#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_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	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_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	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_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	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_IGV	i_Mutation_Status	i_NTotCov_SOL	i_NVaf_SOL	i_NVarCov_SOL	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_TTotCov_SOL	i_TVaf_SOL	i_TVarCov_SOL	i_Transcript_Id	i_Ttot_rna	i_Tvaf_rna	i_Tvar_rna	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_dbSNPPopFreq	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_germline-maf-frequency	i_havana_transcript	i_note	i_refseq_mrna_id	i_secondary_variant_classification
ALDH4A1	8659	hgsc.bcm.edu;mdanderson.org	37	1	19209815	19209815	+	Missense_Mutation	SNP	G	G	T	rs199723895		TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr1:19209815G>T	ENST00000375341.3	-	6	818	c.561C>A	c.(559-561)agC>agA	p.S187R	ALDH4A1_ENST00000538309.1_Missense_Mutation_p.S127R|ALDH4A1_ENST00000290597.5_Missense_Mutation_p.S187R|MIR4695_ENST00000577305.1_RNA|RP13-279N23.2_ENST00000494072.3_3'UTR|ALDH4A1_ENST00000538839.1_Missense_Mutation_p.S187R|ALDH4A1_ENST00000454547.1_5'UTR	NM_003748.3	NP_003739.2	P30038	AL4A1_HUMAN	aldehyde dehydrogenase 4 family, member A1	187					4-hydroxyproline catabolic process (GO:0019470)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate biosynthetic process (GO:0006537)|proline biosynthetic process (GO:0006561)|proline catabolic process (GO:0006562)|proline catabolic process to glutamate (GO:0010133)|proline metabolic process (GO:0006560)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	1-pyrroline-5-carboxylate dehydrogenase activity (GO:0003842)|aldehyde dehydrogenase (NAD) activity (GO:0004029)|electron carrier activity (GO:0009055)|identical protein binding (GO:0042802)			cervix(2)|endometrium(1)|large_intestine(3)|lung(8)|prostate(1)	15		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00479)|BRCA - Breast invasive adenocarcinoma(304;3.67e-05)|Kidney(64;0.000182)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		TCGGGGGCACGCTGATGGGCT	0.642																																					p.S187R													.	.			0			c.C561A												51.0	43.0	46.0					1																	19209815		2203	4300	6503	SO:0001583	missense	8659	exon6			GGGCACGCTGATG	U24266	CCDS188.1, CCDS53272.1	1p36	2008-02-05			ENSG00000159423	ENSG00000159423	1.5.1.12	"""Aldehyde dehydrogenases"""	406	protein-coding gene	gene with protein product		606811		ALDH4		8621661	Standard	NM_003748		Approved	P5CDh	uc001bbc.3	P30038	OTTHUMG00000002443	ENST00000375341.3:c.561C>A	1.37:g.19209815G>T	ENSP00000364490:p.Ser187Arg		Somatic	68	0	0		WXS	Illumina HiSeq	.	54	0.07	4	NM_003748	31	0.00	0	A8K1Q7|B4DGE4|D2D4A3|Q16882|Q53HU4|Q5JNV6|Q8IZ38|Q96IF0|Q9UDI6	Missense_Mutation	SNP	ENST00000375341.3	37	CCDS188.1	.	.	.	.	.	.	.	.	.	.	G	12.70	2.016373	0.35606	.	.	ENSG00000159423	ENST00000290597;ENST00000375341;ENST00000538839;ENST00000538309;ENST00000375335;ENST00000454547;ENST00000375334;ENST00000432718	T;T;T;T;T	0.75938	-0.98;-0.98;-0.98;-0.98;-0.98	5.31	-2.73	0.05950	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.259105	0.50627	D	0.000111	T	0.68393	0.2996	L	0.50333	1.59	0.49051	D	0.999742	P	0.36125	0.538	B	0.42214	0.38	T	0.64685	-0.6349	10	0.72032	D	0.01	-27.23	11.1626	0.48524	0.499:0.0:0.501:0.0	.	187	P30038	AL4A1_HUMAN	R	187;187;187;127;171;85;127;171	ENSP00000290597:S187R;ENSP00000364490:S187R;ENSP00000446071:S187R;ENSP00000442988:S127R;ENSP00000393209:S171R	ENSP00000290597:S187R	S	-	3	2	ALDH4A1	19082402	0.997000	0.39634	0.677000	0.29947	0.272000	0.26649	0.731000	0.26058	-0.591000	0.05859	-1.505000	0.00955	AGC			0.642	ALDH4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000006954.1			
CSMD2	114784	mdanderson.org	37	1	34164479	34164479	+	De_novo_Start_OutOfFrame	SNP	C	C	A			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr1:34164479C>A	ENST00000373388.2	-	0	638				CSMD2_ENST00000373381.4_Missense_Mutation_p.G1267C|CSMD2_ENST00000373380.1_Missense_Mutation_p.G140C			Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				GCAAAATGACCTTCATCATGA	0.547																																					p.G1227C													.	.			0			c.G3679T												81.0	75.0	77.0					1																	34164479		2203	4300	6503			114784	exon24			AATGACCTTCATC	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373388.2:c.-1905G>T	1.37:g.34164479C>A			Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	50	0.06	3	NM_052896	0		0	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373388.2	37		.	.	.	.	.	.	.	.	.	.	C	29.2	4.984803	0.93044	.	.	ENSG00000121904	ENST00000373381;ENST00000373380	T;T	0.26660	1.72;1.72	5.76	5.76	0.90799	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.85682	D	0.000000	T	0.65196	0.2668	H	0.94222	3.51	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.74006	-0.3803	10	0.72032	D	0.01	.	19.3155	0.94211	0.0:1.0:0.0:0.0	.	140;1227;1267	Q7Z408-2;Q7Z408;E7EUA6	.;CSMD2_HUMAN;.	C	1267;140	ENSP00000362479:G1267C;ENSP00000362478:G140C	ENSP00000241312:G1227C	G	-	1	0	CSMD2	33937066	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.776000	0.85560	2.879000	0.98667	0.650000	0.86243	GGT			0.547	CSMD2-202	KNOWN	basic	protein_coding	protein_coding				NM_052896	
SZT2	23334	mdanderson.org	37	1	43908278	43908278	+	Nonsense_Mutation	SNP	C	C	T			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr1:43908278C>T	ENST00000562955.1	+	57	7969	c.7969C>T	c.(7969-7971)Cga>Tga	p.R2657*	SZT2_ENST00000372442.1_Nonsense_Mutation_p.R1815*	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	2714					central nervous system development (GO:0007417)|corpus callosum morphogenesis (GO:0021540)|embryo development (GO:0009790)|pigmentation (GO:0043473)|post-embryonic development (GO:0009791)|regulation of superoxide dismutase activity (GO:1901668)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)				NS(2)|breast(9)|central_nervous_system(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(39)|ovary(4)|pancreas(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	113						CTTCCCCGTGCGAGATGAAAA	0.517																																					p.R2657X													SZT2_ENST00000562955,NS,carcinoma,0,6	SZT2_ENST00000562955	0	6	0			c.C7969T												88.0	90.0	89.0					1																	43908278		2203	4300	6503	SO:0001587	stop_gained	23334	exon57			CCCGTGCGAGATG	AB007936	CCDS30694.1, CCDS30694.2	1p34.2	2012-11-19	2011-06-10	2011-06-10	ENSG00000198198	ENSG00000198198			29040	protein-coding gene	gene with protein product	"""seizure threshold 2 homolog A (mouse)"", ""seizure threshold 2 homolog B (mouse)"""	615463	"""chromosome 1 open reading frame 84"", ""KIAA0467"""	C1orf84, KIAA0467		9455484	Standard	NM_015284		Approved	FLJ10387, SZT2B, RP11-506B15.1, FLJ34502, SZT2A	uc001cjk.3	Q5T011	OTTHUMG00000007423	ENST00000562955.1:c.7969C>T	1.37:g.43908278C>T	ENSP00000457168:p.Arg2657*		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	31	0.10	3	NM_015284	42	0.00	0	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Nonsense_Mutation	SNP	ENST00000562955.1	37	CCDS30694.2	.	.	.	.	.	.	.	.	.	.	C	48	14.644319	0.99804	.	.	ENSG00000198198	ENST00000372442	.	.	.	5.6	5.6	0.85130	.	0.198895	0.42420	D	0.000719	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.6202	0.95653	0.0:1.0:0.0:0.0	.	.	.	.	X	1815	.	ENSP00000361519:R1815X	R	+	1	2	SZT2	43680865	1.000000	0.71417	0.997000	0.53966	0.794000	0.44872	5.821000	0.69257	2.649000	0.89929	0.655000	0.94253	CGA			0.517	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000019517.3		NM_015284	
SEC22B	9554	broad.mit.edu	37	1	145116193	145116193	+	RNA	DEL	G	G	-	rs66989703|rs372891418	byFrequency	TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr1:145116193delG	ENST00000453618.1	+	0	1279							O75396	SC22B_HUMAN	SEC22 vesicle trafficking protein homolog B (S. cerevisiae) (gene/pseudogene)						ER to Golgi vesicle-mediated transport (GO:0006888)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)											AGCACTGGCTGGGGCATTCTC	0.428													GGGG|GGGG|GGG|deletion	1833	0.366014	0.3116	0.4294	5008	,	,		69780	0.3502		0.3847	False		,,,				2504	0.3916				.													.	.			0			.																																											9554	.			CTGGCTGGGGCAT	AF047442		1q21.1	2012-04-20	2010-03-12	2006-04-25	ENSG00000223380				10700	protein-coding gene	gene with protein product		604029	"""SEC22, vesicle trafficking protein (S. cerevisiae)-like 1"", ""SEC22 vesicle trafficking protein-like 1 (S. cerevisiae)"", ""SEC22 vesicle trafficking protein homolog B (S. cerevisiae)"""	SEC22L1		9094723, 16354670	Standard	NM_004892		Approved	sec22b, ERS-24	uc031poa.1	O75396	OTTHUMG00000013745		1.37:g.145116193delG			Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	8	0.38	3	.	167	0.00	0	A8K1G0	RNA	DEL	ENST00000453618.1	37																																																																																						0.428	SEC22B-001	KNOWN	basic	processed_transcript	processed_transcript		OTTHUMT00000038523.5		NM_004892	
OBSCN	84033	hgsc.bcm.edu	37	1	228465295	228465295	+	Intron	SNP	G	G	T			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr1:228465295G>T	ENST00000422127.1	+	25	6798				OBSCN_ENST00000366707.4_Intron|OBSCN_ENST00000570156.2_Nonsense_Mutation_p.E2657*|OBSCN_ENST00000359599.6_Intron|OBSCN_ENST00000366709.4_Intron|OBSCN_ENST00000284548.11_Intron|RP5-1139B12.3_ENST00000602529.1_RNA|RP5-1139B12.3_ENST00000602947.1_RNA	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF						apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CTCCCACGACGAAGTGCCTGG	0.622																																					p.E2657X													.	.			0			c.G7969T																																									SO:0001627	intron_variant	84033	exon29			CACGACGAAGTGC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.6755-160G>T	1.37:g.228465295G>T			Somatic	72	0	0		WXS	Illumina HiSeq	.	76	0.30	23	NM_001271223	8	0.00	0	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Nonsense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																					0.622	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding				NM_052843	
CCDC6	8030	broad.mit.edu	37	10	61666054	61666054	+	Silent	SNP	A	A	C			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr10:61666054A>C	ENST00000263102.6	-	1	360	c.129T>G	c.(127-129)ggT>ggG	p.G43G		NM_005436.4	NP_005427.2	Q16204	CCDC6_HUMAN	coiled-coil domain containing 6	43	Poly-Gly.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	structural constituent of cytoskeleton (GO:0005200)		CCDC6/RET(4)	breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(3)|stomach(1)	18				Kidney(211;0.0597)		CCGACTTCccaccgccgccgc	0.711			T	RET	NSCLC																																p.G43G				Dom	yes		10	10q21	8030	coiled-coil domain containing 6		E	.	CCDC6	44		0			c.T129G												32.0	37.0	35.0					10																	61666054		2203	4300	6503	SO:0001819	synonymous_variant	8030	exon1			CTTCCCACCGCCG	S72869	CCDS7257.1	10q21.2	2006-11-09	2004-01-20		ENSG00000108091	ENSG00000108091			18782	protein-coding gene	gene with protein product	"""DNA segment, single copy, probe pH4 (transforming sequence, thyroid-1"""	601985	"""DNA segment on chromosome 10 (unique) 170"""	TST1, D10S170		8058316, 6745938	Standard	NM_005436		Approved	PTC, TPC, H4	uc001jks.4	Q16204	OTTHUMG00000018284	ENST00000263102.6:c.129T>G	10.37:g.61666054A>C			Somatic	23	0.3043478261	7		WXS	Illumina HiSeq	Phase_I	33	0.30	10	NM_005436	7	0.00	0	Q15250|Q6GSG7	Silent	SNP	ENST00000263102.6	37	CCDS7257.1																																																																																					0.711	CCDC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000048176.2		NM_005436	
PIPSL	266971	broad.mit.edu	37	10	95718367	95718369	+	RNA	DEL	TTC	TTC	-	rs370138833|rs150958812|rs563705611		TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	TTC	TTC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr10:95718367_95718369delTTC	ENST00000480546.1	-	0	2928_2930					NR_002319.2		A2A3N6	PIPSL_HUMAN	PIP5K1A and PSMD4-like, pseudogene							cytoplasm (GO:0005737)	phosphatidylinositol phosphate kinase activity (GO:0016307)										tttcttttctttctttctttctt	0.325																																					.													.	.			0			.																																											0	.			TTTTCTTTCTTTC	BC068549		10q23.33	2010-10-27	2010-10-27	2007-07-06	ENSG00000180764	ENSG00000180764		"""Proteasome (prosome, macropain) subunits"""	23733	pseudogene	pseudogene			"""proteasome (prosome, macropain) 26S subunit, non-ATPase, 4, pseudogene 2"", ""phosphatidylinositol-4-phosphate 5-kinase, type I-like 1"", ""PIP5K1A and PSMD4-like"""	PSMD4P2, PIP5K1L1		16344562	Standard	NR_002319		Approved	PIP5K1A-PSMD4, PIP5K1P3	uc009xuj.2	A2A3N6	OTTHUMG00000137480		10.37:g.95718367_95718369delTTC			Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	14	0.43	6	.	0		0	Q6NUK8	RNA	DEL	ENST00000480546.1	37																																																																																						0.325	PIPSL-002	PUTATIVE	basic	processed_transcript	pseudogene		OTTHUMT00000351483.1		NR_002319	
WNT8B	7479	mdanderson.org	37	10	102242036	102242036	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr10:102242036G>T	ENST00000343737.5	+	6	647	c.519G>T	c.(517-519)aaG>aaT	p.K173N		NM_003393.3	NP_003384.2	Q93098	WNT8B_HUMAN	wingless-type MMTV integration site family, member 8B	173					cell fate commitment (GO:0045165)|cellular response to retinoic acid (GO:0071300)|determination of dorsal identity (GO:0048263)|gastrulation (GO:0007369)|negative regulation of gene expression (GO:0010629)|nervous system development (GO:0007399)|neuron differentiation (GO:0030182)|positive regulation of gene expression (GO:0010628)|response to estradiol (GO:0032355)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			breast(1)|large_intestine(1)|ovary(1)|skin(1)	4		Colorectal(252;0.117)		Epithelial(162;1.87e-10)|all cancers(201;1.64e-08)		AGGCGGTGAAGGGCACCATGA	0.627											OREG0020440	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K173N													.	.			0			c.G519T												16.0	17.0	17.0					10																	102242036		2191	4279	6470	SO:0001583	missense	7479	exon6			GGTGAAGGGCACC	X91940	CCDS7494.1	10q24	2003-11-12			ENSG00000075290	ENSG00000075290		"""Wingless-type MMTV integration sites"""	12789	protein-coding gene	gene with protein product		601396				8661156	Standard	NM_003393		Approved		uc001krb.3	Q93098	OTTHUMG00000018912	ENST00000343737.5:c.519G>T	10.37:g.102242036G>T	ENSP00000340677:p.Lys173Asn		Somatic	9	0	0	1365	WXS	Illumina HiSeq	Phase_I	9	0.22	2	NM_003393	0		0	O00771|Q5VX55|Q8WYK9	Missense_Mutation	SNP	ENST00000343737.5	37	CCDS7494.1	.	.	.	.	.	.	.	.	.	.	G	18.51	3.640290	0.67244	.	.	ENSG00000075290	ENST00000343737	T	0.76839	-1.05	5.43	4.5	0.54988	.	0.086425	0.85682	D	0.000000	D	0.83376	0.5241	M	0.78049	2.395	0.51767	D	0.999939	D	0.67145	0.996	D	0.68039	0.955	T	0.81176	-0.1052	10	0.31617	T	0.26	.	4.0893	0.09962	0.1896:0.0:0.6098:0.2006	.	173	Q93098	WNT8B_HUMAN	N	173	ENSP00000340677:K173N	ENSP00000340677:K173N	K	+	3	2	WNT8B	102232026	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	2.489000	0.45285	1.250000	0.43966	0.462000	0.41574	AAG			0.627	WNT8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000049867.1		NM_003393	
SORCS1	114815	broad.mit.edu;bcgsc.ca;mdanderson.org	37	10	108338921	108338921	+	Intron	SNP	G	G	T			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr10:108338921G>T	ENST00000263054.6	-	25	3379				SORCS1_ENST00000369698.1_Missense_Mutation_p.P689T|SORCS1_ENST00000344440.6_Missense_Mutation_p.P1154T	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1						neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(9)|kidney(2)|large_intestine(24)|lung(69)|ovary(1)|prostate(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	127		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		GGGACATTGGGCCTGCTTTCA	0.463																																					p.P1154T													.	SORCS1	534		0			c.C3460A												141.0	128.0	132.0					10																	108338921		2203	4300	6503	SO:0001627	intron_variant	114815	exon26			CATTGGGCCTGCT	AF284756	CCDS7559.1	10q23-q25	2004-04-20			ENSG00000108018	ENSG00000108018			16697	protein-coding gene	gene with protein product		606283				11499680	Standard	NM_001206570		Approved	sorCS1	uc001kyl.3	Q8WY21	OTTHUMG00000019018	ENST00000263054.6:c.3371+205C>A	10.37:g.108338921G>T			Somatic	95	0.0105263158	1		WXS	Illumina HiSeq	Phase_I	110	0.06	7	NM_001206572	4	0.00	0	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Missense_Mutation	SNP	ENST00000263054.6	37	CCDS7559.1	.	.	.	.	.	.	.	.	.	.	G	10.98	1.503700	0.26949	.	.	ENSG00000108018	ENST00000369698;ENST00000344440	T;T	0.22134	1.97;2.53	5.9	4.03	0.46877	.	0.219926	0.40469	N	0.001097	T	0.24122	0.0584	L	0.29908	0.895	0.42866	D	0.994129	B;P	0.41546	0.059;0.754	B;P	0.47573	0.076;0.55	T	0.01283	-1.1396	9	.	.	.	-5.616	16.9503	0.86243	0.0:0.2244:0.7756:0.0	.	1154;1154	Q8WY21-3;Q8WY21-2	.;.	T	689;1154	ENSP00000358712:P689T;ENSP00000345964:P1154T	.	P	-	1	0	SORCS1	108328911	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	3.123000	0.50453	0.820000	0.34516	0.455000	0.32223	CCC			0.463	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000050232.4		NM_052918	
EMX2	2018	broad.mit.edu	37	10	119303017	119303017	+	Missense_Mutation	SNP	A	A	C			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr10:119303017A>C	ENST00000553456.3	+	1	1063	c.239A>C	c.(238-240)aAc>aCc	p.N80T	EMX2_ENST00000442245.4_Missense_Mutation_p.N80T|EMX2OS_ENST00000551288.1_RNA|EMX2OS_ENST00000440007.1_RNA|EMX2OS_ENST00000450314.2_RNA	NM_004098.3	NP_004089.1	Q04743	EMX2_HUMAN	empty spiracles homeobox 2	80					anterior/posterior pattern specification (GO:0009952)|cell proliferation in forebrain (GO:0021846)|cerebral cortex regionalization (GO:0021796)|dentate gyrus development (GO:0021542)|forebrain cell migration (GO:0021885)|neuron differentiation (GO:0030182)|regulation of transcription, DNA-templated (GO:0006355)|renal system development (GO:0072001)|response to drug (GO:0042493)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|large_intestine(5)|lung(2)|ovary(1)|prostate(2)	12		Colorectal(252;0.109)|Lung NSC(174;0.179)|all_lung(145;0.22)		all cancers(201;0.0133)		CACCCGCCCAACCCCGCCGTG	0.741																																					p.N80T													EMX2,NS,carcinoma,0,1	EMX2	25	1	0			c.A239C												13.0	16.0	15.0					10																	119303017		2185	4241	6426	SO:0001583	missense	2018	exon1			CGCCCAACCCCGC	AF301598	CCDS7601.1, CCDS53583.1	10q26.11	2011-06-20	2007-02-15		ENSG00000170370	ENSG00000170370		"""Homeoboxes / ANTP class : NKL subclass"""	3341	protein-coding gene	gene with protein product		600035	"""empty spiracles homolog 2 (Drosophila)"""			7959790	Standard	NM_004098		Approved		uc001ldh.4	Q04743	OTTHUMG00000019123	ENST00000553456.3:c.239A>C	10.37:g.119303017A>C	ENSP00000450962:p.Asn80Thr		Somatic	58	0.1551724138	9		WXS	Illumina HiSeq	Phase_I	68	0.35	24	NM_001165924	11	0.09	1	G3V305|Q96NN8|Q9BQF4	Missense_Mutation	SNP	ENST00000553456.3	37	CCDS7601.1	.	.	.	.	.	.	.	.	.	.	A	0.961	-0.703392	0.03255	.	.	ENSG00000170370;ENSG00000258614	ENST00000369201;ENST00000553456	D	0.91011	-2.77	5.91	4.78	0.61160	.	0.000000	0.85682	D	0.000000	T	0.79851	0.4517	N	0.08118	0	0.58432	D	0.999995	P;B	0.44816	0.844;0.062	B;B	0.41764	0.366;0.015	T	0.76743	-0.2847	10	0.10377	T	0.69	-20.6656	12.7121	0.57096	0.7406:0.2594:0.0:0.0	.	80;80	G3V305;Q04743	.;EMX2_HUMAN	T	80	ENSP00000450962:N80T	ENSP00000358202:N80T	N	+	2	0	AC005871.1;EMX2	119293007	1.000000	0.71417	1.000000	0.80357	0.182000	0.23217	5.813000	0.69201	1.055000	0.40461	-0.272000	0.10252	AAC			0.741	EMX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000050569.4		NM_004098	
CTBP2	1488	bcgsc.ca	37	10	126678129	126678129	+	Silent	SNP	G	G	T	rs367739342		TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr10:126678129G>T	ENST00000337195.5	-	11	1695	c.1296C>A	c.(1294-1296)ccC>ccA	p.P432P	CTBP2_ENST00000411419.2_Silent_p.P432P|CTBP2_ENST00000494626.2_Silent_p.P432P|CTBP2_ENST00000531469.1_Silent_p.P432P|CTBP2_ENST00000309035.6_Silent_p.P972P|CTBP2_ENST00000334808.6_Silent_p.P500P	NM_001329.2	NP_001320.1	P56545	CTBP2_HUMAN	C-terminal binding protein 2	432					negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)|white fat cell differentiation (GO:0050872)	cell junction (GO:0030054)|nucleus (GO:0005634)|synapse (GO:0045202)|transcriptional repressor complex (GO:0017053)	NAD binding (GO:0051287)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.173)		Colorectal(40;0.00572)|COAD - Colon adenocarcinoma(40;0.0127)|GBM - Glioblastoma multiforme(135;0.147)		CGTGTTTTGTGGGCTGGTTGG	0.542																																					p.P972P													.	CTBP2	100		0			c.C2916A												87.0	89.0	88.0					10																	126678129		2203	4300	6503	SO:0001819	synonymous_variant	1488	exon9			TTTTGTGGGCTGG	AF016507	CCDS7643.1, CCDS7644.1	10q26.13	2008-08-01			ENSG00000175029	ENSG00000175029			2495	protein-coding gene	gene with protein product		602619				9479502, 11864595	Standard	NM_022802		Approved	ribeye	uc001lie.4	P56545	OTTHUMG00000019224	ENST00000337195.5:c.1296C>A	10.37:g.126678129G>T			Somatic	56	0	0		WXS	Illumina HiSeq	Phase_1	62	0.06	4	NM_022802	262	0.00	0	A8K2X5|D3DRF5|O43449|Q5SQP7|Q69YI3|Q86SV0|Q9H2T8	Silent	SNP	ENST00000337195.5	37	CCDS7643.1																																																																																					0.542	CTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000050900.3		NM_001083914	
