#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
MTHFR	4524	broad.mit.edu	37	1	11854879	11854879	+	Missense_Mutation	SNP	C	C	T			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr1:11854879C>T	ENST00000376592.1	-	6	1201	c.1073G>A	c.(1072-1074)cGa>cAa	p.R358Q	MTHFR_ENST00000376585.1_Missense_Mutation_p.R399Q|MTHFR_ENST00000376583.3_Missense_Mutation_p.R399Q|MTHFR_ENST00000376590.3_Missense_Mutation_p.R358Q			P42898	MTHR_HUMAN	methylenetetrahydrofolate reductase (NAD(P)H)	358					blood circulation (GO:0008015)|cellular amino acid metabolic process (GO:0006520)|folic acid metabolic process (GO:0046655)|homocysteine metabolic process (GO:0050667)|methionine biosynthetic process (GO:0009086)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to hypoxia (GO:0001666)|response to interleukin-1 (GO:0070555)|response to vitamin B2 (GO:0033274)|S-adenosylmethionine metabolic process (GO:0046500)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|neuron projection (GO:0043005)	flavin adenine dinucleotide binding (GO:0050660)|methylenetetrahydrofolate reductase (NAD(P)H) activity (GO:0004489)|modified amino acid binding (GO:0072341)|NADP binding (GO:0050661)			NS(4)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(6)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	33	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Benazepril(DB00542)|Cyanocobalamin(DB00115)|Fluorouracil(DB00544)|Folic Acid(DB00158)|L-Methionine(DB00134)|Menadione(DB00170)|Methotrexate(DB00563)|Riboflavin(DB00140)|Tetrahydrofolic acid(DB00116)	ATCTTCCTCTCGGCGCTTGGG	0.612																																					p.R358Q													.	MTHFR	65		0			c.G1073A												65.0	65.0	65.0					1																	11854879		2203	4300	6503	SO:0001583	missense	4524	exon7			TCCTCTCGGCGCT	BC053509	CCDS137.1	1p36.3	2014-09-17	2010-05-04		ENSG00000177000	ENSG00000177000	1.5.1.20		7436	protein-coding gene	gene with protein product		607093	"""5,10-methylenetetrahydrofolate reductase (NADPH)"""			7920641	Standard	NM_005957		Approved		uc001atc.2	P42898	OTTHUMG00000002277	ENST00000376592.1:c.1073G>A	1.37:g.11854879C>T	ENSP00000365777:p.Arg358Gln		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	111	0.04	4	NM_005957	11	0.00	0	B2R7A6|Q5SNW6|Q5SNW9|Q7Z6M6|Q8IU73|Q9UQR2	Missense_Mutation	SNP	ENST00000376592.1	37	CCDS137.1	.	.	.	.	.	.	.	.	.	.	C	18.71	3.681909	0.68042	.	.	ENSG00000177000	ENST00000376592;ENST00000376583;ENST00000376590;ENST00000376585	T;T;T;T	0.73258	-0.73;-0.73;-0.73;-0.73	4.91	4.91	0.64330	.	0.050323	0.85682	D	0.000000	T	0.60573	0.2279	L	0.60067	1.865	0.43729	D	0.996218	B;P	0.46784	0.075;0.884	B;B	0.27380	0.03;0.079	T	0.65030	-0.6267	10	0.25751	T	0.34	.	17.4549	0.87604	0.0:1.0:0.0:0.0	.	358;399	P42898;Q5SNW6	MTHR_HUMAN;.	Q	358;399;358;399	ENSP00000365777:R358Q;ENSP00000365767:R399Q;ENSP00000365775:R358Q;ENSP00000365770:R399Q	ENSP00000365767:R399Q	R	-	2	0	MTHFR	11777466	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	5.253000	0.65452	2.407000	0.81776	0.462000	0.41574	CGA			0.612	MTHFR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000006538.1		NM_005957	
Unknown	0	hgsc.bcm.edu	37	1	16974458	16974458	+	IGR	SNP	G	G	C	rs57783259		TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr1:16974458G>C								CROCCP2 (13404 upstream) : RNU1-3 (18821 downstream)																							GTGAGGTGGGGGGGCGGGCGT	0.657																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	11209	.			GGTGGGGGGGCGG																													1.37:g.16974458G>C			Somatic	244	0	0		WXS	Illumina HiSeq	.	484	0.06	28	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.657										
CROCC	9696	broad.mit.edu	37	1	17270665	17270665	+	Missense_Mutation	SNP	G	G	A	rs199948035		TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr1:17270665G>A	ENST00000375541.5	+	14	1948	c.1879G>A	c.(1879-1881)Gag>Aag	p.E627K	CROCC_ENST00000467938.1_3'UTR	NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin											breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		GCAGGAGCGGGAGAAGCTGCA	0.716																																					p.E627K													.	CROCC	185		0			c.G1879A												7.0	7.0	7.0					1																	17270665		2132	4179	6311	SO:0001583	missense	9696	exon14			GAGCGGGAGAAGC	AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"""rootletin, ciliary rootlet protein"""	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.1879G>A	1.37:g.17270665G>A	ENSP00000364691:p.Glu627Lys		Somatic	75	0.04	3		WXS	Illumina HiSeq	Phase_I	118	0.05	6	NM_014675	26	0.00	0		Missense_Mutation	SNP	ENST00000375541.5	37	CCDS30616.1	.	.	.	.	.	.	.	.	.	.	G	18.29	3.592217	0.66219	.	.	ENSG00000058453	ENST00000375541;ENST00000445545	T	0.13196	2.61	4.48	4.48	0.54585	.	.	.	.	.	T	0.27027	0.0662	M	0.66939	2.045	0.45704	D	0.99861	P;P	0.51537	0.946;0.873	P;B	0.53313	0.723;0.443	T	0.01208	-1.1418	9	0.34782	T	0.22	.	15.4436	0.75208	0.0:0.0:1.0:0.0	.	490;627	A1L0S8;Q5TZA2	.;CROCC_HUMAN	K	627;508	ENSP00000364691:E627K	ENSP00000364691:E627K	E	+	1	0	CROCC	17143252	1.000000	0.71417	1.000000	0.80357	0.784000	0.44337	5.902000	0.69869	2.431000	0.82371	0.561000	0.74099	GAG			0.716	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000006249.2		NM_014675	
UBR4	23352	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;mdanderson.org	37	1	19483407	19483407	+	Nonsense_Mutation	SNP	G	G	A			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr1:19483407G>A	ENST00000375254.3	-	41	5800	c.5773C>T	c.(5773-5775)Cag>Tag	p.Q1925*	UBR4_ENST00000375217.2_Nonsense_Mutation_p.Q1925*|UBR4_ENST00000375226.2_Nonsense_Mutation_p.Q1925*|UBR4_ENST00000375267.2_Nonsense_Mutation_p.Q1925*	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	1925					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		GCAGAGAGCTGCAGAACGGTG	0.453																																					p.Q1925X													.	.			0			c.C5773T												56.0	48.0	51.0					1																	19483407		2203	4300	6503	SO:0001587	stop_gained	23352	exon41			AGAGCTGCAGAAC	AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"""Ubiquitin protein ligase E3 component n-recognins"""	30313	protein-coding gene	gene with protein product		609890	"""zinc finger, UBR1 type 1"""	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.5773C>T	1.37:g.19483407G>A	ENSP00000364403:p.Gln1925*		Somatic	226	0	0		WXS	Illumina HiSeq	.	292	0.15	43	NM_020765	25	0.04	1	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Nonsense_Mutation	SNP	ENST00000375254.3	37	CCDS189.1	.	.	.	.	.	.	.	.	.	.	G	39	7.299759	0.98196	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000417040;ENST00000419533	.	.	.	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	20.1858	0.98214	0.0:0.0:1.0:0.0	.	.	.	.	X	1925;1925;1925;1925;635;1141	.	ENSP00000364365:Q1925X	Q	-	1	0	UBR4	19355994	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.238000	0.95380	2.777000	0.95525	0.591000	0.81541	CAG			0.453	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000007085.1		NM_020765	
PARS2	25973	broad.mit.edu	37	1	55224781	55224781	+	Missense_Mutation	SNP	G	G	T	rs374449269		TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr1:55224781G>T	ENST00000371279.3	-	2	136	c.54C>A	c.(52-54)agC>agA	p.S18R		NM_152268.3	NP_689481.2	Q7L3T8	SYPM_HUMAN	prolyl-tRNA synthetase 2, mitochondrial (putative)	18					gene expression (GO:0010467)|prolyl-tRNA aminoacylation (GO:0006433)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|proline-tRNA ligase activity (GO:0004827)	p.S18R(1)		breast(1)|endometrium(3)|kidney(2)|lung(4)|ovary(2)|prostate(2)|skin(1)	15					L-Proline(DB00172)	AGAGCTGGCGGCTGCAGGTGG	0.602																																					p.S18R													PARS2,NS,carcinoma,0,2	PARS2	29	2	1	Substitution - Missense(1)	kidney(1)	c.C54A												23.0	22.0	23.0					1																	55224781		2202	4297	6499	SO:0001583	missense	25973	exon2			CTGGCGGCTGCAG	AK025585	CCDS597.1	1p32.2	2011-07-01	2007-02-23		ENSG00000162396	ENSG00000162396	6.1.1.15	"""Aminoacyl tRNA synthetases / Class II"""	30563	protein-coding gene	gene with protein product	"""proline tRNA ligase 2, mitochondrial (putative)"""	612036				15779907	Standard	NM_152268		Approved	DKFZp727A071	uc001cxy.3	Q7L3T8	OTTHUMG00000009915	ENST00000371279.3:c.54C>A	1.37:g.55224781G>T	ENSP00000360327:p.Ser18Arg		Somatic	114	0.0087719298	1		WXS	Illumina HiSeq	Phase_I	133	0.05	7	NM_152268	23	0.00	0	A8K0W4|Q9H6S5|Q9UFT1	Missense_Mutation	SNP	ENST00000371279.3	37	CCDS597.1	.	.	.	.	.	.	.	.	.	.	G	0.015	-1.567181	0.00895	.	.	ENSG00000162396	ENST00000371279	T	0.53857	0.6	4.55	1.61	0.23674	.	0.796070	0.11983	N	0.510608	T	0.33000	0.0848	L	0.27053	0.805	0.09310	N	1	B	0.34015	0.435	B	0.30782	0.12	T	0.14671	-1.0464	10	0.12430	T	0.62	-4.5122	8.4699	0.32980	0.2468:0.0:0.7532:0.0	.	18	Q7L3T8	SYPM_HUMAN	R	18	ENSP00000360327:S18R	ENSP00000360327:S18R	S	-	3	2	PARS2	54997369	0.008000	0.16893	0.074000	0.20217	0.011000	0.07611	0.068000	0.14531	0.138000	0.18790	0.467000	0.42956	AGC			0.602	PARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000027436.1		NM_152268	
RPL5	6125	broad.mit.edu	37	1	93300360	93300361	+	Frame_Shift_Ins	INS	-	-	AT			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr1:93300360_93300361insAT	ENST00000370321.3	+	4	304_305	c.214_215insAT	c.(214-216)gatfs	p.D72fs	SNORD21_ENST00000383953.1_RNA	NM_000969.3	NP_000960.2	P46777	RL5_HUMAN	ribosomal protein L5	72					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosomal large subunit biogenesis (GO:0042273)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	5S rRNA binding (GO:0008097)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			endometrium(1)|kidney(2)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	9		all_lung(203;0.00265)|Lung NSC(277;0.0056)|all_neural(321;0.185)|Melanoma(281;0.192)|Glioma(108;0.203)		GBM - Glioblastoma multiforme(16;0.000305)|all cancers(265;0.000343)|Epithelial(280;0.0927)		TATAGAGGGGGATATGATAGTC	0.421																																					p.D72fs													.	RPL5	38		0			c.214_215insAT																																									SO:0001589	frameshift_variant	6125	exon4			GAGGGGGATATGA	U14966	CCDS741.1	1p22.1	2014-06-13			ENSG00000122406	ENSG00000122406		"""L ribosomal proteins"""	10360	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 135"""	603634				7937132, 7772601	Standard	NM_000969		Approved	L5, PPP1R135	uc001doz.3	P46777	OTTHUMG00000010899	ENST00000370321.3:c.217_218dupAT	1.37:g.93300363_93300364dupAT	ENSP00000359345:p.Asp72fs		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	40	0.18	7	NM_000969	2622	0.00	0	Q32LZ3|Q53HH6|Q9H3F4	Frame_Shift_Ins	INS	ENST00000370321.3	37	CCDS741.1																																																																																					0.421	RPL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000030058.2		NM_000969	
TCHH	7062	broad.mit.edu	37	1	152084619	152084621	+	In_Frame_Del	DEL	CTC	CTC	-	rs369048462|rs376670627		TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	CTC	CTC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr1:152084619_152084621delCTC	ENST00000368804.1	-	2	1071_1073	c.1072_1074delGAG	c.(1072-1074)gagdel	p.E358del		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	358	5 X 13 AA tandem repeats of R-R-E-Q-E-E- E-R-R-E-Q-Q-L.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			gctcgcgcctctcctcctcctgc	0.724																																					p.358_358del													.	TCHH	275		0			c.1072_1074del									18,2902		2,14,1444						0.8	0.0			11	42,6426		3,36,3195	no	coding	TCHH	NM_007113.2		5,50,4639	A1A1,A1R,RR		0.6494,0.6164,0.6391				60,9328				SO:0001651	inframe_deletion	7062	exon3			GCGCCTCTCCTCC	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"""EF-hand domain containing"""	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.1072_1074delGAG	1.37:g.152084625_152084627delCTC	ENSP00000357794:p.Glu358del		Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	25	0.28	7	NM_007113	0		0	Q5VUI3	In_Frame_Del	DEL	ENST00000368804.1	37	CCDS41396.1																																																																																					0.724	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000036671.2		NM_007113	
PCP4L1	654790	broad.mit.edu	37	1	161254255	161254255	+	Missense_Mutation	SNP	A	A	G			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr1:161254255A>G	ENST00000504449.1	+	3	439	c.191A>G	c.(190-192)aAg>aGg	p.K64R		NM_001102566.1	NP_001096036.1	A6NKN8	PC4L1_HUMAN	Purkinje cell protein 4 like 1	64	IQ.									endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	4	all_cancers(52;4.16e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			AAAAGGAAAAAGGATCCCAGC	0.517																																					p.K64R													.	PCP4L1	7		0			c.A191G												57.0	59.0	58.0					1																	161254255		1944	4137	6081	SO:0001583	missense	654790	exon3			GGAAAAAGGATCC	BC028905	CCDS53412.1	1q23.3	2006-02-27	2006-02-27		ENSG00000248485	ENSG00000248485			20448	protein-coding gene	gene with protein product			"""purkinje cell protein 4 like 1"""				Standard	NM_001102566		Approved	IQM1	uc001gad.3	A6NKN8	OTTHUMG00000034340	ENST00000504449.1:c.191A>G	1.37:g.161254255A>G	ENSP00000426296:p.Lys64Arg		Somatic	405	0.0049382716	2		WXS	Illumina HiSeq	Phase_I	534	0.01	5	NM_001102566	0		0	B2RV24|B9EJG4	Missense_Mutation	SNP	ENST00000504449.1	37	CCDS53412.1	.	.	.	.	.	.	.	.	.	.	A	17.04	3.287629	0.59976	.	.	ENSG00000248485	ENST00000504449	.	.	.	5.24	5.24	0.73138	.	0.000000	0.64402	D	0.000001	T	0.49047	0.1534	.	.	.	.	.	.	D	0.58268	0.982	P	0.58013	0.831	T	0.54221	-0.8326	7	0.33940	T	0.23	.	9.2707	0.37670	0.8184:0.1816:0.0:0.0	.	64	A6NKN8	PC4L1_HUMAN	R	64	.	ENSP00000426296:K64R	K	+	2	0	PCP4L1	159520879	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.674000	0.61612	2.200000	0.70718	0.459000	0.35465	AAG			0.517	PCP4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000082986.2			
MFSD4	148808	broad.mit.edu;mdanderson.org	37	1	205538281	205538281	+	Silent	SNP	C	C	T			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr1:205538281C>T	ENST00000367147.4	+	1	177	c.84C>T	c.(82-84)ttC>ttT	p.F28F	RNU2-19P_ENST00000517288.1_RNA|MFSD4_ENST00000539267.1_Silent_p.F28F|MFSD4_ENST00000536357.1_Silent_p.F28F	NM_181644.4	NP_857595.3	Q8N468	MFSD4_HUMAN	major facilitator superfamily domain containing 4	28					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16	Breast(84;0.07)		BRCA - Breast invasive adenocarcinoma(75;0.0908)			TCTTCAGCTTCGGCCTGTGCA	0.687																																					p.F28F													.	MFSD4	46		0			c.C84T												26.0	18.0	21.0					1																	205538281		2170	4224	6394	SO:0001819	synonymous_variant	148808	exon1			CAGCTTCGGCCTG	BC036549	CCDS1455.1	1q32.1	2008-02-05			ENSG00000174514	ENSG00000174514			25433	protein-coding gene	gene with protein product							Standard	NM_181644		Approved	DKFZp761N1114, FLJ34577, UNQ3064, FLJ25004	uc001hcv.4	Q8N468	OTTHUMG00000037197	ENST00000367147.4:c.84C>T	1.37:g.205538281C>T			Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	94	0.05	5	NM_181644	0		0	B7Z8X3|Q6UY25|Q8NAY0|Q8TCP4	Silent	SNP	ENST00000367147.4	37	CCDS1455.1																																																																																					0.687	MFSD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000090391.1		NM_181644	
