#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
OGDHL	55753	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	50953529	50953529	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr10:50953529C>T	ENST00000374103.4	-	12	1575	c.1490G>A	c.(1489-1491)cGg>cAg	p.R497Q	OGDHL_ENST00000432695.1_Missense_Mutation_p.R288Q|OGDHL_ENST00000419399.1_Missense_Mutation_p.R440Q	NM_018245.2	NP_060715.2	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like	497					glycolytic process (GO:0006096)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	61						GTGGCCACGCCGGCGGTAACA	0.572																																																0													77.0	72.0	74.0					10																	50953529		2203	4300	6503	SO:0001583	missense	55753			AK001713	CCDS7234.1, CCDS44390.1, CCDS44391.1	10q11.23	2013-09-20			ENSG00000197444	ENSG00000197444			25590	protein-coding gene	gene with protein product						10574462	Standard	NM_018245		Approved	FLJ10851	uc001jie.3	Q9ULD0	OTTHUMG00000018200	ENST00000374103.4:c.1490G>A	10.37:g.50953529C>T	ENSP00000363216:p.Arg497Gln		A8K2G1|B4DKG2|B4E193|Q8TAN9|Q9NVA0	Missense_Mutation	SNP	ENST00000374103.4	37	CCDS7234.1	.	.	.	.	.	.	.	.	.	.	C	33	5.282234	0.95489	.	.	ENSG00000197444	ENST00000374103;ENST00000419399;ENST00000432695	T;T;D	0.95885	2.48;2.48;-3.84	5.3	5.3	0.74995	Dehydrogenase, E1 component (1);	0.000000	0.85682	D	0.000000	D	0.98096	0.9372	M	0.93328	3.405	0.80722	D	1	D;D;D	0.76494	0.999;0.993;0.999	D;D;D	0.71870	0.957;0.931;0.975	D	0.98705	1.0702	10	0.87932	D	0	.	13.6167	0.62112	0.0:0.9252:0.0:0.0748	.	440;288;497	Q9ULD0-2;Q9ULD0-3;Q9ULD0	.;.;OGDHL_HUMAN	Q	497;440;288	ENSP00000363216:R497Q;ENSP00000401356:R440Q;ENSP00000390240:R288Q	ENSP00000363216:R497Q	R	-	2	0	OGDHL	50623535	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.004000	0.70709	2.647000	0.89833	0.650000	0.86243	CGG		0.572	OGDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048007.1	NM_018245		28	80	28	80
ADK	132	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	76360239	76360239	+	Missense_Mutation	SNP	A	A	G	rs541758866		TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr10:76360239A>G	ENST00000286621.2	+	9	915	c.865A>G	c.(865-867)Ata>Gta	p.I289V	ADK_ENST00000539909.1_Missense_Mutation_p.I232V|ADK_ENST00000541550.1_Missense_Mutation_p.I254V|ADK_ENST00000372734.3_Missense_Mutation_p.I272V	NM_006721.3	NP_006712.2	P55263	ADK_HUMAN	adenosine kinase	289				I -> N (in Ref. 1; AA sequence). {ECO:0000305}.	adenosine metabolic process (GO:0046085)|AMP salvage (GO:0044209)|circadian regulation of gene expression (GO:0032922)|dATP biosynthetic process (GO:0006175)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of T cell proliferation (GO:0042102)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|ribonucleoside monophosphate biosynthetic process (GO:0009156)|small molecule metabolic process (GO:0044281)|type B pancreatic cell proliferation (GO:0044342)	cytosol (GO:0005829)|nucleus (GO:0005634)	adenosine kinase activity (GO:0004001)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)|poly(A) RNA binding (GO:0044822)			breast(1)|large_intestine(2)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	8	Prostate(51;0.0112)|Ovarian(15;0.148)				Abacavir(DB01048)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Adenosine(DB00640)|Ribavirin(DB00811)	AGATGACACTATAATGGCTAC	0.348													A|||	1	0.000199681	0.0008	0.0	5008	,	,		10929	0.0		0.0	False		,,,				2504	0.0															0													70.0	58.0	62.0					10																	76360239		2203	4300	6503	SO:0001583	missense	132			U50196	CCDS7343.1, CCDS7344.1, CCDS55716.1, CCDS55717.1	10q22.2	2006-02-21			ENSG00000156110	ENSG00000156110	2.7.1.20		257	protein-coding gene	gene with protein product	"""adenosine 5'-phosphotransferase"""	102750				8577746	Standard	NM_001123		Approved	AK	uc001jwi.3	P55263	OTTHUMG00000018506	ENST00000286621.2:c.865A>G	10.37:g.76360239A>G	ENSP00000286621:p.Ile289Val		B7Z783|B7Z800|O00741|O00742|Q16710|Q5JQ10|Q5JQ11|Q9BTN2	Missense_Mutation	SNP	ENST00000286621.2	37	CCDS7343.1	.	.	.	.	.	.	.	.	.	.	A	0.962	-0.702964	0.03255	.	.	ENSG00000156110	ENST00000539909;ENST00000286621;ENST00000372734;ENST00000541550	D;T;T;T	0.88046	-2.33;-1.06;-1.06;-1.06	5.48	1.98	0.26296	Carbohydrate/purine kinase (1);	0.285757	0.38778	N	0.001561	T	0.71341	0.3328	N	0.16833	0.445	0.34041	D	0.655018	B;B;B;B	0.10296	0.001;0.003;0.0;0.0	B;B;B;B	0.11329	0.003;0.006;0.003;0.004	T	0.62120	-0.6921	10	0.06365	T	0.9	-6.3834	8.6521	0.34040	0.6935:0.0:0.3065:0.0	.	254;232;272;289	B7Z800;B7Z783;Q5JQ10;P55263	.;.;.;ADK_HUMAN	V	232;289;272;254	ENSP00000443965:I232V;ENSP00000286621:I289V;ENSP00000361819:I272V;ENSP00000438321:I254V	ENSP00000286621:I289V	I	+	1	0	ADK	76030245	0.412000	0.25392	0.481000	0.27354	0.992000	0.81027	0.894000	0.28350	0.392000	0.25172	0.460000	0.39030	ATA		0.348	ADK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048763.1	NM_001123, NM_006721		9	34	9	34
FFAR4	338557	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	95326548	95326548	+	Missense_Mutation	SNP	G	G	T			TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr10:95326548G>T	ENST00000371483.4	+	1	127	c.71G>T	c.(70-72)cGc>cTc	p.R24L	FFAR4_ENST00000604414.1_Missense_Mutation_p.R24L|FFAR4_ENST00000371481.4_Missense_Mutation_p.R24L	NM_181745.3	NP_859529.2	Q5NUL3	FFAR4_HUMAN	free fatty acid receptor 4	24					hormone secretion (GO:0046879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of inflammatory response (GO:0050728)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of glucose transport (GO:0010827)	endocytic vesicle (GO:0030139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fatty acid binding (GO:0005504)|taste receptor activity (GO:0008527)										AACCGCACCCGCTTTCCCTTC	0.701																																																0													20.0	18.0	18.0					10																	95326548		2196	4297	6493	SO:0001583	missense	338557				CCDS31248.1, CCDS55720.1	10q23.33	2012-11-16	2012-11-16	2012-11-16	ENSG00000186188	ENSG00000186188		"""GPCR / Class A : Fatty acid receptors"""	19061	protein-coding gene	gene with protein product		609044	"""G protein-coupled receptor 129"", ""G protein-coupled receptor 120"", ""omega-3 fatty acid receptor 1"""	GPR129, GPR120, O3FAR1		20471368, 19723586, 15619630, 20813258	Standard	NM_181745		Approved	PGR4	uc010qnt.2	Q5NUL3	OTTHUMG00000034409	ENST00000371483.4:c.71G>T	10.37:g.95326548G>T	ENSP00000360538:p.Arg24Leu		Q495H1|Q5VY25|Q5VY26|Q7Z605|Q86SM7	Missense_Mutation	SNP	ENST00000371483.4	37	CCDS31248.1	.	.	.	.	.	.	.	.	.	.	G	8.758	0.923019	0.18056	.	.	ENSG00000186188	ENST00000371481;ENST00000371483	T;T	0.35236	1.32;1.32	5.22	2.84	0.33178	.	0.275476	0.31685	N	0.007232	T	0.18173	0.0436	L	0.27053	0.805	0.27748	N	0.94425	B;B	0.12630	0.001;0.006	B;B	0.10450	0.005;0.004	T	0.12915	-1.0529	10	0.12103	T	0.63	-19.4569	2.8994	0.05700	0.3087:0.0:0.3718:0.3195	.	24;24	Q5NUL3-2;Q5NUL3	.;O3FA1_HUMAN	L	24	ENSP00000360536:R24L;ENSP00000360538:R24L	ENSP00000360536:R24L	R	+	2	0	O3FAR1	95316538	.	.	1.000000	0.80357	0.801000	0.45260	.	.	1.088000	0.41272	0.561000	0.74099	CGC		0.701	FFAR4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000083179.1	NM_181745		6	41	6	41
LOXL4	84171	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	100013489	100013489	+	Silent	SNP	C	C	T	rs376068066		TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr10:100013489C>T	ENST00000260702.3	-	11	1806	c.1656G>A	c.(1654-1656)ccG>ccA	p.P552P	RP11-34A14.3_ENST00000433374.1_RNA	NM_032211.6	NP_115587.6	Q96JB6	LOXL4_HUMAN	lysyl oxidase-like 4	552	Lysyl-oxidase like.					extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|receptor complex (GO:0043235)	copper ion binding (GO:0005507)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)			breast(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(8)|ovary(4)|prostate(1)|skin(2)	26		Colorectal(252;0.234)		Epithelial(162;2.14e-11)|all cancers(201;2.49e-09)		GCTGGCTGAGCGGGCGGTCCT	0.627													C|||	1	0.000199681	0.0	0.0	5008	,	,		17484	0.0		0.0	False		,,,				2504	0.001															0								C		0,4406		0,0,2203	80.0	76.0	77.0		1656	-4.1	0.9	10		77	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	LOXL4	NM_032211.6		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		552/757	100013489	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	84171			AF338441	CCDS7473.1	10q24	2008-08-01			ENSG00000138131	ENSG00000138131			17171	protein-coding gene	gene with protein product		607318				11292829	Standard	XM_005270216		Approved	FLJ21889, LOXC	uc001kpa.1	Q96JB6	OTTHUMG00000018874	ENST00000260702.3:c.1656G>A	10.37:g.100013489C>T			Q5W0B3|Q96DY1|Q96PC0|Q9H6T5	Silent	SNP	ENST00000260702.3	37	CCDS7473.1																																																																																				0.627	LOXL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049766.1	NM_032211		25	52	25	52