ODF3	113746	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	11	199447	199447	+	Missense_Mutation	SNP	C	C	A			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr11:199447C>A	ENST00000325113.4	+	6	930	c.613C>A	c.(613-615)Cgt>Agt	p.R205S	BET1L_ENST00000410108.1_Intron|ODF3_ENST00000525282.1_Intron	NM_053280.3	NP_444510.2	Q96PU9	ODF3A_HUMAN	outer dense fiber of sperm tails 3	205					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	outer dense fiber (GO:0001520)		p.R205C(1)		biliary_tract(1)|breast(1)|kidney(1)|large_intestine(2)|ovary(1)|prostate(2)|skin(1)	9		all_cancers(49;9.23e-07)|all_epithelial(84;0.000315)|Breast(177;0.00122)|Ovarian(85;0.0202)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;3.95e-27)|Epithelial(43;2.66e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.55e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)		CATGGCTGCCCGTGTGGAGCC	0.642																																					p.R205S													ODF3,face,carcinoma,0,1	ODF3	0	1	1	Substitution - Missense(1)	skin(1)	c.C613A												28.0	24.0	25.0					11																	199447		2190	4280	6470	SO:0001583	missense	113746	exon6			GCTGCCCGTGTGG	AB067774	CCDS7688.1, CCDS65981.1	11p15.5	2010-04-23			ENSG00000177947	ENSG00000177947			19905	protein-coding gene	gene with protein product	"""cancer/testis antigen 135"""	608356				11870087	Standard	NM_001286136		Approved	SHIPPO1, hSHIPPO, CT135	uc001lob.3	Q96PU9	OTTHUMG00000119073	ENST00000325113.4:c.613C>A	11.37:g.199447C>A	ENSP00000325868:p.Arg205Ser		Somatic	89	0	0		WXS	Illumina HiSeq	.	88	0.42	37	NM_053280	0		0	B7ZLT0|Q69YX0	Missense_Mutation	SNP	ENST00000325113.4	37	CCDS7688.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.188222	0.78789	.	.	ENSG00000177947	ENST00000325113	T	0.39229	1.09	5.0	5.0	0.66597	.	0.000000	0.42964	D	0.000629	T	0.65852	0.2731	M	0.89095	3.005	0.80722	D	1	D	0.61697	0.99	P	0.61800	0.894	T	0.70901	-0.4746	10	0.51188	T	0.08	-14.0033	13.6637	0.62382	0.0:1.0:0.0:0.0	.	205	Q96PU9	ODF3A_HUMAN	S	205	ENSP00000325868:R205S	ENSP00000325868:R205S	R	+	1	0	ODF3	189447	0.757000	0.28394	0.999000	0.59377	0.863000	0.49368	0.632000	0.24583	2.579000	0.87056	0.561000	0.74099	CGT			0.642	ODF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000239287.1			
MUC6	4588	bcgsc.ca	37	11	1016871	1016871	+	Missense_Mutation	SNP	G	G	T	rs554068781		TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr11:1016871G>T	ENST00000421673.2	-	31	5980	c.5930C>A	c.(5929-5931)cCc>cAc	p.P1977H		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1977	Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GGAAGAGAAGGGACTGCTCCC	0.587																																					p.P1977H													.	MUC6	408		0			c.C5930A												1308.0	1300.0	1302.0					11																	1016871		2203	4299	6502	SO:0001583	missense	4588	exon31			GAGAAGGGACTGC	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.5930C>A	11.37:g.1016871G>T	ENSP00000406861:p.Pro1977His		Somatic	337	0.0118694362	4		WXS	Illumina HiSeq	Phase_1	277	0.04	12	NM_005961	1	0.00	0	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	G	12.39	1.923756	0.34002	.	.	ENSG00000184956	ENST00000421673	T	0.18657	2.2	2.69	1.71	0.24356	.	.	.	.	.	T	0.14614	0.0353	L	0.29908	0.895	0.09310	N	1	B	0.29212	0.237	B	0.28553	0.091	T	0.22382	-1.0218	9	0.56958	D	0.05	.	7.0992	0.25327	0.0:0.0:0.7301:0.2699	.	1977	Q6W4X9	MUC6_HUMAN	H	1977	ENSP00000406861:P1977H	ENSP00000406861:P1977H	P	-	2	0	MUC6	1006871	0.015000	0.18098	0.001000	0.08648	0.026000	0.11368	1.250000	0.32850	0.416000	0.25844	0.306000	0.20318	CCC			0.587	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000382120.2		XM_290540	
MUC2	4583	mdanderson.org	37	11	1092966	1092966	+	Silent	SNP	C	C	A			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr11:1092966C>A	ENST00000441003.2	+	30	4812	c.4785C>A	c.(4783-4785)acC>acA	p.T1595T	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	tgaccccaaccccaacaccca	0.637																																					p.T1595T													.	.			0			c.C4785A												48.0	83.0	71.0					11																	1092966		1785	3239	5024	SO:0001819	synonymous_variant	4583	exon30			CCCAACCCCAACA	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4785C>A	11.37:g.1092966C>A			Somatic	30	0.0333333333	1		WXS	Illumina HiSeq	Phase_I	31	0.06	2	NM_002457	17	0.06	1	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																						0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000345894.2		NM_002457	
FOLH1	2346	bcgsc.ca	37	11	49204790	49204790	+	Silent	SNP	A	A	G	rs76509850	byFrequency	TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr11:49204790A>G	ENST00000256999.2	-	7	1091	c.831T>C	c.(829-831)taT>taC	p.Y277Y	FOLH1_ENST00000533034.1_Silent_p.Y262Y|FOLH1_ENST00000343844.4_5'UTR|FOLH1_ENST00000356696.3_Silent_p.Y277Y|FOLH1_ENST00000340334.7_Silent_p.Y262Y	NM_004476.1	NP_004467.1	Q04609	FOLH1_HUMAN	folate hydrolase (prostate-specific membrane antigen) 1	277	NAALADase.				folic acid-containing compound metabolic process (GO:0006760)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(34)|ovary(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	60					Capromab(DB00089)	GCCTATAAGCATATTCTGAAA	0.343																																					p.Y277Y													.	FOLH1	141		0			c.T831C												61.0	61.0	61.0					11																	49204790		2201	4298	6499	SO:0001819	synonymous_variant	2346	exon7			ATAAGCATATTCT	M99487	CCDS7946.1, CCDS31493.1, CCDS53626.1, CCDS53627.1, CCDS53628.1	11p11.2	2011-07-22			ENSG00000086205	ENSG00000086205	3.4.17.21		3788	protein-coding gene	gene with protein product	"""glutamate carboxylase II"", ""glutamate carboxypeptidase II"""	600934		FOLH		9838072	Standard	NM_001193472		Approved	PSM, PSMA, NAALAD1, NAALAdase, GCP2, GCPII	uc001ngy.3	Q04609	OTTHUMG00000166625	ENST00000256999.2:c.831T>C	11.37:g.49204790A>G			Somatic	136	0.0147058824	2		WXS	Illumina HiSeq	Phase_1	113	0.05	6	NM_004476	9	0.00	0	A4UU12|A9CB79|B7Z312|B7Z343|D3DQS5|E9PDX8|O43748|Q16305|Q541A4|Q8TAY3|Q9NP15|Q9NYE2|Q9P1P8	Silent	SNP	ENST00000256999.2	37	CCDS7946.1																																																																																					0.343	FOLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000390896.1		NM_004476	
Unknown	0	bcgsc.ca	37	11	62815368	62815368	+	IGR	SNP	G	G	A	rs150679703|rs374048942|rs7125680|rs372143980	byFrequency	TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr11:62815368G>A								SLC22A8 (32057 upstream) : SLC22A24 (32043 downstream)																							CCAAGGTGCAGCATGCCATGT	0.562																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GGTGCAGCATGCC																													11.37:g.62815368G>A			Somatic	24	0	0		WXS	Illumina HiSeq	Phase_1	30	0.27	8	.	0		0		RNA	SNP		37																																																																																					0	0.562										
ATG2A	23130	mdanderson.org	37	11	64662838	64662838	+	Missense_Mutation	SNP	G	G	T	rs370496305		TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr11:64662838G>T	ENST00000377264.3	-	40	5616	c.5504C>A	c.(5503-5505)gCg>gAg	p.A1835E	ATG2A_ENST00000421419.2_Missense_Mutation_p.A1837E	NM_015104.2	NP_055919.2	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	1835					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(19)|ovary(3)|prostate(5)|skin(1)|stomach(1)|urinary_tract(3)	55						CAGCCTCCGCGCAGAGCGCTT	0.701																																					p.A1835E													.	.			0			c.C5504A												21.0	25.0	24.0					11																	64662838		2197	4287	6484	SO:0001583	missense	23130	exon40			CTCCGCGCAGAGC		CCDS31602.1	11q13.1	2014-02-12	2012-06-06		ENSG00000110046	ENSG00000110046			29028	protein-coding gene	gene with protein product			"""ATG2 autophagy related 2 homolog A (S. cerevisiae)"""			21887408	Standard	NM_015104		Approved	KIAA0404	uc001obx.3	Q2TAZ0	OTTHUMG00000066831	ENST00000377264.3:c.5504C>A	11.37:g.64662838G>T	ENSP00000366475:p.Ala1835Glu		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	34	0.09	3	NM_015104	39	0.00	0	O43154|Q14DM2|Q6ZTV2|Q7Z6K8|Q8IVY5|Q8TAI8|Q96HH7	Missense_Mutation	SNP	ENST00000377264.3	37	CCDS31602.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.020|0.020	-1.434541|-1.434541	0.01108|0.01108	.|.	.|.	ENSG00000110046|ENSG00000110046	ENST00000421419;ENST00000377262;ENST00000377264|ENST00000418259	T;T|.	0.06687|.	3.27;3.27|.	3.29|3.29	1.23|1.23	0.21249|0.21249	.|.	0.283915|.	0.26753|.	N|.	0.022661|.	T|.	0.14743|.	0.0356|.	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	P;P|.	0.36354|.	0.549;0.493|.	B;B|.	0.32211|.	0.142;0.087|.	T|.	0.24012|.	-1.0172|.	10|.	0.05721|.	T|.	0.95|.	.|.	2.9965|2.9965	0.06000|0.06000	0.1964:0.2952:0.5084:0.0|0.1964:0.2952:0.5084:0.0	.|.	1835;1837|.	Q2TAZ0;Q2TAZ0-3|.	ATG2A_HUMAN;.|.	E|X	1837;228;1835|1638	ENSP00000410522:A1837E;ENSP00000366475:A1835E|.	ENSP00000366473:A228E|.	A|C	-|-	2|3	0|2	ATG2A|ATG2A	64419414|64419414	0.005000|0.005000	0.15991|0.15991	0.008000|0.008000	0.14137|0.14137	0.300000|0.300000	0.27592|0.27592	1.586000|1.586000	0.36611|0.36611	0.168000|0.168000	0.19655|0.19655	0.561000|0.561000	0.74099|0.74099	GCG|TGC			0.701	ATG2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000143224.1		NM_015104	
ATG2A	23130	mdanderson.org	37	11	64677638	64677638	+	Silent	SNP	A	A	G			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr11:64677638A>G	ENST00000377264.3	-	13	1849	c.1737T>C	c.(1735-1737)caT>caC	p.H579H	ATG2A_ENST00000421419.2_Silent_p.H579H	NM_015104.2	NP_055919.2	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	579					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(19)|ovary(3)|prostate(5)|skin(1)|stomach(1)|urinary_tract(3)	55						CTGAGTGGCAATGGCAGGCAA	0.687																																					p.H579H													.	.			0			c.T1737C												28.0	34.0	32.0					11																	64677638		2185	4266	6451	SO:0001819	synonymous_variant	23130	exon13			GTGGCAATGGCAG		CCDS31602.1	11q13.1	2014-02-12	2012-06-06		ENSG00000110046	ENSG00000110046			29028	protein-coding gene	gene with protein product			"""ATG2 autophagy related 2 homolog A (S. cerevisiae)"""			21887408	Standard	NM_015104		Approved	KIAA0404	uc001obx.3	Q2TAZ0	OTTHUMG00000066831	ENST00000377264.3:c.1737T>C	11.37:g.64677638A>G			Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	42	0.07	3	NM_015104	34	0.00	0	O43154|Q14DM2|Q6ZTV2|Q7Z6K8|Q8IVY5|Q8TAI8|Q96HH7	Silent	SNP	ENST00000377264.3	37	CCDS31602.1																																																																																					0.687	ATG2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000143224.1		NM_015104	
PCNXL3	399909	mdanderson.org	37	11	65394937	65394937	+	Missense_Mutation	SNP	C	C	T			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr11:65394937C>T	ENST00000355703.3	+	22	4125	c.3586C>T	c.(3586-3588)Ccc>Tcc	p.P1196S		NM_032223.2	NP_115599.2	Q9H6A9	PCX3_HUMAN	pecanex-like 3 (Drosophila)	1196						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)	13						CTTCTGCTGCCCCCCACAGCA	0.632																																					p.P1196S													.	.			0			c.C3586T												99.0	103.0	102.0					11																	65394937		2082	4213	6295	SO:0001583	missense	399909	exon22			TGCTGCCCCCCAC	BX640978	CCDS44650.1	11q12.1	2008-07-21			ENSG00000197136	ENSG00000197136			18760	protein-coding gene	gene with protein product						15146197	Standard	NM_032223		Approved	FLJ22427	uc001oey.2	Q9H6A9	OTTHUMG00000166539	ENST00000355703.3:c.3586C>T	11.37:g.65394937C>T	ENSP00000347931:p.Pro1196Ser		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	50	0.06	3	NM_032223	39	0.00	0	Q6MZN8	Missense_Mutation	SNP	ENST00000355703.3	37	CCDS44650.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.963913	0.74131	.	.	ENSG00000197136	ENST00000355703	T	0.10573	2.86	5.47	4.56	0.56223	.	0.000000	0.85682	D	0.000000	T	0.24812	0.0602	M	0.80183	2.485	0.45183	D	0.998192	P;B	0.47034	0.889;0.384	P;B	0.54312	0.748;0.113	T	0.01140	-1.1439	10	0.52906	T	0.07	.	7.5653	0.27874	0.163:0.7532:0.0:0.0838	.	83;1196	Q9H6A9-3;Q9H6A9	.;PCX3_HUMAN	S	1196	ENSP00000347931:P1196S	ENSP00000347931:P1196S	P	+	1	0	PCNXL3	65151513	1.000000	0.71417	0.997000	0.53966	0.964000	0.63967	7.787000	0.85759	1.454000	0.47793	0.655000	0.94253	CCC			0.632	PCNXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000390321.1		NM_032223	
YIF1A	10897	mdanderson.org	37	11	66052939	66052939	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr11:66052939G>T	ENST00000376901.4	-	6	738	c.554C>A	c.(553-555)gCc>gAc	p.A185D	YIF1A_ENST00000526497.1_5'UTR|YIF1A_ENST00000359461.6_Intron|YIF1A_ENST00000471387.2_Missense_Mutation_p.A42D|YIF1A_ENST00000496746.1_5'Flank	NM_020470.2	NP_065203.2	O95070	YIF1A_HUMAN	Yip1 interacting factor homolog A (S. cerevisiae)	185					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|microtubule organizing center (GO:0005815)		p.A185V(1)		endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|skin(2)|stomach(1)	9						CAGGAGCAGGGCCAGCACCTC	0.642																																					p.A185D													YIF1A,face,carcinoma,0,1	YIF1A	0	1	1	Substitution - Missense(1)	skin(1)	c.C554A												68.0	57.0	61.0					11																	66052939		2200	4295	6495	SO:0001583	missense	10897	exon6			AGCAGGGCCAGCA	AF004876	CCDS8132.1, CCDS73325.1	11q13	2009-01-05	2005-06-07	2005-06-07	ENSG00000174851	ENSG00000174851			16688	protein-coding gene	gene with protein product		611484	"""Yip1 interacting factor homolog (S. cerevisiae)"""	YIF1		8824393, 10970842, 18718466	Standard	NM_020470		Approved	YIF1P, 54TM, FinGER7	uc001ohk.4	O95070	OTTHUMG00000102079	ENST00000376901.4:c.554C>A	11.37:g.66052939G>T	ENSP00000366098:p.Ala185Asp		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	54	0.09	5	NM_020470	132	0.00	0	A6NM00|Q96G83|Q9BVD0	Missense_Mutation	SNP	ENST00000376901.4	37	CCDS8132.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.071939	0.76301	.	.	ENSG00000174851	ENST00000471387;ENST00000376901;ENST00000376904;ENST00000431556	T;T	0.48522	0.81;0.81	4.65	3.73	0.42828	.	0.214164	0.39834	N	0.001258	T	0.66848	0.2831	M	0.80982	2.52	0.39534	D	0.968711	D	0.64830	0.994	D	0.66196	0.942	T	0.72969	-0.4130	10	0.72032	D	0.01	-14.5265	12.3641	0.55219	0.0859:0.0:0.9141:0.0	.	185	O95070	YIF1A_HUMAN	D	42;185;189;197	ENSP00000366098:A185D;ENSP00000401953:A197D	ENSP00000366098:A185D	A	-	2	0	YIF1A	65809515	1.000000	0.71417	0.977000	0.42913	0.952000	0.60782	4.820000	0.62671	1.095000	0.41419	0.462000	0.41574	GCC			0.642	YIF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000219903.3		NM_020470	
PRB2	653247	broad.mit.edu	37	12	11546214	11546214	+	Silent	SNP	T	T	G			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr12:11546214T>G	ENST00000389362.4	-	3	833	c.798A>C	c.(796-798)ccA>ccC	p.P266P	PRB2_ENST00000545829.1_5'Flank|PRB1_ENST00000546254.1_Intron	NM_006248.3	NP_006239.3	P02812	PRB2_HUMAN	proline-rich protein BstNI subfamily 2	266	15 X 20 AA approximate tandem repeats of P-P-G-K-P-Q-G-P-P-P-Q-G-[GD]-[NKS]-[KSQ]- [PRS]-[QRS] [GPS]-[PSAR]-[PSR].					extracellular region (GO:0005576)				NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(5)|skin(4)|stomach(2)|urinary_tract(1)	37		all_cancers(2;0.00558)|Acute lymphoblastic leukemia(2;3.94e-11)|all_hematologic(2;3.6e-09)	OV - Ovarian serous cystadenocarcinoma(49;0.185)			CTTGTGGGGGTGGTCCTTGTG	0.607																																					p.P266P													.	PRB2	168		0			c.A798C												54.0	80.0	72.0					12																	11546214		2067	4150	6217	SO:0001819	synonymous_variant	653247	exon3			TGGGGGTGGTCCT	K03208	CCDS41757.2	12p13.2	2012-10-02			ENSG00000121335	ENSG00000121335			9338	protein-coding gene	gene with protein product		168810				8554050	Standard	NM_006248		Approved	PRPPRB1, Ps, cP7	uc010shk.1	P02812	OTTHUMG00000156975	ENST00000389362.4:c.798A>C	12.37:g.11546214T>G			Somatic	240	0.0666666667	16		WXS	Illumina HiSeq	Phase_I	596	0.07	41	NM_006248	0		0	O00599|P02811|P04281	Silent	SNP	ENST00000389362.4	37	CCDS41757.2																																																																																					0.607	PRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000346925.2		NM_006248	
KRAS	3845	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	12	25380276	25380276	+	Missense_Mutation	SNP	T	T	C	rs121913240		TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr12:25380276T>C	ENST00000256078.4	-	3	245	c.182A>G	c.(181-183)cAa>cGa	p.Q61R	AC087239.1_ENST00000594112.1_5'Flank|KRAS_ENST00000311936.3_Missense_Mutation_p.Q61R|KRAS_ENST00000557334.1_Intron	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	61			Q -> H (in lung carcinoma; dbSNP:rs17851045). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16533793, ECO:0000269|Ref.7}.|Q -> R (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.Q61L(73)|p.Q61R(56)|p.Q61P(12)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			GTACTCCTCTTGACCTGCTGT	0.418	Q61L(NCIH650_LUNG)|Q61L(SW948_LARGE_INTESTINE)|Q61R(PANC0213_PANCREAS)	119	Mis		"""pancreatic, colorectal, lung, thyroid, AML, others"""				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											p.Q61R	Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)			Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"""L, E, M, O"""	KRAS_ENST00000256078,colon,carcinoma,+1,429	KRAS_ENST00000256078	1	429	141	Substitution - Missense(141)	large_intestine(63)|lung(27)|thyroid(14)|haematopoietic_and_lymphoid_tissue(9)|pancreas(6)|skin(5)|stomach(3)|cervix(3)|upper_aerodigestive_tract(2)|soft_tissue(1)|central_nervous_system(1)|biliary_tract(1)|endometrium(1)|urinary_tract(1)|gastrointestinal_tract_(site_indeterminate)(1)|breast(1)|prostate(1)|kidney(1)	c.A182G												109.0	97.0	101.0					12																	25380276		2203	4300	6503	SO:0001583	missense	3845	exon3	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	TCCTCTTGACCTG	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"""v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog"", ""v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"""	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.182A>G	12.37:g.25380276T>C	ENSP00000256078:p.Gln61Arg		Somatic	87	0	0		WXS	Illumina HiSeq	.	193	0.07	14	NM_004985	125	0.02	3	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.022613	0.75275	.	.	ENSG00000133703	ENST00000311936;ENST00000256078	D;D	0.83673	-1.75;-1.75	5.77	5.77	0.91146	Small GTP-binding protein domain (1);	0.049057	0.85682	D	0.000000	D	0.88358	0.6415	M	0.92367	3.3	0.80722	D	1	B;B	0.26744	0.158;0.026	B;B	0.32805	0.135;0.153	D	0.87885	0.2680	10	0.66056	D	0.02	.	15.5753	0.76373	0.0:0.0:0.0:1.0	.	61;61	P01116-2;P01116	.;RASK_HUMAN	R	61	ENSP00000308495:Q61R;ENSP00000256078:Q61R	ENSP00000256078:Q61R	Q	-	2	0	KRAS	25271543	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.983000	0.88140	2.326000	0.78906	0.533000	0.62120	CAA			0.418	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000412232.1		NM_033360	
