#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_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_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_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	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	t_alt_count	t_ref_count
BRAP	8315	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	112110475	112110475	+	Missense_Mutation	SNP	T	T	C	rs150096881		TCGA-HW-8322-01A-11D-2395-08	TCGA-HW-8322-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbb7361c-879c-4964-b6c8-07b5d8d4da46	088c5f2e-ee43-4263-9962-ef89954380a7	g.chr12:112110475T>C	ENST00000327551.6	-	5	787	c.647A>G	c.(646-648)aAa>aGa	p.K216R	BRAP_ENST00000419234.4_Missense_Mutation_p.K246R|BRAP_ENST00000539060.1_Intron			Q6UWU4	CF089_HUMAN	BRCA1 associated protein	0					epithelial cell proliferation (GO:0050673)|positive regulation of cell cycle (GO:0045787)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	20						ATCTTCAGATTTGAGCACTTC	0.363																																					Pancreas(146;846 1904 7830 25130 26065)											0													95.0	83.0	87.0					12																	112110475		2203	4300	6503	SO:0001583	missense	8315			AF035620	CCDS9154.1	12q24.12	2014-09-11			ENSG00000089234	ENSG00000089234		"""RING-type (C3HC4) zinc fingers"""	1099	protein-coding gene	gene with protein product	"""impedes mitogenic signal propagation"", ""galectin-2-binding protein"""	604986				9497340, 19198608	Standard	XM_005253944		Approved	BRAP2, RNF52, IMP	uc001tsn.4	Q7Z569	OTTHUMG00000169600	ENST00000327551.6:c.647A>G	12.37:g.112110475T>C	ENSP00000330813:p.Lys216Arg		B4DTT1|F4NAR0|F4NAR1|Q6ZMG5|Q7Z356|Q8IZ35	Missense_Mutation	SNP	ENST00000327551.6	37		.	.	.	.	.	.	.	.	.	.	T	14.10	2.435454	0.43224	.	.	ENSG00000089234	ENST00000419234;ENST00000327551;ENST00000547043	T;T	0.47177	0.85;0.87	5.49	5.49	0.81192	BRCA1-associated 2 (1);	0.000000	0.85682	D	0.000000	T	0.59783	0.2219	L	0.45228	1.405	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	T	0.54721	-0.8251	10	0.24483	T	0.36	-21.8046	15.5776	0.76404	0.0:0.0:0.0:1.0	.	246	Q7Z569	BRAP_HUMAN	R	246;216;28	ENSP00000403524:K246R;ENSP00000330813:K216R	ENSP00000330813:K216R	K	-	2	0	BRAP	110594858	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.539000	0.82063	2.094000	0.63399	0.454000	0.30748	AAA		0.363	BRAP-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404994.2			27	47	27	47
REC8	9985	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	14	24642224	24642224	+	Missense_Mutation	SNP	A	A	G			TCGA-HW-8322-01A-11D-2395-08	TCGA-HW-8322-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbb7361c-879c-4964-b6c8-07b5d8d4da46	088c5f2e-ee43-4263-9962-ef89954380a7	g.chr14:24642224A>G	ENST00000311457.3	+	4	841	c.242A>G	c.(241-243)tAt>tGt	p.Y81C	REC8_ENST00000559919.1_Missense_Mutation_p.Y81C			O95072	REC8_HUMAN	REC8 meiotic recombination protein	81					double-strand break repair via homologous recombination (GO:0000724)|fertilization (GO:0009566)|linear element assembly (GO:0030999)|male meiosis I (GO:0007141)|meiotic nuclear division (GO:0007126)|oocyte maturation (GO:0001556)|reciprocal meiotic recombination (GO:0007131)|seminiferous tubule development (GO:0072520)|sister chromatid cohesion (GO:0007062)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)	condensed nuclear chromosome kinetochore (GO:0000778)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|nuclear meiotic cohesin complex (GO:0034991)|nucleus (GO:0005634)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	15				GBM - Glioblastoma multiforme(265;0.00839)		ATCCGCGTCTATTCTCAACAA	0.617																																					NSCLC(139;1764 2537 12868 49041)											0													106.0	112.0	110.0					14																	24642224		2008	4170	6178	SO:0001583	missense	9985			AF006264	CCDS41932.1	14q11.2-q12	2013-08-06	2013-08-06	2007-04-03		ENSG00000100918			16879	protein-coding gene	gene with protein product		608193	"""REC8-like 1 (yeast)"", ""REC8 homolog (yeast)"""	REC8L1		10207075, 15935783, 12759374	Standard	NM_005132		Approved	Rec8p, kleisin-alpha	uc001wms.3	O95072		ENST00000311457.3:c.242A>G	14.37:g.24642224A>G	ENSP00000308699:p.Tyr81Cys		A8K576|D3DS62|Q658V5|Q6IA92|Q8WUV8|Q9BTF2|Q9NVQ9	Missense_Mutation	SNP	ENST00000311457.3	37	CCDS41932.1	.	.	.	.	.	.	.	.	.	.	A	19.19	3.780435	0.70222	.	.	ENSG00000100918	ENST00000311457;ENST00000447460	T	0.58797	0.31	5.25	4.08	0.47627	Rad21/Rec8-like protein, N-terminal (1);	0.067648	0.64402	D	0.000011	T	0.77890	0.4198	M	0.90309	3.105	0.43084	D	0.994747	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.991	T	0.80341	-0.1423	10	0.87932	D	0	-10.1516	10.0812	0.42391	0.8307:0.1692:0.0:0.0	.	81;81	O95072-2;O95072	.;REC8_HUMAN	C	81	ENSP00000308699:Y81C	ENSP00000308699:Y81C	Y	+	2	0	REC8	23712064	1.000000	0.71417	0.992000	0.48379	0.919000	0.55068	4.084000	0.57650	0.795000	0.33922	0.459000	0.35465	TAT		0.617	REC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415889.3	NM_005132		58	85	58	85
ADSSL1	122622	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	14	105209429	105209429	+	Missense_Mutation	SNP	G	G	A			TCGA-HW-8322-01A-11D-2395-08	TCGA-HW-8322-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbb7361c-879c-4964-b6c8-07b5d8d4da46	088c5f2e-ee43-4263-9962-ef89954380a7	g.chr14:105209429G>A	ENST00000330877.2	+	10	1059	c.974G>A	c.(973-975)cGc>cAc	p.R325H	ADSSL1_ENST00000555674.1_5'Flank|ADSSL1_ENST00000556623.1_5'Flank|ADSSL1_ENST00000332972.5_Missense_Mutation_p.R368H	NM_152328.3	NP_689541.1			adenylosuccinate synthase like 1											central_nervous_system(1)|cervix(1)|kidney(1)|lung(5)|ovary(2)|prostate(1)	11		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00153)|OV - Ovarian serous cystadenocarcinoma(23;0.0148)|Epithelial(46;0.0396)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.18)		CTGCAGACCCGCGGCCACGAG	0.612																																																0													84.0	82.0	82.0					14																	105209429		2203	4300	6503	SO:0001583	missense	122622			AK095921	CCDS9990.1, CCDS9991.1	14q32.33	2010-08-05			ENSG00000185100	ENSG00000185100			20093	protein-coding gene	gene with protein product		612498					Standard	NM_199165		Approved	FLJ38602	uc001ype.3	Q8N142		ENST00000330877.2:c.974G>A	14.37:g.105209429G>A	ENSP00000331260:p.Arg325His			Missense_Mutation	SNP	ENST00000330877.2	37	CCDS9990.1	.	.	.	.	.	.	.	.	.	.	G	18.04	3.534681	0.64972	.	.	ENSG00000185100	ENST00000330877;ENST00000332972	T;T	0.45668	0.89;0.89	4.82	3.92	0.45320	.	0.000000	0.85682	D	0.000000	T	0.57873	0.2083	M	0.73217	2.22	0.80722	D	1	D;D	0.76494	0.994;0.999	P;P	0.60682	0.806;0.878	T	0.59161	-0.7506	10	0.45353	T	0.12	-18.8102	12.7275	0.57178	0.081:0.0:0.919:0.0	.	368;325	Q8N142-2;Q8N142	.;PURA1_HUMAN	H	325;368	ENSP00000331260:R325H;ENSP00000333019:R368H	ENSP00000331260:R325H	R	+	2	0	ADSSL1	104280474	1.000000	0.71417	0.048000	0.18961	0.325000	0.28411	9.666000	0.98612	0.992000	0.38840	0.561000	0.74099	CGC		0.612	ADSSL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410529.1			46	77	46	77