LINC00467	84791	hgsc.bcm.edu	37	1	211591127	211591127	+	RNA	SNP	A	A	G	rs550651843		TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr1:211591127A>G	ENST00000423222.1	+	0	420					NR_026761.2		Q9BRT7	CA097_HUMAN	long intergenic non-protein coding RNA 467																		AACTGCGGCAATGAGGGCTAG	0.468													a|||	1	0.000199681	0.0	0.0	5008	,	,		19723	0.0		0.001	False		,,,				2504	0.0				.													.	.			0			.																																											84791	.			GCGGCAATGAGGG	BC005997		1q32.3	2014-03-04	2013-12-05	2013-12-05	ENSG00000153363	ENSG00000153363		"""Long non-coding RNAs"""	28227	non-coding RNA	RNA, long non-coding			"""chromosome 1 open reading frame 97"""	C1orf97		24586304	Standard	NR_026761		Approved	MGC14801	uc001hil.4	Q9BRT7	OTTHUMG00000036998		1.37:g.211591127A>G			Somatic	246	0	0		WXS	Illumina HiSeq	.	396	0.17	66	.	4	0.00	0		RNA	SNP	ENST00000423222.1	37																																																																																						0.468	LINC00467-001	KNOWN	basic	processed_transcript	processed_transcript		OTTHUMT00000089831.3		NR_026761	
OR2T4	127074	hgsc.bcm.edu	37	1	248525639	248525640	+	Missense_Mutation	DNP	AT	AT	CC	rs34079073|rs76878172	byFrequency	TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	AT	AT					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr1:248525639_248525640AT>CC	ENST00000366475.1	+	1	757_758	c.757_758AT>CC	c.(757-759)ATc>CCc	p.I253P		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	253						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CTATTTACTCATCCTCCTCACC	0.52																																					p.I253P													OR2T4,brain,glioma,+1,1	OR2T4	1	1	0			c.T758C																																									SO:0001583	missense	127074	exon1			TTACTCATCCTCC	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"""GPCR / Class A : Olfactory receptors"""	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	Exception_encountered	1.37:g.248525639_248525640delinsCC	ENSP00000355431:p.Ile253Pro		Somatic	461	0.0021691974	1		WXS	Illumina HiSeq	.	657	0.03	17	NM_001004696	0		0	Q6IEZ8	Missense_Mutation	DNP	ENST00000366475.1	37	CCDS31113.1																																																																																					0.520	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000097349.2		NM_001004696	
FAM208B	54906	mdanderson.org	37	10	5788743	5788743	+	Missense_Mutation	SNP	G	G	A			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr10:5788743G>A	ENST00000328090.5	+	15	3984	c.3359G>A	c.(3358-3360)gGc>gAc	p.G1120D	RP11-336A10.2_ENST00000411512.2_RNA	NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	1120																	GGACAGAAGGGCACTAAGTAC	0.502																																					p.G1120D													.	.			0			c.G3359A												122.0	118.0	119.0					10																	5788743		1993	4178	6171	SO:0001583	missense	54906	exon15			AGAAGGGCACTAA	BX649177	CCDS41485.1	10p15.1	2011-09-14	2011-09-14	2011-09-14	ENSG00000108021	ENSG00000108021			23484	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 18"""	C10orf18		12477932	Standard	NM_017782		Approved	FLJ20360, bA318E3.2, KIAA2006	uc001iij.3	Q5VWN6	OTTHUMG00000017605	ENST00000328090.5:c.3359G>A	10.37:g.5788743G>A	ENSP00000328426:p.Gly1120Asp		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	87	0.05	4	NM_017782	27	0.00	0	Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	Missense_Mutation	SNP	ENST00000328090.5	37	CCDS41485.1	.	.	.	.	.	.	.	.	.	.	G	1.376	-0.584678	0.03827	.	.	ENSG00000108021	ENST00000328090	T	0.04275	3.66	5.68	0.0766	0.14404	.	0.793883	0.11509	N	0.556885	T	0.03390	0.0098	N	0.25647	0.755	0.09310	N	1	B	0.14438	0.01	B	0.15052	0.012	T	0.43750	-0.9372	10	0.36615	T	0.2	.	4.2749	0.10804	0.4597:0.1716:0.3687:0.0	.	1120	Q5VWN6	F208B_HUMAN	D	1120	ENSP00000328426:G1120D	ENSP00000328426:G1120D	G	+	2	0	C10orf18	5828749	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.083000	0.11286	-0.035000	0.13691	0.591000	0.81541	GGC			0.502	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000046571.2		NM_017782	
TAF5	6877	mdanderson.org	37	10	105147455	105147455	+	Splice_Site	SNP	G	G	T			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr10:105147455G>T	ENST00000369839.3	+	10	2208	c.2185G>T	c.(2185-2187)Ggt>Tgt	p.G729C	TAF5_ENST00000351396.4_Splice_Site_p.G674C	NM_006951.3	NP_008882.2	Q15542	TAF5_HUMAN	TAF5 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 100kDa	729					chromatin modification (GO:0016568)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	protein dimerization activity (GO:0046983)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)	15		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;1.83e-09)|all cancers(201;1.4e-08)|BRCA - Breast invasive adenocarcinoma(275;0.198)		TTTGGCATCAGGTAAATGACT	0.368																																					p.G729C													.	.			0			c.G2185T												131.0	133.0	132.0					10																	105147455		2203	4300	6503	SO:0001630	splice_region_variant	6877	exon10			GCATCAGGTAAAT	X95525	CCDS7547.1	10q24-q25.2	2013-01-10	2002-08-29	2001-12-07	ENSG00000148835	ENSG00000148835		"""WD repeat domain containing"""	11539	protein-coding gene	gene with protein product		601787	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, D, 100kD"""	TAF2D		8884287, 8942982	Standard	NM_006951		Approved	TAFII100	uc001kwv.3	Q15542	OTTHUMG00000018985	ENST00000369839.3:c.2185+1G>T	10.37:g.105147455G>T			Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	24	0.13	3	NM_006951	27	0.00	0	A8K5B4|B2RMR0|B7ZKJ6|Q53EM4|Q5SYD5|Q86UZ7|Q9Y4K5	Missense_Mutation	SNP	ENST00000369839.3	37	CCDS7547.1	.	.	.	.	.	.	.	.	.	.	G	18.90	3.721087	0.68959	.	.	ENSG00000148835	ENST00000369839;ENST00000351396	T;T	0.70749	-0.51;-0.51	5.48	5.48	0.80851	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.81730	0.4884	L	0.51853	1.615	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77557	0.975;0.99	T	0.83013	-0.0171	10	0.87932	D	0	-12.9872	19.359	0.94428	0.0:0.0:1.0:0.0	.	674;729	Q15542-2;Q15542	.;TAF5_HUMAN	C	729;674	ENSP00000358854:G729C;ENSP00000311024:G674C	ENSP00000311024:G674C	G	+	1	0	TAF5	105137445	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.459000	0.97638	2.552000	0.86080	0.557000	0.71058	GGT			0.368	TAF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000050144.1			Missense_Mutation
SPON1	10418	broad.mit.edu	37	11	14101781	14101782	+	RNA	INS	-	-	T	rs11432678	byFrequency	TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr11:14101781_14101782insT	ENST00000310358.7	+	0	1211							Q9HCB6	SPON1_HUMAN	spondin 1, extracellular matrix protein						cell adhesion (GO:0007155)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|endometrium(1)|large_intestine(5)|lung(11)|prostate(2)|upper_aerodigestive_tract(1)	21				Epithelial(150;0.00898)		TAttttttttcttttttttttt	0.441													|||unknown(HR)	1735	0.346446	0.1241	0.2738	5008	,	,		21091	0.4494		0.3917	False		,,,				2504	0.546				.													.	SPON1	65		0			.																																											10418	.			TTTTTTCTTTTTT	AB018305	CCDS73262.1	11p15.2	2014-05-06	2004-03-05		ENSG00000152268	ENSG00000262655			11252	protein-coding gene	gene with protein product		604989	"""spondin 1, (f-spondin) extracellular matrix protein"""			9872452	Standard	NM_006108		Approved	KIAA0762, f-spondin	uc001mle.3	Q9HCB6	OTTHUMG00000181576		11.37:g.14101792_14101792dupT			Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	9	0.33	3	.	0		0	A8K6W5|O94862|Q8NCD7|Q8WUR5	RNA	INS	ENST00000310358.7	37																																																																																						0.441	SPON1-201	KNOWN	basic	processed_transcript	processed_transcript				NM_145584	
FADS1	3992	mdanderson.org	37	11	61582704	61582704	+	5'UTR	SNP	G	G	A			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr11:61582704G>A	ENST00000542506.1	-	0	59				MIR1908_ENST00000410394.1_RNA|FADS2_ENST00000522056.1_5'Flank|FADS2_ENST00000574708.1_Intron|FADS1_ENST00000350997.7_Intron|FADS1_ENST00000541683.1_5'UTR|FADS2_ENST00000517839.1_5'Flank|FADS2_ENST00000522639.1_5'Flank|FADS1_ENST00000433932.1_Intron|FADS2_ENST00000257261.6_5'Flank			O60427	FADS1_HUMAN	fatty acid desaturase 1						alpha-linolenic acid metabolic process (GO:0036109)|cell-cell signaling (GO:0007267)|cellular lipid metabolic process (GO:0044255)|cellular response to starvation (GO:0009267)|icosanoid biosynthetic process (GO:0046456)|linoleic acid metabolic process (GO:0043651)|phospholipid biosynthetic process (GO:0008654)|regulation of cell differentiation (GO:0045595)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid biosynthetic process (GO:0006636)|unsaturated fatty acid metabolic process (GO:0033559)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)	C-5 sterol desaturase activity (GO:0000248)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity (GO:0016491)			central_nervous_system(1)|endometrium(1)|lung(1)|urinary_tract(1)	4					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)	CCCCGCCGCGGCATTCCCGGC	0.726																																					.													.	.			0			.												20.0	24.0	22.0					11																	61582704		692	1591	2283	SO:0001623	5_prime_UTR_variant	100302263	.			GCCGCGGCATTCC		CCDS8011.2	11q12-q13.1	2013-01-25			ENSG00000149485	ENSG00000149485	1.14.19.3	"""Fatty acid desaturases"""	3574	protein-coding gene	gene with protein product	"""delta-5 desaturase"""	606148		LLCDL1			Standard	NM_013402		Approved	D5D, FADSD5, TU12, FADS6	uc010rlm.2	O60427	OTTHUMG00000157155	ENST00000542506.1:c.-485C>T	11.37:g.61582704G>A			Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	45	0.07	3	.	0		0	A8K0I7|B2RAI0|Q53GM5|Q8N3A6|Q8NCC7|Q8NCG0|Q96I39|Q96SV3|Q96T10|Q9NRP8|Q9NYX1	RNA	SNP	ENST00000542506.1	37																																																																																						0.726	FADS1-012	PUTATIVE	basic	protein_coding	protein_coding		OTTHUMT00000398584.1		NM_013402	
RTN3	10313	broad.mit.edu	37	11	63488321	63488321	+	Nonsense_Mutation	SNP	G	G	T			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr11:63488321G>T	ENST00000377819.5	+	3	2501	c.2347G>T	c.(2347-2349)Gaa>Taa	p.E783*	RTN3_ENST00000540798.1_Nonsense_Mutation_p.E671*|RTN3_ENST00000354497.4_Intron|RTN3_ENST00000341307.2_Intron|RTN3_ENST00000356000.3_Intron|RTN3_ENST00000537981.1_Intron|RTN3_ENST00000339997.4_Nonsense_Mutation_p.E764*	NM_001265589.1	NP_001252518.1	O95197	RTN3_HUMAN	reticulon 3	783					apoptotic process (GO:0006915)|endoplasmic reticulum tubular network organization (GO:0071786)|response to stress (GO:0006950)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	20						ATTTGCTCCAGAATCTTGGCC	0.428																																					p.E783X													.	RTN3	104		0			c.G2347T												71.0	64.0	66.0					11																	63488321		2201	4298	6499	SO:0001587	stop_gained	10313	exon3			GCTCCAGAATCTT	AF059524	CCDS8048.1, CCDS8049.1, CCDS8050.1, CCDS41664.1, CCDS58141.1, CCDS58142.1, CCDS58143.1	11q13	2011-01-14			ENSG00000133318	ENSG00000133318			10469	protein-coding gene	gene with protein product	"""neuroendocrine-specific protein-like 2"", ""NSP-like protein II"", ""isoforme III"", ""ASY interacting protein"", ""homolog of ASY protein"""	604249				10331947	Standard	NM_006054		Approved	NSPL2, NSPLII, ASYIP, HAP, RTN3-A1	uc001nxq.3	O95197		ENST00000377819.5:c.2347G>T	11.37:g.63488321G>T	ENSP00000367050:p.Glu783*		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	75	0.07	5	NM_001265589	3	0.00	0	B3KQS2|B7Z308|B7Z4M0|F5H774|Q147U9|Q496K2|Q53GN3|Q59EP0|Q5UEP2|Q6T930|Q7RTM7|Q7RTM8|Q7RTN3	Nonsense_Mutation	SNP	ENST00000377819.5	37	CCDS58141.1	.	.	.	.	.	.	.	.	.	.	G	37	6.143719	0.97320	.	.	ENSG00000133318	ENST00000377819;ENST00000339997;ENST00000540798	.	.	.	5.67	4.72	0.59763	.	5.827120	0.00166	N	0.000009	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	-5.2563	12.4367	0.55602	0.0:0.2345:0.7655:0.0	.	.	.	.	X	783;764;671	.	ENSP00000344106:E764X	E	+	1	0	RTN3	63244897	1.000000	0.71417	0.486000	0.27416	0.172000	0.22775	1.579000	0.36536	1.391000	0.46566	0.655000	0.94253	GAA			0.428	RTN3-002	KNOWN	basic|CCDS	protein_coding	protein_coding		OTTHUMT00000397846.1		NM_006054	
FAM86C2P	645332	bcgsc.ca	37	11	67560715	67560715	+	RNA	SNP	C	C	T	rs184691350		TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr11:67560715C>T	ENST00000528089.1	-	0	1035							A6NEL3	F86C2_HUMAN	family with sequence similarity 86, member C2, pseudogene																		CGTAGGGAAACAGTTTCTGGT	0.512																																					.													.	.			0			.																																											645332	.			GGGAAACAGTTTC			11q13.2	2011-07-07			ENSG00000160172	ENSG00000160172			42392	pseudogene	pseudogene							Standard	NR_024249		Approved		uc001omt.4	A6NEL3	OTTHUMG00000167222		11.37:g.67560715C>T			Somatic	286	0.027972028	8		WXS	Illumina HiSeq	Phase_1	279	0.09	25	.	2	0.00	0		RNA	SNP	ENST00000528089.1	37																																																																																						0.512	FAM86C2P-004	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000393796.1			
FAM86C2P	645332	bcgsc.ca	37	11	67560756	67560757	+	RNA	DNP	CA	CA	TG	rs202203024|rs200464966	byFrequency	TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	CA	CA					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr11:67560756_67560757CA>TG	ENST00000528089.1	-	0	993_994							A6NEL3	F86C2_HUMAN	family with sequence similarity 86, member C2, pseudogene																		CATCTGATCCCAGCCCGGCCTG	0.55																																					.													.	.			0			.																																											645332	.			TGATCCCAGCCCG			11q13.2	2011-07-07			ENSG00000160172	ENSG00000160172			42392	pseudogene	pseudogene							Standard	NR_024249		Approved		uc001omt.4	A6NEL3	OTTHUMG00000167222	Exception_encountered	11.37:g.67560756_67560757delinsTG			Somatic	273	0.0476190476	13		WXS	Illumina HiSeq	Phase_1	289	0.10	28	.	2	0.00	0		RNA	DNP	ENST00000528089.1	37																																																																																						0.550	FAM86C2P-004	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000393796.1			
BUD13	84811	mdanderson.org	37	11	116633790	116633790	+	Nonsense_Mutation	SNP	G	G	T			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr11:116633790G>T	ENST00000260210.4	-	4	538	c.515C>A	c.(514-516)tCa>tAa	p.S172*	BUD13_ENST00000375445.3_Nonsense_Mutation_p.S172*	NM_032725.3	NP_116114.1	Q9BRD0	BUD13_HUMAN	BUD13 homolog (S. cerevisiae)	172	Arg-rich.				mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)	nucleus (GO:0005634)|RES complex (GO:0070274)	poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|pancreas(2)|skin(1)|urinary_tract(1)	22	all_hematologic(175;0.0487)	all_cancers(61;1.72e-06)|all_epithelial(67;0.000735)|Melanoma(852;0.022)|Acute lymphoblastic leukemia(157;0.0255)|Medulloblastoma(222;0.0523)|Breast(348;0.056)|all_hematologic(158;0.0588)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|Epithelial(105;5.81e-06)|all cancers(92;0.000144)|OV - Ovarian serous cystadenocarcinoma(223;0.154)		AGATGTGTCTGAGTCATGACG	0.597																																					p.S172X													.	.			0			c.C515A												95.0	102.0	100.0					11																	116633790		2201	4296	6497	SO:0001587	stop_gained	84811	exon4			GTGTCTGAGTCAT	BC006350	CCDS8374.1, CCDS53712.1	11q23.3	2012-06-07	2007-01-12		ENSG00000137656	ENSG00000137656			28199	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 71"""		"""BUD13 homolog (yeast)"""			12477932	Standard	NM_032725		Approved	MGC13125, fSAP71, Cwc26	uc001ppn.3	Q9BRD0	OTTHUMG00000045136	ENST00000260210.4:c.515C>A	11.37:g.116633790G>T	ENSP00000260210:p.Ser172*		Somatic	56	0.0178571429	1		WXS	Illumina HiSeq	Phase_I	49	0.06	3	NM_001159736	16	0.00	0	A8K0S0|Q96LS7	Nonsense_Mutation	SNP	ENST00000260210.4	37	CCDS8374.1	.	.	.	.	.	.	.	.	.	.	G	17.68	3.448648	0.63178	.	.	ENSG00000137656	ENST00000375445;ENST00000260210	.	.	.	5.08	4.17	0.49024	.	0.263772	0.45126	D	0.000395	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-4.0431	12.7157	0.57113	0.0786:0.0:0.9214:0.0	.	.	.	.	X	172	.	ENSP00000260210:S172X	S	-	2	0	BUD13	116139000	0.903000	0.30736	0.176000	0.23000	0.015000	0.08874	3.682000	0.54656	1.368000	0.46115	0.655000	0.94253	TCA			0.597	BUD13-001	KNOWN	basic|CCDS	protein_coding	protein_coding		OTTHUMT00000104864.1		NM_032725	