ADRBK1	156	hgsc.bcm.edu;broad.mit.edu	37	11	67046685	67046685	+	Missense_Mutation	SNP	C	C	G			TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr11:67046685C>G	ENST00000308595.5	+	3	495	c.205C>G	c.(205-207)Cga>Gga	p.R69G	ADRBK1_ENST00000526285.1_Missense_Mutation_p.R69G	NM_001619.3	NP_001610.2	P25098	ARBK1_HUMAN	adrenergic, beta, receptor kinase 1	69	N-terminal.|RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				activation of phospholipase C activity (GO:0007202)|cardiac muscle contraction (GO:0060048)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of striated muscle contraction (GO:0045988)|negative regulation of the force of heart contraction by chemical signal (GO:0003108)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of catecholamine secretion (GO:0033605)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)|tachykinin receptor signaling pathway (GO:0007217)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|ATP binding (GO:0005524)|beta-adrenergic receptor kinase activity (GO:0047696)|Edg-2 lysophosphatidic acid receptor binding (GO:0031755)|G-protein coupled receptor kinase activity (GO:0004703)|protein kinase activity (GO:0004672)	p.R69R(1)		cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|liver(2)|lung(8)|prostate(2)	22			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)		Adenosine triphosphate(DB00171)	CCTGCTCTTCCGAGACTTCTG	0.592																																																1	Substitution - coding silent(1)	lung(1)											96.0	88.0	91.0					11																	67046685		2200	4295	6495	SO:0001583	missense	156			X61157	CCDS8156.1	11q13	2013-01-10			ENSG00000173020	ENSG00000173020		"""Pleckstrin homology (PH) domain containing"""	289	protein-coding gene	gene with protein product		109635				2037065	Standard	NM_001619		Approved	GRK2, BARK1	uc009yrn.1	P25098	OTTHUMG00000167104	ENST00000308595.5:c.205C>G	11.37:g.67046685C>G	ENSP00000312262:p.Arg69Gly		B0ZBE1|Q13837|Q6GTT3	Missense_Mutation	SNP	ENST00000308595.5	37	CCDS8156.1	.	.	.	.	.	.	.	.	.	.	C	18.41	3.617891	0.66787	.	.	ENSG00000173020	ENST00000308595;ENST00000526285	T;T	0.02498	4.27;4.27	4.5	3.52	0.40303	Regulator of G protein signalling (3);Regulator of G protein signalling superfamily (1);	0.000000	0.44285	D	0.000474	T	0.03695	0.0105	L	0.34521	1.04	0.42422	D	0.99264	P;P	0.43633	0.813;0.653	B;B	0.42798	0.349;0.398	T	0.51787	-0.8661	10	0.72032	D	0.01	-12.0751	12.9449	0.58367	0.1611:0.8389:0.0:0.0	.	69;69	P25098;E9PRV7	ARBK1_HUMAN;.	G	69	ENSP00000312262:R69G;ENSP00000434126:R69G	ENSP00000312262:R69G	R	+	1	2	ADRBK1	66803261	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.656000	0.37355	2.504000	0.84457	0.655000	0.94253	CGA		0.592	ADRBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393153.1	NM_001619		6	77	6	77
TAPBPL	55080	hgsc.bcm.edu;broad.mit.edu	37	12	6567822	6567822	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr12:6567822G>A	ENST00000266556.7	+	5	1081	c.916G>A	c.(916-918)Gta>Ata	p.V306I	TAPBPL_ENST00000544021.1_3'UTR|TAPBPL_ENST00000545700.1_3'UTR	NM_018009.4	NP_060479.3	Q9BX59	TPSNR_HUMAN	TAP binding protein-like	306	Ig-like C1-type.				negative regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002590)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein complex binding (GO:0032403)			endometrium(2)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	6						TTCCCCTAAAGTACGACTGAG	0.522																																																0													125.0	116.0	119.0					12																	6567822		2203	4300	6503	SO:0001583	missense	55080			AK001005	CCDS8546.1	12p13.31	2013-01-11						"""Immunoglobulin superfamily / C1-set domain containing"""	30683	protein-coding gene	gene with protein product		607081				11920573	Standard	NM_018009		Approved	TAPBP-R, FLJ10143, TAPBPR	uc001qog.4	Q9BX59		ENST00000266556.7:c.916G>A	12.37:g.6567822G>A	ENSP00000266556:p.Val306Ile		Q9NWB8	Missense_Mutation	SNP	ENST00000266556.7	37	CCDS8546.1	.	.	.	.	.	.	.	.	.	.	G	13.16	2.153382	0.38021	.	.	ENSG00000139192	ENST00000266556	T	0.16597	2.33	5.05	2.96	0.34315	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.253646	0.39083	N	0.001461	T	0.23410	0.0566	M	0.86268	2.805	0.28738	N	0.902134	B	0.10296	0.003	B	0.14578	0.011	T	0.16778	-1.0391	10	0.54805	T	0.06	-5.7708	8.5151	0.33242	0.2037:0.0:0.7963:0.0	.	306	Q9BX59	TPSNR_HUMAN	I	306	ENSP00000266556:V306I	ENSP00000266556:V306I	V	+	1	0	TAPBPL	6438083	0.982000	0.34865	0.972000	0.41901	0.717000	0.41224	0.843000	0.27640	0.487000	0.27698	0.650000	0.86243	GTA		0.522	TAPBPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399263.1	NM_018009		12	156	12	156
ATF7IP	55729	hgsc.bcm.edu;broad.mit.edu	37	12	14634097	14634097	+	Silent	SNP	T	T	C			TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr12:14634097T>C	ENST00000540793.1	+	12	3413	c.3258T>C	c.(3256-3258)gtT>gtC	p.V1086V	ATF7IP_ENST00000543189.1_Silent_p.V1085V|ATF7IP_ENST00000536444.1_Silent_p.V1085V|ATF7IP_ENST00000544627.1_Silent_p.V1094V|ATF7IP_ENST00000261168.4_Silent_p.V1086V			Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting protein	1086					DNA methylation (GO:0006306)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045898)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)				cervix(1)|endometrium(7)|kidney(5)|large_intestine(10)|liver(2)|lung(22)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	54						CTCCTGCTGTTCGGCAGGTCA	0.453																																																0													63.0	62.0	63.0					12																	14634097		2203	4300	6503	SO:0001819	synonymous_variant	55729			AJ242978	CCDS8663.1, CCDS66326.1, CCDS66327.1, CCDS73449.1	12p13.1	2005-11-18				ENSG00000171681			20092	protein-coding gene	gene with protein product		613644				10976766, 10777215	Standard	XM_005253424		Approved	FLJ10688, p621	uc001rbw.3	Q6VMQ6		ENST00000540793.1:c.3258T>C	12.37:g.14634097T>C			F5GX74|G3V1U0|Q4G0T9|Q6P3T3|Q86XW5|Q9NVJ9|Q9NWC2|Q9Y4X8	Silent	SNP	ENST00000540793.1	37	CCDS8663.1	.	.	.	.	.	.	.	.	.	.	T	10.28	1.306275	0.23736	.	.	ENSG00000171681	ENST00000535738	.	.	.	5.43	-1.77	0.07982	.	.	.	.	.	T	0.37128	0.0992	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33085	-0.9882	4	.	.	.	-12.2358	0.0975	0.00045	0.2825:0.1706:0.2164:0.3305	.	.	.	.	P	100	.	.	S	+	1	0	ATF7IP	14525364	0.961000	0.32948	0.996000	0.52242	0.981000	0.71138	-0.133000	0.10451	0.045000	0.15804	0.528000	0.53228	TCG		0.453	ATF7IP-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401400.1	NM_018179		8	139	8	139
FLT3	2322	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	13	28609684	28609684	+	Silent	SNP	A	A	G			TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr13:28609684A>G	ENST00000241453.7	-	12	1626	c.1545T>C	c.(1543-1545)tgT>tgC	p.C515C	FLT3_ENST00000537084.1_Silent_p.C515C|FLT3_ENST00000380982.4_Silent_p.C515C	NM_004119.2	NP_004110.2	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	515					B cell differentiation (GO:0030183)|cellular response to cytokine stimulus (GO:0071345)|common myeloid progenitor cell proliferation (GO:0035726)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell differentiation (GO:0097028)|hemopoiesis (GO:0030097)|leukocyte homeostasis (GO:0001776)|lymphocyte proliferation (GO:0046651)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|pro-B cell differentiation (GO:0002328)|pro-T cell differentiation (GO:0002572)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor signaling pathway (GO:0038084)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|cytokine receptor activity (GO:0004896)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(12329)|kidney(2)|large_intestine(8)|lung(30)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12390	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Ponatinib(DB08901)|Sorafenib(DB00398)|Sunitinib(DB01268)	AATTGTATGCACAGCACTTGA	0.438			"""Mis, O"""		"""AML, ALL"""																																		Dom	yes		13	13q12	2322	fms-related tyrosine kinase 3		L	0													203.0	180.0	188.0					13																	28609684		2203	4300	6503	SO:0001819	synonymous_variant	2322			U02687	CCDS31953.1	13q12	2014-09-17			ENSG00000122025	ENSG00000122025	2.7.10.1	"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3765	protein-coding gene	gene with protein product		136351				8394751	Standard	NM_004119		Approved	STK1, FLK2, CD135	uc001urw.3	P36888	OTTHUMG00000016646	ENST00000241453.7:c.1545T>C	13.37:g.28609684A>G			A0AVG9|B7ZLT7|B7ZLT8|F5H0A0|Q13414	Silent	SNP	ENST00000241453.7	37	CCDS31953.1																																																																																				0.438	FLT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044319.2			18	163	18	163
FLT3	2322	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	13	28611413	28611413	+	Silent	SNP	A	A	G			TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr13:28611413A>G	ENST00000241453.7	-	10	1299	c.1218T>C	c.(1216-1218)ttT>ttC	p.F406F	FLT3_ENST00000537084.1_Silent_p.F406F|FLT3_ENST00000380982.4_Silent_p.F406F	NM_004119.2	NP_004110.2	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	406					B cell differentiation (GO:0030183)|cellular response to cytokine stimulus (GO:0071345)|common myeloid progenitor cell proliferation (GO:0035726)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell differentiation (GO:0097028)|hemopoiesis (GO:0030097)|leukocyte homeostasis (GO:0001776)|lymphocyte proliferation (GO:0046651)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|pro-B cell differentiation (GO:0002328)|pro-T cell differentiation (GO:0002572)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor signaling pathway (GO:0038084)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|cytokine receptor activity (GO:0004896)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(12329)|kidney(2)|large_intestine(8)|lung(30)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12390	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Ponatinib(DB08901)|Sorafenib(DB00398)|Sunitinib(DB01268)	TATGATTGCAAAACTTGGATA	0.378			"""Mis, O"""		"""AML, ALL"""																																		Dom	yes		13	13q12	2322	fms-related tyrosine kinase 3		L	0													96.0	98.0	97.0					13																	28611413		2203	4300	6503	SO:0001819	synonymous_variant	2322			U02687	CCDS31953.1	13q12	2014-09-17			ENSG00000122025	ENSG00000122025	2.7.10.1	"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3765	protein-coding gene	gene with protein product		136351				8394751	Standard	NM_004119		Approved	STK1, FLK2, CD135	uc001urw.3	P36888	OTTHUMG00000016646	ENST00000241453.7:c.1218T>C	13.37:g.28611413A>G			A0AVG9|B7ZLT7|B7ZLT8|F5H0A0|Q13414	Silent	SNP	ENST00000241453.7	37	CCDS31953.1																																																																																				0.378	FLT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044319.2			10	79	10	79