RAPGEF3	10411	mdanderson.org	37	12	48141588	48141588	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr12:48141588G>T	ENST00000449771.2	-	14	1468	c.1380C>A	c.(1378-1380)aaC>aaA	p.N460K	RAPGEF3_ENST00000405493.2_Missense_Mutation_p.N418K|RAPGEF3_ENST00000171000.4_Missense_Mutation_p.N418K|RAPGEF3_ENST00000395358.3_Missense_Mutation_p.N460K|RAPGEF3_ENST00000389212.3_Missense_Mutation_p.N460K|RAPGEF3_ENST00000548919.1_Missense_Mutation_p.N418K|RAPGEF3_ENST00000549151.1_Missense_Mutation_p.N418K			O95398	RPGF3_HUMAN	Rap guanine nucleotide exchange factor (GEF) 3	460	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cAMP-mediated signaling (GO:0019933)|cell proliferation (GO:0008283)|cellular response to cAMP (GO:0071320)|energy reserve metabolic process (GO:0006112)|establishment of endothelial barrier (GO:0061028)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cAMP catabolic process (GO:0030822)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of stress fiber assembly (GO:0051496)|Rap protein signal transduction (GO:0032486)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cAMP-dependent protein kinase complex (GO:0005952)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase regulator activity (GO:0008603)|guanyl-nucleotide exchange factor activity (GO:0005085)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)			endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|pancreas(1)|prostate(1)|skin(7)	25	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.0375)		GCTGCCTCTTGTTGCAGACGT	0.627																																					p.N460K													.	.			0			c.C1380A												43.0	43.0	43.0					12																	48141588		2203	4300	6503	SO:0001583	missense	10411	exon14			CCTCTTGTTGCAG	AK092448	CCDS31784.1, CCDS41775.1	12q13.1	2006-04-12	2004-03-26		ENSG00000079337	ENSG00000079337			16629	protein-coding gene	gene with protein product	"""exchange protein directly activated by cAMP 1"""	606057	"""RAP guanine-nucleotide-exchange factor (GEF) 3"""			10777494, 9856955	Standard	NM_001098531		Approved	cAMP-GEFI, EPAC, bcm910	uc001rpz.4	O95398	OTTHUMG00000133667	ENST00000449771.2:c.1380C>A	12.37:g.48141588G>T	ENSP00000395708:p.Asn460Lys		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	25	0.08	2	NM_001098531	13	0.00	0	A8K2G5|E7EQC8|O95634|Q8WVN0	Missense_Mutation	SNP	ENST00000449771.2	37	CCDS41775.1	.	.	.	.	.	.	.	.	.	.	G	18.76	3.691833	0.68271	.	.	ENSG00000079337	ENST00000405493;ENST00000449771;ENST00000541821;ENST00000549151;ENST00000171000;ENST00000389211;ENST00000389212;ENST00000397089;ENST00000548919;ENST00000395358	T;T;T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96;0.96;0.96	4.99	3.18	0.36537	Ras guanine nucleotide exchange factor, domain (1);Ras-like guanine nucleotide exchange factor, N-terminal (3);	0.414796	0.26680	N	0.023043	T	0.41834	0.1176	L	0.61218	1.895	0.44175	D	0.996986	P	0.36944	0.574	B	0.42462	0.388	T	0.15954	-1.0419	10	0.29301	T	0.29	.	8.2656	0.31813	0.2465:0.0:0.7535:0.0	.	460	O95398	RPGF3_HUMAN	K	418;460;107;418;418;418;460;472;418;460	ENSP00000384521:N418K;ENSP00000395708:N460K;ENSP00000448619:N418K;ENSP00000171000:N418K;ENSP00000373864:N460K;ENSP00000448480:N418K;ENSP00000378764:N460K	ENSP00000171000:N418K	N	-	3	2	RAPGEF3	46427855	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	0.831000	0.27476	0.825000	0.34637	0.655000	0.94253	AAC			0.627	RAPGEF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000257848.1		NM_006105	
FAM186A	121006	broad.mit.edu	37	12	50746811	50746811	+	Silent	SNP	A	A	G			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr12:50746811A>G	ENST00000327337.5	-	4	3803	c.3804T>C	c.(3802-3804)acT>acC	p.T1268T	FAM186A_ENST00000543111.1_Silent_p.T1268T|FAM186A_ENST00000543096.1_5'Flank	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	1268																	CCTGCTGAGGAGTAAGAGGGA	0.622																																					p.T1268T	NSCLC(138;1796 1887 12511 19463 37884)												.	FAM186A	181		0			c.T3804C												22.0	19.0	20.0					12																	50746811		692	1591	2283	SO:0001819	synonymous_variant	121006	exon4			CTGAGGAGTAAGA		CCDS44878.1	12q13.13	2009-04-22			ENSG00000185958	ENSG00000185958			26980	protein-coding gene	gene with protein product							Standard	NM_001145475		Approved	LOC121006	uc001rwl.2	A6NE01	OTTHUMG00000167889	ENST00000327337.5:c.3804T>C	12.37:g.50746811A>G			Somatic	85	0.0117647059	1		WXS	Illumina HiSeq	Phase_I	109	0.06	6	NM_001145475	0		0		Silent	SNP	ENST00000327337.5	37	CCDS44878.1																																																																																					0.622	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000396838.1		XM_001718353	
EIF4B	1975	mdanderson.org	37	12	53416289	53416289	+	Missense_Mutation	SNP	G	G	A			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr12:53416289G>A	ENST00000262056.9	+	6	871	c.545G>A	c.(544-546)cGt>cAt	p.R182H	EIF4B_ENST00000416762.3_Missense_Mutation_p.R143H|EIF4B_ENST00000420463.3_Missense_Mutation_p.R182H|RP11-983P16.4_ENST00000552905.1_RNA	NM_001417.4	NP_001408.2	P23588	IF4B_HUMAN	eukaryotic translation initiation factor 4B	182	Arg-rich.|Asp-rich.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation initiation factor activity (GO:0003743)			breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)	22						AGGGATGATCGTTCTTTTGGC	0.413																																					p.R182H													EIF4B,NS,carcinoma,0,1	EIF4B	0	1	0			c.G545A												151.0	124.0	132.0					12																	53416289		1858	4096	5954	SO:0001583	missense	1975	exon6			ATGATCGTTCTTT	X55733	CCDS41788.1, CCDS73474.1	12q13.13	2013-02-12			ENSG00000063046	ENSG00000063046		"""RNA binding motif (RRM) containing"""	3285	protein-coding gene	gene with protein product		603928					Standard	XM_005268709		Approved		uc001sbh.4	P23588	OTTHUMG00000169570	ENST00000262056.9:c.545G>A	12.37:g.53416289G>A	ENSP00000262056:p.Arg182His		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	79	0.05	4	NM_001417	576	0.00	0	Q4G0E3|Q53HQ2|Q6GPH5|Q6IB46|Q8WYK5	Missense_Mutation	SNP	ENST00000262056.9	37	CCDS41788.1	.	.	.	.	.	.	.	.	.	.	G	15.58	2.876023	0.51695	.	.	ENSG00000063046	ENST00000262056;ENST00000551002;ENST00000420463;ENST00000430205;ENST00000416762;ENST00000552490	D;D;D;D;D	0.94092	-3.26;-3.26;-3.26;-3.35;-3.26	3.59	3.59	0.41128	.	0.275859	0.34133	N	0.004234	D	0.88127	0.6353	L	0.27053	0.805	0.58432	D	0.999999	P;P;P	0.44380	0.834;0.744;0.744	B;B;B	0.39876	0.312;0.165;0.165	D	0.89089	0.3481	10	0.46703	T	0.11	.	15.041	0.71791	0.0:0.0:1.0:0.0	.	143;182;182	B4DS13;E7EX17;P23588	.;.;IF4B_HUMAN	H	182;136;182;182;143;182	ENSP00000262056:R182H;ENSP00000447192:R136H;ENSP00000388806:R182H;ENSP00000412530:R143H;ENSP00000450324:R182H	ENSP00000262056:R182H	R	+	2	0	EIF4B	51702556	1.000000	0.71417	0.986000	0.45419	0.826000	0.46750	6.053000	0.71089	2.288000	0.76882	0.650000	0.86243	CGT			0.413	EIF4B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000404852.2		NM_001417	
MMP19	4327	mdanderson.org	37	12	56232401	56232401	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr12:56232401G>T	ENST00000322569.4	-	6	975	c.884C>A	c.(883-885)gCc>gAc	p.A295D	MMP19_ENST00000394182.1_5'Flank|MMP19_ENST00000548629.1_Missense_Mutation_p.A272D|MMP19_ENST00000409200.3_Missense_Mutation_p.A213D|TMEM198B_ENST00000478241.1_RNA|MMP19_ENST00000547487.1_5'Flank	NM_002429.4	NP_002420.1	Q99542	MMP19_HUMAN	matrix metallopeptidase 19	295					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|luteolysis (GO:0001554)|ovarian follicle development (GO:0001541)|ovulation from ovarian follicle (GO:0001542)|proteolysis (GO:0006508)|response to cAMP (GO:0051591)|response to hormone (GO:0009725)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(2)|skin(2)	26					Marimastat(DB00786)	CAGCATCATGGCATCCAGTTC	0.602																																					p.A295D													.	.			0			c.C884A												104.0	87.0	93.0					12																	56232401		2203	4300	6503	SO:0001583	missense	4327	exon6			ATCATGGCATCCA	X92521	CCDS8895.1, CCDS61146.1	12q14	2005-08-08	2005-08-08			ENSG00000123342			7165	protein-coding gene	gene with protein product		601807	"""matrix metalloproteinase 19"""	MMP18		9232430	Standard	NM_002429		Approved	RASI-1	uc001sib.4	Q99542	OTTHUMG00000170216	ENST00000322569.4:c.884C>A	12.37:g.56232401G>T	ENSP00000313437:p.Ala295Asp		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	45	0.07	3	NM_002429	19	0.00	0	B4E030|O15278|O95606|Q99580	Missense_Mutation	SNP	ENST00000322569.4	37	CCDS8895.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.034935	0.93575	.	.	ENSG00000123342	ENST00000322569;ENST00000548629;ENST00000409200	T;T;T	0.58060	1.93;1.93;0.36	5.71	5.71	0.89125	Hemopexin/matrixin (2);	0.000000	0.85682	D	0.000000	T	0.80844	0.4701	H	0.94222	3.51	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.988	D	0.85646	0.1279	10	0.72032	D	0.01	.	17.3591	0.87345	0.0:0.0:1.0:0.0	.	213;295	B4E030;Q99542	.;MMP19_HUMAN	D	295;272;213	ENSP00000313437:A295D;ENSP00000446979:A272D;ENSP00000386625:A213D	ENSP00000313437:A295D	A	-	2	0	MMP19	54518668	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.082000	0.89513	2.699000	0.92147	0.514000	0.50259	GCC			0.602	MMP19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000408023.1		NM_002429	
AVIL	10677	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	58204191	58204191	+	Missense_Mutation	SNP	C	C	G			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr12:58204191C>G	ENST00000257861.3	-	6	1132	c.702G>C	c.(700-702)aaG>aaC	p.K234N	AVIL_ENST00000537081.1_Missense_Mutation_p.K227N	NM_006576.3	NP_006567.3	O75366	AVIL_HUMAN	advillin	234	Core. {ECO:0000250}.				actin filament capping (GO:0051693)|cilium morphogenesis (GO:0060271)|cytoskeleton organization (GO:0007010)|nervous system development (GO:0007399)|positive regulation of neuron projection development (GO:0010976)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)	actin binding (GO:0003779)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(9)|ovary(1)|prostate(6)	32	Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)					GGACTGTAGGCTTGATAATGG	0.507																																					p.K234N													.	.			0			c.G702C												123.0	109.0	113.0					12																	58204191		2203	4300	6503	SO:0001583	missense	10677	exon6			TGTAGGCTTGATA	AF041449	CCDS8959.1	12q13.11	2006-03-30				ENSG00000135407			14188	protein-coding gene	gene with protein product		613397				9664034, 12034507	Standard	NM_006576		Approved	p92, FLJ12386, ADVIL, DOC6	uc001sqj.2	O75366	OTTHUMG00000170461	ENST00000257861.3:c.702G>C	12.37:g.58204191C>G	ENSP00000257861:p.Lys234Asn		Somatic	138	0	0		WXS	Illumina HiSeq	.	154	0.33	51	NM_006576	2	0.50	1	B2RAU7|Q2NKM9	Missense_Mutation	SNP	ENST00000257861.3	37	CCDS8959.1	.	.	.	.	.	.	.	.	.	.	C	12.62	1.992208	0.35131	.	.	ENSG00000135407	ENST00000537081;ENST00000257861	T;T	0.15139	2.45;2.45	5.19	4.3	0.51218	.	0.501755	0.23103	N	0.051886	T	0.12987	0.0315	L	0.40543	1.245	0.27512	N	0.95166	B;B	0.10296	0.002;0.003	B;B	0.15870	0.009;0.014	T	0.14671	-1.0464	10	0.28530	T	0.3	-20.1934	6.9291	0.24432	0.0:0.7414:0.0:0.2586	.	227;234	O75366-2;O75366	.;AVIL_HUMAN	N	227;234	ENSP00000443207:K227N;ENSP00000257861:K234N	ENSP00000257861:K234N	K	-	3	2	AVIL	56490458	0.958000	0.32768	1.000000	0.80357	0.986000	0.74619	0.453000	0.21811	1.426000	0.47256	0.655000	0.94253	AAG			0.507	AVIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000409276.1		NM_006576	
DPY19L2	283417	bcgsc.ca	37	12	63964599	63964600	+	Missense_Mutation	DNP	TG	TG	CA	rs577993411|rs557778926	byFrequency	TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	TG	TG					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr12:63964599_63964600TG>CA	ENST00000324472.4	-	20	2121_2122	c.1938_1939CA>TG	c.(1936-1941)agCAtc>agTGtc	p.I647V	DPY19L2_ENST00000413230.2_Missense_Mutation_p.I94V	NM_173812.4	NP_776173.3	Q6NUT2	D19L2_HUMAN	dpy-19-like 2 (C. elegans)	647					multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|nuclear inner membrane (GO:0005637)|nucleus (GO:0005634)	transferase activity, transferring glycosyl groups (GO:0016757)	p.I647V(1)|p.S646>?(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	45			GBM - Glioblastoma multiforme(1;2.77e-05)	GBM - Glioblastoma multiforme(28;0.044)		GACAGCTTGATGCTTGCCATTG	0.376																																					p.I647V													.	DPY19L2	97		2	Substitution - Missense(1)|Complex(1)	prostate(1)|skin(1)	c.C1938T																																									SO:0001583	missense	283417	exon20			GCTTGATGCTTGC		CCDS31851.1	12q14.2	2012-11-14			ENSG00000177990	ENSG00000177990			19414	protein-coding gene	gene with protein product	"""spermatogenesis associated 34"""	613893				12975309	Standard	XM_006719348		Approved	FLJ32949, SPATA34	uc001srp.1	Q6NUT2	OTTHUMG00000168712	ENST00000324472.4:c.1938_1939delinsCA	12.37:g.63964599_63964600delinsCA	ENSP00000315988:p.Ile647Val		Somatic	199	0.0100502513	2		WXS	Illumina HiSeq	Phase_1	207	0.07	14	NM_173812	22	0.00	0	A4FVC1|B4E191|Q3ZCX2|Q6UWG8|Q96LZ9	Missense_Mutation	DNP	ENST00000324472.4	37	CCDS31851.1																																																																																					0.376	DPY19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000400689.2		NM_173812	
VPS33A	65082	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	122734429	122734429	+	Missense_Mutation	SNP	C	C	T			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr12:122734429C>T	ENST00000267199.4	-	6	876	c.764G>A	c.(763-765)gGc>gAc	p.G255D	VPS33A_ENST00000542310.1_5'Flank|RP11-512M8.5_ENST00000535844.1_Missense_Mutation_p.G216D	NM_022916.4	NP_075067.2	Q96AX1	VP33A_HUMAN	vacuolar protein sorting 33 homolog A (S. cerevisiae)	255					lysosome localization (GO:0032418)|melanosome localization (GO:0032400)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of developmental pigmentation (GO:0048070)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	early endosome (GO:0005769)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)				NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(13)|ovary(1)|skin(2)	28	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000336)|Epithelial(86;0.000606)|BRCA - Breast invasive adenocarcinoma(302;0.23)		GTTCTGAATGCCATAAATTTC	0.363																																					p.G255D													.	.			0			c.G764A												135.0	131.0	132.0					12																	122734429		2203	4300	6503	SO:0001583	missense	65082	exon6			TGAATGCCATAAA	AK026048	CCDS9231.1	12q24.31	2008-06-23	2006-04-04		ENSG00000139719	ENSG00000139719			18179	protein-coding gene	gene with protein product		610034	"""vacuolar protein sorting 33A (yeast)"""			11250079	Standard	NM_022916		Approved		uc001ucd.3	Q96AX1	OTTHUMG00000168920	ENST00000267199.4:c.764G>A	12.37:g.122734429C>T	ENSP00000267199:p.Gly255Asp		Somatic	75	0	0		WXS	Illumina HiSeq	.	80	0.35	28	NM_022916	49	0.08	4	Q547V4|Q9H5Q0	Missense_Mutation	SNP	ENST00000267199.4	37	CCDS9231.1	.	.	.	.	.	.	.	.	.	.	C	33	5.201650	0.94997	.	.	ENSG00000139719	ENST00000267199;ENST00000536212	T;T	0.80480	1.4;-1.38	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	D	0.92485	0.7614	M	0.92880	3.355	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93375	0.6738	10	0.59425	D	0.04	-20.7771	19.5736	0.95432	0.0:1.0:0.0:0.0	.	255	Q96AX1	VP33A_HUMAN	D	255;60	ENSP00000267199:G255D;ENSP00000439255:G60D	ENSP00000446319:G216D	G	-	2	0	VPS33A	121300382	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.774000	0.85478	2.636000	0.89361	0.655000	0.94253	GGC			0.363	VPS33A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000401607.2			
RILPL1	353116	mdanderson.org	37	12	123968738	123968738	+	Silent	SNP	G	G	T			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr12:123968738G>T	ENST00000376874.4	-	6	1291	c.1056C>A	c.(1054-1056)ggC>ggA	p.G352G	RILPL1_ENST00000340724.6_Silent_p.G232G|RILPL1_ENST00000544468.1_Silent_p.G25G	NM_178314.3	NP_847884.2	Q5EBL4	RIPL1_HUMAN	Rab interacting lysosomal protein-like 1	352					epithelial cell morphogenesis (GO:0003382)|intracellular protein transport (GO:0006886)|regulation of neuron death (GO:1901214)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)				endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	7	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000224)|Epithelial(86;0.00067)|all cancers(50;0.00836)|BRCA - Breast invasive adenocarcinoma(302;0.197)		GTCGCTTGATGCCCGACTCCG	0.607																																					p.G352G													.	.			0			c.C1056A												26.0	32.0	30.0					12																	123968738		2124	4236	6360	SO:0001819	synonymous_variant	353116	exon6			CTTGATGCCCGAC	AK097550	CCDS45006.1	12q24.31	2007-11-27			ENSG00000188026	ENSG00000188026			26814	protein-coding gene	gene with protein product		614092				14668488	Standard	NM_178314		Approved	FLJ39378	uc001ufe.2	Q5EBL4	OTTHUMG00000168686	ENST00000376874.4:c.1056C>A	12.37:g.123968738G>T			Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	22	0.09	2	NM_178314	42	0.00	0	Q66K36|Q8N1M0	Silent	SNP	ENST00000376874.4	37	CCDS45006.1																																																																																					0.607	RILPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000400595.1		NM_178314	
SCARB1	949	mdanderson.org	37	12	125263108	125263108	+	3'UTR	SNP	G	G	T			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr12:125263108G>T	ENST00000415380.2	-	0	1801				SCARB1_ENST00000261693.6_3'UTR|SCARB1_ENST00000376788.1_3'UTR|SCARB1_ENST00000546215.1_3'UTR|SCARB1_ENST00000339570.5_Missense_Mutation_p.P476T			Q8WTV0	SCRB1_HUMAN	scavenger receptor class B, member 1						adhesion of symbiont to host (GO:0044406)|androgen biosynthetic process (GO:0006702)|blood vessel endothelial cell migration (GO:0043534)|cell adhesion (GO:0007155)|cholesterol catabolic process (GO:0006707)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol import (GO:0070508)|detection of lipopolysaccharide (GO:0032497)|endothelial cell proliferation (GO:0001935)|high-density lipoprotein particle clearance (GO:0034384)|high-density lipoprotein particle remodeling (GO:0034375)|lipopolysaccharide transport (GO:0015920)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid transport (GO:0015914)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of triglyceride biosynthetic process (GO:0010867)|receptor-mediated endocytosis (GO:0006898)|recognition of apoptotic cell (GO:0043654)|regulation of phagocytosis (GO:0050764)|regulation of phosphatidylcholine catabolic process (GO:0010899)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)|viral process (GO:0016032)|wound healing (GO:0042060)	caveola (GO:0005901)|cell surface (GO:0009986)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein binding (GO:0034185)|high-density lipoprotein particle binding (GO:0008035)|high-density lipoprotein particle receptor activity (GO:0070506)|lipopolysaccharide binding (GO:0001530)|lipopolysaccharide receptor activity (GO:0001875)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(7)|prostate(1)	17	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000116)|Epithelial(86;0.000415)|all cancers(50;0.00395)	Phosphatidylserine(DB00144)	GCCAGGCCTGGCTGGCTCACG	0.706																																					p.P476T													.	.			0			c.C1426A												4.0	7.0	6.0					12																	125263108		1745	3787	5532	SO:0001624	3_prime_UTR_variant	949	exon12			GGCCTGGCTGGCT	Z22555	CCDS9259.1, CCDS45008.1	12q24.32	2008-08-05	2002-09-06	2002-09-06	ENSG00000073060	ENSG00000073060			1664	protein-coding gene	gene with protein product		601040	"""CD36 antigen (collagen type I receptor, thrombospondin receptor)-like 1"""	CD36L1		7689561	Standard	NM_001082959		Approved	SRB1, CLA-1, CLA1, SR-BI	uc001ugm.4	Q8WTV0	OTTHUMG00000168544	ENST00000415380.2:c.*17C>A	12.37:g.125263108G>T			Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	46	0.07	3	NM_001082959	53	0.00	0	F8W8N0|Q14016|Q52LZ5|Q6KFX4	Missense_Mutation	SNP	ENST00000415380.2	37		.	.	.	.	.	.	.	.	.	.	G	7.944	0.743468	0.15642	.	.	ENSG00000073060	ENST00000339570	T	0.59772	0.24	4.51	3.6	0.41247	.	.	.	.	.	T	0.40145	0.1105	N	0.22421	0.69	0.22639	N	0.998904	B	0.32829	0.386	B	0.28139	0.086	T	0.24584	-1.0156	9	0.46703	T	0.11	.	8.95	0.35783	0.1094:0.0:0.8906:0.0	.	476	F8W8N0	.	T	476	ENSP00000343795:P476T	ENSP00000343795:P476T	P	-	1	0	SCARB1	123829061	0.127000	0.22367	0.174000	0.22961	0.057000	0.15508	1.202000	0.32271	2.043000	0.60533	0.555000	0.69702	CCA			0.706	SCARB1-006	KNOWN	basic	protein_coding	protein_coding		OTTHUMT00000400165.1		NM_005505	
ADPRHL1	113622	mdanderson.org	37	13	114088091	114088091	+	Silent	SNP	C	C	A			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr13:114088091C>A	ENST00000375418.3	-	3	557	c.471G>T	c.(469-471)gtG>gtT	p.V157V	ADPRHL1_ENST00000356501.4_Silent_p.V75V	NM_138430.3	NP_612439.2	Q8NDY3	ARHL1_HUMAN	ADP-ribosylhydrolase like 1	157					protein de-ADP-ribosylation (GO:0051725)		ADP-ribosylarginine hydrolase activity (GO:0003875)|magnesium ion binding (GO:0000287)			endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|skin(1)	11	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0395)|all_epithelial(44;0.011)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.0195)|GBM - Glioblastoma multiforme(44;0.116)			GGCCGCACTCCACGCTGACCT	0.657																																					p.V157V													ADPRHL1,caecum,carcinoma,-2,1	ADPRHL1	-2	1	0			c.G471T												32.0	26.0	28.0					13																	114088091		2195	4293	6488	SO:0001819	synonymous_variant	113622	exon3			GCACTCCACGCTG	AJ313429	CCDS9535.1, CCDS9536.1	13q34	2003-06-19			ENSG00000153531	ENSG00000153531			21303	protein-coding gene	gene with protein product		610620				12070318	Standard	NM_138430		Approved	ARH2	uc001vtq.1	Q8NDY3	OTTHUMG00000017386	ENST00000375418.3:c.471G>T	13.37:g.114088091C>A			Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	40	0.08	3	NM_138430	3	0.00	0	Q5JUG2|Q96GD1	Silent	SNP	ENST00000375418.3	37	CCDS9535.1																																																																																					0.657	ADPRHL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000045915.2		NM_138430	