KRT73	319101	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	12	53002138	53002138	+	Missense_Mutation	SNP	C	C	T			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr12:53002138C>T	ENST00000305748.3	-	9	1499	c.1465G>A	c.(1465-1467)Ggg>Agg	p.G489R	RP11-641A6.2_ENST00000552364.1_RNA|RP11-641A6.2_ENST00000551089.1_RNA|RP11-641A6.2_ENST00000549180.1_RNA	NM_175068.2	NP_778238.1	Q86Y46	K2C73_HUMAN	keratin 73	489	Tail.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44				BRCA - Breast invasive adenocarcinoma(357;0.189)		CTGTAGCCCCCGCTGACAGAG	0.632																																					p.G489R													.	.			0			c.G1465A												50.0	51.0	50.0					12																	53002138		2203	4300	6503	SO:0001583	missense	319101	exon9			AGCCCCCGCTGAC	AJ508776	CCDS8834.1	12q13.13	2013-06-25			ENSG00000186049	ENSG00000186049		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28928	protein-coding gene	gene with protein product		608247				12648212, 16831889	Standard	NM_175068		Approved	KRT6IRS3, K6IRS3	uc001sas.3	Q86Y46	OTTHUMG00000169746	ENST00000305748.3:c.1465G>A	12.37:g.53002138C>T	ENSP00000307014:p.Gly489Arg		Somatic	52	0	0		WXS	Illumina HiSeq	.	112	0.13	14	NM_175068	0		0	Q32MB2	Missense_Mutation	SNP	ENST00000305748.3	37	CCDS8834.1	.	.	.	.	.	.	.	.	.	.	C	18.35	3.604253	0.66445	.	.	ENSG00000186049	ENST00000305748;ENST00000552855	D;D	0.85773	-1.78;-2.03	4.86	3.02	0.34903	.	0.000000	0.48286	D	0.000185	D	0.87450	0.6180	M	0.73962	2.25	0.31845	N	0.623027	D	0.71674	0.998	P	0.54312	0.748	D	0.86910	0.2060	10	0.56958	D	0.05	.	8.0601	0.30627	0.0:0.8071:0.0:0.1929	.	489	Q86Y46	K2C73_HUMAN	R	489;234	ENSP00000307014:G489R;ENSP00000449081:G234R	ENSP00000307014:G489R	G	-	1	0	KRT73	51288405	0.068000	0.21057	0.523000	0.27875	0.911000	0.54048	0.813000	0.27225	0.563000	0.29222	0.655000	0.94253	GGG			0.632	KRT73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000405700.1		NM_175068	
RP11-511B23.2	0	broad.mit.edu	37	12	93517618	93517619	+	RNA	INS	-	-	A	rs200193906		TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr12:93517618_93517619insA	ENST00000550324.1	-	0	85				RP11-511B23.2_ENST00000549930.1_RNA																							aaaaaataaataaaaaaaaaaG	0.391																																					.													.	.			0			.																																											0	.			AATAAATAAAAAA																													12.37:g.93517628_93517628dupA			Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	6	0.67	4	.	0		0		RNA	INS	ENST00000550324.1	37																																																																																						0.391	RP11-511B23.2-001	KNOWN	basic	antisense	antisense		OTTHUMT00000407311.1			
SELPLG	6404	broad.mit.edu	37	12	109017521	109017521	+	Missense_Mutation	SNP	C	C	G			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr12:109017521C>G	ENST00000550948.1	-	2	787	c.563G>C	c.(562-564)gGc>gCc	p.G188A	SELPLG_ENST00000228463.6_Missense_Mutation_p.G204A|SELPLG_ENST00000388962.3_Missense_Mutation_p.G178A			Q14242	SELPL_HUMAN	selectin P ligand	188	12 X 10 AA tandem repeats.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular response to interleukin-6 (GO:0071354)|leukocyte adhesive activation (GO:0050902)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|prostate(3)|skin(1)	12						TGCCTCCAGGCCTGTGGGTTG	0.637																																					p.G204A													.	SELPLG	138		0			c.G611C												184.0	140.0	155.0					12																	109017521		2203	4300	6503	SO:0001583	missense	0	exon2			TCCAGGCCTGTGG		CCDS31895.1, CCDS31895.2, CCDS55881.1	12q24	2014-01-30						"""CD molecules"", ""Endogenous ligands"""	10722	protein-coding gene	gene with protein product		600738				7505206	Standard	NM_003006		Approved	PSGL-1, CD162	uc010sxe.2	Q14242		ENST00000550948.1:c.563G>C	12.37:g.109017521C>G	ENSP00000447752:p.Gly188Ala		Somatic	113	0.017699115	2		WXS	Illumina HiSeq	Phase_I	185	0.05	9	NM_001206609	75	0.00	0	A8K2Y0|B4DQC3|B7Z5C7|J3KMX6|Q12775|Q6GTW7|Q8N7J7	Missense_Mutation	SNP	ENST00000550948.1	37	CCDS31895.2	.	.	.	.	.	.	.	.	.	.	G	0.199	-1.046801	0.01997	.	.	ENSG00000110876	ENST00000388962;ENST00000550948;ENST00000228463	T;T;T	0.28069	1.63;1.63;1.63	3.31	1.47	0.22746	.	0.737981	0.11117	N	0.597806	T	0.06325	0.0163	N	0.00368	-1.59	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.37731	-0.9693	10	0.02654	T	1	-2.2343	6.622	0.22808	0.1745:0.1505:0.6749:0.0	.	204;188;148	B7Z5C7;Q14242;B4DHR9	.;SELPL_HUMAN;.	A	178;188;204	ENSP00000373614:G178A;ENSP00000447752:G188A;ENSP00000228463:G204A	ENSP00000228463:G204A	G	-	2	0	SELPLG	107541650	0.002000	0.14202	0.001000	0.08648	0.001000	0.01503	0.167000	0.16602	0.410000	0.25675	-0.328000	0.08392	GGC			0.637	SELPLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000403904.1			
CCDC64	92558	mdanderson.org	37	12	120427769	120427769	+	Missense_Mutation	SNP	G	G	A			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr12:120427769G>A	ENST00000397558.2	+	1	97	c.97G>A	c.(97-99)Gca>Aca	p.A33T		NM_207311.2	NP_997194.2	Q6ZP65	BICR1_HUMAN	coiled-coil domain containing 64	33					Golgi to secretory granule transport (GO:0055107)|neuron projection development (GO:0031175)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	dynactin binding (GO:0034452)|Rab GTPase binding (GO:0017137)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(2)|lung(4)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	22	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GGCCGGGGACGCAGTCCGGAG	0.751																																					p.A33T													.	.			0			c.G97A												1.0	2.0	2.0					12																	120427769		1004	2584	3588	SO:0001583	missense	92558	exon1			GGGGACGCAGTCC	U88834, AK129960	CCDS41845.1	12q24.23	2006-01-24				ENSG00000135127			28095	protein-coding gene	gene with protein product							Standard	NM_207311		Approved	FLJ26450	uc001txl.1	Q6ZP65	OTTHUMG00000169311	ENST00000397558.2:c.97G>A	12.37:g.120427769G>A	ENSP00000380690:p.Ala33Thr		Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	23	0.09	2	NM_207311	22	0.00	0	A8MUC8|B4DWL0|B5MDJ0|O95000	Missense_Mutation	SNP	ENST00000397558.2	37	CCDS41845.1	.	.	.	.	.	.	.	.	.	.	G	14.39	2.520266	0.44866	.	.	ENSG00000135127	ENST00000357093;ENST00000397558	T	0.30714	1.52	3.24	1.13	0.20643	.	1.219230	0.06544	U	0.743721	T	0.13329	0.0323	N	0.08118	0	0.80722	D	1	B	0.25048	0.117	B	0.21917	0.037	T	0.43556	-0.9384	10	0.16420	T	0.52	-2.6962	3.2656	0.06864	0.1506:0.0:0.5909:0.2584	.	33	Q6ZP65	BICR1_HUMAN	T	33	ENSP00000380690:A33T	ENSP00000349605:A33T	A	+	1	0	CCDC64	118912152	0.008000	0.16893	0.975000	0.42487	0.796000	0.44982	0.104000	0.15313	1.364000	0.46038	0.450000	0.29827	GCA			0.751	CCDC64-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding		OTTHUMT00000403390.2		NM_207311	
TMEM132B	114795	broad.mit.edu	37	12	125834096	125834096	+	Missense_Mutation	SNP	T	T	C			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr12:125834096T>C	ENST00000299308.3	+	2	159	c.151T>C	c.(151-153)Ttt>Ctt	p.F51L	TMEM132B_ENST00000418253.2_3'UTR	NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	51						integral component of membrane (GO:0016021)				NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(45)|ovary(5)|pancreas(1)|prostate(4)|skin(15)|upper_aerodigestive_tract(3)|urinary_tract(1)	107	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)		AGAGGAGTCCTTTTTCCTTAA	0.527																																					p.F51L													.	TMEM132B	207		0			c.T151C												132.0	132.0	132.0					12																	125834096		1939	4145	6084	SO:0001583	missense	114795	exon2			GAGTCCTTTTTCC	AB067493	CCDS41859.1, CCDS66501.1	12q24.31	2006-03-02							29397	protein-coding gene	gene with protein product						11572484	Standard	NM_001286219		Approved	KIAA1906, KIAA1786	uc001uhe.1	Q14DG7		ENST00000299308.3:c.151T>C	12.37:g.125834096T>C	ENSP00000299308:p.Phe51Leu		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	337	0.01	4	NM_052907	1	0.00	0	A2RRG8|Q8NA73|Q96JN9|Q96PY1	Missense_Mutation	SNP	ENST00000299308.3	37	CCDS41859.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.480918	0.84747	.	.	ENSG00000139364	ENST00000299308	T	0.07216	3.21	5.41	5.41	0.78517	.	.	.	.	.	T	0.21509	0.0518	L	0.39898	1.24	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.00553	-1.1674	9	0.54805	T	0.06	.	15.4399	0.75176	0.0:0.0:0.0:1.0	.	51	Q14DG7	T132B_HUMAN	L	51	ENSP00000299308:F51L	ENSP00000299308:F51L	F	+	1	0	TMEM132B	124400049	1.000000	0.71417	0.943000	0.38184	0.534000	0.34807	7.747000	0.85070	2.034000	0.60081	0.482000	0.46254	TTT			0.527	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000400043.1		NM_052907	
NKX2-1	7080	broad.mit.edu	37	14	36988467	36988467	+	Silent	SNP	G	G	T			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr14:36988467G>T	ENST00000518149.1	-	2	701	c.96C>A	c.(94-96)ggC>ggA	p.G32G	NKX2-1_ENST00000498187.2_Silent_p.G32G|NKX2-1_ENST00000354822.5_Silent_p.G62G|RP11-896J10.3_ENST00000521945.1_RNA|NKX2-1-AS1_ENST00000521292.2_RNA|NKX2-1_ENST00000522719.2_Silent_p.G32G			P43699	NKX21_HUMAN	NK2 homeobox 1	32					anatomical structure formation involved in morphogenesis (GO:0048646)|axon guidance (GO:0007411)|brain development (GO:0007420)|cerebral cortex cell migration (GO:0021795)|cerebral cortex GABAergic interneuron differentiation (GO:0021892)|Clara cell differentiation (GO:0060486)|developmental induction (GO:0031128)|endoderm development (GO:0007492)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|forebrain development (GO:0030900)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain neuron fate commitment (GO:0021877)|globus pallidus development (GO:0021759)|hippocampus development (GO:0021766)|Leydig cell differentiation (GO:0033327)|locomotory behavior (GO:0007626)|lung development (GO:0030324)|lung saccule development (GO:0060430)|menarche (GO:0042696)|negative regulation of cell migration (GO:0030336)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron migration (GO:0001764)|oligodendrocyte differentiation (GO:0048709)|phospholipid metabolic process (GO:0006644)|pituitary gland development (GO:0021983)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|rhythmic process (GO:0048511)|thyroid gland development (GO:0030878)|Type II pneumocyte differentiation (GO:0060510)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(2)	7	all_cancers(3;4.47e-51)|Hepatocellular(127;0.158)|Esophageal squamous(585;0.164)|Breast(36;0.165)		Lung(8;1.8e-08)|LUAD - Lung adenocarcinoma(9;2.16e-07)|Epithelial(34;0.014)|all cancers(34;0.0366)|LUSC - Lung squamous cell carcinoma(13;0.132)	GBM - Glioblastoma multiforme(112;0.0171)		CCCCGAGGCCGCCGCCCTCCA	0.657			A		NSCLC																																p.G62G				Dom	yes		14	14q13	7080	NK2 homeobox 1		E	.	NKX2-1	21		0			c.C186A												9.0	10.0	10.0					14																	36988467		2172	4264	6436	SO:0001819	synonymous_variant	7080	exon2			GAGGCCGCCGCCC		CCDS9659.1, CCDS41945.1	14q13.3	2012-03-09	2007-07-26	2007-07-26	ENSG00000136352	ENSG00000136352		"""Homeoboxes / ANTP class : NKL subclass"""	11825	protein-coding gene	gene with protein product		600635	"""benign chorea"", ""thyroid transcription factor 1"""	NKX2A, BCH, TITF1		1976511	Standard	NM_001079668		Approved	TTF-1, TTF1	uc001wtu.3	P43699	OTTHUMG00000140225	ENST00000518149.1:c.96C>A	14.37:g.36988467G>T			Somatic	79	0.0253164557	2		WXS	Illumina HiSeq	Phase_I	138	0.03	4	NM_001079668	0		0	D3DSA3|O14954|O14955|Q7KZF6|Q9BRJ8	Silent	SNP	ENST00000518149.1	37	CCDS9659.1																																																																																					0.657	NKX2-1-004	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000376225.2		NM_003317	
OTX2	5015	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	14	57271040	57271040	+	Missense_Mutation	SNP	G	G	A			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr14:57271040G>A	ENST00000555006.1	-	3	523	c.115C>T	c.(115-117)Cgc>Tgc	p.R39C	OTX2_ENST00000408990.3_Missense_Mutation_p.R39C|OTX2_ENST00000554788.1_Intron|OTX2_ENST00000339475.5_Missense_Mutation_p.R47C|OTX2_ENST00000554559.1_Intron			P32243	OTX2_HUMAN	orthodenticle homeobox 2	39					axon guidance (GO:0007411)|cell fate specification (GO:0001708)|diencephalon morphogenesis (GO:0048852)|dorsal/ventral pattern formation (GO:0009953)|endoderm development (GO:0007492)|eye photoreceptor cell fate commitment (GO:0042706)|forebrain development (GO:0030900)|inner ear morphogenesis (GO:0042472)|metencephalon development (GO:0022037)|midbrain development (GO:0030901)|neuron fate determination (GO:0048664)|positive regulation of embryonic development (GO:0040019)|positive regulation of gastrulation (GO:2000543)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|primitive streak formation (GO:0090009)|protein complex assembly (GO:0006461)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of smoothened signaling pathway (GO:0008589)|somite rostral/caudal axis specification (GO:0032525)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|nucleus (GO:0005634)|protein complex (GO:0043234)	eukaryotic initiation factor 4E binding (GO:0008190)|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)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	19	Medulloblastoma(1;0.00184)|all_neural(1;0.00414)					CTCTCCCGGCGCTGTTTCCGG	0.632																																					p.R47C													.	.			0			c.C139T												41.0	40.0	40.0					14																	57271040		2203	4300	6503	SO:0001583	missense	5015	exon2			CCCGGCGCTGTTT	AF298117	CCDS9728.1, CCDS41960.1	14q22.3	2014-09-17	2007-02-15		ENSG00000165588	ENSG00000165588		"""Homeoboxes / PRD class"""	8522	protein-coding gene	gene with protein product		600037	"""orthodenticle homolog 2 (Drosophila)"""			7959790	Standard	NM_021728		Approved		uc031qor.1	P32243	OTTHUMG00000152338	ENST00000555006.1:c.115C>T	14.37:g.57271040G>A	ENSP00000452336:p.Arg39Cys		Somatic	109	0	0		WXS	Illumina HiSeq	.	191	0.16	31	NM_001270525	33	0.27	9	B2RAN5|Q6GTV3|Q9HAW3|Q9P2R1	Missense_Mutation	SNP	ENST00000555006.1	37	CCDS41960.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.239855	0.79912	.	.	ENSG00000165588	ENST00000339475;ENST00000408990;ENST00000555006;ENST00000554845;ENST00000555804	D;D;D;D;D	0.97352	-4.35;-4.35;-4.35;-4.35;-4.35	5.58	4.6	0.57074	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.39475	N	0.001353	D	0.99102	0.9691	H	0.99130	4.44	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98383	1.0559	10	0.87932	D	0	.	12.4707	0.55785	0.0:0.0:0.7598:0.2402	.	47;39	F1T0D1;P32243	.;OTX2_HUMAN	C	47;39;39;47;39	ENSP00000343819:R47C;ENSP00000386185:R39C;ENSP00000452336:R39C;ENSP00000451357:R47C;ENSP00000451272:R39C	ENSP00000343819:R47C	R	-	1	0	OTX2	56340793	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.025000	0.41059	2.617000	0.88574	0.655000	0.94253	CGC			0.632	OTX2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000411522.1		NM_021728.	