KHNYN	23351	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	14	24909494	24909494	+	3'UTR	SNP	G	G	T			TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr14:24909494G>T	ENST00000251343.5	+	0	5179				SDR39U1_ENST00000399390.1_Missense_Mutation_p.A131D|SDR39U1_ENST00000399395.3_Missense_Mutation_p.A226D|SDR39U1_ENST00000538105.2_Missense_Mutation_p.A144D|SDR39U1_ENST00000555561.1_5'UTR|SDR39U1_ENST00000555365.1_Missense_Mutation_p.A59D|SDR39U1_ENST00000553930.1_Missense_Mutation_p.A101D|SDR39U1_ENST00000554698.1_Missense_Mutation_p.A118D			O15037	KHNYN_HUMAN	KH and NYN domain containing								RNA binding (GO:0003723)			kidney(1)|large_intestine(3)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(3)	24						GGCAAACTCAGCATTAGTGGC	0.617																																																0													43.0	51.0	49.0					14																	24909494		2049	4202	6251	SO:0001624	3_prime_UTR_variant	56948			AB002321	CCDS32058.1	14q11.2	2010-11-23	2009-10-14	2009-10-14	ENSG00000100441	ENSG00000100441			20166	protein-coding gene	gene with protein product			"""KIAA0323"""	KIAA0323		17114934	Standard	NM_015299		Approved		uc001wph.4	O15037		ENST00000251343.5:c.*3003G>T	14.37:g.24909494G>T			Q86TZ6|Q8IUQ2|Q96BA9	Missense_Mutation	SNP	ENST00000251343.5	37	CCDS32058.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.89|13.89	2.373303|2.373303	0.42105|0.42105	.|.	.|.	ENSG00000100445|ENSG00000100445	ENST00000399395;ENST00000336353;ENST00000399390;ENST00000553930;ENST00000538105;ENST00000554698;ENST00000555365;ENST00000553343;ENST00000555225;ENST00000555355;ENST00000556523|ENST00000556249	T;T;T;T;T;T;T;T;T;T|.	0.33865|.	2.12;1.82;1.82;1.81;1.84;1.86;1.83;1.44;1.39;1.41|.	4.71|4.71	3.77|3.77	0.43336|0.43336	NAD(P)-binding domain (1);|.	0.540943|.	0.19594|.	N|.	0.110542|.	T|T	0.60907|0.60907	0.2305|0.2305	M|M	0.68728|0.68728	2.09|2.09	0.32100|0.32100	N|N	0.590771|0.590771	P;P;P;P;B|.	0.46327|.	0.876;0.646;0.67;0.7;0.415|.	P;B;B;B;B|.	0.49301|.	0.606;0.144;0.299;0.207;0.194|.	T|T	0.66520|0.66520	-0.5903|-0.5903	10|5	0.14656|.	T|.	0.56|.	-2.858|-2.858	11.5707|11.5707	0.50832|0.50832	0.0:0.3179:0.6821:0.0|0.0:0.3179:0.6821:0.0	.|.	101;226;252;144;118|.	G3V5T1;Q9NRG7-2;Q9NRG7;F6RWC2;Q86TZ5|.	.;.;D39U1_HUMAN;.;.|.	D|M	226;252;131;101;144;118;59;120;59;101;59|149	ENSP00000382327:A226D;ENSP00000382322:A131D;ENSP00000452499:A101D;ENSP00000446077:A144D;ENSP00000452438:A118D;ENSP00000451903:A59D;ENSP00000452076:A120D;ENSP00000451593:A59D;ENSP00000450946:A101D;ENSP00000451275:A59D|.	ENSP00000336854:A252D|.	A|L	-|-	2|1	0|2	SDR39U1|SDR39U1	23979334|23979334	0.956000|0.956000	0.32656|0.32656	1.000000|1.000000	0.80357|0.80357	0.907000|0.907000	0.53573|0.53573	1.900000|1.900000	0.39828|0.39828	2.440000|2.440000	0.82611|0.82611	0.563000|0.563000	0.77884|0.77884	GCT|CTG		0.617	KHNYN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412928.1			21	39	21	39
DUOX2	50506	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	45398797	45398797	+	Missense_Mutation	SNP	C	C	T	rs373620034		TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr15:45398797C>T	ENST00000603300.1	-	16	2076	c.1874G>A	c.(1873-1875)cGa>cAa	p.R625Q	DUOX2_ENST00000389039.6_Missense_Mutation_p.R625Q	NM_014080.4	NP_054799.4	Q9NRD8	DUOX2_HUMAN	dual oxidase 2	625					adenohypophysis morphogenesis (GO:0048855)|bone mineralization (GO:0030282)|cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|fertilization (GO:0009566)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|inner ear development (GO:0048839)|multicellular organism growth (GO:0035264)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|response to virus (GO:0009615)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|peroxidase activity (GO:0004601)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	63		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)		CTTGTGTTCTCGGCCCCGGAA	0.557																																																0								C	GLN/ARG	0,4396		0,0,2198	154.0	150.0	151.0		1874	-1.0	1.0	15		151	1,8595	1.2+/-3.3	0,1,4297	no	missense	DUOX2	NM_014080.4	43	0,1,6495	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	625/1549	45398797	1,12991	2198	4298	6496	SO:0001583	missense	50506			AF181972	CCDS10117.1	15q15.3-q21	2013-01-10			ENSG00000140279	ENSG00000140279		"""EF-hand domain containing"""	13273	protein-coding gene	gene with protein product	"""dual oxidase-like domains 2"", ""nicotinamide adenine dinucleotide phosphate oxidase"", ""flavoprotein NADPH oxidase"", ""NADPH thyroid oxidase 2"", ""NADH/NADPH thyroid oxidase p138-tox"", ""NADPH oxidase/peroxidase DUOX2"""	606759				10601291, 10806195	Standard	NM_014080		Approved	P138-TOX, P138(TOX), THOX2, LNOX2	uc010bea.3	Q9NRD8	OTTHUMG00000131355	ENST00000603300.1:c.1874G>A	15.37:g.45398797C>T	ENSP00000475084:p.Arg625Gln		A8MQ13|D2XI64|Q9NR02|Q9UHF9	Missense_Mutation	SNP	ENST00000603300.1	37	CCDS10117.1	.	.	.	.	.	.	.	.	.	.	C	13.84	2.357373	0.41801	0.0	1.16E-4	ENSG00000140279	ENST00000389039	.	.	.	5.42	-1.02	0.10135	.	0.584816	0.18081	N	0.152290	T	0.49287	0.1548	M	0.72894	2.215	0.40470	D	0.980336	B;B	0.31931	0.188;0.347	B;B	0.24701	0.023;0.055	T	0.44467	-0.9326	9	0.42905	T	0.14	-3.1592	9.9682	0.41738	0.0:0.6012:0.0:0.3988	.	625;187	Q9NRD8;Q59GU9	DUOX2_HUMAN;.	Q	625	.	ENSP00000373691:R625Q	R	-	2	0	DUOX2	43186089	0.024000	0.19004	0.990000	0.47175	0.648000	0.38561	-0.235000	0.09016	-0.185000	0.10550	0.455000	0.32223	CGA		0.557	DUOX2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_014080		33	176	33	176
HERC1	8925	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	63972937	63972937	+	Silent	SNP	C	C	T			TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr15:63972937C>T	ENST00000443617.2	-	35	6351	c.6264G>A	c.(6262-6264)acG>acA	p.T2088T	RP11-317G6.1_ENST00000559303.2_RNA	NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	2088	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						CTCCAACACACGTGCCTTCAT	0.373																																																0													188.0	176.0	180.0					15																	63972937		1897	4118	6015	SO:0001819	synonymous_variant	8925			U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"""WD repeat domain containing"""	4867	protein-coding gene	gene with protein product		605109	"""hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"""			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.6264G>A	15.37:g.63972937C>T			Q8IW65	Silent	SNP	ENST00000443617.2	37	CCDS45277.1																																																																																				0.373	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		25	194	25	194
MYO9A	4649	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	72190411	72190411	+	Nonsense_Mutation	SNP	A	A	T			TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr15:72190411A>T	ENST00000356056.5	-	25	4905	c.4433T>A	c.(4432-4434)tTg>tAg	p.L1478*	MYO9A_ENST00000566885.1_Nonsense_Mutation_p.L1098*|MYO9A_ENST00000563542.1_5'UTR|MYO9A_ENST00000424560.1_Nonsense_Mutation_p.L1478*|MYO9A_ENST00000444904.1_Nonsense_Mutation_p.L1459*|MYO9A_ENST00000564571.1_Nonsense_Mutation_p.L1478*	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	1478	Tail.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)			NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						CTCTGTATTCAAAGAAGGAAC	0.393																																																0													103.0	96.0	98.0					15																	72190411		2199	4297	6496	SO:0001587	stop_gained	4649			AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933		"""Myosins / Myosin superfamily : Class IX"""	7608	protein-coding gene	gene with protein product		604875				10409426	Standard	NM_006901		Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000356056.5:c.4433T>A	15.37:g.72190411A>T	ENSP00000348349:p.Leu1478*		B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Nonsense_Mutation	SNP	ENST00000356056.5	37	CCDS10239.1	.	.	.	.	.	.	.	.	.	.	A	17.30	3.355308	0.61293	.	.	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904	.	.	.	5.92	3.6	0.41247	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08837	T	0.75	.	5.9237	0.19096	0.6659:0.1302:0.2039:0.0	.	.	.	.	X	1478;1478;1459	.	ENSP00000348349:L1478X	L	-	2	0	MYO9A	69977465	0.000000	0.05858	0.439000	0.26833	0.747000	0.42532	0.250000	0.18235	1.074000	0.40909	0.528000	0.53228	TTG		0.393	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901		11	123	11	123