ADAM21P1	145241	broad.mit.edu	37	14	70713782	70713782	+	RNA	SNP	A	A	G	rs200469187		TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr14:70713782A>G	ENST00000530196.1	-	0	736					NR_003951.1				ADAM metallopeptidase domain 21 pseudogene 1																		GTCACCAGCAAATTTTGGTTC	0.443																																					.													.	.			0			.																																											0	.			CCAGCAAATTTTG			14q24.2	2014-03-25	2010-01-12	2010-01-12	ENSG00000235812	ENSG00000235812			19822	pseudogene	pseudogene			"""a disintegrin and metalloproteinase domain 21 pseudogene"", ""ADAM metallopeptidase domain 21 pseudogene"""	ADAM21P			Standard	NR_003951		Approved		uc010ttg.2		OTTHUMG00000166565		14.37:g.70713782A>G			Somatic	91	0.021978022	2		WXS	Illumina HiSeq	Phase_I	112	0.09	10	.	0		0		RNA	SNP	ENST00000530196.1	37																																																																																						0.443	ADAM21P1-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000390451.1		NG_002467	
BCL11B	64919	mdanderson.org	37	14	99641120	99641120	+	Missense_Mutation	SNP	C	C	T			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr14:99641120C>T	ENST00000357195.3	-	4	2062	c.2053G>A	c.(2053-2055)Gcc>Acc	p.A685T	BCL11B_ENST00000443726.2_Missense_Mutation_p.A491T|BCL11B_ENST00000345514.2_Missense_Mutation_p.A614T	NM_001282237.1|NM_138576.2	NP_001269166.1|NP_612808.1	Q9C0K0	BC11B_HUMAN	B-cell CLL/lymphoma 11B (zinc finger protein)	685					alpha-beta T cell differentiation (GO:0046632)|epithelial cell morphogenesis (GO:0003382)|keratinocyte development (GO:0003334)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|odontogenesis of dentin-containing tooth (GO:0042475)|olfactory bulb axon guidance (GO:0071678)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive T cell selection (GO:0043368)|post-embryonic camera-type eye development (GO:0031077)|regulation of keratinocyte proliferation (GO:0010837)|regulation of lipid metabolic process (GO:0019216)|regulation of neuron differentiation (GO:0045664)|striatal medium spiny neuron differentiation (GO:0021773)|T cell differentiation in thymus (GO:0033077)|T cell receptor V(D)J recombination (GO:0033153)|thymus development (GO:0048538)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.A685T(1)		NS(3)|breast(1)|central_nervous_system(9)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(9)|prostate(2)|skin(2)	34		Melanoma(154;0.0866)|all_epithelial(191;0.241)		COAD - Colon adenocarcinoma(157;0.103)		ATGCGCTTGGCGGCGCTGTTG	0.741			T	TLX3	T-ALL																																p.A685T				Dom	yes		14	14q32.1	64919	B-cell CLL/lymphoma 11B  (CTIP2)		L	BCL11B,NS,carcinoma,0,1	BCL11B	0	1	1	Substitution - Missense(1)	prostate(1)	c.G2053A												18.0	15.0	16.0					14																	99641120		2174	4246	6420	SO:0001583	missense	64919	exon4			GCTTGGCGGCGCT	AJ404614	CCDS9949.1, CCDS9950.1	14q32	2013-01-08			ENSG00000127152	ENSG00000127152		"""Zinc fingers, C2H2-type"""	13222	protein-coding gene	gene with protein product		606558		ZNF856B		11719382, 16950772	Standard	NM_138576		Approved	CTIP-2, CTIP2, hRIT1-alpha	uc001yga.3	Q9C0K0	OTTHUMG00000028967	ENST00000357195.3:c.2053G>A	14.37:g.99641120C>T	ENSP00000349723:p.Ala685Thr		Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	30	0.10	3	NM_138576	1	0.00	0	Q9H162	Missense_Mutation	SNP	ENST00000357195.3	37	CCDS9950.1	.	.	.	.	.	.	.	.	.	.	C	9.772	1.172876	0.21704	.	.	ENSG00000127152	ENST00000357195;ENST00000345514;ENST00000443726	T;T;T	0.10573	2.87;2.87;2.86	3.73	2.62	0.31277	.	0.710160	0.12469	N	0.466216	T	0.04543	0.0124	N	0.11427	0.14	0.37649	D	0.922324	B;B	0.27823	0.003;0.19	B;B	0.19666	0.003;0.026	T	0.24012	-1.0172	10	0.06891	T	0.86	-10.4805	8.8637	0.35274	0.5384:0.4616:0.0:0.0	.	614;685	Q9C0K0-2;Q9C0K0	.;BC11B_HUMAN	T	685;614;491	ENSP00000349723:A685T;ENSP00000280435:A614T;ENSP00000387419:A491T	ENSP00000280435:A614T	A	-	1	0	BCL11B	98710873	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	3.653000	0.54446	1.790000	0.52503	0.561000	0.74099	GCC			0.741	BCL11B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000072332.2		NM_138576	
PACS2	23241	mdanderson.org	37	14	105858990	105858990	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr14:105858990G>T	ENST00000325438.8	+	22	2749	c.2245G>T	c.(2245-2247)Gtg>Ttg	p.V749L	PACS2_ENST00000447393.1_Missense_Mutation_p.V753L|PACS2_ENST00000430725.2_Missense_Mutation_p.V674L|PACS2_ENST00000551743.1_Missense_Mutation_p.V263L|PACS2_ENST00000547217.1_Missense_Mutation_p.V719L|PACS2_ENST00000458164.2_Missense_Mutation_p.V764L|PACS2_ENST00000551801.1_Intron			Q86VP3	PACS2_HUMAN	phosphofurin acidic cluster sorting protein 2	749					apoptotic process (GO:0006915)|autophagic vacuole assembly (GO:0000045)|protein localization to pre-autophagosomal structure (GO:0034497)|protein targeting to plasma membrane (GO:0072661)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)				endometrium(2)|kidney(2)|lung(7)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	21		all_cancers(154;0.0351)|all_epithelial(191;0.153)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.0145)|Epithelial(46;0.036)	Epithelial(152;0.138)		GGGGCTGCAGGTGGACTACTG	0.607																																					p.V764L													.	.			0			c.G2290T												69.0	60.0	63.0					14																	105858990		2192	4298	6490	SO:0001583	missense	23241	exon23			CTGCAGGTGGACT	AB011174	CCDS32168.1, CCDS45178.1, CCDS45178.2, CCDS58339.1	14q32	2005-02-15	2005-02-15	2005-02-15		ENSG00000179364			23794	protein-coding gene	gene with protein product		610423	"""phosphofurin acidic cluster sorting protein 1-like"""	PACS1L		15692567	Standard	NM_001100913		Approved	KIAA0602	uc001yqu.3	Q86VP3	OTTHUMG00000170450	ENST00000325438.8:c.2245G>T	14.37:g.105858990G>T	ENSP00000321834:p.Val749Leu		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	53	0.06	3	NM_001100913	71	0.00	0	A2VDJ9|G8JLK3|O60342|Q6P191|Q96FL7	Missense_Mutation	SNP	ENST00000325438.8	37	CCDS32168.1	.	.	.	.	.	.	.	.	.	.	G	16.71	3.198224	0.58126	.	.	ENSG00000179364	ENST00000430725;ENST00000325438;ENST00000458164;ENST00000447393;ENST00000547217;ENST00000551743	T;T;T;T;T;T	0.53857	0.6;0.6;0.6;0.6;0.6;0.6	4.0	4.0	0.46444	.	0.074853	0.53938	D	0.000053	T	0.50394	0.1613	L	0.42686	1.345	0.58432	D	0.999999	B;B;B;B	0.33448	0.412;0.039;0.166;0.02	B;B;B;B	0.43916	0.436;0.073;0.143;0.036	T	0.43734	-0.9373	10	0.23891	T	0.37	-36.264	11.1326	0.48356	0.0:0.1882:0.8118:0.0	.	753;764;749;750	E9PB38;Q86VP3-2;Q86VP3;Q86VP3-3	.;.;PACS2_HUMAN;.	L	674;749;764;753;719;263	ENSP00000393524:V674L;ENSP00000321834:V749L;ENSP00000399732:V764L;ENSP00000393559:V753L;ENSP00000449525:V719L;ENSP00000449254:V263L	ENSP00000321834:V749L	V	+	1	0	PACS2	104930035	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	5.345000	0.65987	1.945000	0.56424	0.462000	0.41574	GTG			0.607	PACS2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000409209.1		XM_377355	
RAD51	5888	mdanderson.org	37	15	41021794	41021794	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr15:41021794G>T	ENST00000267868.3	+	8	1004	c.736G>T	c.(736-738)Gcc>Tcc	p.A246S	RAD51_ENST00000423169.2_Missense_Mutation_p.A246S|RAD51_ENST00000532743.1_Missense_Mutation_p.A247S|RAD51_ENST00000557850.1_Missense_Mutation_p.A149S|RAD51_ENST00000530766.1_3'UTR|RAD51_ENST00000382643.3_Missense_Mutation_p.A247S	NM_002875.4	NP_002866.2	Q06609	RAD51_HUMAN	RAD51 recombinase	246	Interaction with PALB2.				ATP catabolic process (GO:0006200)|cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to ionizing radiation (GO:0071479)|DNA recombinase assembly (GO:0000730)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA unwinding involved in DNA replication (GO:0006268)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|meiotic nuclear division (GO:0007126)|mitotic recombination (GO:0006312)|positive regulation of DNA ligation (GO:0051106)|protein homooligomerization (GO:0051260)|reciprocal meiotic recombination (GO:0007131)|regulation of double-strand break repair via homologous recombination (GO:0010569)	condensed chromosome (GO:0000793)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|lateral element (GO:0000800)|mitochondrion (GO:0005739)|nuclear chromosome (GO:0000228)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|PML body (GO:0016605)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA polymerase binding (GO:0070182)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|single-stranded DNA binding (GO:0003697)|single-stranded DNA-dependent ATPase activity (GO:0043142)			breast(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(1)|ovary(1)	9		all_cancers(109;1.19e-18)|all_epithelial(112;2.33e-15)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;1.45e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000421)|COAD - Colon adenocarcinoma(120;0.163)		GATGCACTTGGCCAGGTTTCT	0.522								Homologous recombination																													p.A247S													.	.			0			c.G739T												108.0	91.0	97.0					15																	41021794		2203	4300	6503	SO:0001583	missense	5888	exon8			CACTTGGCCAGGT	D13804	CCDS10062.1, CCDS53931.1, CCDS53932.1	15q15.1	2014-06-12	2013-07-02		ENSG00000051180	ENSG00000051180			9817	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 5"""	179617	"""RAD51 (S. cerevisiae) homolog (E coli RecA homolog)"", ""RAD51 homolog (RecA homolog, E. coli) (S. cerevisiae)"", ""RAD51 homolog (S. cerevisiae)"""	RAD51A, RECA		8358431, 8479919	Standard	NM_002875		Approved	HsRad51, HsT16930, BRCC5	uc010bbx.3	Q06609	OTTHUMG00000130067	ENST00000267868.3:c.736G>T	15.37:g.41021794G>T	ENSP00000267868:p.Ala246Ser		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	67	0.06	4	NM_001164269	186	0.00	0	B0FXP0|B2R8T6|Q6FHX9|Q6ZNA8|Q9BV60	Missense_Mutation	SNP	ENST00000267868.3	37	CCDS10062.1	.	.	.	.	.	.	.	.	.	.	G	36	5.685802	0.96784	.	.	ENSG00000051180	ENST00000423169;ENST00000382642;ENST00000267868;ENST00000532743;ENST00000382643	T;T;T;T	0.41400	1.0;1.0;1.0;1.0	5.51	5.51	0.81932	DNA recombination/repair protein RecA/RadB, ATP-binding domain (1);ATPase, AAA+ type, core (1);DNA recombination and repair protein Rad51, C-terminal (1);	0.105016	0.64402	D	0.000004	T	0.48333	0.1494	L	0.61036	1.89	0.80722	D	1	B;B;B	0.25169	0.119;0.095;0.047	B;B;B	0.32342	0.104;0.144;0.103	T	0.42649	-0.9439	10	0.44086	T	0.13	-9.0152	19.4364	0.94798	0.0:0.0:1.0:0.0	.	246;247;246	Q06609-3;Q6ZNA8;Q06609	.;.;RAD51_HUMAN	S	246;149;246;247;247	ENSP00000406602:A246S;ENSP00000267868:A246S;ENSP00000433924:A247S;ENSP00000372088:A247S	ENSP00000267868:A246S	A	+	1	0	RAD51	38809086	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.772000	0.98984	2.593000	0.87608	0.460000	0.39030	GCC			0.522	RAD51-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding		OTTHUMT00000252358.1		NM_002875, NM_133487	
RPAP1	26015	mdanderson.org	37	15	41817286	41817286	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr15:41817286G>T	ENST00000304330.4	-	15	2094	c.1978C>A	c.(1978-1980)Ctg>Atg	p.L660M	RPAP1_ENST00000568413.1_5'Flank|RPAP1_ENST00000561603.1_Missense_Mutation_p.L660M	NM_015540.2	NP_056355.2	Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1	660						nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(16)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	45		all_cancers(109;6.59e-20)|all_epithelial(112;7.67e-17)|Lung NSC(122;5.34e-11)|all_lung(180;4.17e-10)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		OV - Ovarian serous cystadenocarcinoma(18;2.84e-17)|GBM - Glioblastoma multiforme(113;1.68e-06)|Colorectal(105;0.0163)|BRCA - Breast invasive adenocarcinoma(123;0.117)		GGCAAGGCCAGTTCTTGGGGA	0.607																																					p.L660M													RPAP1,NS,carcinoma,+2,1	RPAP1	2	1	0			c.C1978A												48.0	46.0	47.0					15																	41817286		2203	4300	6503	SO:0001583	missense	26015	exon15			AGGCCAGTTCTTG	BC000246	CCDS10079.1	15q14	2004-03-16			ENSG00000103932	ENSG00000103932			24567	protein-coding gene	gene with protein product		611475				10718198	Standard	XM_005254297		Approved	DKFZP727M111, KIAA1403, MGC858, FLJ12732	uc001zod.3	Q9BWH6	OTTHUMG00000130342	ENST00000304330.4:c.1978C>A	15.37:g.41817286G>T	ENSP00000306123:p.Leu660Met		Somatic	56	0.0178571429	1		WXS	Illumina HiSeq	Phase_I	50	0.06	3	NM_015540	47	0.00	0	Q9H9I2|Q9NSQ5|Q9P2E4|Q9UFS7	Missense_Mutation	SNP	ENST00000304330.4	37	CCDS10079.1	.	.	.	.	.	.	.	.	.	.	G	14.05	2.419321	0.42918	.	.	ENSG00000103932	ENST00000304330	T	0.75367	-0.93	5.38	1.92	0.25849	.	0.075781	0.53938	N	0.000041	T	0.58278	0.2111	L	0.33485	1.01	0.39811	D	0.972707	B	0.31968	0.349	B	0.34093	0.175	T	0.49698	-0.8912	10	0.30078	T	0.28	-4.7015	5.6118	0.17410	0.1464:0.1095:0.6236:0.1206	.	660	Q9BWH6	RPAP1_HUMAN	M	660	ENSP00000306123:L660M	ENSP00000306123:L660M	L	-	1	2	RPAP1	39604578	0.999000	0.42202	0.980000	0.43619	0.991000	0.79684	2.653000	0.46691	0.615000	0.30124	0.455000	0.32223	CTG			0.607	RPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000252694.2		NM_015540	
CSPG4	1464	mdanderson.org	37	15	75979730	75979730	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr15:75979730G>T	ENST00000308508.5	-	3	3768	c.3676C>A	c.(3676-3678)Cta>Ata	p.L1226I		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	1226	Gly/Ser-rich (glycosaminoglycan attachment domain).|Interaction with COL5A1. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						GTCACTTGTAGGGTGGCATCC	0.612																																					p.L1226I													.	.			0			c.C3676A												57.0	57.0	57.0					15																	75979730		2196	4292	6488	SO:0001583	missense	1464	exon3			CTTGTAGGGTGGC	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"""Proteoglycans / Cell surface : Other"""	2466	protein-coding gene	gene with protein product	"""melanoma-associated chondroitin sulfate proteoglycan"""	601172	"""chondroitin sulfate proteoglycan 4 (melanoma-associated)"""			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.3676C>A	15.37:g.75979730G>T	ENSP00000312506:p.Leu1226Ile		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	52	0.06	3	NM_001897	44	0.00	0	D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	37	CCDS10284.1	.	.	.	.	.	.	.	.	.	.	.	11.12	1.546526	0.27652	.	.	ENSG00000173546	ENST00000308508	T	0.20069	2.1	5.07	5.07	0.68467	.	0.132195	0.34959	N	0.003543	T	0.16257	0.0391	L	0.29908	0.895	0.39097	D	0.961205	P	0.34864	0.473	B	0.24848	0.056	T	0.06320	-1.0833	10	0.46703	T	0.11	.	17.4549	0.87604	0.0:0.0:1.0:0.0	.	1226	Q6UVK1	CSPG4_HUMAN	I	1226	ENSP00000312506:L1226I	ENSP00000312506:L1226I	L	-	1	2	CSPG4	73766785	0.997000	0.39634	0.982000	0.44146	0.678000	0.39670	2.918000	0.48829	2.356000	0.79943	0.555000	0.69702	CTA			0.612	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000286472.1		NM_001897	
ACSM2B	348158	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	16	20556521	20556521	+	Missense_Mutation	SNP	C	C	A			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr16:20556521C>A	ENST00000329697.6	-	10	1407	c.1239G>T	c.(1237-1239)agG>agT	p.R413S	ACSM2B_ENST00000567288.1_5'UTR|ACSM2B_ENST00000565322.1_Missense_Mutation_p.R334S|ACSM2B_ENST00000567001.1_Missense_Mutation_p.R413S|ACSM2B_ENST00000565232.1_Missense_Mutation_p.R413S	NM_001105069.1	NP_001098539.1	Q68CK6	ACS2B_HUMAN	acyl-CoA synthetase medium-chain family member 2B	413					fatty acid metabolic process (GO:0006631)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(4)|lung(33)|ovary(1)|prostate(1)|skin(5)	57						TGGGTTTGACCCTGATGCCAA	0.522																																					p.R413S													.	.			0			c.G1239T												148.0	115.0	126.0					16																	20556521		2201	4297	6498	SO:0001583	missense	348158	exon11			TTTGACCCTGATG	AY160217	CCDS10586.1	16p12.3	2014-08-08	2007-06-20	2007-06-20	ENSG00000066813	ENSG00000066813		"""Acyl-CoA synthetase family"""	30931	protein-coding gene	gene with protein product	"""xenobiotic/medium chain fatty acid:CoA ligase"""	614359	"""acyl-CoA synthetase medium-chain family member 2"""	ACSM2		12616642	Standard	NM_182617		Approved	HXMA, HYST1046	uc002dhk.4	Q68CK6	OTTHUMG00000131555	ENST00000329697.6:c.1239G>T	16.37:g.20556521C>A	ENSP00000327453:p.Arg413Ser		Somatic	94	0	0		WXS	Illumina HiSeq	.	63	0.32	20	NM_182617	0		0	Q86YT1	Missense_Mutation	SNP	ENST00000329697.6	37	CCDS10586.1	.	.	.	.	.	.	.	.	.	.	C	8.305	0.820862	0.16678	.	.	ENSG00000066813	ENST00000329697	T	0.48522	0.81	3.38	-3.88	0.04205	AMP-dependent synthetase/ligase (1);	0.114882	0.38326	N	0.001740	T	0.41328	0.1154	M	0.66506	2.035	0.09310	N	0.999996	P;P	0.34724	0.465;0.465	B;B	0.36567	0.228;0.228	T	0.40079	-0.9582	10	0.51188	T	0.08	-27.0483	10.6062	0.45396	0.0:0.3119:0.0:0.6881	.	413;413	A8K051;Q68CK6	.;ACS2B_HUMAN	S	413	ENSP00000327453:R413S	ENSP00000327453:R413S	R	-	3	2	ACSM2B	20464022	0.000000	0.05858	0.105000	0.21289	0.282000	0.26991	0.073000	0.14640	-0.890000	0.03945	-0.180000	0.13094	AGG			0.522	ACSM2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000254417.2		NM_182617	
NPIPB5	100132247	bcgsc.ca	37	16	22545897	22545897	+	Missense_Mutation	SNP	G	G	T	rs143579045		TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr16:22545897G>T	ENST00000517539.1	+	8	1668	c.1593G>T	c.(1591-1593)aaG>aaT	p.K531N	NPIPB5_ENST00000415654.1_3'UTR|NPIPB5_ENST00000424340.1_Missense_Mutation_p.K531N			A8MRT5	NPIB5_HUMAN	nuclear pore complex interacting protein family, member B5	531	Pro-rich.					integral component of membrane (GO:0016021)											ATAATATCAAGACACCTGCCG	0.597																																					p.K531N													RP11-368J21.2_ENST00000424340,NS,carcinoma,0,4	.		4	0			c.G1593T												11.0	7.0	8.0					16																	22545897		686	1576	2262	SO:0001583	missense	0	exon7			TATCAAGACACCT		CCDS45443.1	16p12.2	2013-06-11			ENSG00000243716	ENSG00000243716			37233	protein-coding gene	gene with protein product							Standard	NM_001135865		Approved			A8MRT5	OTTHUMG00000163573	ENST00000517539.1:c.1593G>T	16.37:g.22545897G>T	ENSP00000430633:p.Lys531Asn		Somatic	35	0.0571428571	2		WXS	Illumina HiSeq	Phase_1	42	0.14	6	NM_001135865	187	0.09	17	B4DK13	Missense_Mutation	SNP	ENST00000517539.1	37	CCDS45443.1	.	.	.	.	.	.	.	.	.	.	.	0.526	-0.859889	0.02610	.	.	ENSG00000243716	ENST00000415833;ENST00000424340;ENST00000342168;ENST00000503072;ENST00000517539;ENST00000528249	T;T;T;T	0.20069	2.18;2.1;2.1;2.18	.	.	.	.	.	.	.	.	T	0.17195	0.0413	L	0.50333	1.59	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.0	T	0.25082	-1.0142	6	0.42905	T	0.14	.	.	.	.	.	531;531	F5GWX0;A8MRT5	.;K220L_HUMAN	N	531;531;531;409;531;531	ENSP00000445388:K531N;ENSP00000440703:K531N;ENSP00000430633:K531N;ENSP00000431553:K531N	ENSP00000441680:K531N	K	+	3	2	RP11-368J21.2	22453398	.	.	.	.	.	.	.	.	.	.	.	.	AAG			0.597	NPIPB5-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000374343.2		NM_001135865	
MYBBP1A	10514	mdanderson.org	37	17	4445103	4445103	+	Silent	SNP	G	G	T			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr17:4445103G>T	ENST00000254718.4	-	23	3477	c.3171C>A	c.(3169-3171)ggC>ggA	p.G1057G	MYBBP1A_ENST00000381556.2_Silent_p.G1057G			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	1057					cellular response to glucose starvation (GO:0042149)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleocytoplasmic transport (GO:0006913)|osteoblast differentiation (GO:0001649)|positive regulation of cell cycle arrest (GO:0071158)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|NLS-dependent protein nuclear import complex (GO:0042564)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(2)|stomach(1)	24						CTAGGACCTGGCCCATCAGCT	0.627																																					p.G1057G													MYBBP1A,bladder,carcinoma,-2,1	MYBBP1A	-2	1	0			c.C3171A												83.0	77.0	79.0					17																	4445103		2203	4300	6503	SO:0001819	synonymous_variant	10514	exon23			GACCTGGCCCATC	AF147709	CCDS11046.1, CCDS42238.1	17p13.3	2008-07-18			ENSG00000132382	ENSG00000132382			7546	protein-coding gene	gene with protein product	"""p53-activated protein-2"""	604885				10644447	Standard	NM_014520		Approved	P160, PAP2, FLJ37886	uc002fxz.4	Q9BQG0	OTTHUMG00000090747	ENST00000254718.4:c.3171C>A	17.37:g.4445103G>T			Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	52	0.06	3	NM_014520	109	0.00	0	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Silent	SNP	ENST00000254718.4	37	CCDS11046.1																																																																																					0.627	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000207488.2		NM_014520	