TDRD9	122402	mdanderson.org	37	14	104481101	104481101	+	Nonsense_Mutation	SNP	C	C	T			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr14:104481101C>T	ENST00000409874.4	+	21	2194	c.2146C>T	c.(2146-2148)Cag>Tag	p.Q716*	RN7SL634P_ENST00000485467.2_RNA|TDRD9_ENST00000339063.5_Nonsense_Mutation_p.Q716*	NM_153046.2	NP_694591.2	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9	716					cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|piP-body (GO:0071547)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)				TAGAATCTCACAGTTCAACAT	0.383																																					p.Q716X													.	.			0			c.C2146T												148.0	146.0	146.0					14																	104481101		2203	4300	6503	SO:0001587	stop_gained	122402	exon21			ATCTCACAGTTCA	AK093483	CCDS9987.2	14q32.33	2013-01-23	2004-04-01	2004-04-02	ENSG00000156414	ENSG00000156414		"""Tudor domain containing"""	20122	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 75"""	C14orf75			Standard	NM_153046		Approved	DKFZp434N0820, FLJ36164, NET54	uc001yom.4	Q8NDG6	OTTHUMG00000152876	ENST00000409874.4:c.2146C>T	14.37:g.104481101C>T	ENSP00000387303:p.Gln716*		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	66	0.05	3	NM_153046	4	0.00	0	A1A4S7|Q6ZU54|Q8N7T3|Q8N827|Q8N9V5|Q96AS9	Nonsense_Mutation	SNP	ENST00000409874.4	37	CCDS9987.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	35|35	5.550986|5.550986	0.96501|0.96501	.|.	.|.	ENSG00000156414|ENSG00000156414	ENST00000409874;ENST00000339063|ENST00000557332	.|.	.|.	.|.	5.09|5.09	5.09|5.09	0.68999|0.68999	.|.	0.392290|.	0.24202|.	N|.	0.040602|.	.|T	.|0.60830	.|0.2299	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.68198	.|-0.5472	.|3	0.34782|.	T|.	0.22|.	.|.	11.8569|11.8569	0.52441|0.52441	0.1347:0.7349:0.1304:0.0|0.1347:0.7349:0.1304:0.0	.|.	.|.	.|.	.|.	X|I	716|442	.|.	ENSP00000343545:Q716X|.	Q|T	+|+	1|2	0|0	TDRD9|TDRD9	103550854|103550854	0.867000|0.867000	0.29959|0.29959	0.951000|0.951000	0.38953|0.38953	0.916000|0.916000	0.54674|0.54674	1.633000|1.633000	0.37113|0.37113	2.527000|2.527000	0.85204|0.85204	0.563000|0.563000	0.77884|0.77884	CAG|ACA			0.383	TDRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000328325.3		NM_153046	
UBN1	29855	ucsc.edu	37	16	4925276	4925276	+	Silent	SNP	G	G	A			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr16:4925276G>A	ENST00000396658.4	+	14	3568	c.2865G>A	c.(2863-2865)ggG>ggA	p.G955G	UBN1_ENST00000262376.6_Silent_p.G955G|UBN1_ENST00000545171.1_Silent_p.G955G|UBN1_ENST00000590769.1_Silent_p.G955G	NM_016936.3	NP_058632.2	Q9NPG3	UBN1_HUMAN	ubinuclein 1	955	Ser-rich.				chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|negative regulation of phosphatase activity (GO:0010923)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|tight junction (GO:0005923)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(6)|kidney(4)|large_intestine(10)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38						GTTCAGCAGGGAAAAAAATGC	0.587																																					p.G955G													.	UBN1	88		0			c.G2865A												48.0	54.0	52.0					16																	4925276		2197	4300	6497	SO:0001819	synonymous_variant	29855	exon15			AGCAGGGAAAAAA	AF108460	CCDS10525.1, CCDS73822.1	16p13.3	2010-11-09			ENSG00000118900	ENSG00000118900			12506	protein-coding gene	gene with protein product		609771				10725330	Standard	XM_005255277		Approved		uc002cyb.3	Q9NPG3	OTTHUMG00000129531	ENST00000396658.4:c.2865G>A	16.37:g.4925276G>A			Somatic	81	0	0		RNA-Seq	Illumina HiSeq		97	0.01	1	NM_001079514	34	0.18	6	B7Z6D3|D3DUE8|Q13079|Q9P1P7	Silent	SNP	ENST00000396658.4	37	CCDS10525.1																																																																																					0.587	UBN1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000251719.1		NM_016936	
C16orf62	57020	broad.mit.edu	37	16	19612991	19612991	+	Missense_Mutation	SNP	C	C	A			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr16:19612991C>A	ENST00000251143.5	+	9	742	c.730C>A	c.(730-732)Ctc>Atc	p.L244I	C16orf62_ENST00000538853.1_3'UTR|C16orf62_ENST00000438132.3_Missense_Mutation_p.L333I|C16orf62_ENST00000417362.2_Missense_Mutation_p.L244I|C16orf62_ENST00000448695.1_Splice_Site_p.L94I|C16orf62_ENST00000543152.1_5'UTR|C16orf62_ENST00000542263.1_Missense_Mutation_p.L333I			Q7Z3J2	CP062_HUMAN	chromosome 16 open reading frame 62	244						integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	36						CCCAGGAAAGCTCGTGTACGA	0.488											OREG0023661	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L333I													.	C16orf62	164		0			c.C997A												157.0	124.0	135.0					16																	19612991		2197	4300	6497	SO:0001583	missense	57020	exon9			GGAAAGCTCGTGT		CCDS32397.1, CCDS32397.2, CCDS73840.1	16p12.3	2012-05-30			ENSG00000103544	ENSG00000103544			24641	protein-coding gene	gene with protein product						10493829	Standard	NM_020314		Approved	MGC16824	uc002dgn.3	Q7Z3J2	OTTHUMG00000167925	ENST00000251143.5:c.730C>A	16.37:g.19612991C>A	ENSP00000251143:p.Leu244Ile		Somatic	111	0.009009009	1	734	WXS	Illumina HiSeq	Phase_I	110	0.06	7	NM_020314	33	0.00	0	A8K2M1|O43329|Q69YI1|Q6PDA0|Q7L371|Q86W66|Q8WXA5|Q9H0L7|Q9H7C8	Missense_Mutation	SNP	ENST00000251143.5	37		.	.	.	.	.	.	.	.	.	.	C	17.02	3.283011	0.59867	.	.	ENSG00000103544	ENST00000438132;ENST00000542263;ENST00000251143;ENST00000417362;ENST00000448695	T;T;T;T;T	0.63580	-0.05;-0.05;-0.05;-0.05;-0.05	5.3	1.97	0.26223	.	0.000000	0.64402	D	0.000001	T	0.77665	0.4164	M	0.87547	2.89	0.80722	D	1	D;D;D;D	0.67145	0.984;0.974;0.967;0.996	P;D;P;D	0.67725	0.752;0.953;0.789;0.946	T	0.79077	-0.1951	10	0.66056	D	0.02	-15.1376	10.2431	0.43324	0.0:0.7537:0.0:0.2463	.	244;333;244;333	B3KT69;F5H7K1;Q7Z3J2;E7EWW0	.;.;CP062_HUMAN;.	I	333;333;244;244;94	ENSP00000400815:L333I;ENSP00000442468:L333I;ENSP00000251143:L244I;ENSP00000395973:L244I;ENSP00000398009:L94I	ENSP00000251143:L244I	L	+	1	0	C16orf62	19520492	1.000000	0.71417	0.902000	0.35471	0.635000	0.38103	1.183000	0.32041	0.613000	0.30089	0.462000	0.41574	CTC			0.488	C16orf62-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				NM_020314	
SLC6A10P	386757	broad.mit.edu	37	16	32890622	32890622	+	RNA	SNP	T	T	G	rs200656321		TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr16:32890622T>G	ENST00000330048.5	-	0	3176					NR_003083.2				solute carrier family 6 (neurotransmitter transporter), member 10, pseudogene																		CGTTGGTGTTTTTGTAGACCA	0.617																																					.													.	.			0			.																																											0	.			GGTGTTTTTGTAG	U41163		16p11.2	2013-07-19	2013-07-19	2013-07-19	ENSG00000214617	ENSG00000214617		"""Solute carriers"""	11043	pseudogene	pseudogene	"""creatine transporter-2"""		"""solute carrier family 6 (neurotransmitter transporter, creatine), member 10"""	SLC6A10		9154116	Standard	NR_003083		Approved	CT-2	uc002edh.1		OTTHUMG00000132481		16.37:g.32890622T>G			Somatic	93	0.0107526882	1		WXS	Illumina HiSeq	Phase_I	120	0.08	10	.	1	0.00	0		RNA	SNP	ENST00000330048.5	37																																																																																						0.617	SLC6A10P-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000432081.2			
PKD1L2	114780	mdanderson.org	37	16	81213378	81213378	+	RNA	SNP	A	A	T	rs4889261	byFrequency	TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr16:81213378A>T	ENST00000527937.1	-	0	190				PKD1L2_ENST00000533478.1_RNA|PKD1L2_ENST00000337114.4_RNA|PKD1L2_ENST00000525539.1_RNA|PKD1L2_ENST00000531391.1_RNA			Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						GCAGGCATCCAGGAGGGGCTC	0.597																																					p.L711Q													.	.			0			c.T2132A												43.0	45.0	44.0					16																	81213378		1950	4152	6102			114780	exon13			GCATCCAGGAGGG	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81213378A>T			Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	87	0.02	2	NM_001076780	0		0	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000527937.1	37		.	.	.	.	.	.	.	.	.	.	G	10.27	1.302908	0.23736	.	.	ENSG00000166473	ENST00000531391;ENST00000337114;ENST00000527937	T;T;T	0.68765	2.47;-0.35;2.13	5.02	5.02	0.67125	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);	0.212459	0.34986	N	0.003525	T	0.65450	0.2692	.	.	.	0.39544	P	0.03113200000000005	B;B;B	0.25719	0.0;0.087;0.132	B;B;B	0.36845	0.001;0.053;0.234	T	0.72766	-0.4194	8	0.87932	D	0	-16.099	10.9073	0.47088	0.0886:0.0:0.9114:0.0	.	26;711;711	Q7Z442-6;Q7Z442-3;Q7Z442	.;.;PK1L2_HUMAN	Q	26;711;26	ENSP00000436309:L26Q;ENSP00000337397:L711Q;ENSP00000432818:L26Q	ENSP00000337397:L711Q	L	-	2	0	PKD1L2	79770879	0.998000	0.40836	0.737000	0.30932	0.003000	0.03518	3.419000	0.52728	1.137000	0.42214	-0.355000	0.07637	CTG			0.597	PKD1L2-007	KNOWN	basic|exp_conf	protein_coding	polymorphic_pseudogene		OTTHUMT00000387978.1			
CMIP	80790	mdanderson.org	37	16	81737575	81737575	+	Missense_Mutation	SNP	G	G	A			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr16:81737575G>A	ENST00000537098.3	+	18	2048	c.1976G>A	c.(1975-1977)gGc>gAc	p.G659D	CMIP_ENST00000398040.4_Missense_Mutation_p.G506D|CMIP_ENST00000566513.1_3'UTR|CMIP_ENST00000539778.2_Missense_Mutation_p.G565D	NM_198390.2	NP_938204.2	Q8IY22	CMIP_HUMAN	c-Maf inducing protein	659						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(5)|kidney(1)|lung(7)	13						CTGAGCTCCGGCTCCTTCGGA	0.612																																					p.G659D													CMIP,NS,carcinoma,+1,2	CMIP	1	2	0			c.G1976A												41.0	49.0	46.0					16																	81737575		2188	4283	6471	SO:0001583	missense	80790	exon18			GCTCCGGCTCCTT	AB051481	CCDS54044.1, CCDS54045.1	16q23	2011-08-04			ENSG00000153815	ENSG00000153815			24319	protein-coding gene	gene with protein product		610112				11214970, 12939343	Standard	NM_030629		Approved		uc002fgp.3	Q8IY22		ENST00000537098.3:c.1976G>A	16.37:g.81737575G>A	ENSP00000446100:p.Gly659Asp		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	36	0.08	3	NM_198390	95	0.00	0	Q9C0G9	Missense_Mutation	SNP	ENST00000537098.3	37	CCDS54044.1	.	.	.	.	.	.	.	.	.	.	G	32	5.170759	0.94807	.	.	ENSG00000153815	ENST00000537098;ENST00000539778;ENST00000398040;ENST00000542097	T;T	0.54071	0.59;0.59	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.63153	0.2487	L	0.27053	0.805	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.996;0.986	T	0.67067	-0.5764	10	0.66056	D	0.02	.	18.8746	0.92329	0.0:0.0:1.0:0.0	.	506;565;659	Q8IY22-3;Q8IY22-2;Q8IY22	.;.;CMIP_HUMAN	D	659;565;565;472	ENSP00000446100:G659D;ENSP00000440401:G565D	ENSP00000381120:G565D	G	+	2	0	CMIP	80295076	1.000000	0.71417	0.992000	0.48379	0.992000	0.81027	9.420000	0.97426	2.475000	0.83589	0.549000	0.68633	GGC			0.612	CMIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000432399.2		NM_030629	
ZC3H18	124245	broad.mit.edu	37	16	88677720	88677721	+	In_Frame_Ins	INS	-	-	GAGCGG	rs369086353|rs529387142		TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr16:88677720_88677721insGAGCGG	ENST00000301011.5	+	8	1451_1452	c.1251_1252insGAGCGG	c.(1252-1254)gag>GAGCGGgag	p.418_418E>ERE	ZC3H18_ENST00000452588.2_In_Frame_Ins_p.442_442E>ERE	NM_144604.3	NP_653205.3	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18	418						nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(9)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	42				BRCA - Breast invasive adenocarcinoma(80;0.0542)		agcgcgagcgcgagcgggagcg	0.658																																					p.R417delinsRER	Ovarian(121;375 2276 20373 38669)												ZC3H18,colon,carcinoma,0,2	ZC3H18	90	2	0			c.1251_1252insGAGCGG																																									SO:0001652	inframe_insertion	124245	exon8			CGAGCGCGAGCGG	BC001584	CCDS10967.1, CCDS73924.1	16q24.2-q24.3	2012-07-05			ENSG00000158545	ENSG00000158545		"""Zinc fingers, CCCH-type domain containing"""	25091	protein-coding gene	gene with protein product						17579712	Standard	NM_144604		Approved	NHN1	uc002fky.3	Q86VM9	OTTHUMG00000137679	ENST00000301011.5:c.1264_1269dupGAGCGG	16.37:g.88677721_88677726dupGAGCGG	ENSP00000301011:p.ArgGlu422dup		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	60	0.13	8	NM_144604	40	0.00	0	Q96DG4|Q96MP7	In_Frame_Ins	INS	ENST00000301011.5	37	CCDS10967.1																																																																																					0.658	ZC3H18-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000269168.1		NM_144604	
UBB	7314	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	17	16285479	16285479	+	Silent	SNP	C	C	G			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr17:16285479C>G	ENST00000395837.1	+	2	439	c.258C>G	c.(256-258)ggC>ggG	p.G86G	UBB_ENST00000578649.1_Intron|UBB_ENST00000535788.1_Intron|UBB_ENST00000395839.1_Silent_p.G86G|RP11-138I1.4_ENST00000583934.1_RNA|UBB_ENST00000302182.3_Silent_p.G86G	NM_001281718.1|NM_001281720.1	NP_001268647.1|NP_001268649.1	P0CG47	UBB_HUMAN	ubiquitin B	86	Ubiquitin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00214}.		GMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFV KTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFA GKQLEDGRTLSDYNIQKESTLHLVLRLRGGC -> YADLRE DPDRQDHHPGSGAQ (in UBB(+1); loss of polyubiquitination; impairs the ubiquitin-proteasome pathway; refractory to disassembly by DUBs; slow degradation by UCHL3).		activation of MAPK activity (GO:0000187)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)		CCCTGACCGGCAAGACCATCA	0.552																																					p.G86G	Melanoma(163;1126 3406 34901)												.	.			0			c.C258G												69.0	70.0	69.0					17																	16285479		2203	4297	6500	SO:0001819	synonymous_variant	7314	exon2			GACCGGCAAGACC		CCDS11177.1	17p12-p11.2	2010-11-25			ENSG00000170315	ENSG00000170315			12463	protein-coding gene	gene with protein product	"""polyubiquitin B"""	191339				2154095	Standard	NM_018955		Approved	MGC8385, FLJ25987	uc002gpx.3	P0CG47	OTTHUMG00000058987	ENST00000395837.1:c.258C>G	17.37:g.16285479C>G			Somatic	95	0	0		WXS	Illumina HiSeq	.	106	0.12	13	NM_018955	2236	0.15	330	P02248|P02249|P02250|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Silent	SNP	ENST00000395837.1	37	CCDS11177.1																																																																																					0.552	UBB-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding		OTTHUMT00000130459.1		NM_018955	
KRT17P4	339186	broad.mit.edu	37	17	16748911	16748913	+	RNA	DEL	GCT	GCT	-	rs374561720	byFrequency	TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	GCT	GCT					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr17:16748911_16748913delGCT	ENST00000578037.1	-	0	593				KRT17P1_ENST00000580363.1_RNA																							CGCCCTCAAAGCTGCTGCTGCCA	0.65														2545	0.508187	0.5053	0.536	5008	,	,		12311	0.4067		0.5686	False		,,,				2504	0.5348				.													.	.			0			.																																											0	.			CTCAAAGCTGCTG																													17.37:g.16748917_16748919delGCT			Somatic	170	0.0058823529	1		WXS	Illumina HiSeq	Phase_I	207	0.04	8	.	1	0.00	0		RNA	DEL	ENST00000578037.1	37																																																																																						0.650	AC022596.2-005	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000444295.1			
