4KN-01A-11D-A257-08	TCGA-ET-A4KN-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	178d0486-cb0d-4979-8bdf-bb3fe99149bd	e3d4072c-07ef-4978-a687-43828578a9b3	g.chr9:139235482delC	ENST00000440944.1	+	9	1427				GPSM1_ENST00000392945.3_Frame_Shift_Del_p.L413fs	NM_001145638.1	NP_001139110	Q86YR5	GPSM1_HUMAN	G-protein signaling modulator 1						cell differentiation (GO:0030154)|nervous system development (GO:0007399)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	GDP-dissociation inhibitor activity (GO:0005092)			biliary_tract(1)|endometrium(1)|kidney(2)|lung(4)|upper_aerodigestive_tract(1)	9		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.39e-06)|Epithelial(140;3.24e-06)		GGGTCTTGCTCCCCACAGGCA	0.687													?|CCCC|CCC|unsure	747	0.149161	0.0961	0.0793	5008	,	,		14952	0.252		0.1372	False		,,,				2504	0.1769					ENST00000392945.3																			0				biliary_tract(1)|endometrium(1)|kidney(2)|lung(4)|upper_aerodigestive_tract(1)	9						c.(1237-1239)ctfs		G-protein signaling modulator 1			,	494,3628		54,386,1621	12.0	14.0	14.0		,	0.3	0.0	9	dbSNP_134	15	1203,6943		136,931,3006	no	frameshift,intron	GPSM1	NM_015597.4,NM_001145638.1	,	190,1317,4627	A1A1,A1R,RR		14.768,11.9845,13.8327	,	,	139235482	1697,10571	2116	4195	6311	SO:0001627	intron_variant	26086				cell differentiation|nervous system development|signal transduction	cytosol|endoplasmic reticulum membrane|Golgi membrane|plasma membrane	binding|GTPase activator activity	g.chr9:139235482delC	AI272212	CCDS6996.2, CCDS48055.1, CCDS48056.1	9q34.3	2013-01-10	2010-06-24		ENSG00000160360	ENSG00000160360		"""Tetratricopeptide (TTC) repeat domain containing"""	17858	protein-coding gene	gene with protein product	"""AGS3 homolog (C. elegans)"""	609491	"""G-protein signalling modulator 1 (AGS3-like, C. elegans)"""			11278352, 10969064	Standard	NM_001145639		Approved	AGS3, DKFZP727I051	uc004chd.2	Q86YR5	OTTHUMG00000020930	ENST00000440944.1:c.1207+32C>-	9.37:g.139235482delC						GPSM1_ENST00000440944.1_Intron	p.L413fs	NM_015597.4	NP_056412.4	Q86YR5	GPSM1_HUMAN		OV - Ovarian serous cystadenocarcinoma(145;2.39e-06)|Epithelial(140;3.24e-06)	9	1459	+		Myeloproliferative disorder(178;0.0821)	0			Interaction with STK11/LKB1 (By similarity).|Mediates association with membranes (By similarity).		A9Z1X4|B1B0W3|Q86SR5|Q969T1|Q9UFS8	Frame_Shift_Del	DEL	ENST00000440944.1	37	c.1239delC	CCDS48055.1																																																																																				0.687	GPSM1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015597		3	3						3	3	---	---	---	---
CTB-134H23.3	0	broad.mit.edu	37	16	29113498	29113498	+	RNA	DEL	T	T	-	rs11366120	byFrequency	TCGA-ET-A4KN-01A-11D-A257-08	TCGA-ET-A4KN-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	178d0486-cb0d-4979-8bdf-bb3fe99149bd	e3d4072c-07ef-4978-a687-43828578a9b3	g.chr16:29113498delT	ENST00000562618.1	-	0	1840				RRN3P2_ENST00000564580.1_RNA																							AGGAGGTGGAttttttttttc	0.542													|||unknown(NO_COVERAGE)	2145	0.428315	0.5507	0.4856	5008	,	,		13214	0.248		0.4334	False		,,,				2504	0.4029					ENST00000564580.1																			0																																																			0							g.chr16:29113498delT																													16.37:g.29113498delT														0	1360	+									RNA	DEL	ENST00000562618.1	37																																																																																						0.542	CTB-134H23.3-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000433241.1			4	7						4	7	---	---	---	---