PELP1	27043	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	17	4574813	4574813	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr17:4574813G>T	ENST00000574876.1	-	17	3331	c.3314C>A	c.(3313-3315)aCa>aAa	p.T1105K	PELP1_ENST00000301396.4_Missense_Mutation_p.T1249K|PELP1_ENST00000269230.7_Missense_Mutation_p.T1015K|PELP1_ENST00000572293.1_Missense_Mutation_p.T1155K|PELP1_ENST00000436683.2_Missense_Mutation_p.T881K			Q8IZL8	PELP1_HUMAN	proline, glutamate and leucine rich protein 1	1105					cellular response to estrogen stimulus (GO:0071391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	15						CATGGCAGCTGTGTCATCCTG	0.512																																					p.T1105K													.	PELP1	102		0			c.C3314A												69.0	72.0	71.0					17																	4574813		2132	4252	6384	SO:0001583	missense	27043	exon17			GCAGCTGTGTCAT		CCDS58503.1, CCDS58503.2, CCDS62038.1	17p13.2	2012-05-02	2008-02-21			ENSG00000141456			30134	protein-coding gene	gene with protein product		609455	"""proline, glutamic acid and leucine rich protein 1"""			11481323, 12682072	Standard	NM_014389		Approved	MNAR	uc002fyi.4	Q8IZL8		ENST00000574876.1:c.3314C>A	17.37:g.4574813G>T	ENSP00000461625:p.Thr1105Lys		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	44	0.09	4	NM_014389	176	0.00	0	O15450|Q5EGN3|Q6NTE6|Q96FT1|Q9BU60	Missense_Mutation	SNP	ENST00000574876.1	37	CCDS58503.1	.	.	.	.	.	.	.	.	.	.	G	14.36	2.512170	0.44660	.	.	ENSG00000141456	ENST00000301396;ENST00000269230;ENST00000436683	T;T;T	0.55052	0.56;0.54;0.61	4.74	3.77	0.43336	.	0.208894	0.41001	D	0.000980	T	0.56790	0.2009	L	0.27053	0.805	0.32014	N	0.601682	B;D	0.71674	0.015;0.998	B;D	0.76071	0.004;0.987	T	0.63310	-0.6666	10	0.48119	T	0.1	-8.8691	10.8036	0.46504	0.0928:0.0:0.9072:0.0	.	881;1105	E7EV54;Q8IZL8	.;PELP1_HUMAN	K	1249;1015;881	ENSP00000301396:T1249K;ENSP00000269230:T1015K;ENSP00000416231:T881K	ENSP00000269230:T1015K	T	-	2	0	AC091153.1	4521562	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	4.255000	0.58804	1.207000	0.43291	0.561000	0.74099	ACA			0.512	PELP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000439140.2		NM_014389	
DNAH9	1770	mdanderson.org	37	17	11833287	11833287	+	Silent	SNP	A	A	T	rs2286303	byFrequency	TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr17:11833287A>T	ENST00000262442.4	+	63	12050	c.11982A>T	c.(11980-11982)ccA>ccT	p.P3994P	DNAH9_ENST00000608377.1_Silent_p.P306P|DNAH9_ENST00000454412.2_Intron|DNAH9_ENST00000396001.2_3'UTR	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	3994	AAA 6. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		GTGCAGAGCCAGCACCCTCCC	0.592																																					p.P3994P													.	.			0			c.A11982T												84.0	63.0	70.0					17																	11833287		2203	4300	6503	SO:0001819	synonymous_variant	1770	exon63			AGAGCCAGCACCC	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.11982A>T	17.37:g.11833287A>T			Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	104	0.04	4	NM_001372	3	0.00	0	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																					0.592	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000252756.2		NM_001372	
TVP23C	201158	ucsc.edu	37	17	15457087	15457087	+	Missense_Mutation	SNP	C	C	T			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr17:15457087C>T	ENST00000225576.3	-	3	247	c.152G>A	c.(151-153)tGt>tAt	p.C51Y	TVP23C_ENST00000584811.1_5'UTR|TVP23C_ENST00000428082.2_Missense_Mutation_p.C51Y|TVP23C_ENST00000438826.3_Missense_Mutation_p.C51Y|TVP23C_ENST00000519970.1_Intron|TVP23C_ENST00000518321.1_Missense_Mutation_p.C51Y|TVP23C-CDRT4_ENST00000522212.2_Missense_Mutation_p.C51Y	NM_145301.2	NP_660344.2	Q96ET8	TV23C_HUMAN	trans-golgi network vesicle protein 23 homolog C (S. cerevisiae)	51						integral component of membrane (GO:0016021)											ACAGAGAAGACAGACGATGAT	0.373																																					p.C51Y													.	.			0			c.G152A												274.0	265.0	268.0					17																	15457087		2203	4300	6503	SO:0001583	missense	0	exon3			AGAAGACAGACGA	BC011952	CCDS11170.1, CCDS45617.1	17p12	2012-11-29	2012-11-29	2012-11-29	ENSG00000175106	ENSG00000175106			30453	protein-coding gene	gene with protein product			"""family with sequence similarity 18, member B2"""	FAM18B2			Standard	NM_001135036		Approved	MGC8763	uc002goq.2	Q96ET8	OTTHUMG00000171461	ENST00000225576.3:c.152G>A	17.37:g.15457087C>T	ENSP00000225576:p.Cys51Tyr		Somatic	200	0.05	10		RNA-Seq	Illumina HiSeq		153	0.07	11	NM_145301	24	0.75	18	Q3LIC7	Missense_Mutation	SNP	ENST00000225576.3	37	CCDS11170.1	.	.	.	.	.	.	.	.	.	.	.	2.368	-0.344949	0.05208	.	.	ENSG00000259024;ENSG00000175106;ENSG00000175106;ENSG00000175106	ENST00000522212;ENST00000225576;ENST00000428082;ENST00000438826	T;T;T;T	0.25749	1.78;1.78;1.78;1.78	4.47	4.47	0.54385	.	0.000000	0.85682	N	0.000000	T	0.02571	0.0078	N	0.00004	-3.335	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.0;0.0;0.002	T	0.38457	-0.9660	10	0.02654	T	1	-3.8701	9.492	0.38965	0.0:0.0877:0.0:0.9123	.	51;51;51	Q96ET8-2;Q96ET8-3;Q96ET8	.;.;F18B2_HUMAN	Y	51	ENSP00000429865:C51Y;ENSP00000225576:C51Y;ENSP00000406387:C51Y;ENSP00000413355:C51Y	ENSP00000225576:C51Y	C	-	2	0	RP11-726O12.1;FAM18B2	15397812	1.000000	0.71417	1.000000	0.80357	0.703000	0.40648	6.178000	0.71968	0.670000	0.31165	-0.442000	0.05670	TGT			0.373	TVP23C-001	KNOWN	basic|CCDS	protein_coding	protein_coding		OTTHUMT00000130705.2		NM_145301	
KIAA0100	9703	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	17	26964994	26964994	+	Missense_Mutation	SNP	C	C	T	rs200349785		TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr17:26964994C>T	ENST00000528896.2	-	14	1705	c.1631G>A	c.(1630-1632)cGt>cAt	p.R544H	RP11-192H23.7_ENST00000577814.1_RNA|KIAA0100_ENST00000389003.3_Missense_Mutation_p.R401H|KIAA0100_ENST00000544884.1_Missense_Mutation_p.R401H	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100	544						extracellular region (GO:0005576)				breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(23)|ovary(2)|prostate(2)|skin(6)|stomach(2)|urinary_tract(3)	68	Lung NSC(42;0.00431)					GGATAAGATACGAGACAGACA	0.493																																					p.R544H													.	KIAA0100	175		0			c.G1631A												89.0	78.0	82.0					17																	26964994		2203	4300	6503	SO:0001583	missense	9703	exon14			AAGATACGAGACA	D43947	CCDS32595.1	17q11.2	2012-11-29			ENSG00000007202	ENSG00000007202			28960	protein-coding gene	gene with protein product	"""cancer/testis antigen 101"", ""breast cancer overexpressed gene 1"""	610664				16289875	Standard	NM_014680		Approved	DKFZp686M0843, MGC111488, BCOX1, CT101, BCOX	uc002hbu.3	Q14667	OTTHUMG00000166587	ENST00000528896.2:c.1631G>A	17.37:g.26964994C>T	ENSP00000436773:p.Arg544His		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	41	0.10	4	NM_014680	83	0.00	0	A6NCX3|Q3SYN5|Q49A07|Q5H9T4|Q6WG74|Q6ZP51|Q96HH8	Missense_Mutation	SNP	ENST00000528896.2	37	CCDS32595.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.810128	0.90707	.	.	ENSG00000007202	ENST00000005905;ENST00000389003;ENST00000528896;ENST00000544884	T;T	0.24908	1.83;1.83	5.95	5.95	0.96441	FMP27, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.43787	0.1263	L	0.32530	0.975	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.09335	-1.0679	10	0.44086	T	0.13	.	20.3789	0.98926	0.0:1.0:0.0:0.0	.	544	Q14667	K0100_HUMAN	H	544;544;544;401	ENSP00000436773:R544H;ENSP00000446443:R401H	ENSP00000005905:R544H	R	-	2	0	KIAA0100	23989121	1.000000	0.71417	1.000000	0.80357	0.796000	0.44982	6.863000	0.75489	2.826000	0.97356	0.563000	0.77884	CGT			0.493	KIAA0100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000390571.3		NM_014680	
ANKFN1	162282	mdanderson.org	37	17	54450048	54450048	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr17:54450048G>T	ENST00000318698.2	+	6	687	c.652G>T	c.(652-654)Gtc>Ttc	p.V218F	ANKFN1_ENST00000566473.2_Missense_Mutation_p.V218F	NM_153228.2	NP_694960.2	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain containing 1	218										NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(11)|lung(27)|ovary(1)|prostate(1)|skin(1)	53						CAACACACTGGTCCAGGAAGC	0.493																																					p.V218F													.	.			0			c.G652T												133.0	129.0	130.0					17																	54450048		2203	4300	6503	SO:0001583	missense	162282	exon6			ACACTGGTCCAGG	AK095654	CCDS32686.1	17q23.2	2014-02-12	2005-11-15		ENSG00000153930	ENSG00000153930		"""Ankyrin repeat domain containing"", ""Fibronectin type III domain containing"""	26766	protein-coding gene	gene with protein product							Standard	NM_153228		Approved	FLJ38335	uc002iun.1	Q8N957	OTTHUMG00000155010	ENST00000318698.2:c.652G>T	17.37:g.54450048G>T	ENSP00000321627:p.Val218Phe		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	41	0.07	3	NM_153228	0		0		Missense_Mutation	SNP	ENST00000318698.2	37	CCDS32686.1	.	.	.	.	.	.	.	.	.	.	G	31	5.086711	0.94100	.	.	ENSG00000153930	ENST00000318698	T	0.26810	1.71	5.64	5.64	0.86602	.	0.170706	0.50627	D	0.000106	T	0.47135	0.1429	M	0.70595	2.14	0.58432	D	0.999996	D	0.57899	0.981	P	0.55161	0.77	T	0.45745	-0.9240	10	0.72032	D	0.01	-6.8262	19.7137	0.96107	0.0:0.0:1.0:0.0	.	218	Q8N957	ANKF1_HUMAN	F	218	ENSP00000321627:V218F	ENSP00000321627:V218F	V	+	1	0	ANKFN1	51805047	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.912000	0.87465	2.655000	0.90218	0.462000	0.41574	GTC			0.493	ANKFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000338043.1		NM_153228	
ERN1	2081	mdanderson.org	37	17	62133223	62133223	+	Missense_Mutation	SNP	T	T	A			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr17:62133223T>A	ENST00000433197.3	-	13	1579	c.1484A>T	c.(1483-1485)cAg>cTg	p.Q495L		NM_001433.3	NP_001424.3			endoplasmic reticulum to nucleus signaling 1											central_nervous_system(4)|kidney(1)|lung(2)|ovary(1)|stomach(1)	9						GAAGGGCAgctgctgctgctg	0.632																																					p.Q495L													.	.			0			c.A1484T												5.0	6.0	6.0					17																	62133223		2017	4062	6079	SO:0001583	missense	2081	exon13			GGCAGCTGCTGCT	AF059198	CCDS45762.1	17q23	2011-08-12	2007-08-14			ENSG00000178607			3449	protein-coding gene	gene with protein product	"""inositol-requiring enzyme 1"""	604033	"""ER to nucleus signalling 1"""			9637683	Standard	NM_001433		Approved	IRE1, IRE1P	uc002jdz.2	O75460		ENST00000433197.3:c.1484A>T	17.37:g.62133223T>A	ENSP00000401445:p.Gln495Leu		Somatic	35	0.0285714286	1		WXS	Illumina HiSeq	Phase_I	44	0.09	4	NM_001433	11	0.00	0		Missense_Mutation	SNP	ENST00000433197.3	37	CCDS45762.1	.	.	.	.	.	.	.	.	.	.	T	3.711	-0.059492	0.07317	.	.	ENSG00000178607	ENST00000433197	T	0.16457	2.34	0.14	0.14	0.14804	.	.	.	.	.	T	0.13157	0.0319	L	0.48642	1.525	0.24475	N	0.994376	B	0.22003	0.063	B	0.15052	0.012	T	0.27905	-1.0060	8	0.33141	T	0.24	-15.5741	.	.	.	.	495	O75460	ERN1_HUMAN	L	495	ENSP00000401445:Q495L	ENSP00000401445:Q495L	Q	-	2	0	ERN1	59486955	0.994000	0.37717	0.998000	0.56505	0.867000	0.49689	-0.604000	0.05667	0.157000	0.19338	0.155000	0.16302	CAG			0.632	ERN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000443734.2		NM_001433	
CEP76	79959	mdanderson.org	37	18	12702538	12702538	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr18:12702538G>T	ENST00000262127.2	-	1	235	c.10C>A	c.(10-12)Cct>Act	p.P4T	PSMG2_ENST00000317615.6_5'UTR|CEP76_ENST00000586887.1_5'UTR|CEP76_ENST00000423709.2_Missense_Mutation_p.P4T|PSMG2_ENST00000585331.2_Intron|PSMG2_ENST00000590217.1_5'Flank	NM_024899.2	NP_079175.2	Q8TAP6	CEP76_HUMAN	centrosomal protein 76kDa	4					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of centriole replication (GO:0046599)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|protein complex (GO:0043234)				endometrium(1)|kidney(3)|large_intestine(5)|lung(7)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						TTCTCCGGAGGCAGCGACATG	0.692																																					p.P4T													.	.			0			c.C10A												26.0	24.0	25.0					18																	12702538		2202	4300	6502	SO:0001583	missense	79959	exon1			CCGGAGGCAGCGA	BC026307	CCDS11861.1, CCDS62390.1	18p11.21	2014-02-20	2005-12-01	2005-12-01	ENSG00000101624	ENSG00000101624			25727	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 9"""	C18orf9		14654843	Standard	NM_024899		Approved	HsT1705, FLJ12542	uc002kri.4	Q8TAP6	OTTHUMG00000131701	ENST00000262127.2:c.10C>A	18.37:g.12702538G>T	ENSP00000262127:p.Pro4Thr		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	41	0.07	3	NM_001271989	17	0.00	0	B0YJB2|B4DXG5|B4DZW1|Q658N5|Q9H9U7	Missense_Mutation	SNP	ENST00000262127.2	37	CCDS11861.1	.	.	.	.	.	.	.	.	.	.	g	19.39	3.818856	0.71028	.	.	ENSG00000101624	ENST00000262127;ENST00000423709	T;D	0.84298	-1.41;-1.83	4.6	4.6	0.57074	.	0.056326	0.64402	D	0.000001	D	0.88757	0.6523	M	0.62723	1.935	0.80722	D	1	D;P;P	0.63046	0.992;0.72;0.72	P;B;B	0.57620	0.824;0.26;0.26	D	0.89149	0.3522	10	0.52906	T	0.07	-25.8824	14.1942	0.65659	0.0:0.1503:0.8497:0.0	.	4;4;4	B4DP81;Q8TAP6-2;Q8TAP6	.;.;CEP76_HUMAN	T	4	ENSP00000262127:P4T;ENSP00000403074:P4T	ENSP00000262127:P4T	P	-	1	0	CEP76	12692538	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	6.412000	0.73303	2.394000	0.81467	0.450000	0.29827	CCT			0.692	CEP76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000254611.1		NM_024899	
LOC644669	644669	broad.mit.edu	37	18	15326266	15326284	+	RNA	DEL	ACCTTCTAGCTATCACTTA	ACCTTCTAGCTATCACTTA	-	rs367979780|rs200349884		TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	ACCTTCTAGCTATCACTTA	ACCTTCTAGCTATCACTTA					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr18:15326266_15326284delACCTTCTAGCTATCACTTA	ENST00000455308.2	-	0	198					NR_027417.1																						aaagtctttcaccttctagctatcacttaacctttctgt	0.374																																					.													.	.			0			.																																											0	.			TCTTTCACCTTCT																													18.37:g.15326266_15326284delACCTTCTAGCTATCACTTA			Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	6	0.33	2	.	0		0		RNA	DEL	ENST00000455308.2	37																																																																																						0.374	AP005901.1-001	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000373635.1			
ILF3	3609	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	19	10798137	10798137	+	Silent	SNP	G	G	A			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr19:10798137G>A	ENST00000590261.1	+	17	2175	c.2175G>A	c.(2173-2175)ccG>ccA	p.P725P	ILF3_ENST00000318511.3_Silent_p.P725P|ILF3_ENST00000588657.1_Silent_p.P729P|ILF3_ENST00000449870.1_Silent_p.P729P			Q12906	ILF3_HUMAN	interleukin enhancer binding factor 3, 90kDa	725	Interaction with PRMT1.				defense response to virus (GO:0051607)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|negative regulation of viral genome replication (GO:0045071)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	31			Epithelial(33;6.86e-06)|all cancers(31;1.65e-05)			ACAACTCACCGGTGCCCCCAA	0.662																																					p.P729P													.	.			0			c.G2187A												31.0	31.0	31.0					19																	10798137		2202	4299	6501	SO:0001819	synonymous_variant	3609	exon18			CTCACCGGTGCCC	U10324	CCDS12246.1, CCDS12247.1, CCDS45965.1, CCDS45966.1, CCDS45967.1	19p13.2	2012-08-10	2002-08-29		ENSG00000129351	ENSG00000129351			6038	protein-coding gene	gene with protein product	"""M-phase phosphoprotein 4"""	603182	"""interleukin enhancer binding factor 3, 90kD"""			7519613, 8885239	Standard	NM_012218		Approved	NF90, MPHOSPH4, MPP4, DRBP76, NFAR-1	uc002mpo.3	Q12906		ENST00000590261.1:c.2175G>A	19.37:g.10798137G>A			Somatic	117	0	0		WXS	Illumina HiSeq	.	114	0.12	14	NM_017620	315	0.21	67	A8K6F2|G5E9M5|O43409|Q6P1X1|Q86XY7|Q99544|Q99545|Q9BZH4|Q9BZH5|Q9NQ95|Q9NQ96|Q9NQ97|Q9NQ98|Q9NQ99|Q9NQA0|Q9NQA1|Q9NQA2|Q9NRN2|Q9NRN3|Q9NRN4|Q9UMZ9|Q9UN00|Q9UN84|Q9UNA2	Silent	SNP	ENST00000590261.1	37	CCDS12246.1																																																																																					0.662	ILF3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000452074.1			
RGL3	57139	mdanderson.org	37	19	11512712	11512712	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr19:11512712G>T	ENST00000380456.3	-	13	1522	c.1459C>A	c.(1459-1461)Cag>Aag	p.Q487K	RGL3_ENST00000393423.3_Missense_Mutation_p.Q487K	NM_001035223.2|NM_001161616.1	NP_001030300.2|NP_001155088.1	Q3MIN7	RGL3_HUMAN	ral guanine nucleotide dissociation stimulator-like 3	487	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	Ral guanyl-nucleotide exchange factor activity (GO:0008321)			breast(1)|endometrium(4)|large_intestine(2)|lung(9)|ovary(1)|skin(1)	18						AGCTGGTTCTGGGCATGCAGG	0.657																																					p.Q487K	GBM(174;751 2067 17998 27979 33959)												.	.			0			c.C1459A												39.0	44.0	42.0					19																	11512712		2202	4300	6502	SO:0001583	missense	57139	exon13			GGTTCTGGGCATG	BC014426	CCDS32910.1, CCDS54221.1	19p13.2	2008-02-05				ENSG00000205517			30282	protein-coding gene	gene with protein product						10869344	Standard	NM_001035223		Approved	FLJ32585	uc002mro.2	Q3MIN7		ENST00000380456.3:c.1459C>A	19.37:g.11512712G>T	ENSP00000369823:p.Gln487Lys		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	45	0.07	3	NM_001035223	8	0.00	0	B5ME84|B7ZL22|Q0P6G0	Missense_Mutation	SNP	ENST00000380456.3	37	CCDS32910.1	.	.	.	.	.	.	.	.	.	.	G	17.07	3.295824	0.60086	.	.	ENSG00000205517	ENST00000342684;ENST00000393423;ENST00000380456	T;T	0.29917	1.55;1.55	4.6	4.6	0.57074	Guanine-nucleotide dissociation stimulator CDC25 (3);Ras guanine nucleotide exchange factor, domain (1);	0.378995	0.30126	N	0.010357	T	0.32436	0.0829	L	0.49778	1.585	0.46078	D	0.998856	P;P;P;P	0.49447	0.787;0.924;0.787;0.836	B;B;B;B	0.42188	0.379;0.344;0.379;0.325	T	0.24693	-1.0153	10	0.59425	D	0.04	.	16.2327	0.82356	0.0:0.0:1.0:0.0	.	487;487;487;284	Q3MIN7;B5ME84;B7ZL22;Q8TEP0	RGL3_HUMAN;.;.;.	K	284;487;487	ENSP00000377075:Q487K;ENSP00000369823:Q487K	ENSP00000344665:Q284K	Q	-	1	0	RGL3	11373712	1.000000	0.71417	0.989000	0.46669	0.354000	0.29330	6.815000	0.75242	2.119000	0.64992	0.557000	0.71058	CAG			0.657	RGL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000421208.3		XM_290867	
FAM98C	147965	mdanderson.org	37	19	38893809	38893809	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr19:38893809G>T	ENST00000252530.5	+	1	35	c.16G>T	c.(16-18)Gcg>Tcg	p.A6S	FAM98C_ENST00000343358.7_Missense_Mutation_p.A6S|FAM98C_ENST00000588262.1_Missense_Mutation_p.A6S	NM_174905.3	NP_777565.3	Q17RN3	FA98C_HUMAN	family with sequence similarity 98, member C	6										endometrium(2)|large_intestine(3)|lung(6)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	15	all_cancers(60;3.95e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			GGCGGTGAAGGCGGAAGCGTG	0.726																																					p.A6S													.	.			0			c.G16T												13.0	21.0	18.0					19																	38893809		1979	4128	6107	SO:0001583	missense	147965	exon1			GTGAAGGCGGAAG		CCDS42562.1	19q13.2	2008-02-05				ENSG00000130244			27119	protein-coding gene	gene with protein product						12477932	Standard	NM_174905		Approved	FLJ44669	uc002oin.1	Q17RN3		ENST00000252530.5:c.16G>T	19.37:g.38893809G>T	ENSP00000252530:p.Ala6Ser		Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	12	0.25	3	NM_174905	7	0.00	0	A6NMW3|Q66K45	Missense_Mutation	SNP	ENST00000252530.5	37	CCDS42562.1	.	.	.	.	.	.	.	.	.	.	g	17.61	3.431624	0.62844	.	.	ENSG00000130244	ENST00000252530;ENST00000343358	T;T	0.50813	0.77;0.73	3.87	2.73	0.32206	.	.	.	.	.	T	0.26810	0.0656	N	0.19112	0.55	0.09310	N	1	B;B;B	0.33528	0.416;0.035;0.02	B;B;B	0.23018	0.043;0.031;0.014	T	0.04400	-1.0954	9	0.18710	T	0.47	-18.1445	10.5592	0.45135	0.0:0.0:0.8069:0.1931	.	6;6;6	B7ZLI5;Q17RN3-2;Q17RN3	.;.;FA98C_HUMAN	S	6	ENSP00000252530:A6S;ENSP00000340348:A6S	ENSP00000252530:A6S	A	+	1	0	FAM98C	43585649	0.999000	0.42202	0.252000	0.24328	0.439000	0.31926	3.651000	0.54431	2.186000	0.69663	0.437000	0.28790	GCG			0.726	FAM98C-001	KNOWN	basic|CCDS	protein_coding	protein_coding		OTTHUMT00000459222.1		NM_174905	
IL4I1	259307	mdanderson.org	37	19	50393222	50393222	+	Missense_Mutation	SNP	G	G	A			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr19:50393222G>A	ENST00000391826.2	-	8	1551	c.1409C>T	c.(1408-1410)aCg>aTg	p.T470M	IL4I1_ENST00000595948.1_Missense_Mutation_p.T492M|IL4I1_ENST00000341114.3_Missense_Mutation_p.T492M|MIR4750_ENST00000584564.1_RNA	NM_152899.1	NP_690863.1	Q96RQ9	OXLA_HUMAN	interleukin 4 induced 1	470						extracellular region (GO:0005576)|lysosome (GO:0005764)	L-amino-acid oxidase activity (GO:0001716)			endometrium(3)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	16		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00245)|OV - Ovarian serous cystadenocarcinoma(262;0.0169)	Flavin adenine dinucleotide(DB03147)	ATAAGGGACCGTCCAGTCATC	0.672											OREG0025629	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T492M													.	.			0			c.C1475T												30.0	13.0	19.0					19																	50393222		2184	4285	6469	SO:0001583	missense	259307	exon10			GGGACCGTCCAGT	AF293462	CCDS12786.1, CCDS12787.1	19q13.3-q13.4	2014-06-26				ENSG00000104951			19094	protein-coding gene	gene with protein product		609742				12031486	Standard	NM_152899		Approved	FIG1	uc002pqt.1	Q96RQ9		ENST00000391826.2:c.1409C>T	19.37:g.50393222G>A	ENSP00000375702:p.Thr470Met		Somatic	50	0	0	969	WXS	Illumina HiSeq	Phase_I	51	0.06	3	NM_172374	76	0.00	0	Q1WMJ3|Q4GZN1|Q4GZN2|Q6P2Q3|Q8TEM5|Q96RQ8	Missense_Mutation	SNP	ENST00000391826.2	37	CCDS12787.1	.	.	.	.	.	.	.	.	.	.	G	14.37	2.515532	0.44763	.	.	ENSG00000104951	ENST00000341114;ENST00000391826	D;D	0.92397	-3.03;-3.03	5.22	1.93	0.25924	Amine oxidase (1);	2.131890	0.01530	N	0.018758	D	0.91586	0.7342	L	0.47190	1.495	0.09310	N	1	D;D;D	0.60575	0.986;0.988;0.988	P;P;P	0.49561	0.481;0.615;0.615	T	0.78770	-0.2074	10	0.48119	T	0.1	-14.614	7.0089	0.24851	0.1735:0.1485:0.678:0.0	.	492;492;470	Q96RQ9-2;Q1WMJ3;Q96RQ9	.;.;OXLA_HUMAN	M	492;470	ENSP00000342557:T492M;ENSP00000375702:T470M	ENSP00000342557:T492M	T	-	2	0	IL4I1	55085034	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.060000	0.14342	0.219000	0.20840	-1.268000	0.01426	ACG			0.672	IL4I1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000466413.1			