RBFOX1	54715	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	16	7629894	7629894	+	Missense_Mutation	SNP	G	G	T			TCGA-HW-8322-01A-11D-2395-08	TCGA-HW-8322-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbb7361c-879c-4964-b6c8-07b5d8d4da46	088c5f2e-ee43-4263-9962-ef89954380a7	g.chr16:7629894G>T	ENST00000550418.1	+	6	1374	c.386G>T	c.(385-387)cGg>cTg	p.R129L	RBFOX1_ENST00000436368.2_Missense_Mutation_p.R149L|RBFOX1_ENST00000547372.1_Missense_Mutation_p.R172L|RBFOX1_ENST00000311745.5_Missense_Mutation_p.R149L|RBFOX1_ENST00000552089.1_Missense_Mutation_p.R164L|RBFOX1_ENST00000553186.1_Missense_Mutation_p.R129L|RBFOX1_ENST00000547338.1_Missense_Mutation_p.R129L|RBFOX1_ENST00000355637.4_Missense_Mutation_p.R149L|RBFOX1_ENST00000422070.4_Missense_Mutation_p.R172L|RBFOX1_ENST00000535565.2_Intron|RBFOX1_ENST00000340209.4_Missense_Mutation_p.R134L	NM_018723.3	NP_061193.2	Q9NWB1	RFOX1_HUMAN	RNA binding protein, fox-1 homolog (C. elegans) 1	129	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|neuromuscular process controlling balance (GO:0050885)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|RNA transport (GO:0050658)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	nucleotide binding (GO:0000166)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(11)|lung(17)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)	55						TTCAGGTTCCGGGATCCGGAC	0.542																																					Ovarian(157;934 2567 15163 39509)											0													96.0	88.0	91.0					16																	7629894		2197	4300	6497	SO:0001583	missense	54715			AF107203	CCDS10531.1, CCDS10532.1, CCDS45405.1, CCDS55983.1, CCDS55984.1	16p13.3	2013-02-12			ENSG00000078328	ENSG00000078328		"""RNA binding motif (RRM) containing"""	18222	protein-coding gene	gene with protein product	"""ataxin 2-binding protein 1"", ""hexaribonucleotide binding protein 1"""	605104				10814712, 16260614	Standard	NM_018723		Approved	A2BP1, FOX-1, HRNBP1	uc002cyy.2	Q9NWB1	OTTHUMG00000129551	ENST00000550418.1:c.386G>T	16.37:g.7629894G>T	ENSP00000450031:p.Arg129Leu		Q7Z7I7|Q8TAE3|Q8TAF2|Q8WYB2|Q9NS20	Missense_Mutation	SNP	ENST00000550418.1	37	CCDS55983.1	.	.	.	.	.	.	.	.	.	.	G	35	5.564284	0.96527	.	.	ENSG00000078328	ENST00000547605;ENST00000550418;ENST00000553186;ENST00000547372;ENST00000422070;ENST00000552089;ENST00000551752;ENST00000547338;ENST00000436368;ENST00000311745;ENST00000355637;ENST00000352951;ENST00000340209	T;T;T;T;T;T;T;T;T;T;T;T	0.36157	2.36;2.36;2.36;2.36;2.36;1.27;2.36;2.36;2.36;2.36;2.36;2.36	5.39	5.39	0.77823	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.55289	0.1911	L	0.45352	1.415	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	0.976;0.992;0.999;0.995;0.998;0.995;1.0;0.998	D;D;D;D;D;D;D;D	0.85130	0.919;0.969;0.997;0.977;0.99;0.983;0.996;0.983	T	0.56974	-0.7890	10	0.87932	D	0	-7.8681	19.1841	0.93635	0.0:0.0:1.0:0.0	.	149;172;149;149;149;129;129;172	F8WAC5;B7Z1U7;Q9NWB1-2;Q9NWB1-4;Q9NWB1-5;Q9NWB1-3;Q9NWB1;F8VZG9	.;.;.;.;.;.;RFOX1_HUMAN;.	L	128;129;129;172;172;164;129;129;149;149;149;149;134	ENSP00000450402:R128L;ENSP00000450031:R129L;ENSP00000447753:R129L;ENSP00000446842:R172L;ENSP00000391269:R172L;ENSP00000448496:R164L;ENSP00000447281:R129L;ENSP00000447717:R129L;ENSP00000402745:R149L;ENSP00000309117:R149L;ENSP00000347855:R149L;ENSP00000344196:R134L	ENSP00000309117:R149L	R	+	2	0	RBFOX1	7569895	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.441000	0.97557	2.537000	0.85549	0.655000	0.94253	CGG		0.542	RBFOX1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409492.2	NM_145891		24	50	24	50
METTL16	79066	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	2371168	2371168	+	Missense_Mutation	SNP	C	C	T			TCGA-HW-8322-01A-11D-2395-08	TCGA-HW-8322-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbb7361c-879c-4964-b6c8-07b5d8d4da46	088c5f2e-ee43-4263-9962-ef89954380a7	g.chr17:2371168C>T	ENST00000263092.6	-	5	599	c.472G>A	c.(472-474)Gtg>Atg	p.V158M	METTL16_ENST00000571669.2_5'UTR|METTL16_ENST00000538844.1_Intron	NM_024086.3	NP_076991.3	Q86W50	MET16_HUMAN	methyltransferase like 16	158							methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)			kidney(2)|large_intestine(9)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	19						GGCACTTTCACCACTAGGAGA	0.398																																																0													86.0	78.0	81.0					17																	2371168		1859	4104	5963	SO:0001583	missense	79066			AK027410	CCDS42232.1	17p13.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000127804	ENSG00000127804			28484	protein-coding gene	gene with protein product			"""methyltransferase 10 domain containing"""	METT10D		18021804	Standard	NM_024086		Approved	MGC3329	uc002fut.3	Q86W50		ENST00000263092.6:c.472G>A	17.37:g.2371168C>T	ENSP00000263092:p.Val158Met		D3DTI8|Q86TE5|Q96T16|Q9BVG7	Missense_Mutation	SNP	ENST00000263092.6	37	CCDS42232.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.105114	0.77096	.	.	ENSG00000127804	ENST00000263092;ENST00000399834	T	0.19669	2.13	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.35913	0.0948	L	0.39898	1.24	0.80722	D	1	P;D	0.60575	0.863;0.988	B;P	0.62885	0.403;0.908	T	0.02196	-1.1197	10	0.46703	T	0.11	-6.6255	16.5705	0.84611	0.0:1.0:0.0:0.0	.	158;158	Q86W50-2;Q86W50	.;MET16_HUMAN	M	158	ENSP00000263092:V158M	ENSP00000263092:V158M	V	-	1	0	METTL16	2317918	1.000000	0.71417	1.000000	0.80357	0.868000	0.49771	5.910000	0.69931	2.510000	0.84645	0.491000	0.48974	GTG		0.398	METTL16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437653.2	NM_024086		12	71	12	71