NF1	4763	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	17	29496939	29496939	+	Silent	SNP	C	C	T			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr17:29496939C>T	ENST00000358273.4	+	5	893	c.510C>T	c.(508-510)gaC>gaT	p.D170D	NF1_ENST00000356175.3_Silent_p.D170D|NF1_ENST00000431387.4_Silent_p.D170D	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	170					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(4)|p.E169fs*1(1)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		GTTCAGAAGACAATGTTGATG	0.308			"""D, Mis, N, F, S, O"""		"""neurofibroma, glioma"""	"""neurofibroma, glioma"""			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																											p.D170D			yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	.	.			13	Whole gene deletion(8)|Unknown(4)|Deletion - Frameshift(1)	soft_tissue(8)|autonomic_ganglia(3)|central_nervous_system(2)	c.C510T												94.0	94.0	94.0					17																	29496939		2203	4300	6503	SO:0001819	synonymous_variant	4763	exon5	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	AGAAGACAATGTT		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"""neurofibromatosis"", ""von Recklinghausen disease"", ""Watson disease"""	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.510C>T	17.37:g.29496939C>T			Somatic	93	0	0		WXS	Illumina HiSeq	.	96	0.14	13	NM_001128147	4	0.50	2	O00662|Q14284|Q14930|Q14931|Q9UMK3	Silent	SNP	ENST00000358273.4	37	CCDS42292.1																																																																																					0.308	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000256351.2		NM_000267	
C17orf98	388381	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	17	36997456	36997456	+	Missense_Mutation	SNP	G	G	A			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr17:36997456G>A	ENST00000398575.4	-	1	252	c.187C>T	c.(187-189)Ctt>Ttt	p.L63F		NM_001080465.2	NP_001073934.1	A8MV24	CQ098_HUMAN	chromosome 17 open reading frame 98	63										endometrium(5)|kidney(1)|large_intestine(1)|lung(3)|pancreas(1)|prostate(3)	14						TTCCGCAAAAGGGGCGGAACC	0.592																																					p.L63F													.	.			0			c.C187T												56.0	55.0	55.0					17																	36997456		1929	4131	6060	SO:0001583	missense	388381	exon1			GCAAAAGGGGCGG	AC006449, DY654789	CCDS42310.1	17q12	2014-05-06			ENSG00000214556	ENSG00000275489			34492	protein-coding gene	gene with protein product						16625196	Standard	NM_001080465		Approved	LOC388381	uc002hqv.2	A8MV24	OTTHUMG00000188506	ENST00000398575.4:c.187C>T	17.37:g.36997456G>A	ENSP00000381580:p.Leu63Phe		Somatic	59	0	0		WXS	Illumina HiSeq	.	111	0.16	18	NM_001080465	1	1.00	1		Missense_Mutation	SNP	ENST00000398575.4	37	CCDS42310.1	.	.	.	.	.	.	.	.	.	.	G	16.56	3.157711	0.57368	.	.	ENSG00000214556	ENST00000398575	T	0.48836	0.8	5.16	-6.26	0.02033	.	1.083180	0.07555	U	0.916014	T	0.31638	0.0803	L	0.32530	0.975	0.09310	N	1	B	0.25441	0.126	B	0.29942	0.109	T	0.40850	-0.9541	10	0.66056	D	0.02	-3.5214	4.6506	0.12592	0.1098:0.1895:0.1098:0.5909	.	63	A8MV24	CQ098_HUMAN	F	63	ENSP00000381580:L63F	ENSP00000381580:L63F	L	-	1	0	C17orf98	34250982	0.000000	0.05858	0.004000	0.12327	0.865000	0.49528	-1.752000	0.01819	-1.441000	0.01958	-1.498000	0.00962	CTT			0.592	C17orf98-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000255469.2		NM_001080465	
CDC27	996	mdanderson.org	37	17	45234325	45234325	+	Nonsense_Mutation	SNP	G	G	A			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr17:45234325G>A	ENST00000066544.3	-	7	889	c.796C>T	c.(796-798)Cga>Tga	p.R266*	CDC27_ENST00000527547.1_Nonsense_Mutation_p.R266*|CDC27_ENST00000531206.1_Nonsense_Mutation_p.R266*|CDC27_ENST00000446365.2_Nonsense_Mutation_p.R205*|CDC27_ENST00000528748.1_5'Flank	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	266					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						AATAAACTTCGACCAGTTTTT	0.363																																					p.R266X													.	.			0			c.C796T												60.0	65.0	63.0					17																	45234325		2200	4295	6495	SO:0001587	stop_gained	996	exon7			AACTTCGACCAGT	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.796C>T	17.37:g.45234325G>A	ENSP00000066544:p.Arg266*		Somatic	58	0.0172413793	1		WXS	Illumina HiSeq	Phase_I	64	0.05	3	NM_001114091	42	0.00	0	G3V1C4|Q16349|Q96F35	Nonsense_Mutation	SNP	ENST00000066544.3	37	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.117088	0.77323	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547;ENST00000526866	.	.	.	5.64	4.66	0.58398	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-17.5002	13.5956	0.61987	0.0:0.0:0.8433:0.1567	.	.	.	.	X	266;266;205;266;266	.	ENSP00000066544:R266X	R	-	1	2	CDC27	42589324	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.123000	0.71614	1.354000	0.45846	0.460000	0.39030	CGA			0.363	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding		OTTHUMT00000389742.2			
HOXB9	3219	mdanderson.org	37	17	46703562	46703562	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr17:46703562G>T	ENST00000311177.5	-	1	277	c.70C>A	c.(70-72)Cct>Act	p.P24T	HOXB-AS4_ENST00000480386.1_RNA|HOXB9_ENST00000550387.1_Missense_Mutation_p.P24T|HOXB7_ENST00000567101.2_Intron	NM_024017.4	NP_076922.1	P17482	HXB9_HUMAN	homeobox B9	24					anterior/posterior pattern specification (GO:0009952)|canonical Wnt signaling pathway (GO:0060070)|cell chemotaxis (GO:0060326)|embryonic skeletal system development (GO:0048706)|mammary gland development (GO:0030879)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(2)|endometrium(1)|large_intestine(1)|liver(1)|lung(6)|prostate(1)	12						TTGGCTGGAGGCGCGTCCTCA	0.607																																					p.P24T													.	.			0			c.C70A												20.0	23.0	22.0					17																	46703562		2192	4273	6465	SO:0001583	missense	3219	exon1			CTGGAGGCGCGTC		CCDS11534.1	17q21.32	2011-06-20	2005-12-22		ENSG00000170689	ENSG00000170689		"""Homeoboxes / ANTP class : HOXL subclass"""	5120	protein-coding gene	gene with protein product		142964	"""homeo box B9"""	HOX2E, HOX2		1973146, 1358459	Standard	NM_024017		Approved		uc002inx.3	P17482	OTTHUMG00000159907	ENST00000311177.5:c.70C>A	17.37:g.46703562G>T	ENSP00000309439:p.Pro24Thr		Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	10	0.20	2	NM_024017	0		0	B2RDB7|Q9H1I1	Missense_Mutation	SNP	ENST00000311177.5	37	CCDS11534.1	.	.	.	.	.	.	.	.	.	.	G	10.56	1.383104	0.25031	.	.	ENSG00000170689	ENST00000311177;ENST00000442657;ENST00000550387	D	0.92699	-3.09	4.66	4.66	0.58398	Hox9, N-terminal activation domain (1);	0.204155	0.42172	D	0.000757	D	0.88555	0.6468	L	0.47016	1.485	0.38439	D	0.946664	P	0.38300	0.626	B	0.34722	0.188	D	0.88196	0.2880	10	0.23302	T	0.38	.	17.8979	0.88895	0.0:0.0:1.0:0.0	.	24	P17482	HXB9_HUMAN	T	24	ENSP00000309439:P24T	ENSP00000309439:P24T	P	-	1	0	HOXB9	44058561	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.357000	0.34090	2.277000	0.76020	0.555000	0.69702	CCT			0.607	HOXB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000358101.2			
GGA3	23163	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	17	73237088	73237088	+	Missense_Mutation	SNP	C	C	A			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr17:73237088C>A	ENST00000245541.6	-	11	1213	c.997G>T	c.(997-999)Gac>Tac	p.D333Y	GGA3_ENST00000537686.1_3'UTR|GGA3_ENST00000582486.1_Missense_Mutation_p.D261Y|GGA3_ENST00000578348.1_Missense_Mutation_p.D211Y|GGA3_ENST00000351904.7_Missense_Mutation_p.D300Y|GGA3_ENST00000579743.1_5'Flank|GGA3_ENST00000538886.1_Missense_Mutation_p.D211Y|GGA3_ENST00000582717.1_Missense_Mutation_p.D261Y	NM_138619.2	NP_619525.1	Q9NZ52	GGA3_HUMAN	golgi-associated, gamma adaptin ear containing, ARF binding protein 3	333	Unstructured hinge.				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|endosome (GO:0005768)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)			breast(2)|endometrium(3)|large_intestine(4)|liver(1)|lung(4)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	20			all cancers(21;2.39e-06)|Epithelial(20;2.38e-05)			TTGGTCGTGTCCAGCTCCGCA	0.577											OREG0024730	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D333Y													.	.			0			c.G997T												139.0	133.0	135.0					17																	73237088		2203	4300	6503	SO:0001583	missense	23163	exon11			TCGTGTCCAGCTC	AF190864	CCDS11716.1, CCDS11717.1, CCDS54164.1, CCDS58597.1	17q25	2010-02-12	2010-02-12			ENSG00000125447			17079	protein-coding gene	gene with protein product		606006				10747089, 10749927	Standard	NR_033345		Approved	KIAA0154	uc002jni.2	Q9NZ52		ENST00000245541.6:c.997G>T	17.37:g.73237088C>A	ENSP00000245541:p.Asp333Tyr		Somatic	112	0	0	1143	WXS	Illumina HiSeq	.	176	0.11	20	NM_138619	35	0.29	10	B7Z7E2|B7Z7M9|J3KRN0|Q15017|Q6IS16|Q9UJY3	Missense_Mutation	SNP	ENST00000245541.6	37	CCDS11717.1	.	.	.	.	.	.	.	.	.	.	C	10.31	1.314908	0.23908	.	.	ENSG00000125447	ENST00000245541;ENST00000351904;ENST00000537584;ENST00000538886	T;T	0.56444	1.85;0.46	5.4	5.4	0.78164	.	0.259992	0.35585	N	0.003104	T	0.65575	0.2704	L	0.46157	1.445	0.80722	D	1	D;P;D	0.65815	0.977;0.93;0.995	P;P;P	0.60345	0.75;0.873;0.855	T	0.67110	-0.5753	10	0.72032	D	0.01	-24.1664	19.5504	0.95315	0.0:1.0:0.0:0.0	.	211;300;333	B7Z7E2;Q9NZ52-2;Q9NZ52	.;.;GGA3_HUMAN	Y	333;300;261;211	ENSP00000245541:D333Y;ENSP00000326575:D300Y	ENSP00000245541:D333Y	D	-	1	0	GGA3	70748683	1.000000	0.71417	0.397000	0.26308	0.082000	0.17680	5.287000	0.65645	2.688000	0.91661	0.655000	0.94253	GAC			0.577	GGA3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000446645.1		NM_138619	
ELP2	55250	mdanderson.org	37	18	33726314	33726314	+	Silent	SNP	G	G	A	rs143713231		TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr18:33726314G>A	ENST00000358232.6	+	11	1158	c.1095G>A	c.(1093-1095)ttG>ttA	p.L365L	ELP2_ENST00000542824.1_Intron|ELP2_ENST00000442325.2_Silent_p.L430L|ELP2_ENST00000423854.2_Silent_p.L295L|ELP2_ENST00000350494.6_Intron|ELP2_ENST00000351393.6_Silent_p.L339L	NM_018255.2	NP_060725.1	Q6IA86	ELP2_HUMAN	elongator acetyltransferase complex subunit 2	365					chromatin organization (GO:0006325)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|nucleolus (GO:0005730)|transcription elongation factor complex (GO:0008023)				NS(1)|breast(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|skin(2)|urinary_tract(2)	30						ACGGAGCGTTGCACCTTTGGA	0.373													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18733	0.0		0.0	False		,,,				2504	0.0				p.L430L													.	.			0			c.G1290A							G	,,,,,	4,4402	8.1+/-20.4	0,4,2199	159.0	150.0	153.0		1290,,1017,,885,1095	2.9	0.8	18	dbSNP_134	153	0,8600		0,0,4300	no	coding-synonymous,intron,coding-synonymous,intron,coding-synonymous,coding-synonymous	ELP2	NM_001242875.1,NM_001242876.1,NM_001242877.1,NM_001242878.1,NM_001242879.1,NM_018255.2	,,,,,	0,4,6499	AA,AG,GG		0.0,0.0908,0.0308	,,,,,	430/892,,339/801,,295/757,365/827	33726314	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	55250	exon12			AGCGTTGCACCTT	AK001741	CCDS11918.1, CCDS56065.1, CCDS56066.1, CCDS56067.1, CCDS56068.1, CCDS56069.1	18q12.1	2013-01-10	2012-08-08	2007-04-20	ENSG00000134759	ENSG00000134759		"""Elongator acetyltransferase complex subunits"", ""WD repeat domain containing"""	18248	protein-coding gene	gene with protein product			"""signal transducer and activator of transcription 3 interacting protein 1"", ""elongation protein 2 homolog (S. cerevisiae)"""	STATIP1		11714725, 10954736	Standard	NM_001242875		Approved	FLJ10879, StIP	uc002kzk.2	Q6IA86	OTTHUMG00000132589	ENST00000358232.6:c.1095G>A	18.37:g.33726314G>A			Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	99	0.05	5	NM_001242875	69	0.00	0	A8KAI6|B4DTG0|B4DXP0|E7EP23|E9PCX0|Q53GZ0|Q687Y8|Q8N5C2|Q96GV4|Q96PI7|Q9H9N0|Q9NV81	Silent	SNP	ENST00000358232.6	37	CCDS11918.1	.	.	.	.	.	.	.	.	.	.	G	8.545	0.874117	0.17395	9.08E-4	0.0	ENSG00000134759	ENST00000535093	.	.	.	5.6	2.86	0.33363	.	.	.	.	.	T	0.58264	0.2110	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50825	-0.8782	4	.	.	.	-4.3353	9.0044	0.36102	0.242:0.0:0.758:0.0	.	.	.	.	Y	186	.	.	C	+	2	0	ELP2	31980312	0.996000	0.38824	0.824000	0.32777	0.935000	0.57460	0.310000	0.19356	0.323000	0.23307	0.313000	0.20887	TGC	0.001		0.373	ELP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000255800.2		NM_018255	
PLIN5	440503	mdanderson.org	37	19	4531721	4531721	+	Silent	SNP	G	G	T	rs377467819		TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr19:4531721G>T	ENST00000381848.3	-	3	254	c.174C>A	c.(172-174)cgC>cgA	p.R58R	CTB-50L17.14_ENST00000586020.1_Missense_Mutation_p.A76D	NM_001013706.2	NP_001013728.2	Q00G26	PLIN5_HUMAN	perilipin 5	58	Essential for lipid droplet targeting. {ECO:0000250}.|Interaction with LIPE. {ECO:0000250}.				lipid particle organization (GO:0034389)|lipid storage (GO:0019915)|mitochondrion localization (GO:0051646)|negative regulation of fatty acid beta-oxidation (GO:0031999)|negative regulation of lipase activity (GO:0060192)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of triglyceride catabolic process (GO:0010897)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of lipase activity (GO:0060193)|positive regulation of lipid storage (GO:0010884)|positive regulation of sequestering of triglyceride (GO:0010890)|positive regulation of triglyceride biosynthetic process (GO:0010867)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|lipid particle (GO:0005811)|mitochondrion (GO:0005739)				endometrium(4)|lung(3)|skin(2)|upper_aerodigestive_tract(1)	10						TCTCAGCCAGGCGGCAGGCGG	0.706																																					p.R58R													.	.			0			c.C174A												8.0	13.0	11.0					19																	4531721		2128	4209	6337	SO:0001819	synonymous_variant	440503	exon3			AGCCAGGCGGCAG	DQ839131	CCDS42473.1	19p13.3	2009-08-12			ENSG00000214456	ENSG00000214456		"""Perilipins"""	33196	protein-coding gene	gene with protein product	"""lipid storage droplet protein 5"""	613248				17234449, 19638644	Standard	NM_001013706		Approved	LSDP5, LSDA5, OXPAT, MLDP	uc002mas.3	Q00G26		ENST00000381848.3:c.174C>A	19.37:g.4531721G>T			Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	44	0.07	3	NM_001013706	0		0	A2RRC1|Q6ZS68	Silent	SNP	ENST00000381848.3	37	CCDS42473.1																																																																																					0.706	PLIN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000458647.1		NM_001013706	