AC021021.2	0	bcgsc.ca	37	2	6636082	6636082	+	lincRNA	SNP	G	G	T	rs306191		TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr2:6636082G>T	ENST00000436082.1	+	0	0																											GGAGGGCTTCGTTAAACTTCA	0.577																																					.													.	.			0			.																																											0	.			GGCTTCGTTAAAC																													2.37:g.6636082G>T			Somatic	36	0	0		WXS	Illumina HiSeq	Phase_1	42	0.10	4	.	0		0		RNA	SNP	ENST00000436082.1	37																																																																																						0.577	AC021021.2-001	KNOWN	basic|exp_conf	lincRNA	lincRNA		OTTHUMT00000322748.1			
ATL2	64225	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;mdanderson.org	37	2	38527452	38527452	+	Nonsense_Mutation	SNP	G	G	A			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr2:38527452G>A	ENST00000378954.4	-	10	1091	c.1090C>T	c.(1090-1092)Caa>Taa	p.Q364*	ATL2_ENST00000332337.4_Nonsense_Mutation_p.Q346*|ATL2_ENST00000402054.1_Nonsense_Mutation_p.Q193*|ATL2_ENST00000539122.1_Nonsense_Mutation_p.Q193*|ATL2_ENST00000546051.1_Nonsense_Mutation_p.Q193*|ATL2_ENST00000406122.1_Nonsense_Mutation_p.Q193*|ATL2_ENST00000452935.2_Nonsense_Mutation_p.Q346*|ATL2_ENST00000419554.2_Nonsense_Mutation_p.Q364*	NM_001135673.1|NM_022374.2	NP_001129145.1|NP_071769.2	Q8NHH9	ATLA2_HUMAN	atlastin GTPase 2	364					endoplasmic reticulum organization (GO:0007029)|Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	22						TCTTCTCCTTGATAGATTTTG	0.358																																					p.Q364X													.	.			0			c.C1090T												138.0	136.0	137.0					2																	38527452		2203	4300	6503	SO:0001587	stop_gained	64225	exon10			CTCCTTGATAGAT		CCDS1795.1, CCDS46260.1	2p22.3	2008-09-17	2008-09-17	2008-09-17	ENSG00000119787	ENSG00000119787			24047	protein-coding gene	gene with protein product		609368	"""ADP-ribosylation factor-like 6 interacting protein 2"""	ARL6IP2		10508919, 18270207	Standard	NM_022374		Approved		uc002rqq.3	Q8NHH9	OTTHUMG00000102074	ENST00000378954.4:c.1090C>T	2.37:g.38527452G>A	ENSP00000368237:p.Gln364*		Somatic	25	0	0		WXS	Illumina HiSeq	.	24	0.25	6	NM_001135673	46	0.13	6	B7Z1X2|B7Z7X8|Q4ZG30|Q7Z630|Q8NHH8|Q9H5M7	Nonsense_Mutation	SNP	ENST00000378954.4	37	CCDS46260.1	.	.	.	.	.	.	.	.	.	.	G	40	7.956548	0.98580	.	.	ENSG00000119787	ENST00000378954;ENST00000406122;ENST00000402054;ENST00000539122;ENST00000332337;ENST00000419554;ENST00000452935;ENST00000546051	.	.	.	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.18710	T	0.47	-17.3875	18.7695	0.91885	0.0:0.0:1.0:0.0	.	.	.	.	X	364;193;193;193;346;364;346;193	.	ENSP00000333393:Q346X	Q	-	1	0	ATL2	38380956	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.529000	0.98049	2.736000	0.93811	0.655000	0.94253	CAA			0.358	ATL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000219886.2		NM_022374	
ANKRD20A8P	729171	broad.mit.edu	37	2	95514650	95514651	+	RNA	INS	-	-	A			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr2:95514650_95514651insA	ENST00000432432.2	-	0	712				RNU6-1320P_ENST00000390838.1_RNA	NR_040113.1		Q5CZ79	AN20B_HUMAN	ankyrin repeat domain 20 family, member A8, pseudogene																		gactccatctcaaaaaaaaaaa	0.386																																					.													.	.			0			.																																											0	.			CCATCTCAAAAAA			2q11.1	2011-09-16	2010-12-15	2010-12-15	ENSG00000229089	ENSG00000229089			23666	pseudogene	pseudogene			"""ankyrin repeat domain 20B"""	ANKRD20B			Standard	NR_003366		Approved		uc010fhq.2	Q5CZ79	OTTHUMG00000155138		2.37:g.95514661_95514661dupA			Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	8	0.63	5	.	0		0	A6NC18	RNA	INS	ENST00000432432.2	37																																																																																						0.386	ANKRD20A8P-002	KNOWN	not_best_in_genome_evidence|basic	processed_transcript	pseudogene		OTTHUMT00000451404.1			
TMEM182	130827	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	2	103380804	103380804	+	Silent	SNP	C	C	G			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr2:103380804C>G	ENST00000412401.2	+	3	454	c.249C>G	c.(247-249)tcC>tcG	p.S83S	TMEM182_ENST00000409173.1_Silent_p.S40S|TMEM182_ENST00000409528.1_5'UTR|TMEM182_ENST00000486293.1_3'UTR	NM_144632.3	NP_653233.3	Q6ZP80	TM182_HUMAN	transmembrane protein 182	83						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)	11						AGCCACCGTCCAAGAACTGCA	0.473																																					p.S83S													.	.			0			c.C249G												173.0	132.0	146.0					2																	103380804		2203	4300	6503	SO:0001819	synonymous_variant	130827	exon3			ACCGTCCAAGAAC	AK054856	CCDS2064.1	2q12.1	2009-08-25			ENSG00000170417	ENSG00000170417			26391	protein-coding gene	gene with protein product						12477932	Standard	NM_144632		Approved	FLJ30294	uc010fjb.3	Q6ZP80	OTTHUMG00000130779	ENST00000412401.2:c.249C>G	2.37:g.103380804C>G			Somatic	100	0	0		WXS	Illumina HiSeq	.	88	0.34	30	NM_144632	20	0.30	6	C9JML7|Q3B7B8|Q53TT9|Q6GMU0|Q8WW45|Q96NR4	Silent	SNP	ENST00000412401.2	37	CCDS2064.1																																																																																					0.473	TMEM182-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000253293.1		NM_144632	
KCNE4	23704	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	2	223918008	223918008	+	Missense_Mutation	SNP	C	C	T			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr2:223918008C>T	ENST00000281830.3	+	2	944	c.613C>T	c.(613-615)Ccc>Tcc	p.P205S	KCNE4_ENST00000488477.2_Intron|KCNE4_ENST00000604125.1_Missense_Mutation_p.P154S			Q8WWG9	KCNE4_HUMAN	potassium voltage-gated channel, Isk-related family, member 4	205						apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)	voltage-gated potassium channel activity (GO:0005249)			large_intestine(2)|lung(5)|ovary(2)|skin(1)	10		Renal(207;0.0183)|Lung NSC(271;0.137)|all_lung(227;0.175)		Epithelial(121;4.48e-11)|all cancers(144;2.88e-08)|Lung(261;0.00688)|LUSC - Lung squamous cell carcinoma(224;0.008)		CTCGGAGACGCCCCTCAACGA	0.637																																					p.P205S													.	.			0			c.C613T												32.0	37.0	36.0					2																	223918008		2203	4296	6499	SO:0001583	missense	23704	exon2			GAGACGCCCCTCA	AY065987	CCDS2456.1, CCDS2456.2	2q36.1	2008-02-05			ENSG00000152049	ENSG00000152049		"""Potassium channels"""	6244	protein-coding gene	gene with protein product		607775				10219239, 12670483	Standard	NM_080671		Approved	MiRP3	uc002vnl.5	Q8WWG9	OTTHUMG00000133161	ENST00000281830.3:c.613C>T	2.37:g.223918008C>T	ENSP00000281830:p.Pro205Ser		Somatic	92	0	0		WXS	Illumina HiSeq	.	129	0.26	34	NM_080671	39	0.26	10	B7Z275|Q53SM4|Q96CC4	Missense_Mutation	SNP	ENST00000281830.3	37		.	.	.	.	.	.	.	.	.	.	C	11.97	1.796529	0.31777	.	.	ENSG00000152049	ENST00000281830	.	.	.	6.17	6.17	0.99709	.	0.352176	0.30473	N	0.009560	T	0.31544	0.0800	N	0.19112	0.55	0.31552	N	0.6586	B	0.27559	0.181	B	0.22880	0.042	T	0.26121	-1.0112	9	0.16420	T	0.52	-21.0667	13.9957	0.64397	0.0:0.9315:0.0:0.0685	.	154	Q8WWG9	KCNE4_HUMAN	S	154	.	ENSP00000281830:P154S	P	+	1	0	KCNE4	223626252	0.345000	0.24835	1.000000	0.80357	0.737000	0.42083	1.361000	0.34136	2.941000	0.99782	0.655000	0.94253	CCC			0.637	KCNE4-001	KNOWN	basic	protein_coding	protein_coding		OTTHUMT00000330997.2		NM_080671	
TIGD1	200765	broad.mit.edu	37	2	233414313	233414313	+	Missense_Mutation	SNP	T	T	G			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr2:233414313T>G	ENST00000408957.3	-	1	913	c.280A>C	c.(280-282)Acc>Ccc	p.T94P	EIF4E2_ENST00000409394.1_5'Flank|EIF4E2_ENST00000258416.3_5'Flank|EIF4E2_ENST00000409495.1_5'Flank|EIF4E2_ENST00000409514.1_5'Flank|EIF4E2_ENST00000409167.3_5'Flank|EIF4E2_ENST00000409098.1_5'Flank|EIF4E2_ENST00000409322.1_5'Flank|MIR5001_ENST00000580185.1_RNA	NM_145702.1	NP_663748.1	Q96MW7	TIGD1_HUMAN	tigger transposable element derived 1	94	HTH CENPB-type. {ECO:0000255|PROSITE- ProRule:PRU00583}.					nucleus (GO:0005634)	DNA binding (GO:0003677)	p.T94P(1)		endometrium(1)|skin(1)	2		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;2e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000771)|LUSC - Lung squamous cell carcinoma(224;0.00746)|Lung(119;0.00842)|GBM - Glioblastoma multiforme(43;0.233)		ttgcggctggtctgatcttct	0.433																																					p.T94P													TIGD1,NS,carcinoma,0,1	TIGD1	17	1	1	Substitution - Missense(1)	endometrium(1)	c.A280C												3.0	4.0	4.0					2																	233414313		1230	2187	3417	SO:0001583	missense	200765	exon1			GGCTGGTCTGATC		CCDS2495.1	2q37.1	2011-01-17			ENSG00000221944	ENSG00000221944			14523	protein-coding gene	gene with protein product		612972					Standard	NM_145702		Approved	EEYORE	uc002vsy.2	Q96MW7	OTTHUMG00000133260	ENST00000408957.3:c.280A>C	2.37:g.233414313T>G	ENSP00000386186:p.Thr94Pro		Somatic	22	0.1818181818	4		WXS	Illumina HiSeq	Phase_I	25	0.40	10	NM_145702	13	0.31	4	Q6P4D2|Q6PIF9	Missense_Mutation	SNP	ENST00000408957.3	37	CCDS2495.1	.	.	.	.	.	.	.	.	.	.	T	12.48	1.949454	0.34377	.	.	ENSG00000221944	ENST00000408957	T	0.32023	1.47	0.685	0.685	0.18009	Homeodomain-related (1);Pogo transposase / Cenp-B / PDC2, DNA-binding HTH domain (3);Homeodomain-like (1);	.	.	.	.	T	0.46464	0.1394	M	0.80183	2.485	0.21256	N	0.999748	P	0.48407	0.91	P	0.56648	0.803	T	0.28522	-1.0041	8	0.33940	T	0.23	.	.	.	.	.	94	Q96MW7	TIGD1_HUMAN	P	94	ENSP00000386186:T94P	ENSP00000386186:T94P	T	-	1	0	TIGD1	233122557	0.692000	0.27719	0.615000	0.29064	0.610000	0.37248	0.449000	0.21744	0.539000	0.28788	0.528000	0.53228	ACC			0.433	TIGD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000257037.1		NM_145702	
INSM1	3642	broad.mit.edu	37	20	20350192	20350192	+	Frame_Shift_Del	DEL	G	G	-			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr20:20350192delG	ENST00000310227.1	+	1	1428	c.1281delG	c.(1279-1281)gagfs	p.E427fs		NM_002196.2	NP_002187.1	Q01101	INSM1_HUMAN	insulinoma-associated 1	427					adrenal chromaffin cell differentiation (GO:0061104)|cell cycle (GO:0007049)|endocrine pancreas development (GO:0031018)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|noradrenergic neuron development (GO:0003358)|norepinephrine biosynthetic process (GO:0042421)|pancreatic A cell differentiation (GO:0003310)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of cell differentiation (GO:0045597)|positive regulation of neural precursor cell proliferation (GO:2000179)|regulation of gene expression (GO:0010468)|regulation of protein complex assembly (GO:0043254)|sympathetic ganglion development (GO:0061549)|transcription, DNA-templated (GO:0006351)|transdifferentiation (GO:0060290)|type B pancreatic cell development (GO:0003323)|type B pancreatic cell differentiation (GO:0003309)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|cyclin binding (GO:0030332)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			liver(1)|lung(3)|ovary(1)|prostate(1)	6				READ - Rectum adenocarcinoma(2;0.0649)		GCGACGGCGAGGGGGCCGGCG	0.756																																					p.E427fs													.	INSM1	17		0			c.1281delG												4.0	7.0	6.0					20																	20350192		1919	3877	5796	SO:0001589	frameshift_variant	3642	exon1			CGGCGAGGGGGCC		CCDS13143.1	20p11.2	2012-07-10			ENSG00000173404	ENSG00000173404			6090	protein-coding gene	gene with protein product		600010				8188699, 16569215	Standard	NM_002196		Approved	IA-1, IA1	uc002wrx.3	Q01101	OTTHUMG00000032004	ENST00000310227.1:c.1281delG	20.37:g.20350192delG	ENSP00000312631:p.Glu427fs		Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	6	0.33	2	NM_002196	0		0		Frame_Shift_Del	DEL	ENST00000310227.1	37	CCDS13143.1																																																																																					0.756	INSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000078223.1		NM_002196	
BCRP7	100133163	broad.mit.edu	37	22	18843613	18843613	+	Intron	DEL	G	G	-	rs201642685	byFrequency	TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr22:18843613delG	ENST00000412938.1	+	4	2337																											AGGAGAGGCAGGGGCGGGGGT	0.622													gggg|GGGG|GGG|deletion	680	0.135783	0.2247	0.0994	5008	,	,		26818	0.003		0.1948	False		,,,				2504	0.1176				.													.	.			0			.																																									SO:0001627	intron_variant	0	.			GAGGCAGGGGCGG																												ENST00000412938.1:c.2337+182G>-	22.37:g.18843613delG			Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	16	0.19	3	.	1	0.00	0		RNA	DEL	ENST00000412938.1	37																																																																																						0.622	AC008132.13-002	KNOWN	basic	processed_transcript	protein_coding		OTTHUMT00000471615.1			
CARD10	29775	mdanderson.org	37	22	37912202	37912202	+	Silent	SNP	G	G	T			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr22:37912202G>T	ENST00000403299.1	-	4	693	c.477C>A	c.(475-477)gcC>gcA	p.A159A	CARD10_ENST00000251973.5_Silent_p.A159A|CARD10_ENST00000494166.1_5'Flank			Q9BWT7	CAR10_HUMAN	caspase recruitment domain family, member 10	159					activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein complex assembly (GO:0006461)|regulation of apoptotic process (GO:0042981)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)	receptor signaling complex scaffold activity (GO:0030159)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	17	Melanoma(58;0.0574)					CCCGGCCCCGGGCCTGCAGTT	0.701																																					p.A159A													.	.			0			c.C477A																																									SO:0001819	synonymous_variant	29775	exon3			GCCCCGGGCCTGC	AF086324	CCDS13948.1	22q13.1	2008-05-22			ENSG00000100065	ENSG00000100065			16422	protein-coding gene	gene with protein product		607209				11259443, 11356195	Standard	NM_014550		Approved	CARMA3, BIMP1	uc003asu.1	Q9BWT7	OTTHUMG00000150592	ENST00000403299.1:c.477C>A	22.37:g.37912202G>T			Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	42	0.07	3	NM_014550	31	0.00	0	Q14CQ8|Q5TFG6|Q8NC81|Q9UGR5|Q9UGR6|Q9Y3H0	Silent	SNP	ENST00000403299.1	37	CCDS13948.1																																																																																					0.701	CARD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000318997.1		NM_014550	
TSEN2	80746	broad.mit.edu	37	3	12544861	12544861	+	Nonsense_Mutation	SNP	G	G	T			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr3:12544861G>T	ENST00000284995.6	+	5	796	c.409G>T	c.(409-411)Gag>Tag	p.E137*	TSEN2_ENST00000402228.3_Nonsense_Mutation_p.E137*|RNU6-404P_ENST00000515968.1_RNA|TSEN2_ENST00000454502.2_Nonsense_Mutation_p.E137*|TSEN2_ENST00000415684.1_Nonsense_Mutation_p.E137*|TSEN2_ENST00000444864.1_Nonsense_Mutation_p.E137*|TSEN2_ENST00000383797.5_Nonsense_Mutation_p.E137*|TSEN2_ENST00000314571.7_Nonsense_Mutation_p.E137*	NM_025265.3	NP_079541.1	Q8NCE0	SEN2_HUMAN	TSEN2 tRNA splicing endonuclease subunit	137					mRNA processing (GO:0006397)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|tRNA-intron endonuclease complex (GO:0000214)	lyase activity (GO:0016829)|nucleic acid binding (GO:0003676)|tRNA-intron endonuclease activity (GO:0000213)			central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(7)	19						GAAACCGCTTGAGCATCCTCC	0.512																																					p.E137X													.	TSEN2	46		0			c.G409T												108.0	100.0	103.0					3																	12544861		2203	4300	6503	SO:0001587	stop_gained	80746	exon5			CCGCTTGAGCATC	BC019582	CCDS2611.1, CCDS46757.1, CCDS46758.1, CCDS46759.1	3p25.2	2013-08-06	2013-08-06		ENSG00000154743	ENSG00000154743		"""tRNA splicing endonuclease subunits"""	28422	protein-coding gene	gene with protein product		608753	"""tRNA splicing endonuclease 2 homolog (SEN2, S. cerevisiae)"", ""tRNA splicing endonuclease 2 homolog (S. cerevisiae)"""			15109492	Standard	NM_025265		Approved	SEN2, SEN2L, MGC2776	uc003bxb.3	Q8NCE0	OTTHUMG00000129765	ENST00000284995.6:c.409G>T	3.37:g.12544861G>T	ENSP00000284995:p.Glu137*		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	106	0.04	4	NM_001145394	32	0.00	0	B7Z6K1|C9IZI7|G5E9Q3|Q8WTW7|Q9BPU7	Nonsense_Mutation	SNP	ENST00000284995.6	37	CCDS2611.1	.	.	.	.	.	.	.	.	.	.	G	37	6.005520	0.97195	.	.	ENSG00000154743	ENST00000446004;ENST00000314571;ENST00000454502;ENST00000383797;ENST00000402228;ENST00000284995;ENST00000444864;ENST00000537959;ENST00000415684	.	.	.	4.4	1.44	0.22558	.	0.375032	0.27172	N	0.020585	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-13.727	12.1571	0.54083	0.0:0.5158:0.4842:0.0	.	.	.	.	X	137;137;137;137;137;137;137;110;137	.	ENSP00000284995:E137X	E	+	1	0	TSEN2	12519861	0.000000	0.05858	0.000000	0.03702	0.134000	0.20937	0.194000	0.17135	0.176000	0.19873	0.609000	0.83330	GAG			0.512	TSEN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000251981.1		NM_025265	
NEK10	152110	broad.mit.edu;ucsc.edu	37	3	27157448	27157448	+	Nonsense_Mutation	SNP	G	G	T			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr3:27157448G>T	ENST00000429845.2	-	38	3815	c.3453C>A	c.(3451-3453)taC>taA	p.Y1151*	NEK10_ENST00000383771.4_Nonsense_Mutation_p.Y453*|NEK10_ENST00000383770.3_Nonsense_Mutation_p.Y406*|NEK10_ENST00000295720.6_Nonsense_Mutation_p.Y463*			Q6ZWH5	NEK10_HUMAN	NIMA-related kinase 10	1151					positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein autophosphorylation (GO:0031954)|protein phosphorylation (GO:0006468)|regulation of cell cycle G2/M phase transition (GO:1902749)|regulation of ERK1 and ERK2 cascade (GO:0070372)	protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						ATGTAAAATTGTAATAGCCAC	0.303																																					.													.	.			0			.												69.0	70.0	70.0					3																	27157448		2203	4298	6501	SO:0001587	stop_gained	152110	.			AAAATTGTAATAG	AK123061, AK057247	CCDS46781.1	3p24.1	2012-11-15	2012-11-15		ENSG00000163491	ENSG00000163491			18592	protein-coding gene	gene with protein product			"""NIMA (never in mitosis gene a)- related kinase 10"""			15289607	Standard	NM_199347		Approved	FLJ32685	uc003cdt.2	Q6ZWH5	OTTHUMG00000130571	ENST00000429845.2:c.3453C>A	3.37:g.27157448G>T	ENSP00000395849:p.Tyr1151*		Somatic	431	0.0023201856	1		WXS	Illumina HiSeq	Phase_I	344	0.37	126	.	2	0.50	1	A8MWG1|B9ZVR0|Q45VJ4|Q6ZR11|Q7Z671|Q86XB1|Q96MB3	Nonsense_Mutation	SNP	ENST00000429845.2	37		.	.	.	.	.	.	.	.	.	.	G	44	10.816970	0.99472	.	.	ENSG00000163491	ENST00000295720;ENST00000383771;ENST00000383770	.	.	.	5.73	3.94	0.45596	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.378	0.44094	0.1592:0.0:0.8408:0.0	.	.	.	.	X	463;453;406	.	ENSP00000295720:Y463X	Y	-	3	2	NEK10	27132452	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.046000	0.30354	0.876000	0.35872	0.655000	0.94253	TAC			0.303	NEK10-016	NOVEL	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000438156.1		NM_152534	
CMTM6	54918	mdanderson.org	37	3	32544117	32544117	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr3:32544117G>T	ENST00000205636.3	-	1	783	c.121C>A	c.(121-123)Ctc>Atc	p.L41I		NM_017801.2	NP_060271.1	Q9NX76	CKLF6_HUMAN	CKLF-like MARVEL transmembrane domain containing 6	41	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				chemotaxis (GO:0006935)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|endometrium(1)	2						AAGCCCTTGAGAACGCGCCGG	0.726																																					p.L41I													.	.			0			c.C121A												7.0	10.0	9.0					3																	32544117		2166	4243	6409	SO:0001583	missense	54918	exon1			CCTTGAGAACGCG	AK000403	CCDS2653.1	3p22.2	2006-08-25	2005-11-08	2005-11-08	ENSG00000091317	ENSG00000091317			19177	protein-coding gene	gene with protein product		607889	"""chemokine-like factor super family 6"", ""chemokine-like factor superfamily 6"""	CKLFSF6			Standard	NM_017801		Approved	FLJ20396	uc003cfa.1	Q9NX76	OTTHUMG00000130747	ENST00000205636.3:c.121C>A	3.37:g.32544117G>T	ENSP00000205636:p.Leu41Ile		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	23	0.13	3	NM_017801	40	0.00	0	Q6IAC4	Missense_Mutation	SNP	ENST00000205636.3	37	CCDS2653.1	.	.	.	.	.	.	.	.	.	.	G	16.84	3.233909	0.58886	.	.	ENSG00000091317	ENST00000205636	T	0.34275	1.37	4.64	-2.03	0.07365	Marvel (1);MARVEL-like domain (1);	0.373415	0.26241	N	0.025515	T	0.22704	0.0548	L	0.46157	1.445	0.09310	N	1	B	0.06786	0.001	B	0.17098	0.017	T	0.13469	-1.0508	10	0.52906	T	0.07	.	1.3014	0.02080	0.3629:0.1388:0.3565:0.1418	.	41	Q9NX76	CKLF6_HUMAN	I	41	ENSP00000205636:L41I	ENSP00000205636:L41I	L	-	1	0	CMTM6	32519121	.	.	0.001000	0.08648	0.713000	0.41058	.	.	-0.561000	0.06094	0.467000	0.42956	CTC			0.726	CMTM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000253247.1			