SMARCA4	6597	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	11143994	11143994	+	Missense_Mutation	SNP	G	G	A			TCGA-HW-8322-01A-11D-2395-08	TCGA-HW-8322-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbb7361c-879c-4964-b6c8-07b5d8d4da46	088c5f2e-ee43-4263-9962-ef89954380a7	g.chr19:11143994G>A	ENST00000429416.3	+	27	3856	c.3575G>A	c.(3574-3576)cGc>cAc	p.R1192H	SMARCA4_ENST00000358026.2_Missense_Mutation_p.R1192H|SMARCA4_ENST00000541122.2_Missense_Mutation_p.R1192H|SMARCA4_ENST00000444061.3_Missense_Mutation_p.R1192H|SMARCA4_ENST00000590574.1_Missense_Mutation_p.R1192H|SMARCA4_ENST00000450717.3_Missense_Mutation_p.R1192H|SMARCA4_ENST00000589677.1_Missense_Mutation_p.R1192H|SMARCA4_ENST00000413806.3_Missense_Mutation_p.R1192H|SMARCA4_ENST00000344626.4_Missense_Mutation_p.R1192H	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	1192	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				CGAGCCCACCGCATCGGGCAG	0.612			"""F, N, Mis"""		NSCLC																																		Rec	yes		19	19p13.2	6597	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"""		E	1	Unknown(1)	lung(1)											63.0	62.0	62.0					19																	11143994		2203	4300	6503	SO:0001583	missense	6597			D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"""SNF2-like 4"", ""global transcription activator homologous sequence"", ""sucrose nonfermenting-like 4"", ""mitotic growth and transcription activator"", ""BRM/SWI2-related gene 1"", ""homeotic gene regulator"", ""nuclear protein GRB1"", ""brahma protein-like 1"", ""ATP-dependent helicase SMARCA4"""	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.3575G>A	19.37:g.11143994G>A	ENSP00000395654:p.Arg1192His		B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	37	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.769759	0.90020	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	D;D;D;D;D;D;D	0.97850	-4.57;-4.57;-4.57;-4.57;-4.57;-4.57;-4.57	4.74	4.74	0.60224	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.99426	0.9797	H	0.99863	4.86	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D	0.97804	1.0246	10	0.87932	D	0	-34.1151	16.7067	0.85374	0.0:0.0:1.0:0.0	.	1192;1192;1192;1192;1192;412;1192	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;B4E0F1;P51532	.;.;.;.;.;.;SMCA4_HUMAN	H	1192;1192;1256;1192;1192;1192;1192;1192	ENSP00000395654:R1192H;ENSP00000350720:R1192H;ENSP00000343896:R1192H;ENSP00000445036:R1192H;ENSP00000392837:R1192H;ENSP00000397783:R1192H;ENSP00000414727:R1192H	ENSP00000343896:R1192H	R	+	2	0	SMARCA4	11004994	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	9.319000	0.96338	2.488000	0.83962	0.558000	0.71614	CGC		0.612	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		38	79	38	79
GIPC1	10755	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	14591417	14591417	+	Silent	SNP	G	G	A			TCGA-HW-8322-01A-11D-2395-08	TCGA-HW-8322-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbb7361c-879c-4964-b6c8-07b5d8d4da46	088c5f2e-ee43-4263-9962-ef89954380a7	g.chr19:14591417G>A	ENST00000393033.4	-	5	731	c.462C>T	c.(460-462)taC>taT	p.Y154Y	GIPC1_ENST00000345425.2_Silent_p.Y154Y|GIPC1_ENST00000586027.1_Silent_p.Y154Y|GIPC1_ENST00000393029.3_Silent_p.Y57Y|GIPC1_ENST00000393028.1_Silent_p.Y57Y|GIPC1_ENST00000591349.1_Silent_p.Y57Y	NM_005716.3	NP_005707.1	O14908	GIPC1_HUMAN	GIPC PDZ domain containing family, member 1	154	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				endothelial cell migration (GO:0043542)|G-protein coupled receptor signaling pathway (GO:0007186)|glutamate secretion (GO:0014047)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of cytokinesis (GO:0032467)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein targeting (GO:0006605)|regulation of protein stability (GO:0031647)|regulation of synaptic plasticity (GO:0048167)|synaptic transmission (GO:0007268)	brush border (GO:0005903)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|myosin binding (GO:0017022)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			endometrium(1)|lung(4)|upper_aerodigestive_tract(1)	6						TGATGAAGGCGTAGCCAGCCC	0.657											OREG0025316	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									Pancreas(33;78 923 2910 41023 52850)											0													104.0	93.0	97.0					19																	14591417		2203	4300	6503	SO:0001819	synonymous_variant	10755			AF089816	CCDS12310.1, CCDS12311.1	19p13.1	2009-09-22	2005-06-28	2005-06-28					1226	protein-coding gene	gene with protein product		605072	"""chromosome 19 open reading frame 3"", ""regulator of G-protein signalling 19 interacting protein 1"""	C19orf3, RGS19IP1		9770488, 9482110	Standard	NM_005716		Approved	TIP-2, Hs.6454, GIPC, SEMCAP, GLUT1CBP, SYNECTIN, NIP	uc002myx.4	O14908		ENST00000393033.4:c.462C>T	19.37:g.14591417G>A		696	A8K4I3|A8MZG3|Q9BTC9	Silent	SNP	ENST00000393033.4	37	CCDS12310.1																																																																																				0.657	GIPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460239.2			57	63	57	63