PNPLA6	10908	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;mdanderson.org	37	19	7615464	7615464	+	Nonsense_Mutation	SNP	C	C	T			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr19:7615464C>T	ENST00000221249.6	+	19	2322	c.1891C>T	c.(1891-1893)Cag>Tag	p.Q631*	PNPLA6_ENST00000600737.1_Nonsense_Mutation_p.Q670*|PNPLA6_ENST00000414982.3_Nonsense_Mutation_p.Q679*|PNPLA6_ENST00000594864.1_3'UTR|PNPLA6_ENST00000545201.2_Nonsense_Mutation_p.Q605*|PNPLA6_ENST00000450331.3_Nonsense_Mutation_p.Q631*	NM_006702.4	NP_006693.3	Q8IY17	PLPL6_HUMAN	patatin-like phospholipase domain containing 6	670					angiogenesis (GO:0001525)|cell death (GO:0008219)|lipid catabolic process (GO:0016042)|organ morphogenesis (GO:0009887)|phosphatidylcholine metabolic process (GO:0046470)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	lysophospholipase activity (GO:0004622)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(14)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)	35						TAGCGTGATCCAGCGAGGCAG	0.667																																					p.Q679X													.	.			0			c.C2035T												58.0	48.0	51.0					19																	7615464		2203	4300	6503	SO:0001587	stop_gained	10908	exon18			GTGATCCAGCGAG	AJ004832	CCDS32891.1, CCDS54206.1, CCDS54207.1, CCDS59343.1	19p13.2	2013-09-11						"""Patatin-like phospholipase domain containing"""	16268	protein-coding gene	gene with protein product	"""neuropathy target esterase"""	603197				9576844, 16799181, 19029121	Standard	NM_006702		Approved	NTE, sws, iPLA2delta, SPG39	uc010xjq.2	Q8IY17		ENST00000221249.6:c.1891C>T	19.37:g.7615464C>T	ENSP00000221249:p.Gln631*		Somatic	74	0	0		WXS	Illumina HiSeq	.	160	0.13	20	NM_001166111	64	0.09	6	A6NGQ0|B4DFB9|B7Z7T2|F5H5K9|J3KQS3|O60859|Q86W58|Q9UG58	Nonsense_Mutation	SNP	ENST00000221249.6	37	CCDS32891.1	.	.	.	.	.	.	.	.	.	.	C	42	9.602034	0.99216	.	.	ENSG00000032444	ENST00000221249;ENST00000545201;ENST00000414982;ENST00000450331	.	.	.	4.85	4.85	0.62838	.	0.065897	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10902	T	0.67	.	10.7002	0.45922	0.1907:0.8093:0.0:0.0	.	.	.	.	X	631;605;679;631	.	ENSP00000221249:Q631X	Q	+	1	0	PNPLA6	7521464	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	4.563000	0.60823	2.245000	0.73994	0.591000	0.81541	CAG			0.667	PNPLA6-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000459275.1		NM_006702	
ZNF699	374879	broad.mit.edu;ucsc.edu	37	19	9407511	9407511	+	Missense_Mutation	SNP	G	G	C			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr19:9407511G>C	ENST00000591998.1	-	6	797	c.569C>G	c.(568-570)aCt>aGt	p.T190S	CTC-325H20.4_ENST00000591336.1_RNA|ZNF699_ENST00000308650.3_Missense_Mutation_p.T190S			Q32M78	ZN699_HUMAN	zinc finger protein 699	190					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						TTTTACTTCAGTATTTCTCTT	0.388																																					p.T190S													ZNF699,NS,carcinoma,-1,1	ZNF699	67	1	0			c.C569G												107.0	96.0	100.0					19																	9407511		1938	4149	6087	SO:0001583	missense	374879	exon5			ACTTCAGTATTTC	BC109268	CCDS42495.1	19p13.2	2013-01-08				ENSG00000196110		"""Zinc fingers, C2H2-type"", ""-"""	24750	protein-coding gene	gene with protein product	hangover homolog (Drosophila)	609571				16940975	Standard	NM_198535		Approved	FLJ38144, hang	uc002mlc.1	Q32M78		ENST00000591998.1:c.569C>G	19.37:g.9407511G>C	ENSP00000467723:p.Thr190Ser		Somatic	142	0.014084507	2		WXS	Illumina HiSeq	Phase_I	183	0.15	27	NM_198535	11	0.09	1	Q8N9A1	Missense_Mutation	SNP	ENST00000591998.1	37	CCDS42495.1	.	.	.	.	.	.	.	.	.	.	G	8.675	0.903772	0.17760	.	.	ENSG00000196110	ENST00000308650	T	0.17528	2.27	3.07	0.79	0.18613	.	0.772090	0.10636	N	0.651617	T	0.12050	0.0293	L	0.35414	1.06	0.09310	N	1	B	0.13594	0.008	B	0.12156	0.007	T	0.29822	-0.9999	10	0.45353	T	0.12	.	5.7594	0.18190	0.1226:0.2017:0.6757:0.0	.	190	Q32M78	ZN699_HUMAN	S	190	ENSP00000311596:T190S	ENSP00000311596:T190S	T	-	2	0	ZNF699	9268511	0.000000	0.05858	0.001000	0.08648	0.079000	0.17450	0.615000	0.24329	0.289000	0.22422	0.555000	0.69702	ACT			0.388	ZNF699-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000449010.1		NM_198535	
BST2	684	broad.mit.edu	37	19	17516586	17516587	+	5'Flank	INS	-	-	T	rs28413175|rs397830624	byFrequency	TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr19:17516586_17516587insT	ENST00000252593.6	-	0	0				CTD-2521M24.9_ENST00000500836.2_lincRNA|BST2_ENST00000527220.1_5'Flank	NM_004335.2	NP_004326.1	Q10589	BST2_HUMAN	bone marrow stromal cell antigen 2						B cell activation (GO:0042113)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|multicellular organismal development (GO:0007275)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of intracellular transport of viral material (GO:1901253)|negative regulation of plasmacytoid dendritic cell cytokine production (GO:0002737)|negative regulation of viral genome replication (GO:0045071)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of actin cytoskeleton organization (GO:0032956)|response to interferon-alpha (GO:0035455)|response to interferon-beta (GO:0035456)|response to interferon-gamma (GO:0034341)|response to virus (GO:0009615)|signal transduction (GO:0007165)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metalloendopeptidase inhibitor activity (GO:0008191)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)			endometrium(1)|large_intestine(2)|lung(1)|ovary(3)|prostate(2)	9						AGGAGGTGGGCTTTTTTTTCAC	0.525													?|TTTTTTTT|TTTTTTTTT|unsure	4318	0.86222	0.8767	0.9366	5008	,	,		17780	0.6081		0.9692	False		,,,				2504	0.9417				.													.	BST2	28		0			.																																									SO:0001631	upstream_gene_variant	0	.			GGTGGGCTTTTTT		CCDS12358.1	19p13.2	2009-10-30				ENSG00000130303		"""CD molecules"""	1119	protein-coding gene	gene with protein product		600534				7607676	Standard	NM_004335		Approved	CD317, tetherin	uc002ngl.3	Q10589			19.37:g.17516594_17516594dupT	Exception_encountered		Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	8	0.63	5	.	0		0	A8K4Y4|Q53G07	RNA	INS	ENST00000252593.6	37	CCDS12358.1																																																																																					0.525	BST2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding		OTTHUMT00000387346.1		NM_004335	
ZNF676	163223	bcgsc.ca	37	19	22363736	22363736	+	Silent	SNP	T	T	G	rs559970266	byFrequency	TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr19:22363736T>G	ENST00000397121.2	-	3	1100	c.783A>C	c.(781-783)ggA>ggC	p.G261G		NM_001001411.2	NP_001001411.2	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	261					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(49)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	67		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)				CGCTACTAAATCCTTTGCCAC	0.388																																					p.G261G													.	ZNF676	146		0			c.A783C												89.0	95.0	93.0					19																	22363736		2160	4274	6434	SO:0001819	synonymous_variant	163223	exon3			ACTAAATCCTTTG	AK097798	CCDS42539.1	19p12	2013-01-08				ENSG00000196109		"""Zinc fingers, C2H2-type"""	20429	protein-coding gene	gene with protein product							Standard	NM_001001411		Approved		uc002nqs.1	Q8N7Q3		ENST00000397121.2:c.783A>C	19.37:g.22363736T>G			Somatic	55	0	0		WXS	Illumina HiSeq	Phase_1	71	0.04	3	NM_001001411	81	0.00	0	A8MVX5	Silent	SNP	ENST00000397121.2	37	CCDS42539.1																																																																																					0.388	ZNF676-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000464392.1		NM_001001411	
ZNF99	7652	hgsc.bcm.edu	37	19	22940462	22940463	+	Missense_Mutation	DNP	AC	AC	CT			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	AC	AC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr19:22940462_22940463AC>CT	ENST00000596209.1	-	4	2338_2339	c.2248_2249GT>AG	c.(2248-2250)GTa>AGa	p.V750R	ZNF99_ENST00000397104.3_Missense_Mutation_p.V659R|CTC-451A6.4_ENST00000442497.2_lincRNA	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	750					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				TACCTTATGTACAGTAAGTTTT	0.356																																					p.V659R													ZNF99,colon,carcinoma,+2,1	ZNF99	2	1	0			c.G2248A																																									SO:0001583	missense	7652	exon4			TTATGTACAGTAA	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"""Zinc fingers, C2H2-type"", ""-"""	13175	protein-coding gene	gene with protein product		603981	"""zinc finger protein 99 (F8281)"", ""chromosome 19 open reading frame 9"""	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.2248_2249delinsCT	19.37:g.22940462_22940463delinsCT	ENSP00000472969:p.Val750Arg		Somatic	34	0.0294117647	1		WXS	Illumina HiSeq	.	54	0.07	4	NM_001080409	7	0.00	0	M0R335	Missense_Mutation	DNP	ENST00000596209.1	37	CCDS59369.1																																																																																					0.356	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding		OTTHUMT00000464591.1		XM_065124	
LGI4	163175	broad.mit.edu	37	19	35625538	35625538	+	Missense_Mutation	SNP	A	A	C			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr19:35625538A>C	ENST00000310123.3	-	1	566	c.47T>G	c.(46-48)gTg>gGg	p.V16G	LGI4_ENST00000591633.1_Missense_Mutation_p.V16G|LGI4_ENST00000493050.1_Intron|LGI4_ENST00000392225.3_Missense_Mutation_p.V16G	NM_139284.2	NP_644813.1	Q8N135	LGI4_HUMAN	leucine-rich repeat LGI family, member 4	16					adult locomotory behavior (GO:0008344)|glial cell proliferation (GO:0014009)|myelination in peripheral nervous system (GO:0022011)|neuron maturation (GO:0042551)	extracellular space (GO:0005615)		p.V16G(1)		endometrium(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10	all_lung(56;7.56e-09)|Lung NSC(56;1.1e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.54e-20)|OV - Ovarian serous cystadenocarcinoma(14;1.33e-18)|all cancers(14;4.27e-17)|LUSC - Lung squamous cell carcinoma(66;0.0849)			GGCCACCACCACCCCCGCCCC	0.701																																					p.V16G													LGI4,pharynx,carcinoma,0,1	LGI4	32	1	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.T47G												18.0	22.0	21.0					19																	35625538		2183	4277	6460	SO:0001583	missense	163175	exon1			ACCACCACCCCCG	AJ487519	CCDS12444.1	19q13.13	2008-07-03			ENSG00000153902	ENSG00000153902			18712	protein-coding gene	gene with protein product		608303				12023020	Standard	NM_139284		Approved		uc002nxx.2	Q8N135	OTTHUMG00000044558	ENST00000310123.3:c.47T>G	19.37:g.35625538A>C	ENSP00000312273:p.Val16Gly		Somatic	55	0.1090909091	6		WXS	Illumina HiSeq	Phase_I	82	0.22	18	NM_139284	1	0.00	0	B2RN53|B9EGS7|Q5M8T1	Missense_Mutation	SNP	ENST00000310123.3	37	CCDS12444.1	.	.	.	.	.	.	.	.	.	.	A	10.47	1.357956	0.24598	.	.	ENSG00000153902	ENST00000310123;ENST00000392225;ENST00000437421	T;T	0.65549	-0.16;-0.09	4.15	-6.63	0.01807	.	2.430960	0.01731	N	0.028842	T	0.43033	0.1229	N	0.08118	0	0.09310	N	1	B;B	0.18968	0.032;0.005	B;B	0.24701	0.055;0.015	T	0.33317	-0.9873	10	0.23302	T	0.38	.	14.5335	0.67942	0.163:0.0:0.837:0.0	.	16;16	Q8N135-2;Q8N135	.;LGI4_HUMAN	G	16	ENSP00000312273:V16G;ENSP00000376059:V16G	ENSP00000312273:V16G	V	-	2	0	LGI4	40317378	0.000000	0.05858	0.004000	0.12327	0.043000	0.13939	-0.603000	0.05674	-1.470000	0.01888	-1.039000	0.02377	GTG			0.701	LGI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000103963.1			
ZNF567	163081	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	19	37211070	37211071	+	Frame_Shift_Del	DEL	TG	TG	-			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	TG	TG					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr19:37211070_37211071delTG	ENST00000536254.2	+	6	1666_1667	c.1444_1445delTG	c.(1444-1446)tgtfs	p.C482fs	ZNF850_ENST00000589390.1_Intron|ZNF567_ENST00000588311.1_Frame_Shift_Del_p.C451fs|ZNF567_ENST00000392163.2_Frame_Shift_Del_p.C451fs|ZNF567_ENST00000585696.1_Frame_Shift_Del_p.C451fs|ZNF567_ENST00000360729.4_Frame_Shift_Del_p.C451fs			Q8N184	ZN567_HUMAN	zinc finger protein 567	482					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			ATGTCCTCACTGTGGGAAGGCC	0.411																																					p.450_451del													.	ZNF567	61		0			c.1350_1351del																																									SO:0001589	frameshift_variant	163081	exon4			CCTCACTGTGGGA	AK093034	CCDS12495.1, CCDS74349.1	19q13.12	2013-10-08				ENSG00000189042		"""Zinc fingers, C2H2-type"", ""-"""	28696	protein-coding gene	gene with protein product						12477932	Standard	XM_006723064		Approved	MGC45586	uc002oep.4	Q8N184		ENST00000536254.2:c.1444_1445delTG	19.37:g.37211072_37211073delTG	ENSP00000441838:p.Cys482fs		Somatic	125	0	0		WXS	Illumina HiSeq	.	134	0.14	19	NM_152603	24	0.00	0	B3KX49|Q6N044	Frame_Shift_Del	DEL	ENST00000536254.2	37																																																																																						0.411	ZNF567-001	KNOWN	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000453549.1		NM_152603	
RYR1	6261	mdanderson.org	37	19	38958286	38958286	+	Missense_Mutation	SNP	G	G	A			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr19:38958286G>A	ENST00000359596.3	+	25	3215	c.3215G>A	c.(3214-3216)cGc>cAc	p.R1072H	RYR1_ENST00000360985.3_Missense_Mutation_p.R1072H|RYR1_ENST00000355481.4_Missense_Mutation_p.R1072H			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	1072	6 X approximate repeats.|B30.2/SPRY 2. {ECO:0000255|PROSITE- ProRule:PRU00548}.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GACCGGGTGCGCATCTTCCGG	0.572																																					p.R1072H													RYR1,colon,carcinoma,0,3	RYR1	0	3	0			c.G3215A												104.0	97.0	99.0					19																	38958286		2203	4300	6503	SO:0001583	missense	6261	exon25			GGGTGCGCATCTT	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.3215G>A	19.37:g.38958286G>A	ENSP00000352608:p.Arg1072His		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	72	0.06	4	NM_001042723	14	0.00	0	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	g	11.77	1.736858	0.30774	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.97642	-4.47;-4.47;-4.47	2.92	2.92	0.33932	B30.2/SPRY domain (1);	0.000000	0.64402	U	0.000016	D	0.98635	0.9543	M	0.92367	3.3	0.50632	D	0.999887	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.99143	1.0856	10	0.87932	D	0	.	14.736	0.69416	0.0:0.0:1.0:0.0	.	1072;1072	P21817-2;P21817	.;RYR1_HUMAN	H	1072	ENSP00000352608:R1072H;ENSP00000347667:R1072H;ENSP00000354254:R1072H	ENSP00000347667:R1072H	R	+	2	0	RYR1	43650126	1.000000	0.71417	1.000000	0.80357	0.611000	0.37282	9.294000	0.96088	1.966000	0.57179	0.154000	0.16183	CGC			0.572	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000462137.1			