GDPD1	284161	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	57348316	57348316	+	Missense_Mutation	SNP	A	A	G			TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr17:57348316A>G	ENST00000284116.4	+	8	867	c.730A>G	c.(730-732)Atg>Gtg	p.M244V	GDPD1_ENST00000581276.1_Missense_Mutation_p.M244V|GDPD1_ENST00000581140.1_Missense_Mutation_p.M244V	NM_182569.3	NP_872375.2	Q8N9F7	GDPD1_HUMAN	glycerophosphodiester phosphodiesterase domain containing 1	244	GP-PDE.				glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycerophosphodiester phosphodiesterase activity (GO:0008889)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|liver(1)|lung(2)|upper_aerodigestive_tract(1)	6	all_neural(34;0.0837)|Medulloblastoma(34;0.0922)					ACCACACACCATGTCCAGAAG	0.279																																																0													105.0	110.0	109.0					17																	57348316		2203	4297	6500	SO:0001583	missense	284161			AK094770	CCDS11616.1, CCDS58583.1, CCDS58584.1	17q23.2	2011-01-25				ENSG00000153982			20883	protein-coding gene	gene with protein product						14612981	Standard	NM_182569		Approved	FLJ37451, GDE4	uc002ixk.2	Q8N9F7		ENST00000284116.4:c.730A>G	17.37:g.57348316A>G	ENSP00000284116:p.Met244Val		A8W735|Q56VR1|Q8N4E3	Missense_Mutation	SNP	ENST00000284116.4	37	CCDS11616.1	.	.	.	.	.	.	.	.	.	.	A	9.701	1.154470	0.21371	.	.	ENSG00000153982	ENST00000284116	T	0.09538	2.97	5.44	5.44	0.79542	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);	0.230980	0.51477	D	0.000098	T	0.10035	0.0246	L	0.40543	1.245	0.39854	D	0.973289	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.17077	-1.0381	10	0.17832	T	0.49	.	13.2241	0.59905	1.0:0.0:0.0:0.0	.	244;244	Q8N9F7;Q8N9F7-2	GDPD1_HUMAN;.	V	244	ENSP00000284116:M244V	ENSP00000284116:M244V	M	+	1	0	GDPD1	54703098	0.998000	0.40836	0.998000	0.56505	0.924000	0.55760	3.530000	0.53539	2.068000	0.61886	0.482000	0.46254	ATG		0.279	GDPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446024.1	NM_182569		37	92	37	92
SMARCD2	6603	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	61911645	61911645	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr17:61911645C>T	ENST00000448276.2	-	8	1230	c.965G>A	c.(964-966)gGa>gAa	p.G322E	SMARCD2_ENST00000225742.9_Missense_Mutation_p.G247E|SMARCD2_ENST00000323347.10_Missense_Mutation_p.G274E	NM_001098426.1	NP_001091896.1	Q92925	SMRD2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2	322	SWIB.				ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|nucleosome disassembly (GO:0006337)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	transcription coactivator activity (GO:0003713)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(1)	8						CGTGTGCACTCCCAGCAGCCT	0.567											OREG0024642	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0													26.0	27.0	27.0					17																	61911645		2014	4165	6179	SO:0001583	missense	6603			U66618	CCDS45756.1	17q23.3	2014-07-16			ENSG00000108604	ENSG00000108604			11107	protein-coding gene	gene with protein product	"""mammalian chromatin remodeling complex BRG1-associated factor 60B"", ""Swp73-like protein"", ""chromatin remodeling complex BAF60B subunit"", ""SWI/SNF complex 60 kDa subunit B"""	601736				8804307, 9693044	Standard	NM_001098426		Approved	BAF60B, Rsc6p, CRACD2, PRO2451	uc010deb.1	Q92925	OTTHUMG00000179045	ENST00000448276.2:c.965G>A	17.37:g.61911645C>T	ENSP00000392617:p.Gly322Glu	1057	A5PLL5|A6NNQ7|B4DV56|B4E1R6|Q7L2I6|Q9UHZ1	Missense_Mutation	SNP	ENST00000448276.2	37	CCDS45756.1	.	.	.	.	.	.	.	.	.	.	.	10.91	1.484002	0.26598	.	.	ENSG00000108604	ENST00000448276;ENST00000225742;ENST00000450364;ENST00000323347	T;T	0.58940	0.3;0.37	5.55	5.55	0.83447	SWIB/MDM2 domain (2);	0.000000	0.85682	D	0.000000	D	0.82412	0.5031	M	0.93638	3.44	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.998	D	0.86256	0.1652	10	0.87932	D	0	-22.3518	17.0466	0.86505	0.0:1.0:0.0:0.0	.	274;285;322	Q92925-3;B9EGA3;Q92925	.;.;SMRD2_HUMAN	E	322;264;285;274	ENSP00000392617:G322E;ENSP00000318451:G274E	ENSP00000225742:G264E	G	-	2	0	SMARCD2	59265377	1.000000	0.71417	1.000000	0.80357	0.032000	0.12392	7.651000	0.83577	2.894000	0.99253	0.655000	0.94253	GGA		0.567	SMARCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444544.1	NM_001098426		7	25	7	25
SMARCA4	6597	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	11135091	11135091	+	Missense_Mutation	SNP	G	G	T			TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr19:11135091G>T	ENST00000429416.3	+	22	3339	c.3058G>T	c.(3058-3060)Gat>Tat	p.D1020Y	SMARCA4_ENST00000413806.3_Missense_Mutation_p.D1020Y|SMARCA4_ENST00000589677.1_Missense_Mutation_p.D1020Y|SMARCA4_ENST00000590574.1_Missense_Mutation_p.D1020Y|SMARCA4_ENST00000344626.4_Missense_Mutation_p.D1020Y|SMARCA4_ENST00000450717.3_Missense_Mutation_p.D1020Y|SMARCA4_ENST00000444061.3_Missense_Mutation_p.D1020Y|SMARCA4_ENST00000358026.2_Missense_Mutation_p.D1020Y|SMARCA4_ENST00000541122.2_Missense_Mutation_p.D1020Y	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	1020					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)				GCTGCTGACTGATGGCTCCGA	0.627			"""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)											73.0	59.0	64.0					19																	11135091		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.3058G>T	19.37:g.11135091G>T	ENSP00000395654:p.Asp1020Tyr		B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	37	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	G	19.74	3.884577	0.72410	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	D;D;D;D;D;D;D	0.81499	-1.5;-1.5;-1.5;-1.5;-1.5;-1.5;-1.5	4.76	4.76	0.60689	SNF2-related (1);	0.000000	0.85682	D	0.000000	D	0.89157	0.6635	M	0.74647	2.275	0.58432	D	0.999999	D;D;D;P;D;P;D;D	0.89917	0.999;0.997;1.0;0.944;0.999;0.537;1.0;1.0	D;D;D;D;D;P;D;D	0.77004	0.989;0.981;0.986;0.918;0.989;0.722;0.989;0.989	D	0.90510	0.4480	10	0.87932	D	0	-36.5944	16.6873	0.85312	0.0:0.0:1.0:0.0	.	1020;1020;1020;1020;1020;240;1020;1020	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;B4E0F1;A7E2E1;P51532	.;.;.;.;.;.;.;SMCA4_HUMAN	Y	1020;1020;1084;1020;1020;1020;1020;1020	ENSP00000395654:D1020Y;ENSP00000350720:D1020Y;ENSP00000343896:D1020Y;ENSP00000445036:D1020Y;ENSP00000392837:D1020Y;ENSP00000397783:D1020Y;ENSP00000414727:D1020Y	ENSP00000343896:D1020Y	D	+	1	0	SMARCA4	10996091	1.000000	0.71417	0.933000	0.37362	0.503000	0.33858	9.411000	0.97342	2.468000	0.83385	0.655000	0.94253	GAT		0.627	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		18	37	18	37
ZNF490	57474	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	12692359	12692359	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr19:12692359G>A	ENST00000311437.6	-	5	652	c.530C>T	c.(529-531)tCt>tTt	p.S177F	ZNF490_ENST00000465656.1_5'Flank|CTD-2192J16.20_ENST00000593682.1_5'Flank	NM_020714.2	NP_065765.1	Q9ULM2	ZN490_HUMAN	zinc finger protein 490	177					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	18						TTCAGTGTGAGATCTCATGTG	0.443																																																0													218.0	177.0	191.0					19																	12692359		2203	4300	6503	SO:0001583	missense	57474			AB033024	CCDS12272.1	19p13.2	2013-01-08			ENSG00000188033	ENSG00000188033		"""Zinc fingers, C2H2-type"", ""-"""	23705	protein-coding gene	gene with protein product							Standard	NM_020714		Approved	KIAA1198	uc002mtz.2	Q9ULM2	OTTHUMG00000156398	ENST00000311437.6:c.530C>T	19.37:g.12692359G>A	ENSP00000311521:p.Ser177Phe			Missense_Mutation	SNP	ENST00000311437.6	37	CCDS12272.1	.	.	.	.	.	.	.	.	.	.	G	0.024	-1.394836	0.01175	.	.	ENSG00000188033	ENST00000311437;ENST00000440366	T;T	0.18338	2.22;4.71	0.996	-0.188	0.13264	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.18130	0.0435	L	0.31845	0.965	0.09310	N	1	D	0.54601	0.967	P	0.54856	0.762	T	0.13548	-1.0505	9	0.51188	T	0.08	.	3.8373	0.08899	0.1842:0.2595:0.5564:0.0	.	177	Q9ULM2	ZN490_HUMAN	F	177;124	ENSP00000311521:S177F;ENSP00000404112:S124F	ENSP00000311521:S177F	S	-	2	0	ZNF490	12553359	0.000000	0.05858	0.024000	0.17045	0.017000	0.09413	-0.060000	0.11712	-0.013000	0.14199	0.491000	0.48974	TCT		0.443	ZNF490-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344073.1	NM_020714		72	138	72	138
IL27RA	9466	hgsc.bcm.edu;broad.mit.edu	37	19	14157294	14157294	+	Silent	SNP	G	G	A			TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr19:14157294G>A	ENST00000263379.2	+	8	1130	c.1005G>A	c.(1003-1005)acG>acA	p.T335T		NM_004843.3	NP_004834.1	Q6UWB1	I27RA_HUMAN	interleukin 27 receptor, alpha	335	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|defense response to Gram-positive bacterium (GO:0050830)|immune response (GO:0006955)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T-helper 1 type immune response (GO:0002827)|regulation of isotype switching to IgG isotypes (GO:0048302)	integral component of plasma membrane (GO:0005887)	interleukin-27 receptor activity (GO:0045509)|transmembrane signaling receptor activity (GO:0004888)			breast(3)|endometrium(3)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	26						CTGGGAGCACGGAGCTACTGG	0.627																																					Colon(164;1849 1896 4443 37792 47834)											0													90.0	95.0	93.0					19																	14157294		2203	4300	6503	SO:0001819	synonymous_variant	9466			AF053004	CCDS12303.1	19p13.11	2013-02-11				ENSG00000104998		"""Interleukins and interleukin receptors"", ""Fibronectin type III domain containing"""	17290	protein-coding gene	gene with protein product	"""T-cell cytokine receptor type 1"""	605350				9600072, 11057672	Standard	NM_004843		Approved	WSX-1, TCCR, CRL1, WSX1, zcytor1, IL-27R	uc002mxx.4	Q6UWB1		ENST00000263379.2:c.1005G>A	19.37:g.14157294G>A			A0N0L1|O60624	Silent	SNP	ENST00000263379.2	37	CCDS12303.1																																																																																				0.627	IL27RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458539.1	NM_004843		15	216	15	216