TFPT	29844	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	54611508	54611508	+	Missense_Mutation	SNP	G	G	A	rs201891249		TCGA-HW-8322-01A-11D-2395-08	TCGA-HW-8322-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbb7361c-879c-4964-b6c8-07b5d8d4da46	088c5f2e-ee43-4263-9962-ef89954380a7	g.chr19:54611508G>A	ENST00000391759.1	-	5	872	c.467C>T	c.(466-468)gCg>gTg	p.A156V	TFPT_ENST00000391757.1_Missense_Mutation_p.R144W|NDUFA3_ENST00000391764.3_Intron|TFPT_ENST00000391758.1_Missense_Mutation_p.A147V	NM_013342.3	NP_037474.1	P0C1Z6	TFPT_HUMAN	TCF3 (E2A) fusion partner (in childhood Leukemia)	156					apoptotic signaling pathway (GO:0097190)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	actin filament (GO:0005884)|cytoplasm (GO:0005737)|Ino80 complex (GO:0031011)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			large_intestine(2)|lung(2)	4	all_cancers(19;0.004)|all_epithelial(19;0.00195)|all_lung(19;0.0193)|Lung NSC(19;0.0358)|Breast(117;0.137)|Ovarian(34;0.19)					CTCATTCTCCGCATTGCCTGG	0.677			T	TCF3	pre-B ALL								G|||	1	0.000199681	0.0	0.0	5008	,	,		14953	0.001		0.0	False		,,,				2504	0.0						Dom	yes		19	19q13	29844	TCF3 (E2A) fusion partner (in childhood Leukemia)		L	0								G	VAL/ALA	1,4401		0,1,2200	20.0	21.0	21.0		467	4.0	0.1	19		21	0,8598		0,0,4299	no	missense	TFPT	NM_013342.3	64	0,1,6499	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging	156/254	54611508	1,12999	2201	4299	6500	SO:0001583	missense	29844			AF052052	CCDS12878.1	19q13	2011-07-06			ENSG00000105619	ENSG00000105619		"""INO80 complex subunits"""	13630	protein-coding gene	gene with protein product	"""amida, partner of the E2A"", ""INO80 complex subunit F"""	609519				10644725, 16230350	Standard	NM_013342		Approved	FB1, amida, INO80F	uc010yej.1	P0C1Z6	OTTHUMG00000065906	ENST00000391759.1:c.467C>T	19.37:g.54611508G>A	ENSP00000375639:p.Ala156Val			Missense_Mutation	SNP	ENST00000391759.1	37	CCDS12878.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0017482517482517483|0.0017482517482517483	0|0	0.0|0.0	G|G	11.75|11.75	1.730432|1.730432	0.30684|0.30684	2.27E-4|2.27E-4	0.0|0.0	ENSG00000105619|ENSG00000105619	ENST00000391759;ENST00000391758|ENST00000391757	.|.	.|.	.|.	5.04|5.04	3.98|3.98	0.46160|0.46160	.|.	0.536722|.	0.19144|.	N|.	0.121602|.	T|T	0.43033|0.43033	0.1229|0.1229	L|L	0.36672|0.36672	1.1|1.1	0.09310|0.09310	N|N	1|1	P|.	0.39920|.	0.695|.	B|.	0.30495|.	0.116|.	T|T	0.37384|0.37384	-0.9708|-0.9708	9|6	0.21540|0.66056	T|D	0.41|0.02	-2.9054|-2.9054	13.0878|13.0878	0.59151|0.59151	0.0807:0.0:0.9193:0.0|0.0807:0.0:0.9193:0.0	.|.	156|.	P0C1Z6|.	TFPT_HUMAN|.	V|W	156;147|144	.|.	ENSP00000375638:A147V|ENSP00000375637:R144W	A|R	-|-	2|1	0|2	TFPT|TFPT	59303320|59303320	0.010000|0.010000	0.17322|0.17322	0.060000|0.060000	0.19600|0.19600	0.271000|0.271000	0.26615|0.26615	1.285000|1.285000	0.33261|0.33261	1.234000|1.234000	0.43709|0.43709	0.655000|0.655000	0.94253|0.94253	GCG|CGG		0.677	TFPT-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141215.4	NM_013342		11	9	11	9
KCNT2	343450	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	196250118	196250118	+	Splice_Site	SNP	T	T	C			TCGA-HW-8322-01A-11D-2395-08	TCGA-HW-8322-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbb7361c-879c-4964-b6c8-07b5d8d4da46	088c5f2e-ee43-4263-9962-ef89954380a7	g.chr1:196250118T>C	ENST00000294725.9	-	25	3697	c.2782A>G	c.(2782-2784)Atg>Gtg	p.M928V	KCNT2_ENST00000367431.4_Splice_Site_p.M854V|KCNT2_ENST00000367433.5_Splice_Site_p.M904V|KCNT2_ENST00000498426.1_5'UTR|KCNT2_ENST00000451324.2_3'UTR|KCNT2_ENST00000609185.1_Splice_Site_p.M854V			Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	928					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(16)|lung(43)|ovary(5)|pancreas(1)|prostate(1)|skin(11)|stomach(2)|upper_aerodigestive_tract(1)	97						GTGATTTTCATCTATAACACA	0.348																																																0													72.0	72.0	72.0					1																	196250118		2202	4300	6502	SO:0001630	splice_region_variant	343450			BX647852, AY359444, AK127807	CCDS1384.1, CCDS72994.1, CCDS72995.1	1q31.3	2012-07-05			ENSG00000162687	ENSG00000162687		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	18866	protein-coding gene	gene with protein product	"""sodium and chloride activated ATP sensitive potassium channel"""	610044				16382103	Standard	NM_198503		Approved	KCa4.2, SLICK, SLO2.1	uc001gtd.1	Q6UVM3	OTTHUMG00000035611	ENST00000294725.9:c.2782-1A>G	1.37:g.196250118T>C			Q3SY59|Q5VTN1|Q6ZMT3	Splice_Site	SNP	ENST00000294725.9	37	CCDS1384.1	.	.	.	.	.	.	.	.	.	.	T	14.58	2.578464	0.46006	.	.	ENSG00000162687	ENST00000367433;ENST00000367431;ENST00000294725	T;T;T	0.75704	-0.96;-0.96;-0.96	5.52	5.52	0.82312	.	0.072539	0.64402	D	0.000017	T	0.77909	0.4201	M	0.83953	2.67	0.80722	D	1	B;B;B;B;B	0.27068	0.104;0.082;0.167;0.082;0.104	B;B;B;B;B	0.35114	0.065;0.059;0.196;0.087;0.065	T	0.73920	-0.3830	10	0.17369	T	0.5	-26.5936	14.9129	0.70773	0.0:0.0:0.0:1.0	.	928;886;904;854;928	A9LNM6;Q6UVM3-4;Q6UVM3-2;Q6UVM3-3;Q6UVM3	.;.;.;.;KCNT2_HUMAN	V	904;854;928	ENSP00000356403:M904V;ENSP00000356401:M854V;ENSP00000294725:M928V	ENSP00000294725:M928V	M	-	1	0	KCNT2	194516741	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	7.404000	0.79996	2.222000	0.72286	0.455000	0.32223	ATG		0.348	KCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086418.2	NM_198503	Missense_Mutation	9	16	9	16
C1orf186	440712	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	206243208	206243208	+	Silent	SNP	G	G	A			TCGA-HW-8322-01A-11D-2395-08	TCGA-HW-8322-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbb7361c-879c-4964-b6c8-07b5d8d4da46	088c5f2e-ee43-4263-9962-ef89954380a7	g.chr1:206243208G>A	ENST00000331555.5	-	3	692	c.54C>T	c.(52-54)tcC>tcT	p.S18S		NM_001007544.1	NP_001007545.1	Q6ZWK4	CA186_HUMAN	chromosome 1 open reading frame 186	18						integral component of membrane (GO:0016021)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.0754)			GCAGGAAGAGGGACACCACCG	0.527																																																0													129.0	112.0	118.0					1																	206243208		2203	4300	6503	SO:0001819	synonymous_variant	0			AK122631	CCDS73014.1	1q32.1	2014-05-06			ENSG00000196533	ENSG00000263961			25341	protein-coding gene	gene with protein product							Standard	XM_005272738		Approved	FLJ16052	uc001hdt.2	Q6ZWK4	OTTHUMG00000184376	ENST00000331555.5:c.54C>T	1.37:g.206243208G>A				Silent	SNP	ENST00000331555.5	37	CCDS30995.1																																																																																				0.527	C1orf186-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088002.1	NM_001007544		35	54	35	54