VPS8	23355	mdanderson.org	37	3	184682325	184682325	+	Missense_Mutation	SNP	G	G	T	rs373762204		TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr3:184682325G>T	ENST00000437079.3	+	38	3424	c.3253G>T	c.(3253-3255)Gcc>Tcc	p.A1085S	VPS8_ENST00000436792.2_Missense_Mutation_p.A1083S|VPS8_ENST00000446204.2_Missense_Mutation_p.A993S|VPS8_ENST00000287546.4_Missense_Mutation_p.A1085S	NM_001009921.2	NP_001009921.1	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog (S. cerevisiae)	1085							zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	54	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)			TATTCATGGTGCCTTCCTAAT	0.289																																					p.A1085S													.	.			0			c.G3253T												93.0	93.0	93.0					3																	184682325		1691	3679	5370	SO:0001583	missense	23355	exon37			CATGGTGCCTTCC	AK056661	CCDS46972.1	3q27.2	2006-07-07	2006-07-07	2006-07-07	ENSG00000156931	ENSG00000156931			29122	protein-coding gene	gene with protein product			"""KIAA0804"""	KIAA0804		9872452	Standard	NM_001009921		Approved	FLJ32099	uc003fpb.1	Q8N3P4	OTTHUMG00000156707	ENST00000437079.3:c.3253G>T	3.37:g.184682325G>T	ENSP00000397879:p.Ala1085Ser		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	52	0.06	3	NM_001009921	18	0.00	0	A8K8Q8|B9EIQ1|C9JB61|O94896|Q63HP2|Q9BVP9|Q9H9B0	Missense_Mutation	SNP	ENST00000437079.3	37	CCDS46971.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.593592	0.86953	.	.	ENSG00000156931	ENST00000287546;ENST00000437079;ENST00000436792;ENST00000446204	T;T;T;T	0.36520	1.25;1.25;1.25;1.26	5.8	5.8	0.92144	Quinonprotein alcohol dehydrogenase-like (1);	0.000000	0.85682	D	0.000000	T	0.63628	0.2527	M	0.81614	2.55	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;1.0;0.998	T	0.64892	-0.6300	10	0.54805	T	0.06	-0.8454	16.9805	0.86326	0.0:0.0:1.0:0.0	.	1085;993;1083	Q8N3P4;Q8N3P4-2;Q8N3P4-3	VPS8_HUMAN;.;.	S	1085;1085;1083;993	ENSP00000287546:A1085S;ENSP00000397879:A1085S;ENSP00000404704:A1083S;ENSP00000405483:A993S	ENSP00000287546:A1085S	A	+	1	0	VPS8	186165019	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.718000	0.74713	2.751000	0.94390	0.650000	0.86243	GCC			0.289	VPS8-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				NM_015303	
DGKQ	1609	mdanderson.org	37	4	960807	960807	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr4:960807G>T	ENST00000273814.3	-	10	1329	c.1256C>A	c.(1255-1257)cCg>cAg	p.P419Q	DGKQ_ENST00000502309.1_5'UTR	NM_001347.3	NP_001338.2	P52824	DGKQ_HUMAN	diacylglycerol kinase, theta 110kDa	419	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				blood coagulation (GO:0007596)|cAMP-mediated signaling (GO:0019933)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|protein kinase C signaling (GO:0070528)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to ATP (GO:0033198)|thrombin receptor signaling pathway (GO:0070493)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|kinase binding (GO:0019900)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|phospholipase binding (GO:0043274)			breast(1)|endometrium(2)|kidney(2)|lung(2)|prostate(2)	9			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			CGTGCTCTTCGGGGTCACTCG	0.721																																					p.P419Q	Esophageal Squamous(17;537 645 4447 26373)												.	.			0			c.C1256A												19.0	23.0	22.0					4																	960807		2157	4251	6408	SO:0001583	missense	1609	exon10			CTCTTCGGGGTCA	L38707	CCDS3342.1	4p16.3	2008-08-29	2002-08-29		ENSG00000145214	ENSG00000145214			2856	protein-coding gene	gene with protein product		601207	"""diacylglycerol kinase, theta (110kD)"""	DAGK4		8617502, 9099683	Standard	NM_001347		Approved	DAGK, DAGK7	uc003gbw.4	P52824	OTTHUMG00000088629	ENST00000273814.3:c.1256C>A	4.37:g.960807G>T	ENSP00000273814:p.Pro419Gln		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	26	0.08	2	NM_001347	12	0.00	0	Q6P3W4	Missense_Mutation	SNP	ENST00000273814.3	37	CCDS3342.1	.	.	.	.	.	.	.	.	.	.	G	1.407	-0.576566	0.03854	.	.	ENSG00000145214	ENST00000273814	T	0.17528	2.27	3.77	2.04	0.26737	Ras-association (3);	0.542144	0.18633	N	0.135529	T	0.11196	0.0273	L	0.40543	1.245	0.09310	N	1	P;P	0.41624	0.757;0.757	B;B	0.38264	0.209;0.269	T	0.17501	-1.0367	10	0.20519	T	0.43	.	5.7679	0.18237	0.2432:0.0:0.7568:0.0	.	419;419	E9KL49;P52824	.;DGKQ_HUMAN	Q	419	ENSP00000273814:P419Q	ENSP00000273814:P419Q	P	-	2	0	DGKQ	950807	0.000000	0.05858	0.005000	0.12908	0.002000	0.02628	-1.170000	0.03118	0.583000	0.29574	-0.142000	0.14014	CCG			0.721	DGKQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000200888.1			
HGFAC	3083	broad.mit.edu	37	4	3443798	3443800	+	In_Frame_Del	DEL	CTG	CTG	-	rs372137428		TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	CTG	CTG					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr4:3443798_3443800delCTG	ENST00000382774.3	+	1	185_187	c.70_72delCTG	c.(70-72)ctgdel	p.L29del	HGFAC_ENST00000511533.1_In_Frame_Del_p.L29del	NM_001528.2	NP_001519.1	Q04756	HGFA_HUMAN	HGF activator	29					proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|rough endoplasmic reticulum (GO:0005791)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		CCTCCTCCTCCTGCTGCTGCTGC	0.714																																					p.24_24del													.	HGFAC	69		0			c.70_72del									1,155,2800		0,0,1,8,139,1330						2.2	1.0			15	2,247,5979		0,0,2,8,231,2873	no	codingComplex	HGFAC	NM_001528.2		0,0,3,16,370,4203	A1A1,A1A2,A1R,A2A2,A2R,RR		3.9981,5.2774,4.4098				3,402,8779				SO:0001651	inframe_deletion	3083	exon1			CTCCTCCTGCTGC	D14012	CCDS3369.1, CCDS75098.1	4p16	2008-02-07			ENSG00000109758	ENSG00000109758	3.4.21.-		4894	protein-coding gene	gene with protein product		604552				7683665, 8226803	Standard	XM_005247966		Approved	HGFAP, HGFA	uc003ghc.3	Q04756	OTTHUMG00000090281	ENST00000382774.3:c.70_72delCTG	4.37:g.3443807_3443809delCTG	ENSP00000372224:p.Leu29del		Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	6	0.33	2	NM_001528	0		0	Q14726|Q2M1W7|Q53X47	In_Frame_Del	DEL	ENST00000382774.3	37	CCDS3369.1																																																																																					0.714	HGFAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000206607.3			
KIAA1109	84162	bcgsc.ca;mdanderson.org	37	4	123120533	123120533	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr4:123120533G>T	ENST00000264501.4	+	14	1681	c.1308G>T	c.(1306-1308)aaG>aaT	p.K436N	KIAA1109_ENST00000495260.1_3'UTR|KIAA1109_ENST00000388738.3_Missense_Mutation_p.K436N|KIAA1109_ENST00000455637.1_Missense_Mutation_p.K436N			Q2LD37	K1109_HUMAN	KIAA1109	436					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						CTGCTATTAAGGGACAACTCT	0.363																																					p.K436N													.	KIAA1109	424		0			c.G1308T												191.0	161.0	171.0					4																	123120533		1848	4090	5938	SO:0001583	missense	84162	exon12			TATTAAGGGACAA	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"""fragile site-associated"""	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.1308G>T	4.37:g.123120533G>T	ENSP00000264501:p.Lys436Asn		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_1	72	0.07	5	NM_015312	5	0.00	0	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	37	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.23|18.23	3.578374|3.578374	0.65878|0.65878	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000424425|ENST00000264501;ENST00000388738;ENST00000455637	.|D;D;D	.|0.94184	.|-3.37;-3.37;-3.37	5.53|5.53	4.35|4.35	0.52113|0.52113	.|.	.|0.958552	.|0.08596	.|N	.|0.922248	D|D	0.95166|0.95166	0.8433|0.8433	L|L	0.48642|0.48642	1.525|1.525	0.54753|0.54753	D|D	0.999981|0.999981	.|D	.|0.71674	.|0.998	.|D	.|0.76071	.|0.987	D|D	0.89203|0.89203	0.3559|0.3559	5|10	.|0.41790	.|T	.|0.15	.|.	11.2948|11.2948	0.49272|0.49272	0.9285:0.0:0.0715:0.0|0.9285:0.0:0.0715:0.0	.|.	.|436	.|Q2LD37	.|K1109_HUMAN	W|N	269|436	.|ENSP00000264501:K436N;ENSP00000373390:K436N;ENSP00000389925:K436N	.|ENSP00000264501:K436N	G|K	+|+	1|3	0|2	KIAA1109|KIAA1109	123339983|123339983	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.981000|0.981000	0.71138|0.71138	5.194000|5.194000	0.65125|0.65125	0.956000|0.956000	0.37904|0.37904	-0.312000|-0.312000	0.09012|0.09012	GGG|AAG			0.363	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000316415.1		NM_020797	
ZDHHC11	79844	ucsc.edu	37	5	840644	840644	+	Missense_Mutation	SNP	G	G	C	rs200038670		TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr5:840644G>C	ENST00000283441.8	-	5	1133	c.750C>G	c.(748-750)caC>caG	p.H250Q	ZDHHC11_ENST00000503758.2_5'UTR|ZDHHC11_ENST00000511539.1_Missense_Mutation_p.H37Q|ZDHHC11_ENST00000424784.2_Missense_Mutation_p.H250Q	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	250						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)	p.H250Q(2)		haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(10)|pancreas(1)|prostate(5)|skin(2)|urinary_tract(1)	21			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)			GCTGGCCCAGGTGCACCAAGC	0.602																																					p.H250Q													.	ZDHHC11	97		2	Substitution - Missense(2)	lung(2)	c.C750G												137.0	146.0	143.0					5																	840644		2203	4300	6503	SO:0001583	missense	79844	exon5			GCCCAGGTGCACC	AK023215	CCDS3857.1	5p15.2	2011-02-09			ENSG00000188818	ENSG00000188818		"""Zinc fingers, DHHC-type"""	19158	protein-coding gene	gene with protein product							Standard	NM_024786		Approved	ZNF399, FLJ13153	uc011cma.1	Q9H8X9	OTTHUMG00000090319	ENST00000283441.8:c.750C>G	5.37:g.840644G>C	ENSP00000283441:p.His250Gln		Somatic	34	0.0294117647	1		WXS	Illumina HiSeq		28	0.21	6	NM_024786	6	0.33	2	Q6UWR9	Missense_Mutation	SNP	ENST00000283441.8	37	CCDS3857.1	.	.	.	.	.	.	.	.	.	.	g	5.277	0.236438	0.10023	.	.	ENSG00000188818	ENST00000424784;ENST00000283441;ENST00000511193;ENST00000511539	T;T;T;T	0.43688	1.86;1.86;0.99;0.94	2.74	-0.394	0.12434	.	642.914000	0.00961	U	0.003101	T	0.25494	0.0620	N	0.03608	-0.345	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.15870	0.014;0.001	T	0.27606	-1.0069	10	0.29301	T	0.29	-6.9343	13.336	0.60518	0.0:0.2548:0.7452:0.0	.	250;37	Q9H8X9;Q6UWR9	ZDH11_HUMAN;.	Q	250;250;25;37	ENSP00000397719:H250Q;ENSP00000283441:H250Q;ENSP00000426873:H25Q;ENSP00000427067:H37Q	ENSP00000283441:H250Q	H	-	3	2	ZDHHC11	893644	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.474000	0.06607	-0.110000	0.12022	-2.048000	0.00412	CAC			0.602	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000206681.3		NM_024786	
ZDHHC11	79844	ucsc.edu	37	5	840704	840704	+	Silent	SNP	G	G	A	rs139300052	byFrequency	TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr5:840704G>A	ENST00000283441.8	-	5	1073	c.690C>T	c.(688-690)acC>acT	p.T230T	ZDHHC11_ENST00000503758.2_5'UTR|ZDHHC11_ENST00000511539.1_Silent_p.T17T|ZDHHC11_ENST00000424784.2_Silent_p.T230T	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	230						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(10)|pancreas(1)|prostate(5)|skin(2)|urinary_tract(1)	21			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)			CGACTATCAGGGTCTGCACCT	0.567													G|||	34	0.00678914	0.0083	0.0	5008	,	,		28789	0.0208		0.002	False		,,,				2504	0.0				p.T230T													.	ZDHHC11	97		0			c.C690T												237.0	270.0	258.0					5																	840704		2203	4300	6503	SO:0001819	synonymous_variant	79844	exon5			TATCAGGGTCTGC	AK023215	CCDS3857.1	5p15.2	2011-02-09			ENSG00000188818	ENSG00000188818		"""Zinc fingers, DHHC-type"""	19158	protein-coding gene	gene with protein product							Standard	NM_024786		Approved	ZNF399, FLJ13153	uc011cma.1	Q9H8X9	OTTHUMG00000090319	ENST00000283441.8:c.690C>T	5.37:g.840704G>A			Somatic	36	0.0277777778	1		WXS	Illumina HiSeq		31	0.19	6	NM_024786	2	1.00	2	Q6UWR9	Silent	SNP	ENST00000283441.8	37	CCDS3857.1																																																																																					0.567	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000206681.3		NM_024786	
JARID2	3720	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	6	15374463	15374463	+	Missense_Mutation	SNP	G	G	A			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr6:15374463G>A	ENST00000341776.2	+	2	405	c.161G>A	c.(160-162)gGg>gAg	p.G54E	JARID2_ENST00000397311.3_5'UTR	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	54					central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|liver development (GO:0001889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone methylation (GO:0031061)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K9 methylation (GO:0051574)|spleen development (GO:0048536)|stem cell differentiation (GO:0048863)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	59	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)				GGCATTGCTGGGAGCCTGAAA	0.453																																					p.G54E													.	.			0			c.G161A												134.0	134.0	134.0					6																	15374463		2203	4300	6503	SO:0001583	missense	3720	exon2			TTGCTGGGAGCCT	U57592	CCDS4533.1, CCDS58996.1	6p24-p23	2008-02-05	2006-10-06	2004-01-30	ENSG00000008083	ENSG00000008083			6196	protein-coding gene	gene with protein product		601594	"""jumonji (mouse) homolog"", ""Jumonji, AT rich interactive domain 2"""	JMJ		8894700	Standard	NM_001267040		Approved		uc003nbj.4	Q92833	OTTHUMG00000014293	ENST00000341776.2:c.161G>A	6.37:g.15374463G>A	ENSP00000341280:p.Gly54Glu		Somatic	91	0	0		WXS	Illumina HiSeq	.	102	0.26	27	NM_004973	19	0.37	7	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	Missense_Mutation	SNP	ENST00000341776.2	37	CCDS4533.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.276368	0.80580	.	.	ENSG00000008083	ENST00000341776	T	0.54071	0.59	5.07	5.07	0.68467	.	0.114027	0.64402	D	0.000013	T	0.43144	0.1234	L	0.50333	1.59	0.80722	D	1	P	0.43477	0.808	B	0.42112	0.376	T	0.52719	-0.8538	10	0.72032	D	0.01	-16.7274	18.4912	0.90848	0.0:0.0:1.0:0.0	.	54	Q92833	JARD2_HUMAN	E	54	ENSP00000341280:G54E	ENSP00000341280:G54E	G	+	2	0	JARID2	15482442	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.944000	0.70219	2.368000	0.80403	0.655000	0.94253	GGG			0.453	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000039926.1		NM_004973	
VARS2	57176	bcgsc.ca	37	6	30890754	30890754	+	Splice_Site	SNP	G	G	T			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr6:30890754G>T	ENST00000321897.5	+	22	2817		c.e22+1		VARS2_ENST00000416670.2_Splice_Site|VARS2_ENST00000542001.1_Splice_Site|VARS2_ENST00000541562.1_Splice_Site|VARS2_ENST00000476162.1_Splice_Site			Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial						gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(3)|prostate(3)|skin(4)|urinary_tract(1)	46						GGAGTTCAGGGTAAGCCTGGG	0.607																																					.													.	VARS2	60		0			c.2185+1G>T												75.0	82.0	79.0					6																	30890754		1509	2707	4216	SO:0001630	splice_region_variant	57176	exon23			TTCAGGGTAAGCC	AB067472	CCDS34387.1, CCDS54980.1	6p21.33	2012-10-26	2012-10-26	2007-02-23	ENSG00000137411	ENSG00000137411	6.1.1.9	"""Aminoacyl tRNA synthetases / Class I"""	21642	protein-coding gene	gene with protein product	"""valine tRNA ligase 2, mitochondrial"""	612802	"""valyl-tRNA synthetase 2-like"", ""valyl-tRNA synthetase like"", ""valyl-tRNA synthetase 2, mitochondrial (putative)"""	VARS2L, VARSL		1898367, 11572484, 18400783	Standard	NM_001167734		Approved	DKFZP434L1435, KIAA1885, G7a	uc011dmz.2	Q5ST30	OTTHUMG00000031263	ENST00000321897.5:c.2185+1G>T	6.37:g.30890754G>T			Somatic	92	0.0108695652	1		WXS	Illumina HiSeq	Phase_1	150	0.04	6	NM_020442	0		0	A2ABL7|B4DET4|B4E3P5|F5GXJ0|F5H323|Q2M2A0|Q59FI1|Q5SQ96|Q5SS98|Q6DKJ5|Q6ZV24|Q96GN2|Q96H77|Q96Q02|Q9H6R2|Q9UFH7	Splice_Site	SNP	ENST00000321897.5	37	CCDS34387.1	.	.	.	.	.	.	.	.	.	.	G	16.88	3.244229	0.59103	.	.	ENSG00000137411	ENST00000321897;ENST00000416670;ENST00000542001;ENST00000541562	.	.	.	5.37	5.37	0.77165	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.9531	0.86251	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	VARS2	30998733	1.000000	0.71417	1.000000	0.80357	0.589000	0.36550	8.889000	0.92470	2.686000	0.91538	0.561000	0.74099	.			0.607	VARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000076566.2		NM_020442	Intron
RUNX2	860	mdanderson.org	37	6	45390498	45390498	+	Missense_Mutation	SNP	C	C	A			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr6:45390498C>A	ENST00000371438.1	+	2	585	c.227C>A	c.(226-228)gCg>gAg	p.A76E	RP1-244F24.1_ENST00000606796.1_RNA|RUNX2_ENST00000576263.1_Missense_Mutation_p.A76E|RUNX2_ENST00000352853.5_Missense_Mutation_p.A144E|RUNX2_ENST00000541979.1_Missense_Mutation_p.A144E|RUNX2_ENST00000465038.2_Missense_Mutation_p.A76E|RUNX2_ENST00000371436.6_Missense_Mutation_p.A76E|RUNX2_ENST00000359524.5_Missense_Mutation_p.A62E|RUNX2_ENST00000371432.3_Missense_Mutation_p.A62E	NM_001024630.3	NP_001019801.3	Q13950	RUNX2_HUMAN	runt-related transcription factor 2	76	Poly-Ala.				BMP signaling pathway (GO:0030509)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|chondrocyte development (GO:0002063)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic forelimb morphogenesis (GO:0035115)|endochondral ossification (GO:0001958)|gene expression (GO:0010467)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|osteoblast development (GO:0002076)|osteoblast differentiation (GO:0001649)|osteoblast fate commitment (GO:0002051)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|stem cell differentiation (GO:0048863)|T cell differentiation (GO:0030217)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(18)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						gcggcggcggcggctgcggcg	0.726																																					p.A76E													.	.			0			c.C227A												3.0	6.0	5.0					6																	45390498		1038	2382	3420	SO:0001583	missense	860	exon3			CGGCGGCGGCTGC	AF001450	CCDS43467.1, CCDS43468.1, CCDS43467.2, CCDS43468.2	6p21	2010-08-20			ENSG00000124813	ENSG00000124813			10472	protein-coding gene	gene with protein product		600211		CCD, CBFA1, CCD1		7835892	Standard	NM_001024630		Approved	AML3, PEBP2A1, PEBP2aA1	uc011dvx.2	Q13950	OTTHUMG00000014774	ENST00000371438.1:c.227C>A	6.37:g.45390498C>A	ENSP00000360493:p.Ala76Glu		Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	16	0.13	2	NM_001024630	1	0.00	0	O14614|O14615|O95181	Missense_Mutation	SNP	ENST00000371438.1	37	CCDS43467.2	.	.	.	.	.	.	.	.	.	.	C	7.966	0.748078	0.15710	.	.	ENSG00000124813	ENST00000465038;ENST00000352853;ENST00000541979;ENST00000371438;ENST00000371436;ENST00000359524;ENST00000371432	T;T;T;T;T;T;T	0.78003	-1.14;-1.14;-1.14;-1.14;-1.14;-1.14;-1.14	2.95	2.95	0.34219	.	0.453907	0.16126	N	0.228395	T	0.44726	0.1307	N	0.14661	0.345	0.33802	D	0.626795	B;B;B	0.31837	0.342;0.231;0.342	B;B;B	0.38056	0.264;0.135;0.264	T	0.25433	-1.0132	10	0.10111	T	0.7	.	11.9419	0.52905	0.0:1.0:0.0:0.0	.	144;76;62	F6RGB9;Q13950;Q13950-2	.;RUNX2_HUMAN;.	E	76;144;144;76;76;62;62	ENSP00000420707:A76E;ENSP00000319087:A144E;ENSP00000446290:A144E;ENSP00000360493:A76E;ENSP00000360491:A76E;ENSP00000352514:A62E;ENSP00000360486:A62E	ENSP00000319087:A144E	A	+	2	0	RUNX2	45498476	0.998000	0.40836	0.988000	0.46212	0.871000	0.50021	0.187000	0.16998	1.349000	0.45751	0.407000	0.27541	GCG			0.726	RUNX2-003	KNOWN	not_organism_supported|upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000040755.2		NM_004348	