ZNF681	148213	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	23927189	23927189	+	Missense_Mutation	SNP	T	T	C	rs145416258	byFrequency	TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr19:23927189T>C	ENST00000402377.3	-	4	1304	c.1163A>G	c.(1162-1164)cAt>cGt	p.H388R	ZNF681_ENST00000395385.3_Missense_Mutation_p.H319R	NM_138286.2	NP_612143.2	Q96N22	ZN681_HUMAN	zinc finger protein 681	388					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(3)	21		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				CTCTCCAGTATGAATTATCTT	0.398																																																0													65.0	71.0	69.0					19																	23927189		2201	4300	6501	SO:0001583	missense	148213			AK056088	CCDS12414.2	19p12	2013-01-08			ENSG00000196172	ENSG00000196172		"""Zinc fingers, C2H2-type"", ""-"""	26457	protein-coding gene	gene with protein product	"""hypothetical protein FLJ31526"""						Standard	NM_138286		Approved	FLJ31526	uc002nrk.4	Q96N22	OTTHUMG00000150831	ENST00000402377.3:c.1163A>G	19.37:g.23927189T>C	ENSP00000384000:p.His388Arg		B3KVF7	Missense_Mutation	SNP	ENST00000402377.3	37	CCDS12414.2	.	.	.	.	.	.	.	.	.	.	.	11.45	1.642813	0.29246	.	.	ENSG00000196172	ENST00000402377;ENST00000395385	T;T	0.67523	-0.27;-0.27	1.51	1.51	0.23008	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.77778	0.4181	M	0.76838	2.35	0.33311	D	0.566147	D	0.89917	1.0	D	0.79784	0.993	T	0.79584	-0.1743	9	0.87932	D	0	.	6.6698	0.23062	0.0:0.0:0.0:1.0	.	388	Q96N22	ZN681_HUMAN	R	388;319	ENSP00000384000:H388R;ENSP00000378783:H319R	ENSP00000378783:H319R	H	-	2	0	ZNF681	23719029	1.000000	0.71417	0.114000	0.21550	0.315000	0.28087	3.827000	0.55745	0.663000	0.31027	0.260000	0.18958	CAT		0.398	ZNF681-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320248.2	NM_138286		30	62	30	62
THEMIS2	9473	hgsc.bcm.edu;broad.mit.edu	37	1	28209255	28209255	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr1:28209255G>A	ENST00000373921.3	+	4	1424	c.1420G>A	c.(1420-1422)Ggc>Agc	p.G474S	THEMIS2_ENST00000373927.3_Intron|THEMIS2_ENST00000328928.7_Missense_Mutation_p.G345S|THEMIS2_ENST00000373925.1_Intron	NM_001105556.1	NP_001099026.1	Q5TEJ8	THMS2_HUMAN	thymocyte selection associated family member 2	474	CABIT 2.				cell adhesion (GO:0007155)|inflammatory response (GO:0006954)|T cell receptor signaling pathway (GO:0050852)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											CTCCTTCCTGGGCCTGCGGCT	0.602																																																0													69.0	70.0	69.0					1																	28209255		2064	4206	6270	SO:0001583	missense	9473			AF044896	CCDS30653.1, CCDS30654.1, CCDS41290.1, CCDS65461.1	1p35.2	2012-07-10	2012-07-10	2012-07-10	ENSG00000130775	ENSG00000130775			16839	protein-coding gene	gene with protein product	"""induced by contact to basement membrane 1"""		"""chromosome 1 open reading frame 38"""	C1orf38		16219472	Standard	XM_005246041		Approved	ICB-1, Icb-1	uc001bpc.4	Q5TEJ8	OTTHUMG00000003735	ENST00000373921.3:c.1420G>A	1.37:g.28209255G>A	ENSP00000363031:p.Gly474Ser		A2RTZ3|B4DZT9|B4DZY3|O60560|Q5TEJ1|Q5TEJ9|Q5TEK1|Q68DP4|Q9BYB6|Q9NS90	Missense_Mutation	SNP	ENST00000373921.3	37	CCDS41290.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.09|11.09	1.536510|1.536510	0.27475|0.27475	.|.	.|.	ENSG00000130775|ENSG00000130775	ENST00000328928;ENST00000373921|ENST00000456990	T;T|.	0.13538|.	2.58;2.58|.	4.98|4.98	4.98|4.98	0.66077|0.66077	.|.	0.280340|.	0.38778|.	N|.	0.001563|.	T|.	0.53850|.	0.1822|.	L|L	0.58669|0.58669	1.825|1.825	0.20403|0.20403	N|N	0.99991|0.99991	P;D;P|.	0.89917|.	0.649;1.0;0.63|.	B;D;B|.	0.83275|.	0.256;0.996;0.403|.	T|.	0.47812|.	-0.9088|.	10|.	0.41790|.	T|.	0.15|.	-23.9582|-23.9582	12.448|12.448	0.55662|0.55662	0.0:0.0:0.7225:0.2775|0.0:0.0:0.7225:0.2775	.|.	345;278;474|.	Q5TEJ8-5;Q5TEJ8-6;Q5TEJ8|.	.;.;THMS2_HUMAN|.	S|X	345;474|221	ENSP00000329862:G345S;ENSP00000363031:G474S|.	ENSP00000329862:G345S|.	G|W	+|+	1|3	0|0	C1orf38|C1orf38	28081842|28081842	0.262000|0.262000	0.24073|0.24073	0.952000|0.952000	0.39060|0.39060	0.090000|0.090000	0.18270|0.18270	1.176000|1.176000	0.31957|0.31957	2.489000|2.489000	0.83994|0.83994	0.555000|0.555000	0.69702|0.69702	GGC|TGG		0.602	THEMIS2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011148.1	NM_004848		6	91	6	91
KCNA10	3744	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	111060317	111060317	+	Missense_Mutation	SNP	C	C	T	rs190117605		TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr1:111060317C>T	ENST00000369771.2	-	1	1480	c.1093G>A	c.(1093-1095)Ggg>Agg	p.G365R		NM_005549.2	NP_005540.1	Q16322	KCA10_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 10	365					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|intracellular cyclic nucleotide activated cation channel activity (GO:0005221)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(3)|skin(1)|urinary_tract(1)	35		all_cancers(81;4.57e-06)|all_epithelial(167;1.52e-05)|all_lung(203;0.000152)|Lung NSC(277;0.000301)		Lung(183;0.0238)|all cancers(265;0.0874)|Colorectal(144;0.103)|Epithelial(280;0.116)|LUSC - Lung squamous cell carcinoma(189;0.134)	Dalfampridine(DB06637)	AGTGTTTGCCCGAGGATCTGC	0.557													C|||	1	0.000199681	0.0	0.0	5008	,	,		20618	0.0		0.001	False		,,,				2504	0.0															0													98.0	95.0	96.0					1																	111060317		2203	4300	6503	SO:0001583	missense	3744			U96110	CCDS826.1	1p13.1	2012-07-05			ENSG00000143105	ENSG00000143105		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6219	protein-coding gene	gene with protein product		602420				16382104	Standard	NM_005549		Approved	Kv1.8	uc001dzt.1	Q16322	OTTHUMG00000022785	ENST00000369771.2:c.1093G>A	1.37:g.111060317C>T	ENSP00000358786:p.Gly365Arg			Missense_Mutation	SNP	ENST00000369771.2	37	CCDS826.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	16.76	3.211498	0.58343	.	.	ENSG00000143105	ENST00000369771	D	0.98701	-5.08	5.63	5.63	0.86233	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99287	0.9751	M	0.89287	3.02	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99544	1.0964	10	0.87932	D	0	.	18.3064	0.90184	0.0:1.0:0.0:0.0	.	365	Q16322	KCA10_HUMAN	R	365	ENSP00000358786:G365R	ENSP00000358786:G365R	G	-	1	0	KCNA10	110861840	1.000000	0.71417	1.000000	0.80357	0.269000	0.26545	7.815000	0.86186	2.676000	0.91093	0.558000	0.71614	GGG		0.557	KCNA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059081.1	NM_005549		76	62	76	62
DUSP27	92235	hgsc.bcm.edu;broad.mit.edu	37	1	167096396	167096396	+	Silent	SNP	G	G	A	rs376593703		TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr1:167096396G>A	ENST00000361200.2	+	6	2194	c.2028G>A	c.(2026-2028)acG>acA	p.T676T	DUSP27_ENST00000271385.5_Silent_p.T676T|DUSP27_ENST00000443333.1_Silent_p.T676T|DUSP27_ENST00000485151.1_Intron			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	676					protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						GGGACACGACGTCAGTACTGA	0.637																																																0								G		0,4406		0,0,2203	48.0	49.0	49.0		2028	-9.1	0.0	1		49	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	DUSP27	NM_001080426.1		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		676/1159	167096396	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	92235			AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.2028G>A	1.37:g.167096396G>A			A0AUM4|Q9C074	Silent	SNP	ENST00000361200.2	37	CCDS30932.1																																																																																				0.637	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426		5	49	5	49
PRG4	10216	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	186276487	186276487	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr1:186276487C>T	ENST00000445192.2	+	7	1681	c.1636C>T	c.(1636-1638)Ccc>Tcc	p.P546S	PRG4_ENST00000367485.4_Missense_Mutation_p.P453S|PRG4_ENST00000367486.3_Missense_Mutation_p.P503S|PRG4_ENST00000367483.4_Missense_Mutation_p.P505S|PRG4_ENST00000367484.3_Intron	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	546	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						CAAGTCTGCACCCACCACTCC	0.642																																																0													141.0	125.0	130.0					1																	186276487		2203	4299	6502	SO:0001583	missense	10216			U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"""lubricin"", ""megakaryocyte stimulating factor"", ""articular superficial zone protein"", ""Jacobs camptodactyly-arthropathy-pericarditis syndrome"", ""camptodactyly, arthropathy, coxa vara, pericarditis syndrome"", ""bG174L6.2 (MSF: megakaryocyte stimulating factor )"""	604283	"""proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"""	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.1636C>T	1.37:g.186276487C>T	ENSP00000399679:p.Pro546Ser		Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Missense_Mutation	SNP	ENST00000445192.2	37	CCDS1369.1	.	.	.	.	.	.	.	.	.	.	c	3.432	-0.115969	0.06881	.	.	ENSG00000116690	ENST00000367486;ENST00000367482;ENST00000367483;ENST00000367485;ENST00000445192	T;T;T;T	0.07688	3.18;3.27;3.17;3.29	2.25	1.25	0.21368	.	.	.	.	.	T	0.05914	0.0154	L	0.34521	1.04	0.09310	N	0.999995	B;B;B;B	0.26081	0.087;0.087;0.141;0.041	B;B;B;B	0.23574	0.047;0.047;0.021;0.047	T	0.39418	-0.9615	8	.	.	.	.	5.0698	0.14600	0.0:0.6095:0.2425:0.1479	.	412;453;546;505	Q92954-4;Q92954-3;Q92954;Q92954-2	.;.;PRG4_HUMAN;.	S	503;412;505;453;546	ENSP00000356456:P503S;ENSP00000356453:P505S;ENSP00000356455:P453S;ENSP00000399679:P546S	.	P	+	1	0	PRG4	184543110	0.000000	0.05858	0.008000	0.14137	0.013000	0.08279	-0.001000	0.12947	0.982000	0.38575	0.437000	0.28790	CCC		0.642	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807		49	104	49	104