MIA3	375056	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	222805521	222805521	+	Missense_Mutation	SNP	C	C	T			TCGA-HW-8322-01A-11D-2395-08	TCGA-HW-8322-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbb7361c-879c-4964-b6c8-07b5d8d4da46	088c5f2e-ee43-4263-9962-ef89954380a7	g.chr1:222805521C>T	ENST00000344922.5	+	5	3209	c.3184C>T	c.(3184-3186)Cat>Tat	p.H1062Y	MIA3_ENST00000344507.1_Intron|MIA3_ENST00000344441.6_Missense_Mutation_p.H1062Y|MIA3_ENST00000470521.1_3'UTR	NM_198551.2	NP_940953.2	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	1062					chondrocyte development (GO:0002063)|collagen fibril organization (GO:0030199)|exocytosis (GO:0006887)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|positive regulation of bone mineralization (GO:0030501)|positive regulation of leukocyte migration (GO:0002687)|protein transport (GO:0015031)|wound healing (GO:0042060)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(5)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(15)|lung(37)|ovary(5)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|urinary_tract(1)	80				GBM - Glioblastoma multiforme(131;0.0199)		GCAACCACTGCATGAAGATAA	0.498																																																0													110.0	106.0	108.0					1																	222805521		1998	4157	6155	SO:0001583	missense	375056				CCDS41470.1, CCDS73035.1	1p36.33	2012-12-13		2006-07-25	ENSG00000154305	ENSG00000154305			24008	protein-coding gene	gene with protein product	"""C219 reactive peptide"", ""transport and golgi organization"""	613455				15183315	Standard	XM_005273121		Approved	UNQ6077, FLJ39207, KIAA0268, TANGO	uc001hnl.3	Q5JRA6	OTTHUMG00000037543	ENST00000344922.5:c.3184C>T	1.37:g.222805521C>T	ENSP00000340900:p.His1062Tyr		A8K2S0|A8MT05|A8MT13|B7Z430|Q14083|Q3S4X3|Q5JRA5|Q5JRB0|Q5JRB1|Q5JRB2|Q6UVY8|Q86Y60|Q8N8M5|Q92580	Missense_Mutation	SNP	ENST00000344922.5	37	CCDS41470.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.016|0.016	-1.513894|-1.513894	0.00975|0.00975	.|.	.|.	ENSG00000154305|ENSG00000154305	ENST00000354906|ENST00000344922;ENST00000344441;ENST00000320831	.|T;T	.|0.04360	.|3.64;3.64	3.81|3.81	2.88|2.88	0.33553|0.33553	.|.	.|.	.|.	.|.	.|.	T|T	0.04182|0.04182	0.0116|0.0116	N|N	0.25647|0.25647	0.755|0.755	0.09310|0.09310	N|N	1|1	.|P;B	.|0.42296	.|0.775;0.367	.|B;B	.|0.37692	.|0.256;0.062	T|T	0.40213|0.40213	-0.9575|-0.9575	5|9	.|0.56958	.|D	.|0.05	.|.	9.4291|9.4291	0.38599|0.38599	0.0:0.7831:0.2169:0.0|0.0:0.7831:0.2169:0.0	.|.	.|1062;1062	.|Q5JRA6-2;Q5JRA6	.|.;MIA3_HUMAN	V|Y	644|1062	.|ENSP00000340900:H1062Y;ENSP00000340587:H1062Y	.|ENSP00000325973:H1062Y	A|H	+|+	2|1	0|0	MIA3|MIA3	220872144|220872144	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.017000|0.017000	0.09413|0.09413	0.419000|0.419000	0.21247|0.21247	1.149000|1.149000	0.42402|0.42402	0.557000|0.557000	0.71058|0.71058	GCA|CAT		0.498	MIA3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091489.4	NM_198551		17	106	17	106
APOL1	8542	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	22	36661324	36661324	+	Missense_Mutation	SNP	A	A	G			TCGA-HW-8322-01A-11D-2395-08	TCGA-HW-8322-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbb7361c-879c-4964-b6c8-07b5d8d4da46	088c5f2e-ee43-4263-9962-ef89954380a7	g.chr22:36661324A>G	ENST00000397278.3	+	6	671	c.442A>G	c.(442-444)Aaa>Gaa	p.K148E	APOL1_ENST00000319136.4_Missense_Mutation_p.K164E|APOL1_ENST00000397279.4_Missense_Mutation_p.K148E|APOL1_ENST00000422706.1_Missense_Mutation_p.K148E|APOL1_ENST00000347595.7_Missense_Mutation_p.K27E|APOL1_ENST00000426053.1_Missense_Mutation_p.K130E|APOL1_ENST00000440669.2_3'UTR	NM_003661.3	NP_003652.2	O14791	APOL1_HUMAN	apolipoprotein L, 1	148					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|cholesterol metabolic process (GO:0008203)|cytolysis (GO:0019835)|innate immune response (GO:0045087)|killing of cells of other organism (GO:0031640)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|high-density lipoprotein particle (GO:0034364)|intrinsic component of membrane (GO:0031224)|very-low-density lipoprotein particle (GO:0034361)	chloride channel activity (GO:0005254)|lipid binding (GO:0008289)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	14						TCCTCGGTTGAAAAGTGAGCT	0.478																																																0													111.0	101.0	105.0					22																	36661324		2203	4300	6503	SO:0001583	missense	8542			AF019225	CCDS13925.1, CCDS13926.1, CCDS46702.1	22q13.1	2014-09-17			ENSG00000100342	ENSG00000100342		"""Apolipoproteins"""	618	protein-coding gene	gene with protein product		603743		APOL		9325276, 11374903, 16020735	Standard	NM_003661		Approved		uc011amp.2	O14791	OTTHUMG00000030427	ENST00000397278.3:c.442A>G	22.37:g.36661324A>G	ENSP00000380448:p.Lys148Glu		A5PLQ4|B4DU12|E9PF24|O60804|Q5R3P7|Q5R3P8|Q96AB8|Q96PM4|Q9BQ03	Missense_Mutation	SNP	ENST00000397278.3	37	CCDS13926.1	.	.	.	.	.	.	.	.	.	.	a	9.687	1.150754	0.21371	.	.	ENSG00000100342	ENST00000397278;ENST00000422706;ENST00000426053;ENST00000319136;ENST00000427990;ENST00000347595;ENST00000397279	T;T;T;T;T;T;T	0.05199	3.48;3.48;3.48;3.48;3.48;3.48;3.48	3.38	1.21	0.21127	.	0.308968	0.35320	N	0.003294	T	0.06872	0.0175	L	0.60904	1.88	0.09310	N	1	B;B;B	0.31256	0.316;0.186;0.27	B;B;B	0.32022	0.139;0.08;0.086	T	0.25222	-1.0138	10	0.48119	T	0.1	.	5.6062	0.17381	0.7427:0.0:0.2573:0.0	.	130;148;164	E9PF24;O14791;O14791-2	.;APOL1_HUMAN;.	E	148;148;130;164;148;27;148	ENSP00000380448:K148E;ENSP00000411507:K148E;ENSP00000388477:K130E;ENSP00000317674:K164E;ENSP00000391302:K148E;ENSP00000216178:K27E;ENSP00000380449:K148E	ENSP00000317674:K164E	K	+	1	0	APOL1	34991270	0.023000	0.18921	0.024000	0.17045	0.011000	0.07611	1.460000	0.35244	-0.072000	0.12864	-1.140000	0.01884	AAA		0.478	APOL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319100.4	NM_145343		63	97	63	97