HNRNPL	3191	broad.mit.edu	37	19	39338057	39338057	+	Silent	SNP	C	C	T			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr19:39338057C>T	ENST00000221419.5	-	2	651	c.285G>A	c.(283-285)ccG>ccA	p.P95P	HNRNPL_ENST00000600873.1_5'UTR|AC008982.2_ENST00000600473.1_RNA	NM_001533.2	NP_001524.2	P14866	HNRPL_HUMAN	heterogeneous nuclear ribonucleoprotein L	95					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription regulatory region DNA binding (GO:0044212)	p.P95P(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	30	all_cancers(60;6.83e-06)|Ovarian(47;0.0454)		Lung(45;0.00342)|LUSC - Lung squamous cell carcinoma(53;0.00575)			GGGTTTTGTGCGGGTCATCGT	0.522																																					p.P95P													HNRNPL,NS,carcinoma,0,2	HNRNPL	67	2	1	Substitution - coding silent(1)	endometrium(1)	c.G285A												85.0	75.0	78.0					19																	39338057		2203	4300	6503	SO:0001819	synonymous_variant	3191	exon2			TTTGTGCGGGTCA	X16135	CCDS33015.1, CCDS33016.1	19q13.2	2013-06-12		2007-08-16	ENSG00000104824	ENSG00000104824		"""RNA binding motif (RRM) containing"""	5045	protein-coding gene	gene with protein product		603083		HNRPL		2687284	Standard	NM_001533		Approved		uc021uuh.1	P14866	OTTHUMG00000182612	ENST00000221419.5:c.285G>A	19.37:g.39338057C>T			Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	106	0.04	4	NM_001533	382	0.00	0	A6ND69|A6NIT8|Q9H3P3	Silent	SNP	ENST00000221419.5	37	CCDS33015.1																																																																																					0.522	HNRNPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000462670.1			
ZNF528	84436	mdanderson.org	37	19	52919465	52919465	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr19:52919465G>T	ENST00000360465.3	+	7	1786	c.1360G>T	c.(1360-1362)Gcc>Tcc	p.A454S	ZNF528_ENST00000391788.2_3'UTR	NM_032423.2	NP_115799.2	Q3MIS6	ZN528_HUMAN	zinc finger protein 528	454					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(6)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	39				GBM - Glioblastoma multiforme(134;0.00249)|OV - Ovarian serous cystadenocarcinoma(262;0.00817)		AGACCTTACTGCCCATTTTCT	0.373																																					p.A454S													.	.			0			c.G1360T												72.0	73.0	73.0					19																	52919465		2202	4300	6502	SO:0001583	missense	84436	exon7			CTTACTGCCCATT	AB058730	CCDS33091.1	19q13	2013-01-08			ENSG00000167555	ENSG00000167555		"""Zinc fingers, C2H2-type"", ""-"""	29384	protein-coding gene	gene with protein product		615580				11347906	Standard	NM_032423		Approved	KIAA1827	uc002pzh.3	Q3MIS6	OTTHUMG00000156494	ENST00000360465.3:c.1360G>T	19.37:g.52919465G>T	ENSP00000353652:p.Ala454Ser		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	123	0.04	5	NM_032423	35	0.00	0	B3KPN4|Q86T88|Q96JK0	Missense_Mutation	SNP	ENST00000360465.3	37	CCDS33091.1	.	.	.	.	.	.	.	.	.	.	G	2.948	-0.217374	0.06101	.	.	ENSG00000167555	ENST00000360465	T	0.17854	2.25	1.96	-3.92	0.04155	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.08223	0.0205	N	0.04018	-0.295	0.09310	N	1	P	0.45212	0.853	P	0.51974	0.686	T	0.06023	-1.0850	9	0.07030	T	0.85	.	3.5526	0.07853	0.4075:0.0:0.4193:0.1732	.	454	Q3MIS6	ZN528_HUMAN	S	454	ENSP00000353652:A454S	ENSP00000353652:A454S	A	+	1	0	ZNF528	57611277	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.704000	0.00388	-1.111000	0.02988	-0.355000	0.07637	GCC			0.373	ZNF528-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000344336.1		NM_032423	
DNAH6	1768	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	2	84838859	84838859	+	Missense_Mutation	SNP	A	A	T			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr2:84838859A>T	ENST00000237449.6	+	21	3364	c.3356A>T	c.(3355-3357)gAc>gTc	p.D1119V	DNAH6_ENST00000389394.3_Missense_Mutation_p.D1119V|DNAH6_ENST00000398278.2_Missense_Mutation_p.D1119V			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	1119	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						AATGCTCCAGACATTCAGAGG	0.438																																					p.D1119V													.	DNAH6	194		0			c.A3356T												62.0	63.0	62.0					2																	84838859		692	1591	2283	SO:0001583	missense	1768	exon22			CTCCAGACATTCA	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"""Axonemal dyneins"""	2951	protein-coding gene	gene with protein product		603336	"""dynein, axonemal, heavy polypeptide 6"", ""dynein heavy chain-like 1"""	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.3356A>T	2.37:g.84838859A>T	ENSP00000237449:p.Asp1119Val		Somatic	497	0.0020120724	1		WXS	Illumina HiSeq	Phase_I	558	0.14	76	NM_001370	0		0	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	37	CCDS46348.1	.	.	.	.	.	.	.	.	.	.	A	20.5	4.001535	0.74818	.	.	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	T;T;T	0.71103	-0.54;-0.54;-0.54	5.46	4.29	0.51040	Dynein heavy chain, domain-2 (1);	.	.	.	.	D	0.88855	0.6550	H	0.97707	4.06	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	D	0.90816	0.4705	9	0.87932	D	0	.	11.7832	0.52026	0.8526:0.1474:0.0:0.0	.	1119	Q9C0G6	DYH6_HUMAN	V	1119	ENSP00000374045:D1119V;ENSP00000381326:D1119V;ENSP00000237449:D1119V	ENSP00000237449:D1119V	D	+	2	0	DNAH6	84692370	1.000000	0.71417	0.992000	0.48379	0.975000	0.68041	8.279000	0.89901	0.874000	0.35823	0.533000	0.62120	GAC			0.438	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000328537.2		NM_001370	
CNNM3	26505	mdanderson.org	37	2	97482998	97482998	+	Silent	SNP	C	C	T			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr2:97482998C>T	ENST00000305510.3	+	1	1012	c.984C>T	c.(982-984)gaC>gaT	p.D328D	CNNM3_ENST00000377060.3_Silent_p.D328D	NM_017623.4	NP_060093.3	Q8NE01	CNNM3_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 3	328	CBS 1. {ECO:0000255|PROSITE- ProRule:PRU00703}.				ion transport (GO:0006811)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)			NS(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(2)|skin(1)|urinary_tract(2)	13						TCATGCTGGACGCCAGCACCG	0.677																																					p.D328D													.	.			0			c.C984T												48.0	47.0	47.0					2																	97482998		2203	4299	6502	SO:0001819	synonymous_variant	26505	exon1			GCTGGACGCCAGC	AF216965	CCDS2025.1, CCDS2026.1	2q11.2	2014-08-08	2014-08-07		ENSG00000168763	ENSG00000168763			104	protein-coding gene	gene with protein product		607804	"""cyclin M3"""	ACDP3		21393841, 24632616	Standard	XM_005263917		Approved		uc002swy.3	Q8NE01	OTTHUMG00000130531	ENST00000305510.3:c.984C>T	2.37:g.97482998C>T			Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	42	0.07	3	NM_017623	33	0.00	0	B3KX67|Q8TBV4|Q96IW4|Q9NRK4|Q9NXW6	Silent	SNP	ENST00000305510.3	37	CCDS2025.1																																																																																					0.677	CNNM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000252952.2		NM_017623	
KIF5C	3800	broad.mit.edu	37	2	149866823	149866823	+	Missense_Mutation	SNP	C	C	T			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr2:149866823C>T	ENST00000435030.1	+	24	3093	c.2725C>T	c.(2725-2727)Cgg>Tgg	p.R909W	KIF5C_ENST00000464066.1_3'UTR|KIF5C_ENST00000414838.2_Missense_Mutation_p.R814W|KIF5C_ENST00000397413.1_Missense_Mutation_p.R677W			O60282	KIF5C_HUMAN	kinesin family member 5C	909	Globular.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mRNA transport (GO:0051028)|organelle organization (GO:0006996)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(221;0.108)		GGAGGCCGTGCGGGCCAAGAA	0.632																																					p.R909W													.	KIF5C	166		0			c.C2725T												22.0	27.0	25.0					2																	149866823		2169	4287	6456	SO:0001583	missense	3800	exon24			GCCGTGCGGGCCA	AB011103	CCDS74586.1	2q23	2008-02-05			ENSG00000168280	ENSG00000168280		"""Kinesins"""	6325	protein-coding gene	gene with protein product		604593				7514426	Standard	NM_004522		Approved		uc010zbu.2	O60282	OTTHUMG00000153779	ENST00000435030.1:c.2725C>T	2.37:g.149866823C>T	ENSP00000393379:p.Arg909Trp		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	261	0.03	7	NM_004522	1	0.00	0	O95079|Q2YDC5	Missense_Mutation	SNP	ENST00000435030.1	37		.	.	.	.	.	.	.	.	.	.	C	19.71	3.879120	0.72294	.	.	ENSG00000168280	ENST00000435030;ENST00000414838;ENST00000334436;ENST00000397413	D;D;D	0.84800	-1.9;-1.9;-1.9	5.42	-0.379	0.12493	.	0.067237	0.56097	D	0.000021	D	0.91317	0.7262	.	.	.	0.46458	D	0.999053	D;D	0.89917	1.0;0.971	D;P	0.78314	0.991;0.709	D	0.90813	0.4703	8	.	.	.	.	16.402	0.83643	0.7923:0.2077:0.0:0.0	.	909;217	O60282;Q59GB8	KIF5C_HUMAN;.	W	909;814;812;677	ENSP00000393379:R909W;ENSP00000410115:R814W;ENSP00000380560:R677W	.	R	+	1	2	KIF5C	149575069	0.543000	0.26434	0.408000	0.26446	0.950000	0.60333	0.796000	0.26986	0.061000	0.16311	0.650000	0.86243	CGG			0.632	KIF5C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000332562.3		NM_004522	
TTN	7273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	2	179399008	179399008	+	Missense_Mutation	SNP	A	A	T			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr2:179399008A>T	ENST00000591111.1	-	308	97635	c.97411T>A	c.(97411-97413)Tcc>Acc	p.S32471T	TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.S25172T|TTN_ENST00000460472.2_Missense_Mutation_p.S25047T|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.S34112T|TTN_ENST00000342992.6_Missense_Mutation_p.S31544T|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.S25239T|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000586831.1_RNA			Q8WZ42	TITIN_HUMAN	titin	32471					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CCACCACAGGAGATCCGGGCT	0.453																																					p.S34112T													.	.			0			c.T102334A												115.0	112.0	113.0					2																	179399008		1949	4157	6106	SO:0001583	missense	7273	exon358			CACAGGAGATCCG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.97411T>A	2.37:g.179399008A>T	ENSP00000465570:p.Ser32471Thr		Somatic	131	0	0		WXS	Illumina HiSeq	.	181	0.29	53	NM_001267550	0		0	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	A	12.60	1.985346	0.35036	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.63417	-0.04;0.19;0.17;0.16	5.48	5.48	0.80851	Protein kinase-like domain (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.46639	0.1403	N	0.08118	0	0.33419	D	0.579631	B;B;B;B	0.22800	0.075;0.075;0.075;0.035	B;B;B;B	0.27715	0.055;0.055;0.082;0.074	T	0.59091	-0.7519	9	0.87932	D	0	.	14.8527	0.70309	1.0:0.0:0.0:0.0	.	25047;25172;25239;32471	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	T	31544;25047;25239;25172;25044	ENSP00000343764:S31544T;ENSP00000434586:S25047T;ENSP00000340554:S25239T;ENSP00000352154:S25172T	ENSP00000340554:S25239T	S	-	1	0	TTN	179107254	1.000000	0.71417	0.986000	0.45419	0.992000	0.81027	5.578000	0.67450	2.213000	0.71641	0.454000	0.30748	TCC			0.453	TTN-019	PUTATIVE	basic	protein_coding	protein_coding		OTTHUMT00000460310.1		NM_133378	
MPP4	58538	broad.mit.edu	37	2	202549823	202549823	+	Missense_Mutation	SNP	C	C	A			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr2:202549823C>A	ENST00000409474.3	-	7	745	c.538G>T	c.(538-540)Gcc>Tcc	p.A180S	MPP4_ENST00000409143.1_Missense_Mutation_p.A153S|MPP4_ENST00000315506.7_Missense_Mutation_p.A180S|MPP4_ENST00000396886.3_Missense_Mutation_p.A136S|MPP4_ENST00000359962.5_Missense_Mutation_p.A180S|MPP4_ENST00000447335.2_Missense_Mutation_p.A180S|MPP4_ENST00000428900.2_Missense_Mutation_p.A180S	NM_033066.2	NP_149055	Q96JB8	MPP4_HUMAN	membrane protein, palmitoylated 4 (MAGUK p55 subfamily member 4)	180	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				protein localization to synapse (GO:0035418)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|presynaptic membrane (GO:0042734)		p.A180S(2)		kidney(1)|lung(11)	12						ATGATCCTGGCCACCAAGATG	0.527																																					p.A180S													MPP4,NS,carcinoma,0,1	MPP4	93	1	2	Substitution - Missense(2)	lung(2)	c.G538T												45.0	45.0	45.0					2																	202549823		2012	4189	6201	SO:0001583	missense	58538	exon7			TCCTGGCCACCAA	AF316032	CCDS46491.1	2q33.2	2008-05-15			ENSG00000082126	ENSG00000082126			13680	protein-coding gene	gene with protein product		606575		DLG6		11414766	Standard	NM_033066		Approved		uc002uyk.4	Q96JB8	OTTHUMG00000154525	ENST00000409474.3:c.538G>T	2.37:g.202549823C>A	ENSP00000387278:p.Ala180Ser		Somatic	108	0.0092592593	1		WXS	Illumina HiSeq	Phase_I	145	0.05	7	NM_033066	0		0	C9IZK4|Q53TT3|Q6ZNH6|Q96Q43|Q96Q44	Missense_Mutation	SNP	ENST00000409474.3	37	CCDS46491.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.033366	0.93575	.	.	ENSG00000082126	ENST00000409474;ENST00000315506;ENST00000396886;ENST00000359962;ENST00000315549;ENST00000374605;ENST00000428900;ENST00000409143;ENST00000447335	T;T;T;T;T;T	0.23552	1.9;1.9;1.9;1.9;1.9;1.9	5.89	5.89	0.94794	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.45316	0.1336	L	0.41079	1.255	0.80722	D	1	D;D;D;D;D;D;D;D;D;P	0.89917	1.0;1.0;0.999;0.999;0.999;1.0;0.996;1.0;0.997;0.809	D;D;D;D;D;D;D;D;D;P	0.87578	0.981;0.998;0.992;0.989;0.981;0.992;0.94;0.991;0.977;0.682	T	0.28004	-1.0057	10	0.87932	D	0	.	18.4188	0.90582	0.0:1.0:0.0:0.0	.	153;136;180;180;180;180;136;193;180;136	F6Q0Y6;B4DUF3;E7ET46;B7ZM19;Q96JB8-2;E7EUL8;F8WC25;F8WBH8;Q96JB8;Q96JB8-4	.;.;.;.;.;.;.;.;MPP4_HUMAN;.	S	180;180;136;180;136;109;180;153;180	ENSP00000387278:A180S;ENSP00000319363:A180S;ENSP00000353047:A180S;ENSP00000416781:A180S;ENSP00000387293:A153S;ENSP00000406160:A180S	ENSP00000319363:A180S	A	-	1	0	MPP4	202258068	1.000000	0.71417	1.000000	0.80357	0.776000	0.43924	7.413000	0.80104	2.786000	0.95864	0.655000	0.94253	GCC			0.527	MPP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000335748.2			
IKZF2	22807	broad.mit.edu	37	2	214012404	214012405	+	Intron	DEL	AA	AA	-	rs550073377|rs6738070|rs547307585|rs112988286	byFrequency	TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	AA	AA					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr2:214012404_214012405delAA	ENST00000434687.1	-	4	449				IKZF2_ENST00000421754.2_Intron|IKZF2_ENST00000457361.1_Intron|IKZF2_ENST00000374327.4_Intron|IKZF2_ENST00000374319.4_Intron|IKZF2_ENST00000442445.1_Frame_Shift_Del_p.L62fs|IKZF2_ENST00000342002.2_Intron|IKZF2_ENST00000451136.2_Intron|IKZF2_ENST00000413091.3_Intron			Q9UKS7	IKZF2_HUMAN	IKAROS family zinc finger 2 (Helios)						positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(7)|lung(7)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		Esophageal squamous(248;0.0559)|Renal(323;0.218)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;2.97e-07)|all cancers(144;1.53e-05)|LUSC - Lung squamous cell carcinoma(224;0.00599)|Lung(261;0.00792)		ACACACACACAAAAAAAAATCA	0.411																																					.													.	IKZF2	71		0			.																																									SO:0001627	intron_variant	22807	.			ACACACAAAAAAA	AF130863	CCDS2395.1, CCDS46507.1	2q13.1	2013-01-08	2006-08-25	2006-08-25	ENSG00000030419	ENSG00000030419		"""Zinc fingers, C2H2-type"", ""IKAROS zinc fingers"""	13177	protein-coding gene	gene with protein product		606234	"""zinc finger protein, subfamily 1A, 2 (Helios)"""	ZNFN1A2		9512513, 9560339	Standard	NM_001079526		Approved	Helios	uc002vem.3	Q9UKS7	OTTHUMG00000133005	ENST00000434687.1:c.139+26TT>-	2.37:g.214012410_214012411delAA			Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	63	0.00	0	.	0		0	Q53YJ5|Q6PQC5|Q6PQC6|Q6PQC7|Q6PQC8|Q6PQD0|Q6PQD1|Q8N6S1	Frame_Shift_Del	DEL	ENST00000434687.1	37	CCDS2395.1																																																																																					0.411	IKZF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000256593.3		NM_016260	