OR13G1	441933	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	247835570	247835570	+	Silent	SNP	G	G	T			TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr1:247835570G>T	ENST00000359688.2	-	1	795	c.774C>A	c.(772-774)cgC>cgA	p.R258R	RP11-634B7.4_ENST00000449298.1_RNA	NM_001005487.1	NP_001005487.1	Q8NGZ3	O13G1_HUMAN	olfactory receptor, family 13, subfamily G, member 1	258						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|kidney(1)|large_intestine(2)|lung(28)|skin(2)	35	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			TGGAAGCAGGGCGGATATAGG	0.463																																																0													137.0	124.0	129.0					1																	247835570		2203	4300	6503	SO:0001819	synonymous_variant	441933			AB065623	CCDS31094.1	1q44	2012-08-09			ENSG00000197437	ENSG00000197437		"""GPCR / Class A : Olfactory receptors"""	14999	protein-coding gene	gene with protein product		611677					Standard	NM_001005487		Approved		uc001idi.1	Q8NGZ3	OTTHUMG00000040212	ENST00000359688.2:c.774C>A	1.37:g.247835570G>T			B2RN80|Q5T2T2|Q6IF86	Silent	SNP	ENST00000359688.2	37	CCDS31094.1																																																																																				0.463	OR13G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096869.1	NM_001005487		29	157	29	157
HELZ2	85441	hgsc.bcm.edu;ucsc.edu	37	20	62194934	62194934	+	Silent	SNP	C	C	T			TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr20:62194934C>T	ENST00000467148.1	-	8	5310	c.5241G>A	c.(5239-5241)gtG>gtA	p.V1747V	HELZ2_ENST00000427522.2_Silent_p.V1178V	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	1747					cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										AGCCCGCCTCCACGTCCACCA	0.711																																																0													6.0	8.0	7.0					20																	62194934		2056	4098	6154	SO:0001819	synonymous_variant	85441			AB201715	CCDS13527.1, CCDS33508.1	20q13.33	2012-09-26			ENSG00000130589	ENSG00000130589			30021	protein-coding gene	gene with protein product	"""peroxisomal proliferator activated receptor A interacting complex 285"", ""PPARG-DBD-interacting protein 1"""	611265				11214970, 12189208, 16239304	Standard	NM_001037335		Approved	PDIP1, PRIC285, KIAA1769	uc002yfm.2	Q9BYK8	OTTHUMG00000032969	ENST00000467148.1:c.5241G>A	20.37:g.62194934C>T			Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Silent	SNP	ENST00000467148.1	37	CCDS33508.1																																																																																				0.711	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335		4	10	4	10
FBLN7	129804	hgsc.bcm.edu;broad.mit.edu	37	2	112944825	112944825	+	Silent	SNP	C	C	T			TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr2:112944825C>T	ENST00000331203.2	+	8	1333	c.1062C>T	c.(1060-1062)ctC>ctT	p.L354L	FBLN7_ENST00000409903.1_Intron|FBLN7_ENST00000409667.3_Silent_p.L220L|FBLN7_ENST00000409450.3_Silent_p.L308L	NM_001128165.1|NM_153214.2	NP_001121637.1|NP_694946.2	Q53RD9	FBLN7_HUMAN	fibulin 7	354					cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						CCATCACGCTCTTCCGCATGG	0.647																																																0													87.0	90.0	89.0					2																	112944825		2203	4300	6503	SO:0001819	synonymous_variant	129804				CCDS2095.1, CCDS46391.1	2q13	2010-06-15			ENSG00000144152	ENSG00000144152		"""Fibulins"""	26740	protein-coding gene	gene with protein product		611551				17699513	Standard	NM_153214		Approved	FLJ37440, TM14	uc002tho.1	Q53RD9	OTTHUMG00000153267	ENST00000331203.2:c.1062C>T	2.37:g.112944825C>T			A0JNV1|A0JNV2|Q5H9P5|Q8N9G0	Silent	SNP	ENST00000331203.2	37	CCDS2095.1																																																																																				0.647	FBLN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330505.1	NM_153214		17	190	17	190
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000446179.1_Missense_Mutation_p.R132H|IDH1_ENST00000345146.2_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			31	81	31	81
ASIC5	51802	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	156764859	156764859	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr4:156764859C>T	ENST00000537611.2	-	5	881	c.835G>A	c.(835-837)Gca>Aca	p.A279T		NM_017419.2	NP_059115.1	Q9NY37	ASIC5_HUMAN	acid-sensing (proton-gated) ion channel family member 5	279					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrogen ion channel activity (GO:0015252)|ligand-gated sodium channel activity (GO:0015280)										GTTACCCTTGCGTGCATTCCC	0.448																																																0													156.0	131.0	139.0					4																	156764859		2203	4300	6503	SO:0001583	missense	51802			AJ252011	CCDS3793.1	4q32.1	2012-10-03	2012-03-02	2012-03-02	ENSG00000256394	ENSG00000256394			17537	protein-coding gene	gene with protein product			"""amiloride-sensitive cation channel 5, intestinal"""	ACCN5		10767424	Standard	NM_017419		Approved	INAC, HINAC	uc003ipe.1	Q9NY37	OTTHUMG00000161941	ENST00000537611.2:c.835G>A	4.37:g.156764859C>T	ENSP00000442477:p.Ala279Thr			Missense_Mutation	SNP	ENST00000537611.2	37	CCDS3793.1	.	.	.	.	.	.	.	.	.	.	C	4.481	0.089072	0.08583	.	.	ENSG00000256394	ENST00000537611	T	0.58940	0.3	4.4	-1.76	0.08006	.	0.582071	0.16428	N	0.214858	T	0.35248	0.0925	L	0.28344	0.845	0.09310	N	1	B	0.09022	0.002	B	0.12837	0.008	T	0.33954	-0.9848	10	0.02654	T	1	-0.0696	11.6158	0.51090	0.0:0.6517:0.0:0.3483	.	279	Q9NY37	ACCN5_HUMAN	T	279	ENSP00000442477:A279T	ENSP00000264432:A279T	A	-	1	0	ACCN5	156984309	0.001000	0.12720	0.002000	0.10522	0.186000	0.23388	-0.149000	0.10204	-0.588000	0.05882	-1.287000	0.01368	GCA		0.448	ASIC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366464.1			35	120	35	120
DNAH5	1767	hgsc.bcm.edu;broad.mit.edu	37	5	13919350	13919350	+	Silent	SNP	A	A	G			TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr5:13919350A>G	ENST00000265104.4	-	7	1014	c.910T>C	c.(910-912)Ttg>Ctg	p.L304L		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	304	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					GGGCTTTTCAATTGTTCCAAA	0.507									Kartagener syndrome																																							0													127.0	138.0	135.0					5																	13919350		2203	4300	6503	SO:0001819	synonymous_variant	1767	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.910T>C	5.37:g.13919350A>G			Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																				0.507	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		29	234	29	234
ATP6AP1L	92270	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	81608458	81608458	+	Missense_Mutation	SNP	T	T	G			TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr5:81608458T>G	ENST00000380167.4	+	9	1485	c.160T>G	c.(160-162)Tcc>Gcc	p.S54A	ATP6AP1L_ENST00000508366.1_3'UTR|ATP6AP1L_ENST00000439350.1_Missense_Mutation_p.S54A			Q52LC2	VAS1L_HUMAN	ATPase, H+ transporting, lysosomal accessory protein 1-like	54					ATP hydrolysis coupled proton transport (GO:0015991)	integral component of membrane (GO:0016021)|proton-transporting V-type ATPase, V1 domain (GO:0033180)	proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|urinary_tract(1)	12						CAACAAGTTGTCCATCCAGAG	0.413											OREG0016689	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0													178.0	173.0	175.0					5																	81608458		2203	4300	6503	SO:0001583	missense	92270			AK022625	CCDS34196.1	5q14.2	2010-03-10				ENSG00000205464			28091	protein-coding gene	gene with protein product							Standard	XR_112744		Approved		uc003khw.3	Q52LC2		ENST00000380167.4:c.160T>G	5.37:g.81608458T>G	ENSP00000369513:p.Ser54Ala	1207		Missense_Mutation	SNP	ENST00000380167.4	37	CCDS34196.1	.	.	.	.	.	.	.	.	.	.	T	7.732	0.699430	0.15106	.	.	ENSG00000205464	ENST00000380167;ENST00000439350	.	.	.	5.58	-1.29	0.09288	.	0.517808	0.20520	N	0.090713	T	0.40619	0.1124	M	0.70903	2.155	0.23396	N	0.997761	B	0.17268	0.021	B	0.20184	0.028	T	0.37384	-0.9708	9	0.51188	T	0.08	.	5.8611	0.18747	0.0:0.1962:0.2255:0.5783	.	54	Q52LC2	VAS1L_HUMAN	A	54	.	ENSP00000369513:S54A	S	+	1	0	ATP6AP1L	81644214	0.997000	0.39634	0.020000	0.16555	0.038000	0.13279	0.589000	0.23939	-0.196000	0.10366	-0.290000	0.09829	TCC		0.413	ATP6AP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369562.3	NM_001017971		17	221	17	221
HTR4	3360	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	147889456	147889456	+	Nonsense_Mutation	SNP	G	G	T			TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr5:147889456G>T	ENST00000377888.3	-	6	777	c.639C>A	c.(637-639)taC>taA	p.Y213*	HTR4_ENST00000354217.2_Nonsense_Mutation_p.Y213*|HTR4_ENST00000521735.1_Nonsense_Mutation_p.Y213*|HTR4_ENST00000517929.1_Nonsense_Mutation_p.Y213*|HTR4_ENST00000360693.3_Nonsense_Mutation_p.Y213*|HTR4_ENST00000362016.2_Nonsense_Mutation_p.Y227*|HTR4_ENST00000520514.1_Nonsense_Mutation_p.Y213*|HTR4_ENST00000314512.6_Nonsense_Mutation_p.Y213*|HTR4_ENST00000521530.1_Nonsense_Mutation_p.Y213*	NM_000870.5	NP_000861.1	Q13639	5HT4R_HUMAN	5-hydroxytryptamine (serotonin) receptor 4, G protein-coupled	213					G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of cell proliferation (GO:0008284)|regulation of appetite (GO:0032098)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	serotonin receptor activity (GO:0004993)			endometrium(5)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Cinitapride(DB08810)|Cisapride(DB00604)|Ergoloid mesylate(DB01049)|Metoclopramide(DB01233)|Ondansetron(DB00904)	CATAGATGCGGTAATAGGCCA	0.542																																					GBM(120;370 1604 14007 17804 41573)											0													104.0	89.0	94.0					5																	147889456		2203	4300	6503	SO:0001587	stop_gained	3360			Y08756	CCDS4291.1, CCDS34270.1, CCDS34271.1, CCDS34272.1, CCDS34273.1, CCDS34273.2, CCDS75353.1	5q31-q33	2012-08-08	2012-02-03		ENSG00000164270	ENSG00000164270		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5299	protein-coding gene	gene with protein product		602164	"""5-hydroxytryptamine (serotonin) receptor 4"""			9371406, 9276448	Standard	NM_199453		Approved	5-HT4	uc021yfj.1	Q13639	OTTHUMG00000129931	ENST00000377888.3:c.639C>A	5.37:g.147889456G>T	ENSP00000367120:p.Tyr213*		C4WYH4|Q546Q1|Q684M0|Q712M9|Q96KH9|Q96KI0|Q9H199|Q9NY73|Q9UBM6|Q9UBT4|Q9UE22|Q9UE23|Q9UQR6	Nonsense_Mutation	SNP	ENST00000377888.3	37	CCDS4291.1	.	.	.	.	.	.	.	.	.	.	G	6.963	0.547576	0.13312	.	.	ENSG00000164270	ENST00000521530;ENST00000354217;ENST00000314512;ENST00000521735;ENST00000517929;ENST00000520514;ENST00000377888;ENST00000360693;ENST00000362016	.	.	.	6.02	-3.32	0.04973	.	0.104499	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.2689	0.66140	0.4032:0.0:0.5968:0.0	.	.	.	.	X	213;213;213;213;213;213;213;213;227	.	ENSP00000314906:Y213X	Y	-	3	2	HTR4	147869649	0.853000	0.29707	0.979000	0.43373	0.004000	0.04260	0.069000	0.14552	-0.457000	0.07033	-0.136000	0.14681	TAC		0.542	HTR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252187.2	NM_000870		23	41	23	41