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-HW-8322-01A-11D-2395-08	TCGA-HW-8322-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbb7361c-879c-4964-b6c8-07b5d8d4da46	088c5f2e-ee43-4263-9962-ef89954380a7	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000345146.2_Missense_Mutation_p.R132H|IDH1_ENST00000446179.1_Missense_Mutation_p.R132H	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393			Mis		gliobastoma																																Pancreas(158;264 1958 3300 35450 36047)		Dom	yes		2	2q33.3	3417	"""isocitrate dehydrogenase 1 (NADP+), soluble"""		O	2835	Substitution - Missense(2834)|Complex - compound substitution(1)	central_nervous_system(2579)|haematopoietic_and_lymphoid_tissue(205)|bone(43)|prostate(4)|biliary_tract(2)|urinary_tract(1)|skin(1)											79.0	73.0	75.0					2																	209113112		2203	4300	6503	SO:0001583	missense	3417				CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.395G>A	2.37:g.209113112C>T	ENSP00000390265:p.Arg132His		Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.657324	0.88154	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	5.57	4.69	0.59074	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.93145	0.7817	H	0.99379	4.54	0.80722	D	1	B	0.25486	0.127	B	0.25405	0.06	D	0.92324	0.5868	10	0.87932	D	0	-20.0399	14.3783	0.66895	0.0:0.9288:0.0:0.0712	.	132	O75874	IDHC_HUMAN	H	132	ENSP00000260985:R132H;ENSP00000410513:R132H;ENSP00000390265:R132H;ENSP00000391075:R132H	ENSP00000260985:R132H	R	-	2	0	IDH1	208821357	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	6.088000	0.71371	1.356000	0.45884	0.555000	0.69702	CGT		0.393	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			32	53	32	53
ROBO1	6091	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	78685111	78685111	+	Missense_Mutation	SNP	C	C	T			TCGA-HW-8322-01A-11D-2395-08	TCGA-HW-8322-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbb7361c-879c-4964-b6c8-07b5d8d4da46	088c5f2e-ee43-4263-9962-ef89954380a7	g.chr3:78685111C>T	ENST00000464233.1	-	23	3298	c.3185G>A	c.(3184-3186)cGt>cAt	p.R1062H	ROBO1_ENST00000467549.1_Intron|ROBO1_ENST00000495273.1_Missense_Mutation_p.R1017H|ROBO1_ENST00000436010.2_Missense_Mutation_p.R1023H	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	1062					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)	p.R1039H(1)		breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		ATTGACAAAACGCCCATCCTT	0.473																																																1	Substitution - Missense(1)	ovary(1)											155.0	159.0	157.0					3																	78685111		2107	4225	6332	SO:0001583	missense	6091			AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	10249	protein-coding gene	gene with protein product		602430	"""roundabout (axon guidance receptor, Drosophila) homolog 1"""			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.3185G>A	3.37:g.78685111C>T	ENSP00000420321:p.Arg1062His		B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Missense_Mutation	SNP	ENST00000464233.1	37	CCDS54611.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.437230	0.83885	.	.	ENSG00000169855	ENST00000436010;ENST00000398412;ENST00000464233;ENST00000495273;ENST00000398414	T;T;T	0.62105	0.08;0.05;0.12	6.05	6.05	0.98169	.	0.000000	0.85682	D	0.000000	T	0.74680	0.3748	L	0.44542	1.39	0.80722	D	1	D;D;D;D	0.76494	0.999;0.996;0.999;0.999	D;P;D;D	0.80764	0.994;0.731;0.926;0.921	T	0.69720	-0.5069	9	.	.	.	.	20.6087	0.99469	0.0:1.0:0.0:0.0	.	1026;1062;1017;1023	Q9Y6N7-3;Q9Y6N7;B2RXI1;Q9Y6N7-4	.;ROBO1_HUMAN;.;.	H	1023;1017;1062;1017;1066	ENSP00000406043:R1023H;ENSP00000420321:R1062H;ENSP00000420637:R1017H	.	R	-	2	0	ROBO1	78767801	1.000000	0.71417	1.000000	0.80357	0.835000	0.47333	7.291000	0.78721	2.866000	0.98385	0.650000	0.86243	CGT		0.473	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		60	77	60	77
RAD17	5884	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	68689027	68689027	+	Missense_Mutation	SNP	T	T	C			TCGA-HW-8322-01A-11D-2395-08	TCGA-HW-8322-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbb7361c-879c-4964-b6c8-07b5d8d4da46	088c5f2e-ee43-4263-9962-ef89954380a7	g.chr5:68689027T>C	ENST00000509734.1	+	13	1946	c.1268T>C	c.(1267-1269)tTa>tCa	p.L423S	RAD17_ENST00000380774.3_Missense_Mutation_p.L423S|RAD17_ENST00000354312.3_Missense_Mutation_p.L412S|RAD17_ENST00000305138.4_Missense_Mutation_p.L412S|RAD17_ENST00000354868.5_Missense_Mutation_p.L412S|RAD17_ENST00000345306.6_Missense_Mutation_p.L412S|RAD17_ENST00000358030.2_Missense_Mutation_p.L247S|RAD17_ENST00000282891.6_Missense_Mutation_p.L326S|RAD17_ENST00000504177.1_Intron|RAD17_ENST00000521422.1_Missense_Mutation_p.L247S|RAD17_ENST00000361732.2_Missense_Mutation_p.L412S			O75943	RAD17_HUMAN	RAD17 homolog (S. pombe)	423					cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of DNA replication (GO:0008156)|regulation of phosphorylation (GO:0042325)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)						Lung NSC(167;5.19e-05)|Prostate(74;0.0143)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;9.36e-57)|Epithelial(20;1.21e-52)|all cancers(19;3.34e-48)|Lung(70;0.0183)		CCCTCTCATTTATCAGAATAT	0.313								Other conserved DNA damage response genes																																								0													96.0	93.0	94.0					5																	68689027		2203	4297	6500	SO:0001583	missense	5884			AF085736	CCDS4003.1, CCDS4004.1, CCDS4005.1, CCDS47226.1	5q13	2010-09-24	2001-11-28		ENSG00000152942	ENSG00000152942			9807	protein-coding gene	gene with protein product		603139	"""RAD1 (S. pombe) homolog"""			9869296, 9660800	Standard	NM_133343		Approved	Rad24, RAD17Sp, CCYC	uc003jwo.3	O75943	OTTHUMG00000099357	ENST00000509734.1:c.1268T>C	5.37:g.68689027T>C	ENSP00000426191:p.Leu423Ser		A8K8X2|D3DWA5|O75714|Q7Z3S4|Q9UNK7|Q9UNR7|Q9UNR8|Q9UPF5	Missense_Mutation	SNP	ENST00000509734.1	37	CCDS4003.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.384546	0.82792	.	.	ENSG00000152942	ENST00000361732;ENST00000509734;ENST00000354868;ENST00000521422;ENST00000354312;ENST00000345306;ENST00000305138;ENST00000282891;ENST00000358030;ENST00000380774;ENST00000513214	T;T;T;T;T;T;T;T;T;T;T	0.56103	1.18;1.18;1.18;1.18;1.18;1.18;1.18;1.18;1.18;1.18;0.48	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.77994	0.4214	M	0.90870	3.155	0.58432	D	0.999997	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.994;0.995	D	0.83484	0.0066	10	0.87932	D	0	-26.216	14.4894	0.67639	0.0:0.0:0.0:1.0	.	423;326;412	O75943;O75943-4;O75943-2	RAD17_HUMAN;.;.	S	412;423;412;247;412;412;412;326;247;423;31	ENSP00000355226:L412S;ENSP00000426191:L423S;ENSP00000346938:L412S;ENSP00000427743:L247S;ENSP00000346271:L412S;ENSP00000311227:L412S;ENSP00000303134:L412S;ENSP00000282891:L326S;ENSP00000350725:L247S;ENSP00000370151:L423S;ENSP00000425005:L31S	ENSP00000282891:L326S	L	+	2	0	RAD17	68724783	1.000000	0.71417	0.867000	0.34043	0.926000	0.56050	6.464000	0.73534	2.059000	0.61396	0.383000	0.25322	TTA		0.313	RAD17-008	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369171.1	NM_133344		13	27	13	27