C6orf165	154313	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	6	88119658	88119658	+	Missense_Mutation	SNP	C	C	G			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr6:88119658C>G	ENST00000507897.1	+	2	184	c.101C>G	c.(100-102)gCt>gGt	p.A34G	C6ORF165_ENST00000369562.4_Missense_Mutation_p.A34G			Q8IYR0	CF165_HUMAN	chromosome 6 open reading frame 165	34										NS(1)|central_nervous_system(1)|large_intestine(5)|lung(8)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0419)		ACTCTGATTGCTTTTATGGTA	0.358																																					p.A34G													.	.			0			c.C101G												127.0	131.0	130.0					6																	88119658		2203	4300	6503	SO:0001583	missense	154313	exon2			TGATTGCTTTTAT	BC035083	CCDS34498.1	6q15	2012-02-07			ENSG00000213204	ENSG00000213204			21405	protein-coding gene	gene with protein product							Standard	NM_001031743		Approved	FLJ25974, dJ382I10.1	uc003plv.3	Q8IYR0	OTTHUMG00000015173	ENST00000507897.1:c.101C>G	6.37:g.88119658C>G	ENSP00000426769:p.Ala34Gly		Somatic	53	0	0		WXS	Illumina HiSeq	.	23	0.43	10	NM_001031743	12	0.58	7	A8K969|E1P507|Q8N9U4	Missense_Mutation	SNP	ENST00000507897.1	37	CCDS34498.1	.	.	.	.	.	.	.	.	.	.	C	17.76	3.469569	0.63625	.	.	ENSG00000213204	ENST00000369562;ENST00000480123	T;T	0.37752	1.25;1.18	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	T	0.31231	0.0790	L	0.57536	1.79	0.80722	D	1	P;P	0.49307	0.512;0.922	B;P	0.44518	0.228;0.452	T	0.09185	-1.0686	10	0.44086	T	0.13	.	18.5254	0.90969	0.0:1.0:0.0:0.0	.	34;34	Q8IYR0;E1P509	CF165_HUMAN;.	G	34	ENSP00000358575:A34G;ENSP00000422494:A34G	ENSP00000358575:A34G	A	+	2	0	C6orf165	88176377	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.003000	0.76310	2.521000	0.84997	0.655000	0.94253	GCT			0.358	C6orf165-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding		OTTHUMT00000470406.1		NM_178823	
SERINC1	57515	mdanderson.org	37	6	122773072	122773072	+	Nonsense_Mutation	SNP	G	G	T			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr6:122773072G>T	ENST00000339697.4	-	6	804	c.720C>A	c.(718-720)tgC>tgA	p.C240*		NM_020755.2	NP_065806.1	Q9NRX5	SERC1_HUMAN	serine incorporator 1	240					L-serine transport (GO:0015825)|phosphatidylserine metabolic process (GO:0006658)|phospholipid biosynthetic process (GO:0008654)|positive regulation of transferase activity (GO:0051347)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	L-serine transmembrane transporter activity (GO:0015194)			endometrium(2)|kidney(2)|large_intestine(4)|liver(1)|lung(2)|ovary(1)|skin(1)	13				GBM - Glioblastoma multiforme(226;0.126)		AAGCACCAACGCAGAGGAGCA	0.383																																					p.C240X													.	.			0			c.C720A												97.0	85.0	89.0					6																	122773072		2203	4300	6503	SO:0001587	stop_gained	57515	exon6			ACCAACGCAGAGG	AF087902	CCDS5125.1	6q22.32	2006-02-09	2005-10-14	2005-10-14	ENSG00000111897	ENSG00000111897			13464	protein-coding gene	gene with protein product		614548	"""tumor differentially expressed 2"""	TDE2		10637174	Standard	NM_020755		Approved	TMS-2, TDE1L, KIAA1253	uc003pyy.1	Q9NRX5	OTTHUMG00000015487	ENST00000339697.4:c.720C>A	6.37:g.122773072G>T	ENSP00000342962:p.Cys240*		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	50	0.06	3	NM_020755	201	0.00	0	B3KY69|E1P565|O75655|Q7Z2F5|Q8TAG1|Q9NTH8|Q9ULG7	Nonsense_Mutation	SNP	ENST00000339697.4	37	CCDS5125.1	.	.	.	.	.	.	.	.	.	.	G	35	5.517088	0.96416	.	.	ENSG00000111897	ENST00000339697;ENST00000368454	.	.	.	5.71	3.91	0.45181	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.3065	10.8122	0.46553	0.2584:0.0:0.7416:0.0	.	.	.	.	X	240	.	ENSP00000342962:C240X	C	-	3	2	SERINC1	122814771	1.000000	0.71417	0.993000	0.49108	0.954000	0.61252	3.904000	0.56325	0.740000	0.32651	0.650000	0.86243	TGC			0.383	SERINC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000042031.2		NM_020755	
VNN1	8876	broad.mit.edu;mdanderson.org	37	6	133013412	133013412	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr6:133013412G>T	ENST00000367928.4	-	5	1151	c.1138C>A	c.(1138-1140)Cta>Ata	p.L380I		NM_004666.2	NP_004657.2	O95497	VNN1_HUMAN	vanin 1	380					acute inflammatory response (GO:0002526)|cellular component movement (GO:0006928)|chronic inflammatory response (GO:0002544)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|pantothenate metabolic process (GO:0015939)|positive regulation of T cell differentiation in thymus (GO:0033089)|response to oxidative stress (GO:0006979)|single organismal cell-cell adhesion (GO:0016337)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	GPI anchor binding (GO:0034235)|pantetheine hydrolase activity (GO:0017159)			NS(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)	31	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.0027)|GBM - Glioblastoma multiforme(226;0.0189)		AATGCCCCTAGAGCGTACACT	0.403																																					p.L380I													.	VNN1	69		0			c.C1138A												112.0	107.0	108.0					6																	133013412		2203	4300	6503	SO:0001583	missense	8876	exon5			CCCCTAGAGCGTA	AJ132099	CCDS5159.1	6q23-q24	2013-02-13			ENSG00000112299	ENSG00000112299	3.5.1.92	"""Vanins"""	12705	protein-coding gene	gene with protein product		603570				9790769	Standard	NM_004666		Approved	Tiff66	uc003qdo.3	O95497	OTTHUMG00000015587	ENST00000367928.4:c.1138C>A	6.37:g.133013412G>T	ENSP00000356905:p.Leu380Ile		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	80	0.06	5	NM_004666	1	0.00	0	A8K310|Q4JFW6|Q4VAS7|Q4VAS8|Q4VAS9|Q9UF16|Q9UJF4	Missense_Mutation	SNP	ENST00000367928.4	37	CCDS5159.1	.	.	.	.	.	.	.	.	.	.	G	13.41	2.230367	0.39399	.	.	ENSG00000112299	ENST00000367928	D	0.95853	-3.83	5.7	0.513	0.17000	.	0.212122	0.32175	N	0.006476	D	0.95014	0.8386	M	0.92268	3.29	0.09310	N	1	P	0.47350	0.894	P	0.50860	0.652	D	0.91124	0.4932	10	0.72032	D	0.01	-28.8786	8.0056	0.30323	0.2526:0.1071:0.6404:0.0	.	380	O95497	VNN1_HUMAN	I	380	ENSP00000356905:L380I	ENSP00000356905:L380I	L	-	1	2	VNN1	133055105	0.948000	0.32251	0.038000	0.18304	0.205000	0.24178	1.526000	0.35964	0.322000	0.23283	0.563000	0.77884	CTA			0.403	VNN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000042263.1			
LINC00957	255031	broad.mit.edu	37	7	44080453	44080453	+	lincRNA	SNP	G	G	A	rs116887274	byFrequency	TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr7:44080453G>A	ENST00000441052.1	+	0	1138				RASA4CP_ENST00000446874.1_RNA					long intergenic non-protein coding RNA 957																		CACAGCAGCCGGGACACGGAC	0.677													A|||	706	0.140974	0.2791	0.121	5008	,	,		13459	0.0694		0.1163	False		,,,				2504	0.0675				.													.	.			0			.																																											0	.			GCAGCCGGGACAC	BC014556		7p13	2013-06-04			ENSG00000235314	ENSG00000235314		"""Long non-coding RNAs"""	22332	non-coding RNA	RNA, long non-coding							Standard	NR_015401		Approved				OTTHUMG00000155351		7.37:g.44080453G>A			Somatic	40	0.025	1		WXS	Illumina HiSeq	Phase_I	33	0.24	8	.	1	0.00	0		RNA	SNP	ENST00000441052.1	37																																																																																						0.677	LINC00957-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000339589.1			
MUC17	140453	hgsc.bcm.edu	37	7	100682117	100682117	+	Missense_Mutation	SNP	G	G	A	rs555953599	byFrequency	TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr7:100682117G>A	ENST00000306151.4	+	3	7484	c.7420G>A	c.(7420-7422)Ggc>Agc	p.G2474S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2474	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					TTCTGAGGCTGGCACCCTTTC	0.522													N|||	3	0.000599042	0.0	0.0	5008	,	,		27478	0.0		0.0	False		,,,				2504	0.0031				p.G2474S													MUC17,right_upper_lobe,carcinoma,-2,1	MUC17	-2	1	0			c.G7420A																																									SO:0001583	missense	140453	exon3			GAGGCTGGCACCC	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"""Mucins"""	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.7420G>A	7.37:g.100682117G>A	ENSP00000302716:p.Gly2474Ser		Somatic	82	0	0		WXS	Illumina HiSeq	.	104	0.06	6	NM_001040105	0		0	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	N	2.617	-0.289370	0.05605	.	.	ENSG00000169876	ENST00000306151	T	0.03468	3.92	0.869	-0.297	0.12820	.	.	.	.	.	T	0.01254	0.0041	N	0.02916	-0.46	0.09310	N	1	B	0.27286	0.174	B	0.19148	0.024	T	0.45131	-0.9282	9	0.02654	T	1	.	5.8185	0.18514	0.4085:0.0:0.5915:0.0	.	2474	Q685J3	MUC17_HUMAN	S	2474	ENSP00000302716:G2474S	ENSP00000302716:G2474S	G	+	1	0	MUC17	100468837	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-0.476000	0.06591	-0.655000	0.05387	-1.616000	0.00795	GGC			0.522	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000347161.1		NM_001040105	
EBAG9	9166	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	8	110569202	110569202	+	Silent	SNP	C	C	A			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr8:110569202C>A	ENST00000337573.5	+	5	660	c.360C>A	c.(358-360)atC>atA	p.I120I	EBAG9_ENST00000529502.1_3'UTR|EBAG9_ENST00000531677.1_Silent_p.I120I|EBAG9_ENST00000395785.2_Silent_p.I120I	NM_001278938.1|NM_004215.3	NP_001265867.1|NP_004206.1	O00559	RCAS1_HUMAN	estrogen receptor binding site associated, antigen, 9	120					regulation of cell growth (GO:0001558)	focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)	peptidase activator activity involved in apoptotic process (GO:0016505)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(2)	10			OV - Ovarian serous cystadenocarcinoma(57;1.39e-14)			ATTTTGGCATCCCAGATGGGA	0.343																																					p.I120I													.	.			0			c.C360A												98.0	91.0	93.0					8																	110569202		2203	4299	6502	SO:0001819	synonymous_variant	9166	exon5			TGGCATCCCAGAT	AB007619	CCDS6313.1	8q23	2013-03-07			ENSG00000147654	ENSG00000147654			3123	protein-coding gene	gene with protein product		605772					Standard	NM_004215		Approved	EB9, RCAS1	uc003ynf.3	O00559	OTTHUMG00000165346	ENST00000337573.5:c.360C>A	8.37:g.110569202C>A			Somatic	100	0	0		WXS	Illumina HiSeq	.	158	0.23	37	NM_004215	111	0.23	26	A8K3N6|Q5Y8C7|Q6IB20|Q9BS76	Silent	SNP	ENST00000337573.5	37	CCDS6313.1																																																																																					0.343	EBAG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000383536.1		NM_004215	
ZHX1	11244	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	8	124267671	124267671	+	Silent	SNP	A	A	G			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr8:124267671A>G	ENST00000522655.1	-	3	1056	c.516T>C	c.(514-516)tcT>tcC	p.S172S	ZHX1_ENST00000297857.2_Silent_p.S172S|ZHX1_ENST00000395571.3_Silent_p.S172S|ZHX1_ENST00000522595.1_5'Flank|ZHX1-C8ORF76_ENST00000357082.4_Intron			Q9UKY1	ZHX1_HUMAN	zinc fingers and homeoboxes 1	172					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(37;1.25e-09)|Ovarian(258;0.0154)		STAD - Stomach adenocarcinoma(47;0.00527)			TTCCCGAAGAAGAAACTTCTG	0.338																																					p.S172S													.	.			0			c.T516C												103.0	104.0	104.0					8																	124267671		2203	4300	6503	SO:0001819	synonymous_variant	11244	exon3			CGAAGAAGAAACT	AF106862	CCDS6342.1	8q24.13	2012-03-09	2004-01-23		ENSG00000165156	ENSG00000165156		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	12871	protein-coding gene	gene with protein product		604764	"""zinc-fingers and homeoboxes 1"""			10441475	Standard	NM_001017926		Approved		uc003yqe.3	Q9UKY1	OTTHUMG00000165088	ENST00000522655.1:c.516T>C	8.37:g.124267671A>G			Somatic	74	0	0		WXS	Illumina HiSeq	.	139	0.22	30	NM_007222	21	0.19	4	Q8IWD8	Silent	SNP	ENST00000522655.1	37	CCDS6342.1																																																																																					0.338	ZHX1-003	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding		OTTHUMT00000381759.1			
PPP1R16A	84988	mdanderson.org	37	8	145726559	145726559	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr8:145726559G>T	ENST00000292539.4	+	10	2002	c.1085G>T	c.(1084-1086)cGc>cTc	p.R362L	GPT_ENST00000528431.1_5'Flank|PPP1R16A_ENST00000435887.1_Missense_Mutation_p.R362L|CTD-2517M22.14_ENST00000532766.1_RNA|GPT_ENST00000394955.2_5'Flank|CTD-2517M14.5_ENST00000569326.1_RNA			Q96I34	PP16A_HUMAN	protein phosphatase 1, regulatory subunit 16A	362						plasma membrane (GO:0005886)				NS(1)|endometrium(1)|kidney(2)|lung(3)|prostate(1)	8	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			GACCTGTACCGCAAGCAGCAC	0.697																																					p.R362L													.	.			0			c.G1085T												24.0	25.0	24.0					8																	145726559		2188	4285	6473	SO:0001583	missense	84988	exon9			TGTACCGCAAGCA		CCDS6429.1	8q24.3	2013-01-10	2011-10-04		ENSG00000160972	ENSG00000160972		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	14941	protein-coding gene	gene with protein product		609172	"""protein phosphatase 1, regulatory (inhibitor) subunit 16A"""			11948623	Standard	NM_032902		Approved	MGC14333, MYPT3	uc003zdf.3	Q96I34	OTTHUMG00000165173	ENST00000292539.4:c.1085G>T	8.37:g.145726559G>T	ENSP00000292539:p.Arg362Leu		Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	35	0.09	3	NM_032902	70	0.00	0	D3DWM5	Missense_Mutation	SNP	ENST00000292539.4	37	CCDS6429.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	33|33	5.195103|5.195103	0.94960|0.94960	.|.	.|.	ENSG00000160972|ENSG00000160972	ENST00000528430|ENST00000292539;ENST00000435887	.|T;T	.|0.72394	.|-0.65;-0.65	4.72|4.72	3.78|3.78	0.43462|0.43462	.|.	.|0.062558	.|0.64402	.|D	.|0.000007	T|T	0.81403|0.81403	0.4815|0.4815	M|M	0.73962|0.73962	2.25|2.25	0.53688|0.53688	D|D	0.999979|0.999979	.|D	.|0.89917	.|1.0	.|D	.|0.81914	.|0.995	T|T	0.82123|0.82123	-0.0613|-0.0613	5|10	.|0.51188	.|T	.|0.08	.|.	11.3091|11.3091	0.49353|0.49353	0.0:0.0:0.817:0.183|0.0:0.0:0.817:0.183	.|.	.|362	.|Q96I34	.|PP16A_HUMAN	S|L	30|362	.|ENSP00000292539:R362L;ENSP00000391126:R362L	.|ENSP00000292539:R362L	A|R	+|+	1|2	0|0	PPP1R16A|PPP1R16A	145697367|145697367	0.987000|0.987000	0.35691|0.35691	1.000000|1.000000	0.80357|0.80357	0.961000|0.961000	0.63080|0.63080	3.895000|3.895000	0.56258|0.56258	2.153000|2.153000	0.67306|0.67306	0.462000|0.462000	0.41574|0.41574	GCA|CGC			0.697	PPP1R16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000382459.1		NM_032902	
GPR144	347088	mdanderson.org	37	9	127217258	127217258	+	Missense_Mutation	SNP	G	G	A	rs574266662	byFrequency	TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr9:127217258G>A	ENST00000334810.1	+	7	1301	c.1301G>A	c.(1300-1302)cGc>cAc	p.R434H				Q7Z7M1	GP144_HUMAN	G protein-coupled receptor 144	434					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)	4						GCTGTTGTCCGCTTCCTGAAG	0.672													G|||	2	0.000399361	0.0	0.0	5008	,	,		15749	0.002		0.0	False		,,,				2504	0.0				p.R434H													.	.			0			c.G1301A												33.0	39.0	37.0					9																	127217258		692	1591	2283	SO:0001583	missense	347088	exon7			TTGTCCGCTTCCT	AY278562		9q34.11	2014-08-08			ENSG00000180264	ENSG00000180264		"""-"", ""GPCR / Class B : Orphans"""	18651	protein-coding gene	gene with protein product							Standard	XM_006710216		Approved	PGR24	uc010mwn.3	Q7Z7M1	OTTHUMG00000020652	ENST00000334810.1:c.1301G>A	9.37:g.127217258G>A	ENSP00000335156:p.Arg434His		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	23	0.09	2	NM_001161808	0		0	Q86SL4|Q8NH12	Missense_Mutation	SNP	ENST00000334810.1	37	CCDS48016.1	.	.	.	.	.	.	.	.	.	.	G	0.208	-1.038720	0.02013	.	.	ENSG00000180264	ENST00000334810;ENST00000439837	T	0.47869	0.83	4.99	-1.78	0.07957	.	.	.	.	.	T	0.15522	0.0374	N	0.00707	-1.245	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.29336	-1.0015	9	0.23302	T	0.38	.	9.9041	0.41366	0.5968:0.0:0.4032:0.0	.	434	Q7Z7M1	GP144_HUMAN	H	434;130	ENSP00000335156:R434H	ENSP00000335156:R434H	R	+	2	0	GPR144	126257079	0.000000	0.05858	0.233000	0.24025	0.187000	0.23431	-0.357000	0.07651	-0.234000	0.09782	-0.768000	0.03414	CGC			0.672	GPR144-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000054026.2		NM_182611	
MT-ND2	4536	hgsc.bcm.edu	37	M	4492	4492	+	Missense_Mutation	SNP	T	T	C			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chrM:4492T>C	ENST00000361453.3	+	1	23	c.23T>C	c.(22-24)gTc>gCc	p.V8A	MT-TQ_ENST00000387372.1_RNA|MT-TM_ENST00000387377.1_RNA|MT-TL1_ENST00000386347.1_RNA|MT-CO1_ENST00000361624.2_5'Flank|MT-TC_ENST00000387405.1_RNA|MT-TS1_ENST00000387416.2_RNA|MT-TW_ENST00000387382.1_RNA|MT-TA_ENST00000387392.1_RNA|MT-TI_ENST00000387365.1_RNA|MT-TN_ENST00000387400.1_RNA|MT-RNR1_ENST00000389680.2_RNA|MT-TV_ENST00000387342.1_RNA|MT-RNR2_ENST00000387347.2_RNA|MT-TY_ENST00000387409.1_RNA			P03891	NU2M_HUMAN	mitochondrially encoded NADH dehydrogenase 2	8					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|reactive oxygen species metabolic process (GO:0072593)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|lung(1)	3						GGCCCAACCCGTCATCTACTC	0.458																																					p.V8A													.	.			0			c.T23C																																									SO:0001583	missense	0	exon1			AACCCGTCATCTA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198763	ENSG00000198763	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7456	protein-coding gene	gene with protein product	"""complex I ND2 subunit"", ""NADH-ubiquinone oxidoreductase chain 2"""	516001	"""NADH dehydrogenase 2"""	MTND2			Standard			Approved	ND2, NAD2		P03891		ENST00000361453.3:c.23T>C	M.37:g.4492T>C	ENSP00000355046:p.Val8Ala		Somatic	15	0	0		WXS	Illumina HiSeq	.	18	0.50	9	ENST00000361453	0		0	Q34769|Q9TGI0|Q9TGI1|Q9TGI2|Q9TGI3|Q9TGI4	Missense_Mutation	SNP	ENST00000361453.3	37																																																																																						0.458	MT-ND2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				YP_003024027	
ARMCX5	64860	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	X	101857554	101857554	+	Missense_Mutation	SNP	C	C	A			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chrX:101857554C>A	ENST00000604957.1	+	1	3107	c.485C>A	c.(484-486)tCc>tAc	p.S162Y	ARMCX5_ENST00000372742.1_Missense_Mutation_p.S162Y|RP4-769N13.7_ENST00000602441.1_RNA|ARMCX5_ENST00000537008.1_Missense_Mutation_p.S162Y|ARMCX5_ENST00000541409.1_Missense_Mutation_p.S162Y|ARMCX5_ENST00000246174.2_Missense_Mutation_p.S162Y|ARMCX5_ENST00000536530.1_Missense_Mutation_p.S162Y|RP4-769N13.6_ENST00000476910.2_RNA	NM_001168478.1	NP_001161950.1	Q6P1M9	ARMX5_HUMAN	armadillo repeat containing, X-linked 5	162										breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|upper_aerodigestive_tract(2)	22						GGGATGAAATCCAGTGATGAG	0.473																																					p.S162Y													.	.			0			c.C485A												153.0	144.0	147.0					X																	101857554		2203	4300	6503	SO:0001583	missense	64860	exon3			TGAAATCCAGTGA		CCDS14500.1	Xq22.1-q22.3	2014-03-21			ENSG00000125962	ENSG00000125962		"""Armadillo repeat containing"""	25772	protein-coding gene	gene with protein product						16221301, 22569362	Standard	NM_022838		Approved	FLJ12969, GASP5	uc004ejh.3	Q6P1M9	OTTHUMG00000022062	ENST00000604957.1:c.485C>A	X.37:g.101857554C>A	ENSP00000474720:p.Ser162Tyr		Somatic	84	0	0		WXS	Illumina HiSeq	.	153	0.52	80	NM_022838	45	0.44	20	B3KU88|D3DX99|Q68DB4|Q9BVZ3|Q9H969	Missense_Mutation	SNP	ENST00000604957.1	37	CCDS14500.1	.	.	.	.	.	.	.	.	.	.	C	8.561	0.877751	0.17395	.	.	ENSG00000125962	ENST00000246174;ENST00000537008;ENST00000541409;ENST00000536530;ENST00000372742	T;T;T;T;T	0.22134	1.97;1.97;1.97;1.97;1.97	3.59	-0.251	0.13003	.	1.077630	0.07296	N	0.873194	T	0.07773	0.0195	N	0.14661	0.345	0.09310	N	1	B	0.32283	0.362	B	0.22753	0.041	T	0.21042	-1.0257	10	0.02654	T	1	13.8044	4.0151	0.09641	0.0:0.381:0.1801:0.439	.	162	Q6P1M9	ARMX5_HUMAN	Y	162	ENSP00000246174:S162Y;ENSP00000439001:S162Y;ENSP00000446385:S162Y;ENSP00000445851:S162Y;ENSP00000361827:S162Y	ENSP00000246174:S162Y	S	+	2	0	ARMCX5	101744210	0.009000	0.17119	0.000000	0.03702	0.196000	0.23810	0.242000	0.18087	-0.180000	0.10637	-0.975000	0.02590	TCC			0.473	ARMCX5-013	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000469659.1		NM_022838	
SHANK2	22941	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	11	70653201	70653201	+	Silent	SNP	G	G	A			TCGA-2G-AAG3-01A-11D-A42Y-10	TCGA-2G-AAG3-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	edec0ae4-0d21-40ef-87fb-9bf99b9d20d3	aee66dc1-135a-44d7-8f3d-b4e02426e898	g.chr11:70653201G>A	ENST00000423696.2	-	3	468	c.432C>T	c.(430-432)taC>taT	p.Y144Y	SHANK2_ENST00000338508.4_Silent_p.Y524Y|SHANK2_ENST00000468619.1_5'UTR			Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2	144					adult behavior (GO:0030534)|learning (GO:0007612)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|ionotropic glutamate receptor binding (GO:0035255)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(30)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)			GCACGGCACTGTAGAGCTTCC	0.622																																					.													SHANK2_ENST00000338508,colon,carcinoma,-1,1	SHANK2_ENST00000338508	-1	1	0			.												58.0	73.0	69.0					11																	70653201		692	1591	2283	SO:0001819	synonymous_variant	22941	.			GGCACTGTAGAGC	AF141901		11q13.2	2013-01-10			ENSG00000162105	ENSG00000162105		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	14295	protein-coding gene	gene with protein product		603290	"""cortactin binding protein 1"""	CORTBP1		10506216	Standard	XM_005277930		Approved	CTTNBP1, ProSAP1, SHANK, SPANK-3	uc001oqc.3	Q9UPX8	OTTHUMG00000154615	ENST00000423696.2:c.432C>T	11.37:g.70653201G>A			Somatic	88	0	0		WXS	Illumina HiSeq	.	77	0.09	7	.	4	0.25	1	C0SPG8|C0SPG9|Q3Y8G9|Q52LK2|Q9UKP1	Silent	SNP	ENST00000423696.2	37																																																																																						0.622	SHANK2-203	KNOWN	basic	protein_coding	protein_coding				NM_012309	