TENM2	57451	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	167674102	167674102	+	Missense_Mutation	SNP	A	A	G			TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr5:167674102A>G	ENST00000518659.1	+	27	6197	c.6158A>G	c.(6157-6159)aAc>aGc	p.N2053S	TENM2_ENST00000545108.1_Missense_Mutation_p.N2052S|TENM2_ENST00000519204.1_Missense_Mutation_p.N1932S|TENM2_ENST00000403607.2_Missense_Mutation_p.N1877S|TENM2_ENST00000520394.1_Missense_Mutation_p.N1814S	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	2053					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)										AAGATGGTCAACCTCCAAAGT	0.522																																																0													80.0	79.0	80.0					5																	167674102		1943	4144	6087	SO:0001583	missense	57451			AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"""odz, odd Oz/ten-m homolog 2 (Drosophila)"""	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.6158A>G	5.37:g.167674102A>G	ENSP00000429430:p.Asn2053Ser		Q9ULU2	Missense_Mutation	SNP	ENST00000518659.1	37		.	.	.	.	.	.	.	.	.	.	A	16.01	3.002530	0.54254	.	.	ENSG00000145934	ENST00000518659;ENST00000545108;ENST00000519204;ENST00000520394;ENST00000403607	D;D;D;D;D	0.89270	-2.02;-2.01;-2.12;-2.45;-2.49	5.44	3.02	0.34903	.	0.039655	0.85682	N	0.000000	D	0.92688	0.7676	M	0.80028	2.48	0.40758	D	0.982977	D;D;D	0.89917	1.0;1.0;0.99	D;D;D	0.91635	0.999;0.997;0.979	D	0.89580	0.3820	10	0.18276	T	0.48	.	9.4562	0.38756	0.8602:0.0:0.1398:0.0	.	2052;2053;1814	F5H2D1;Q9NT68;F8VNQ3	.;TEN2_HUMAN;.	S	2053;2052;1932;1814;1877	ENSP00000429430:N2053S;ENSP00000438635:N2052S;ENSP00000428964:N1932S;ENSP00000427874:N1814S;ENSP00000384905:N1877S	ENSP00000384905:N1877S	N	+	2	0	ODZ2	167606680	1.000000	0.71417	0.998000	0.56505	0.957000	0.61999	3.846000	0.55888	0.360000	0.24265	0.459000	0.35465	AAC		0.522	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679		65	126	65	126
FAM83B	222584	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	54735129	54735129	+	Nonsense_Mutation	SNP	C	C	T			TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr6:54735129C>T	ENST00000306858.7	+	2	201	c.85C>T	c.(85-87)Cga>Tga	p.R29*		NM_001010872.1	NP_001010872.1	Q5T0W9	FA83B_HUMAN	family with sequence similarity 83, member B	29										autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(28)|ovary(6)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	71	Lung NSC(77;0.0178)|Renal(3;0.122)					GGAATGGTATCGAGTAGCCAT	0.403																																																0													137.0	126.0	129.0					6																	54735129		2203	4300	6503	SO:0001587	stop_gained	222584			AK055204	CCDS34479.1	6p12.1	2014-03-13	2006-03-23	2006-03-23	ENSG00000168143	ENSG00000168143			21357	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 143"""	C6orf143		22886302	Standard	NM_001010872		Approved	FLJ30642	uc003pck.4	Q5T0W9	OTTHUMG00000014899	ENST00000306858.7:c.85C>T	6.37:g.54735129C>T	ENSP00000304078:p.Arg29*		Q2M1P3|Q96DQ2	Nonsense_Mutation	SNP	ENST00000306858.7	37	CCDS34479.1	.	.	.	.	.	.	.	.	.	.	C	37	6.365651	0.97507	.	.	ENSG00000168143	ENST00000306858	.	.	.	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.776	14.5555	0.68097	0.1469:0.8531:0.0:0.0	.	.	.	.	X	29	.	ENSP00000304078:R29X	R	+	1	2	FAM83B	54843088	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	4.614000	0.61183	2.525000	0.85131	0.467000	0.42956	CGA		0.403	FAM83B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040994.1	XM_294139		63	148	63	148
TACC1	6867	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	8	38678119	38678119	+	Missense_Mutation	SNP	G	G	C			TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr8:38678119G>C	ENST00000317827.4	+	3	1736	c.1357G>C	c.(1357-1359)Gaa>Caa	p.E453Q	TACC1_ENST00000518415.1_Missense_Mutation_p.E408Q|TACC1_ENST00000520615.1_Missense_Mutation_p.E258Q|TACC1_ENST00000379931.3_Missense_Mutation_p.E453Q|TACC1_ENST00000443286.2_Missense_Mutation_p.E469Q|TACC1_ENST00000330691.6_Intron|TACC1_ENST00000520340.1_Missense_Mutation_p.E417Q|TACC1_ENST00000519416.1_Missense_Mutation_p.E258Q|TACC1_ENST00000276520.8_Intron|TACC1_ENST00000520973.1_Missense_Mutation_p.E258Q|TACC1_ENST00000522752.1_Intron|TACC1_ENST00000348567.4_Intron|TACC1_ENST00000520611.1_5'UTR	NM_006283.2	NP_006274.2	O75410	TACC1_HUMAN	transforming, acidic coiled-coil containing protein 1	453	SPAZ 2.				cell cycle (GO:0007049)|cell division (GO:0051301)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)				breast(4)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|skin(3)	17		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.065)	LUSC - Lung squamous cell carcinoma(45;1.7e-09)|COAD - Colon adenocarcinoma(9;0.235)			TGAAATCTTAGAATCACCCAA	0.453																																																0													133.0	144.0	140.0					8																	38678119		2203	4300	6503	SO:0001583	missense	6867			AF049910	CCDS6109.1, CCDS47845.1, CCDS55224.1	8p11	2012-12-20			ENSG00000147526	ENSG00000147526			11522	protein-coding gene	gene with protein product		605301					Standard	NM_006283		Approved		uc010lwp.3	O75410	OTTHUMG00000164018	ENST00000317827.4:c.1357G>C	8.37:g.38678119G>C	ENSP00000321703:p.Glu453Gln		B2RBD9|D3DSX6|Q6Y687|Q86YG7|Q8IUJ2|Q8IUJ3|Q8IUJ4|Q8IZG2|Q8NEY7|Q9UPP9	Missense_Mutation	SNP	ENST00000317827.4	37	CCDS6109.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.67|17.67	3.446301|3.446301	0.63178|0.63178	.|.	.|.	ENSG00000147526|ENSG00000147526	ENST00000519416;ENST00000520615;ENST00000443388;ENST00000443286;ENST00000518415;ENST00000522904;ENST00000317827;ENST00000379931;ENST00000520973|ENST00000521866;ENST00000518809	T;T;T;T;T;T;T;T|.	0.10192|.	2.93;2.93;3.04;3.05;2.91;3.08;3.02;2.9|.	5.69|5.69	5.69|5.69	0.88448|0.88448	.|.	0.366777|.	0.28665|.	N|.	0.014559|.	T|.	0.63355|.	0.2504|.	L|L	0.56769|0.56769	1.78|1.78	0.30873|0.30873	N|N	0.732218|0.732218	P;B;B;P;D;B;P;B|.	0.63046|.	0.948;0.046;0.046;0.935;0.992;0.124;0.951;0.08|.	P;B;B;B;P;B;P;B|.	0.58660|.	0.628;0.008;0.008;0.398;0.843;0.051;0.503;0.047|.	T|.	0.63625|.	-0.6595|.	10|.	0.21014|.	T|.	0.42|.	-5.1624|-5.1624	17.9839|17.9839	0.89150|0.89150	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	258;258;258;469;453;453;258;408|.	B7Z3G3;E7EVI4;B4DH49;B4E302;O75410-2;O75410;E7ET87;O75410-7|.	.;.;.;.;.;TACC1_HUMAN;.;.|.	Q|Y	258;258;258;469;408;425;453;453;258|227;90	ENSP00000428687:E258Q;ENSP00000428450:E258Q;ENSP00000393647:E469Q;ENSP00000428706:E408Q;ENSP00000430355:E425Q;ENSP00000321703:E453Q;ENSP00000369263:E453Q;ENSP00000430959:E258Q|.	ENSP00000321703:E453Q|.	E|X	+|+	1|3	0|2	TACC1|TACC1	38797276|38797276	1.000000|1.000000	0.71417|0.71417	0.989000|0.989000	0.46669|0.46669	0.421000|0.421000	0.31385|0.31385	6.485000|6.485000	0.73625|0.73625	2.669000|2.669000	0.90835|0.90835	0.655000|0.655000	0.94253|0.94253	GAA|TAG		0.453	TACC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376768.1	NM_006283		107	236	107	236
KIF24	347240	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	34257924	34257924	+	Missense_Mutation	SNP	G	G	A	rs144983593		TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr9:34257924G>A	ENST00000402558.2	-	10	1705	c.1681C>T	c.(1681-1683)Cgg>Tgg	p.R561W	KIF24_ENST00000345050.2_Missense_Mutation_p.R427W|KIF24_ENST00000379166.2_Missense_Mutation_p.R561W|KIF24_ENST00000379174.3_Missense_Mutation_p.R427W			Q5T7B8	KIF24_HUMAN	kinesin family member 24	561					ATP catabolic process (GO:0006200)|cilium assembly (GO:0042384)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)	centriole (GO:0005814)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|liver(1)|lung(13)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	32			LUSC - Lung squamous cell carcinoma(29;0.0107)			CCAGATGTCCGATTTCGACTG	0.398													G|||	1	0.000199681	0.0	0.0	5008	,	,		19997	0.0		0.0	False		,,,				2504	0.001															0													121.0	131.0	128.0					9																	34257924		2203	4300	6503	SO:0001583	missense	347240			AK001795	CCDS6551.2	9p13.3	2013-01-10			ENSG00000186638	ENSG00000186638		"""Kinesins"", ""Sterile alpha motif (SAM) domain containing"""	19916	protein-coding gene	gene with protein product		613747	"""chromosome 9 open reading frame 48"""	C9orf48		12477932	Standard	NM_194313		Approved	bA571F15.4, FLJ10933, FLJ43884	uc003zua.4	Q5T7B8	OTTHUMG00000019810	ENST00000402558.2:c.1681C>T	9.37:g.34257924G>A	ENSP00000384433:p.Arg561Trp		Q2TB93|Q5T7B5|Q5T7B7|Q6ZU97|Q6ZUZ2|Q86XZ0|Q9NV43	Missense_Mutation	SNP	ENST00000402558.2	37	CCDS6551.2	.	.	.	.	.	.	.	.	.	.	G	16.88	3.244799	0.59103	.	.	ENSG00000186638	ENST00000402558;ENST00000379174;ENST00000379166;ENST00000345050;ENST00000420188	T;T;T;T	0.73575	-0.54;-0.76;-0.54;-0.76	5.53	4.62	0.57501	.	0.454742	0.16183	N	0.225744	T	0.77765	0.4179	M	0.67953	2.075	0.21416	N	0.999692	D	0.76494	0.999	P	0.47528	0.549	T	0.71609	-0.4541	10	0.66056	D	0.02	.	15.5999	0.76616	0.0:0.0:0.8611:0.1389	.	561	Q5T7B8	KIF24_HUMAN	W	561;427;561;427;561	ENSP00000384433:R561W;ENSP00000368472:R427W;ENSP00000368464:R561W;ENSP00000340179:R427W	ENSP00000340179:R427W	R	-	1	2	KIF24	34247924	0.967000	0.33354	0.513000	0.27749	0.516000	0.34256	3.145000	0.50623	1.299000	0.44798	0.655000	0.94253	CGG		0.398	KIF24-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052150.5			126	62	126	62