KCNN2	3781	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	113698887	113698887	+	Missense_Mutation	SNP	C	C	T			TCGA-HW-8322-01A-11D-2395-08	TCGA-HW-8322-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbb7361c-879c-4964-b6c8-07b5d8d4da46	088c5f2e-ee43-4263-9962-ef89954380a7	g.chr5:113698887C>T	ENST00000512097.3	+	2	1433	c.415C>T	c.(415-417)Ctc>Ttc	p.L139F	KCNN2_ENST00000507750.1_3'UTR|KCNN2_ENST00000264773.3_Missense_Mutation_p.L139F			Q9H2S1	KCNN2_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2	139					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of potassium ion transmembrane transport (GO:1901379)|synaptic transmission (GO:0007268)	dendritic spine (GO:0043197)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calcium-activated potassium channel activity (GO:0015269)|calmodulin binding (GO:0005516)|protein homodimerization activity (GO:0042803)|small conductance calcium-activated potassium channel activity (GO:0016286)			breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(21)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_cancers(142;2.86e-05)|all_epithelial(76;9.33e-06)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Breast(839;0.159)|Lung NSC(810;0.174)|all_lung(232;0.206)		OV - Ovarian serous cystadenocarcinoma(64;1.89e-08)|Epithelial(69;2.04e-08)|all cancers(49;3.74e-06)|COAD - Colon adenocarcinoma(37;0.142)|Colorectal(14;0.195)	Miconazole(DB01110)|Procaine(DB00721)	CGACTACGCGCTCATCTTCGG	0.597																																																0													36.0	36.0	36.0					5																	113698887		2202	4300	6502	SO:0001583	missense	3781			AF239613	CCDS4114.1, CCDS43352.1	5q22.3	2012-07-05			ENSG00000080709	ENSG00000080709		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	6291	protein-coding gene	gene with protein product		605879				16382103	Standard	NM_001278204		Approved	KCa2.2, hSK2	uc003kqo.3	Q9H2S1	OTTHUMG00000128836	ENST00000512097.3:c.415C>T	5.37:g.113698887C>T	ENSP00000427120:p.Leu139Phe		A6NF94|Q0VFZ4|Q6PJI0|Q6X2Y2	Missense_Mutation	SNP	ENST00000512097.3	37	CCDS4114.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.030982	0.75504	.	.	ENSG00000080709	ENST00000512097;ENST00000264773	D;D	0.99042	-5.36;-5.36	5.44	5.44	0.79542	Potassium channel, calcium-activated, SK, conserved region (1);	0.000000	0.85682	D	0.000000	D	0.99408	0.9791	M	0.89095	3.005	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98922	1.0784	10	0.87932	D	0	.	18.8802	0.92353	0.0:1.0:0.0:0.0	.	139	Q9H2S1	KCNN2_HUMAN	F	139	ENSP00000427120:L139F;ENSP00000264773:L139F	ENSP00000264773:L139F	L	+	1	0	KCNN2	113726786	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.702000	0.54800	2.536000	0.85505	0.655000	0.94253	CTC		0.597	KCNN2-001	KNOWN	not_organism_supported|upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250775.2	NM_021614		18	58	18	58
SERPINE1	5054	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	100779018	100779018	+	Silent	SNP	G	G	A			TCGA-HW-8322-01A-11D-2395-08	TCGA-HW-8322-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbb7361c-879c-4964-b6c8-07b5d8d4da46	088c5f2e-ee43-4263-9962-ef89954380a7	g.chr7:100779018G>A	ENST00000223095.4	+	7	1180	c.1023G>A	c.(1021-1023)gcG>gcA	p.A341A	SERPINE1_ENST00000445463.2_Silent_p.A326A	NM_000602.4	NP_000593.1	P05121	PAI1_HUMAN	serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1	341					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular response to lipopolysaccharide (GO:0071222)|chronological cell aging (GO:0001300)|defense response to Gram-negative bacterium (GO:0050829)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|gene expression (GO:0010467)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell migration (GO:0030336)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of plasminogen activation (GO:0010757)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell-matrix adhesion (GO:2000098)|negative regulation of vascular wound healing (GO:0061044)|negative regulation of wound healing (GO:0061045)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of leukotriene production involved in inflammatory response (GO:0035491)|positive regulation of monocyte chemotaxis (GO:0090026)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell proliferation (GO:0042127)|regulation of receptor activity (GO:0010469)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(3)	20	Lung NSC(181;0.136)|all_lung(186;0.182)				Alteplase(DB00009)|Anistreplase(DB00029)|Drotrecogin alfa(DB00055)|Reteplase(DB00015)|Tenecteplase(DB00031)|Urokinase(DB00013)	TCCACGTCGCGCAGGCGCTGC	0.587																																																0													88.0	81.0	84.0					7																	100779018		2203	4300	6503	SO:0001819	synonymous_variant	5054			M16006	CCDS5711.1	7q22.1	2014-02-18	2005-08-18		ENSG00000106366	ENSG00000106366		"""Serine (or cysteine) peptidase inhibitors"""	8583	protein-coding gene	gene with protein product	"""plasminogen activator inhibitor, type I"""	173360	"""serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1"""	PLANH1, PAI1		3097076, 2891140, 24172014	Standard	NM_000602		Approved	PAI	uc003uxt.4	P05121	OTTHUMG00000157107	ENST00000223095.4:c.1023G>A	7.37:g.100779018G>A			B7Z4S0|F8WD53	Silent	SNP	ENST00000223095.4	37	CCDS5711.1																																																																																				0.587	SERPINE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347458.1	NM_000602		36	118	36	118
TAS1R3	83756	broad.mit.edu;hgsc.bcm.edu	37	1	1267913	1267913	+	Frame_Shift_Del	DEL	C	C	-			TCGA-HW-8322-01A-11D-2395-08	TCGA-HW-8322-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbb7361c-879c-4964-b6c8-07b5d8d4da46	088c5f2e-ee43-4263-9962-ef89954380a7	g.chr1:1267913delC	ENST00000339381.5	+	3	1034	c.1002delC	c.(1000-1002)ttcfs	p.F334fs		NM_152228.1	NP_689414	Q7RTX0	TS1R3_HUMAN	taste receptor, type 1, member 3	334					detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			kidney(2)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	12	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;3.01e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.88e-21)|Colorectal(212;0.000157)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00251)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.146)		TGCACGAGTTCCCCCAGTACG	0.692																																																0													36.0	38.0	37.0					1																	1267913		2199	4292	6491	SO:0001589	frameshift_variant	83756			AC026283	CCDS30556.1	1p36	2012-08-22			ENSG00000169962	ENSG00000169962		"""Taste receptors / Type 1"", ""GPCR / Unclassified : Taste receptors"""	15661	protein-coding gene	gene with protein product		605865				11319557	Standard	XM_006710939		Approved	T1R3	uc010nyk.2	Q7RTX0	OTTHUMG00000003071	ENST00000339381.5:c.1002delC	1.37:g.1267913delC	ENSP00000344411:p.Phe334fs		Q5TA49|Q8NGW9	Frame_Shift_Del	DEL	ENST00000339381.5	37	CCDS30556.1																																																																																				0.692	TAS1R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008493.1			15	29	15	29
NEU2	4759	broad.mit.edu;hgsc.bcm.edu	37	2	233898908	233898909	+	Frame_Shift_Ins	INS	-	-	G	rs201616110		TCGA-HW-8322-01A-11D-2395-08	TCGA-HW-8322-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbb7361c-879c-4964-b6c8-07b5d8d4da46	088c5f2e-ee43-4263-9962-ef89954380a7	g.chr2:233898908_233898909insG	ENST00000233840.3	+	2	284_285	c.284_285insG	c.(283-288)acggggfs	p.TG95fs		NM_005383.2	NP_005374.2	Q9Y3R4	NEUR2_HUMAN	sialidase 2 (cytosolic sialidase)	95					ganglioside catabolic process (GO:0006689)|glycosphingolipid metabolic process (GO:0006687)|oligosaccharide catabolic process (GO:0009313)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	exo-alpha-(2->3)-sialidase activity (GO:0052794)|exo-alpha-(2->6)-sialidase activity (GO:0052795)|exo-alpha-(2->8)-sialidase activity (GO:0052796)			endometrium(3)|large_intestine(2)|lung(10)|skin(2)|urinary_tract(1)	18		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0271)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0839)		Epithelial(121;7.17e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000311)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)|GBM - Glioblastoma multiforme(43;0.0488)	Oseltamivir(DB00198)|Zanamivir(DB00558)	GACGCGCAGACGGGGACCCTCT	0.619																																																0																																										SO:0001589	frameshift_variant	4759			Y16535	CCDS2501.1	2q37	2008-05-27			ENSG00000115488	ENSG00000115488			7759	protein-coding gene	gene with protein product	"""N-acetyl-alpha-neuraminidase 2"""	605528				10191093, 14613940	Standard	NM_005383		Approved	SIAL2	uc010zmn.2	Q9Y3R4	OTTHUMG00000133274	ENST00000233840.3:c.288dupG	2.37:g.233898912_233898912dupG	ENSP00000233840:p.Thr95fs		Q3KNW4|Q6NTB4	Frame_Shift_Ins	INS	ENST00000233840.3	37	CCDS2501.1																																																																																				0.619	NEU2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257053.2	NM_005383		32	161	32	161
NOTCH1	4851	broad.mit.edu	37	9	139399848	139399848	+	Frame_Shift_Del	DEL	G	G	-			TCGA-HW-8322-01A-11D-2395-08	TCGA-HW-8322-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbb7361c-879c-4964-b6c8-07b5d8d4da46	088c5f2e-ee43-4263-9962-ef89954380a7	g.chr9:139399848delG	ENST00000277541.6	-	25	4575	c.4500delC	c.(4498-4500)ttcfs	p.F1500fs		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	1500					anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		GGCCGTCACTGAAGTACTTCC	0.617			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)																													Dom	yes		9	9q34.3	4851	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""		L	0													26.0	33.0	31.0					9																	139399848		2152	4251	6403	SO:0001589	frameshift_variant	4851			AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"""Ankyrin repeat domain containing"""	7881	protein-coding gene	gene with protein product		190198	"""Notch (Drosophila) homolog 1 (translocation-associated)"", ""Notch homolog 1, translocation-associated (Drosophila)"""	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.4500delC	9.37:g.139399848delG	ENSP00000277541:p.Phe1500fs		Q59ED8|Q5SXM3	Frame_Shift_Del	DEL	ENST00000277541.6	37	CCDS43905.1																																																																																				0.617	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617		18	21	18	21
NOTCH1	4851	broad.mit.edu	37	9	139395301	139395301	+	Splice_Site	SNP	T	T	G			TCGA-HW-8322-01A-11D-2395-08	TCGA-HW-8322-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbb7361c-879c-4964-b6c8-07b5d8d4da46	088c5f2e-ee43-4263-9962-ef89954380a7	g.chr9:139395301T>G	ENST00000277541.6	-	31	5714		c.e31-2			NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1						anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		TGAAGCCATCTGCAGAGGCAG	0.701			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)																													Dom	yes		9	9q34.3	4851	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""		L	0													10.0	12.0	11.0					9																	139395301		1987	4133	6120	SO:0001630	splice_region_variant	4851			AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"""Ankyrin repeat domain containing"""	7881	protein-coding gene	gene with protein product		190198	"""Notch (Drosophila) homolog 1 (translocation-associated)"", ""Notch homolog 1, translocation-associated (Drosophila)"""	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.5639-2A>C	9.37:g.139395301T>G			Q59ED8|Q5SXM3	Splice_Site	SNP	ENST00000277541.6	37	CCDS43905.1	.	.	.	.	.	.	.	.	.	.	t	17.32	3.359465	0.61403	.	.	ENSG00000148400	ENST00000277541	.	.	.	4.6	4.6	0.57074	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.5941	0.61979	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	NOTCH1	138515122	1.000000	0.71417	0.998000	0.56505	0.586000	0.36452	7.786000	0.85741	1.870000	0.54199	0.438000	0.28831	.		0.701	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617	Intron	3	30	3	30