FAM120A	23196	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	96324505	96324505	+	Silent	SNP	T	T	A			TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr9:96324505T>A	ENST00000277165.6	+	17	3158	c.2964T>A	c.(2962-2964)gtT>gtA	p.V988V	FAM120A_ENST00000340893.4_Silent_p.V942V|FAM120A_ENST00000333936.5_Silent_p.V1016V	NM_014612.3	NP_055427.2	Q9NZB2	F120A_HUMAN	family with sequence similarity 120A	988	RNA binding.					cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(3)|large_intestine(8)|lung(12)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						CAAGAGGAGTTATTTCCACCC	0.368																																																0													159.0	138.0	145.0					9																	96324505		2203	4300	6503	SO:0001819	synonymous_variant	23196			AF214737	CCDS6706.1, CCDS75859.1	9q22.31	2013-03-08	2006-07-04	2006-07-04	ENSG00000048828	ENSG00000048828			13247	protein-coding gene	gene with protein product	"""DNA polymerase-transactivated protein 1"", ""oxidative stess-associated Src activator"""	612265	"""chromosome 9 open reading frame 10"""	C9orf10		14585507	Standard	NM_001286722		Approved	KIAA0183, DNAPTP1, OSSA	uc004atw.3	Q9NZB2	OTTHUMG00000020252	ENST00000277165.6:c.2964T>A	9.37:g.96324505T>A			A6NGU0|C4AMC6|O60649|Q14688|Q4VXF4|Q4VXF5|Q4VXG2|Q86V69|Q96I21|Q9NZB1	Silent	SNP	ENST00000277165.6	37	CCDS6706.1																																																																																				0.368	FAM120A-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053160.2	NM_014612		18	51	18	51
GBGT1	26301	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	136029281	136029281	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr9:136029281G>A	ENST00000372040.3	-	7	1038	c.727C>T	c.(727-729)Cgc>Tgc	p.R243C	GBGT1_ENST00000540636.1_Missense_Mutation_p.R226C|GBGT1_ENST00000372043.3_Silent_p.S236S|RALGDS_ENST00000542690.1_Intron|GBGT1_ENST00000472281.1_5'UTR	NM_001282629.1	NP_001269558.1	Q8N5D6	GBGT1_HUMAN	globoside alpha-1,3-N-acetylgalactosaminyltransferase 1	243					glycolipid biosynthetic process (GO:0009247)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	globoside alpha-N-acetylgalactosaminyltransferase activity (GO:0047277)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(4)|lung(2)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(145;3.49e-06)|Epithelial(140;2.59e-05)		ACACGCCTGCGCTCATAGGGG	0.602																																																0													79.0	80.0	80.0					9																	136029281		2203	4300	6503	SO:0001583	missense	26301			AY358175	CCDS6960.1, CCDS65175.1, CCDS65176.1	9q34.13-q34.3	2014-07-18			ENSG00000148288	ENSG00000148288		"""Glycosyltransferase family 6 domain containing"""	20460	protein-coding gene	gene with protein product	"""Forssman glycolipid synthetase (FS)"", ""Forssman synthetase"""	606074				10506200, 8855242	Standard	NM_021996		Approved	UDP-GalNAc, A3GALNT, MGC44848, FS		Q8N5D6	OTTHUMG00000020853	ENST00000372040.3:c.727C>T	9.37:g.136029281G>A	ENSP00000361110:p.Arg243Cys		A8K633|B2RA95|B7Z8S5|Q45F07|Q5T7U9|Q5T7V1|Q8N2K4|Q9UKI5	Missense_Mutation	SNP	ENST00000372040.3	37	CCDS6960.1	.	.	.	.	.	.	.	.	.	.	G	17.76	3.469318	0.63625	.	.	ENSG00000148288	ENST00000372040;ENST00000540636	T;T	0.02421	4.3;4.3	5.25	3.2	0.36748	.	0.000000	0.85682	D	0.000000	T	0.19644	0.0472	M	0.92604	3.325	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.07158	-1.0787	10	0.87932	D	0	-12.131	13.9166	0.63902	0.0:0.0:0.779:0.221	.	226;243	B7Z8S5;Q8N5D6	.;GBGT1_HUMAN	C	243;226	ENSP00000361110:R243C;ENSP00000437663:R226C	ENSP00000361110:R243C	R	-	1	0	GBGT1	135019102	0.311000	0.24536	0.999000	0.59377	0.880000	0.50808	1.623000	0.37008	2.451000	0.82905	0.561000	0.74099	CGC		0.602	GBGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054815.1	NM_021996		47	106	47	106
DDIT3	1649	broad.mit.edu;ucsc.edu	37	12	57911132	57911132	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr12:57911132C>T	ENST00000346473.3	-	3	237	c.58G>A	c.(58-60)Gcc>Acc	p.A20T	MIR616_ENST00000385293.1_RNA|DDIT3_ENST00000547303.1_Missense_Mutation_p.A20T|DDIT3_ENST00000552740.1_Missense_Mutation_p.A43T|DDIT3_ENST00000551116.1_Missense_Mutation_p.A43T	NM_001195057.1|NM_004083.5	NP_001181986.1|NP_004074.2	P35638	DDIT3_HUMAN	DNA-damage-inducible transcript 3	20	N-terminal.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|blood vessel maturation (GO:0001955)|cell cycle arrest (GO:0007050)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of determination of dorsal identity (GO:2000016)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of transcription involved in anterior/posterior axis specification (GO:0044324)|regulation of transcription, DNA-templated (GO:0006355)|release of sequestered calcium ion into cytosol (GO:0051209)|response to endoplasmic reticulum stress (GO:0034976)|response to starvation (GO:0042594)|response to unfolded protein (GO:0006986)|Wnt signaling pathway (GO:0016055)	late endosome (GO:0005770)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)		EWSR1/DDIT3(45)|FUS/DDIT3(631)	central_nervous_system(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(2)|skin(1)	16						TCATACCAGGCTTCCAGCTCC	0.493			T	FUS	liposarcoma																																GBM(112;1383 1547 7626 23045 28770)		Dom	yes		12	12q13.1-q13.2	1649	DNA-damage-inducible transcript 3		M	0													64.0	58.0	60.0					12																	57911132		2203	4300	6503	SO:0001583	missense	1649			BC003637	CCDS8943.1, CCDS55838.1	12q13.1-q13.2	2008-02-05				ENSG00000175197			2726	protein-coding gene	gene with protein product	"""C/EBP zeta"""	126337				1990262	Standard	NM_001195053		Approved	CHOP10, GADD153, CHOP	uc021qzk.1	P35638		ENST00000346473.3:c.58G>A	12.37:g.57911132C>T	ENSP00000340671:p.Ala20Thr		F8VS99	Missense_Mutation	SNP	ENST00000346473.3	37	CCDS8943.1	.	.	.	.	.	.	.	.	.	.	C	18.20	3.570252	0.65765	.	.	ENSG00000175197	ENST00000547303;ENST00000551116;ENST00000346473;ENST00000552740;ENST00000547526	T;T;T;T	0.55234	0.61;0.53;0.61;0.53	5.01	5.01	0.66863	.	0.120501	0.53938	D	0.000049	T	0.58119	0.2100	L	0.32530	0.975	0.38163	D	0.939105	D;P	0.76494	0.999;0.941	D;P	0.65323	0.934;0.527	T	0.62760	-0.6786	10	0.72032	D	0.01	-12.9575	11.1156	0.48258	0.2844:0.7156:0.0:0.0	.	43;20	F8VS99;P35638	.;DDIT3_HUMAN	T	20;43;20;43;43	ENSP00000447188:A20T;ENSP00000448665:A43T;ENSP00000340671:A20T;ENSP00000447803:A43T	ENSP00000340671:A20T	A	-	1	0	DDIT3	56197399	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.038000	0.49783	2.776000	0.95493	0.655000	0.94253	GCC		0.493	DDIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407137.1	NM_004083		21	39	21	39
ZNF271	10778	broad.mit.edu;ucsc.edu	37	18	32887852	32887852	+	RNA	SNP	G	G	A			TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr18:32887852G>A	ENST00000399070.3	+	0	2246					NR_024565.1|NR_024566.1		Q14591	ZN271_HUMAN	zinc finger protein 271						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(3)|lung(9)	12						GAATGCTGTTGATTATTGATG	0.373																																																0													48.0	47.0	47.0					18																	32887852		2203	4300	6503			10778			X78930		18q12.2	2013-04-03			ENSG00000257267	ENSG00000257267		"""Zinc fingers, C2H2-type"""	13065	other	unknown		604754				7865130, 11777961	Standard	NR_024565		Approved	HZF7, ZNFEB	uc002kyp.4	Q14591	OTTHUMG00000132563		18.37:g.32887852G>A			B3KN34|Q96T29|Q9BSX2|Q9UN33|Q9Y5B7	RNA	SNP	ENST00000399070.3	37																																																																																					0.373	ZNF271-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000255767.2	NR_024565		15	31	15	31
ARID4B	51742	broad.mit.edu;hgsc.bcm.edu	37	1	235345238	235345244	+	Frame_Shift_Del	DEL	TCTTCAA	TCTTCAA	-			TCGA-HT-8109-01A-11D-2395-08	TCGA-HT-8109-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61523043-c989-4ebc-8d20-80f1c578aa38	a2939a7a-eec5-4cf0-821a-f0bb89ad36e7	g.chr1:235345238_235345244delTCTTCAA	ENST00000264183.3	-	20	3487_3493	c.2990_2996delTTGAAGA	c.(2989-2997)attgaagaafs	p.IEE997fs	ARID4B_ENST00000494543.1_5'Flank|ARID4B_ENST00000366603.2_Frame_Shift_Del_p.IEE997fs|ARID4B_ENST00000349213.3_Frame_Shift_Del_p.IEE911fs	NM_016374.5	NP_057458.4	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B (RBP1-like)	997					histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|large_intestine(2)|lung(1)|ovary(2)	8	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)			TACTGTTTTTTCTTCAATGGGTTTACT	0.444																																																0																																										SO:0001589	frameshift_variant	51742			AF214114	CCDS31060.1, CCDS31061.1	1q42.1-q43	2013-02-07	2006-11-08	2004-01-30	ENSG00000054267	ENSG00000054267		"""-"""	15550	protein-coding gene	gene with protein product		609696	"""retinoblastoma binding protein 1-like 1"", ""AT rich interactive domain 4B (RBP1- like)"""	RBP1L1		11481388	Standard	NM_016374		Approved	BCAA, BRCAA1, SAP180	uc001hwq.3	Q4LE39	OTTHUMG00000039621	ENST00000264183.3:c.2990_2996delTTGAAGA	1.37:g.235345238_235345244delTCTTCAA	ENSP00000264183:p.Ile997fs		A1L465|Q3MHV4|Q5HY99|Q5T2C2|Q5T2C3|Q5T2C4|Q5T2C5|Q5T2C6|Q6P600|Q86UX1|Q86WR4|Q9H915|Q9NYU3|Q9NZB6|Q9NZG4|Q9P2W4|Q9UF62|Q9Y6E1	Frame_Shift_Del	DEL	ENST00000264183.3	37	CCDS31061.1																																																																																				0.444	ARID4B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095566.3	NM_016374		53	82	53	82