ANO7	50636	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	2	242163124	242163124	+	Missense_Mutation	SNP	C	C	G			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr2:242163124C>G	ENST00000274979.8	+	23	2725	c.2622C>G	c.(2620-2622)gaC>gaG	p.D874E		NM_001001891.3	NP_001001891.2	Q6IWH7	ANO7_HUMAN	anoctamin 7	874					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)			NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(14)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	32						TGGTGCCTGACATCCCAGAGT	0.592																																					p.D874E													ANO7,colon,carcinoma,+1,1	ANO7	1	1	0			c.C2622G												68.0	63.0	65.0					2																	242163124		2203	4300	6503	SO:0001583	missense	50636	exon23			GCCTGACATCCCA	AY617079	CCDS33423.1, CCDS46563.1	2q37.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000146205	ENSG00000146205		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	31677	protein-coding gene	gene with protein product		605096	"""transmembrane protein 16G"""	PCANAP5, TMEM16G		14981236, 15375614, 24692353	Standard	NM_001001891		Approved	NGEP, PCANAP5L, IPCA-5	uc002wax.2	Q6IWH7	OTTHUMG00000151702	ENST00000274979.8:c.2622C>G	2.37:g.242163124C>G	ENSP00000274979:p.Asp874Glu		Somatic	129	0	0		WXS	Illumina HiSeq	.	212	0.24	50	NM_001001891	5	0.20	1	Q6IWH6	Missense_Mutation	SNP	ENST00000274979.8	37	CCDS33423.1	.	.	.	.	.	.	.	.	.	.	C	16.33	3.092761	0.56075	.	.	ENSG00000146205	ENST00000274979	T	0.68624	-0.34	3.85	2.96	0.34315	.	0.242401	0.31301	N	0.007895	T	0.80385	0.4613	M	0.83384	2.64	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.81837	-0.0749	10	0.54805	T	0.06	.	10.6407	0.45592	0.0:0.9048:0.0:0.0952	.	874	Q6IWH7	ANO7_HUMAN	E	874	ENSP00000274979:D874E	ENSP00000274979:D874E	D	+	3	2	ANO7	241811797	0.558000	0.26554	0.143000	0.22291	0.646000	0.38490	1.028000	0.30128	1.710000	0.51325	0.467000	0.42956	GAC			0.592	ANO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000323509.1		NM_001001891	
FRG1B	284802	hgsc.bcm.edu	37	20	29625928	29625928	+	Missense_Mutation	SNP	G	G	C			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr20:29625928G>C	ENST00000278882.3	+	5	552	c.172G>C	c.(172-174)Gtt>Ctt	p.V58L	FRG1B_ENST00000439954.2_Missense_Mutation_p.V63L|FRG1B_ENST00000358464.4_Missense_Mutation_p.V58L			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	58										endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						AGATGAACTTGTTGGGCATTC	0.333																																					.													.	.			0			.																																									SO:0001583	missense	284802	.			GAACTTGTTGGGC			20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531			15792	other	unknown			"""chromosome 20 open reading frame 80"""	C20orf80			Standard	NR_003579		Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.172G>C	20.37:g.29625928G>C	ENSP00000278882:p.Val58Leu		Somatic	138	0	0		WXS	Illumina HiSeq	.	123	0.05	6	.	113	0.00	0	C4AME5	RNA	SNP	ENST00000278882.3	37		.	.	.	.	.	.	.	.	.	.	g	11.29	1.593880	0.28445	.	.	ENSG00000149531	ENST00000278882;ENST00000439954;ENST00000358464	T	0.51817	0.69	1.68	1.68	0.24146	.	0.127131	0.52532	D	0.000065	T	0.38639	0.1048	.	.	.	0.26463	N	0.975418	B	0.19817	0.039	B	0.34385	0.181	T	0.36648	-0.9739	9	0.36615	T	0.2	.	9.3557	0.38164	0.0:0.0:1.0:0.0	.	63	F5H5R5	.	L	58;63;58	ENSP00000408863:V63L	ENSP00000278882:V58L	V	+	1	0	FRG1B	28239589	1.000000	0.71417	1.000000	0.80357	0.023000	0.10783	8.114000	0.89570	1.250000	0.43966	0.184000	0.17185	GTT			0.333	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000078494.2		NR_003579	
KCNS1	3787	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	20	43726455	43726455	+	Silent	SNP	G	G	A			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr20:43726455G>A	ENST00000306117.1	-	4	1354	c.958C>T	c.(958-960)Ctg>Ttg	p.L320L	KCNS1_ENST00000537075.1_Silent_p.L320L	NM_002251.3	NP_002242.2	Q96KK3	KCNS1_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 1	320					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel regulator activity (GO:0015459)			endometrium(1)|lung(3)|ovary(1)|stomach(1)	6		Myeloproliferative disorder(115;0.0122)				CCAGCCAGCAGCGTGAGATAG	0.637																																					p.L320L													.	.			0			c.C958T												70.0	54.0	60.0					20																	43726455		2203	4300	6503	SO:0001819	synonymous_variant	3787	exon4			CCAGCAGCGTGAG	AF043473	CCDS13342.1	20q12	2011-07-05			ENSG00000124134	ENSG00000124134		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6300	protein-coding gene	gene with protein product		602905				9305895, 16382104	Standard	NM_002251		Approved	Kv9.1	uc002xnc.3	Q96KK3	OTTHUMG00000033079	ENST00000306117.1:c.958C>T	20.37:g.43726455G>A			Somatic	39	0	0		WXS	Illumina HiSeq	.	62	0.26	16	NM_002251	5	0.40	2	A2RUL9|B7ZM31|O43652|Q6DJU6	Silent	SNP	ENST00000306117.1	37	CCDS13342.1																																																																																					0.637	KCNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000080507.3		NM_002251	
BAGE2	85319	broad.mit.edu	37	21	11045626	11045626	+	RNA	DEL	G	G	-	rs60108847|rs56675609		TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr21:11045626delG	ENST00000470054.1	-	0	774							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2							extracellular region (GO:0005576)								Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TCCAAAATAAGATGTGAAAAG	0.363																																					.													.	.			0			.																																											85319	.			AAATAAGATGTGA	AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172			15723	protein-coding gene	gene with protein product	"""cancer/testis antigen family 2, member 2"""					12461691	Standard	NM_182482		Approved	CT2.2		Q86Y30	OTTHUMG00000074128		21.37:g.11045626delG			Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	6	0.67	4	.	0		0	A8K925|Q08ER0	RNA	DEL	ENST00000470054.1	37																																																																																						0.363	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000157417.3		NM_182482	
MORC3	23515	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	21	37705948	37705948	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr21:37705948G>T	ENST00000400485.1	+	2	120	c.44G>T	c.(43-45)tGc>tTc	p.C15F	MORC3_ENST00000487909.1_Intron	NM_015358.2	NP_056173.1	Q14149	MORC3_HUMAN	MORC family CW-type zinc finger 3	15					cell aging (GO:0007569)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of fibroblast proliferation (GO:0048147)|peptidyl-serine phosphorylation (GO:0018105)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)	PML body (GO:0016605)	zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	35						TTTCAGCTTTGCCCGAAGTTT	0.333																																					p.C15F													.	.			0			c.G44T												142.0	130.0	134.0					21																	37705948		1825	4088	5913	SO:0001583	missense	23515	exon2			AGCTTTGCCCGAA	AK025327	CCDS42924.1	21q22.13	2005-06-15	2005-06-15	2005-06-15	ENSG00000159256	ENSG00000159256			23572	protein-coding gene	gene with protein product		610078	"""zinc finger, CW-type with coiled-coil domain 3"", ""zinc finger, CW type with coiled-coil domain 3"""	ZCWCC3		14607086	Standard	NM_015358		Approved	ZCW5, NXP2, KIAA0136	uc002yvi.3	Q14149	OTTHUMG00000086620	ENST00000400485.1:c.44G>T	21.37:g.37705948G>T	ENSP00000383333:p.Cys15Phe		Somatic	103	0	0		WXS	Illumina HiSeq	.	155	0.13	20	NM_015358	16	0.19	3	A8KA92|Q9UEZ2	Missense_Mutation	SNP	ENST00000400485.1	37	CCDS42924.1	.	.	.	.	.	.	.	.	.	.	G	17.70	3.454059	0.63290	.	.	ENSG00000159256	ENST00000400485	T	0.28666	1.6	5.54	5.54	0.83059	.	0.292956	0.43416	D	0.000562	T	0.33294	0.0858	L	0.36672	1.1	0.38838	D	0.956001	D	0.54397	0.966	P	0.47299	0.543	T	0.13019	-1.0525	10	0.59425	D	0.04	-10.4785	16.4921	0.84205	0.0:0.1306:0.8694:0.0	.	15	Q14149	MORC3_HUMAN	F	15	ENSP00000383333:C15F	ENSP00000383333:C15F	C	+	2	0	MORC3	36627818	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.660000	0.54496	2.616000	0.88540	0.650000	0.86243	TGC			0.333	MORC3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding		OTTHUMT00000194640.1		NM_015358	
COL18A1	80781	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	21	46909431	46909431	+	Missense_Mutation	SNP	C	C	T			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr21:46909431C>T	ENST00000359759.4	+	18	3221	c.3200C>T	c.(3199-3201)gCg>gTg	p.A1067V	COL18A1_ENST00000400337.2_Missense_Mutation_p.A652V|COL18A1_ENST00000355480.5_Missense_Mutation_p.A832V			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	1067	Triple-helical region 4 (COL4).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		CTGCCGGGGGCGAAGGTAAGC	0.711																																					p.A832V													.	.			0			c.C2495T												13.0	17.0	16.0					21																	46909431		1985	4129	6114	SO:0001583	missense	80781	exon18			CGGGGGCGAAGGT		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"""Collagens"""	2195	protein-coding gene	gene with protein product	"""endostatin"""	120328	"""Knobloch syndrome, type 1"""	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.3200C>T	21.37:g.46909431C>T	ENSP00000352798:p.Ala1067Val		Somatic	56	0	0		WXS	Illumina HiSeq	.	126	0.11	14	NM_030582	115	0.04	5	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Missense_Mutation	SNP	ENST00000359759.4	37		.	.	.	.	.	.	.	.	.	.	C	13.24	2.179450	0.38511	.	.	ENSG00000182871	ENST00000400337;ENST00000400347;ENST00000355480;ENST00000359759;ENST00000539645	D;D;D	0.93712	-3.27;-3.27;-3.27	3.74	-1.6	0.08426	.	0.715484	0.12324	U	0.478983	T	0.81049	0.4742	N	0.20685	0.6	0.09310	N	1	B;B;B	0.24576	0.106;0.086;0.086	B;B;B	0.13407	0.009;0.005;0.005	T	0.67158	-0.5741	10	0.16420	T	0.52	.	0.5017	0.00581	0.1801:0.3128:0.1765:0.3306	.	1067;832;652	P39060;P39060-1;P39060-2	COIA1_HUMAN;.;.	V	652;652;832;1067;1067	ENSP00000383191:A652V;ENSP00000347665:A832V;ENSP00000352798:A1067V	ENSP00000347665:A832V	A	+	2	0	COL18A1	45733859	0.000000	0.05858	0.001000	0.08648	0.048000	0.14542	-0.759000	0.04761	-0.203000	0.10251	0.650000	0.86243	GCG			0.711	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000206827.1			
CARD10	29775	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	22	37912055	37912055	+	Missense_Mutation	SNP	C	C	A			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr22:37912055C>A	ENST00000403299.1	-	4	840	c.624G>T	c.(622-624)atG>atT	p.M208I	CARD10_ENST00000251973.5_Missense_Mutation_p.M208I|CARD10_ENST00000494166.1_5'Flank			Q9BWT7	CAR10_HUMAN	caspase recruitment domain family, member 10	208					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)					GCATGGCGATCATGTAGTTCT	0.657																																					p.M208I													.	.			0			c.G624T												21.0	20.0	20.0					22																	37912055		2203	4298	6501	SO:0001583	missense	29775	exon3			GGCGATCATGTAG	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.624G>T	22.37:g.37912055C>A	ENSP00000384570:p.Met208Ile		Somatic	117	0	0		WXS	Illumina HiSeq	.	224	0.14	31	NM_014550	75	0.24	18	Q14CQ8|Q5TFG6|Q8NC81|Q9UGR5|Q9UGR6|Q9Y3H0	Missense_Mutation	SNP	ENST00000403299.1	37	CCDS13948.1	.	.	.	.	.	.	.	.	.	.	C	13.91	2.377154	0.42105	.	.	ENSG00000100065	ENST00000403299;ENST00000251973	T;T	0.34472	1.36;1.36	5.4	4.32	0.51571	.	0.218245	0.48767	D	0.000176	T	0.21921	0.0528	N	0.16478	0.41	0.27640	N	0.947746	B	0.15473	0.013	B	0.08055	0.003	T	0.07366	-1.0776	10	0.35671	T	0.21	-37.4489	11.0027	0.47616	0.1439:0.7172:0.1389:0.0	.	208	Q9BWT7	CAR10_HUMAN	I	208	ENSP00000384570:M208I;ENSP00000251973:M208I	ENSP00000251973:M208I	M	-	3	0	CARD10	36242001	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.844000	0.27654	2.679000	0.91253	0.655000	0.94253	ATG			0.657	CARD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000318997.1		NM_014550	
CELSR1	9620	broad.mit.edu	37	22	46765084	46765084	+	Silent	SNP	T	T	C			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr22:46765084T>C	ENST00000262738.3	-	27	7943	c.7944A>G	c.(7942-7944)aaA>aaG	p.K2648K		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	2648					anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		ACACGATCCCTTTTTTCCCAT	0.537																																					p.K2648K													.	CELSR1	242		0			c.A7944G												162.0	149.0	153.0					22																	46765084		2203	4300	6503	SO:0001819	synonymous_variant	9620	exon27			GATCCCTTTTTTC	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	1850	protein-coding gene	gene with protein product	"""flamingo homolog 2 (Drosophila)"""	604523	"""cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"""			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.7944A>G	22.37:g.46765084T>C			Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	220	0.02	4	NM_014246	16	0.00	0	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Silent	SNP	ENST00000262738.3	37	CCDS14076.1																																																																																					0.537	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000318037.1		NM_014246	
TUBGCP6	85378	mdanderson.org	37	22	50657310	50657310	+	Missense_Mutation	SNP	G	G	T	rs144740402		TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr22:50657310G>T	ENST00000248846.5	-	21	4747	c.4643C>A	c.(4642-4644)aCg>aAg	p.T1548K	TUBGCP6_ENST00000491449.1_5'UTR|TUBGCP6_ENST00000439308.2_3'UTR			Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	1548					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)			breast(4)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(13)|ovary(3)|prostate(2)|skin(2)	45		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)		CTCTCCGGGCGTTTGCCCAGC	0.662																																					p.T1548K													TUBGCP6,NS,carcinoma,+1,1	TUBGCP6	1	1	0			c.C4643A												41.0	45.0	43.0					22																	50657310		2203	4300	6503	SO:0001583	missense	85378	exon21			CCGGGCGTTTGCC	AB051456	CCDS14087.1	22q13.31-q13.33	2008-07-01			ENSG00000128159	ENSG00000128159			18127	protein-coding gene	gene with protein product	"""gamma-tubulin complex component 6"""	610053				11694571, 11258795	Standard	XR_244458		Approved	GCP6, KIAA1669, DJ402G11.6	uc003bkb.1	Q96RT7	OTTHUMG00000030150	ENST00000248846.5:c.4643C>A	22.37:g.50657310G>T	ENSP00000248846:p.Thr1548Lys		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	59	0.05	3	NM_020461	48	0.00	0	Q5JZ80|Q6PJ40|Q86YE9|Q9BY91|Q9UGX3|Q9UGX4	Missense_Mutation	SNP	ENST00000248846.5	37	CCDS14087.1	.	.	.	.	.	.	.	.	.	.	G	13.15	2.152245	0.38021	.	.	ENSG00000128159	ENST00000248846;ENST00000425018	T;T	0.06528	3.29;3.29	5.16	1.58	0.23477	.	0.389307	0.30850	N	0.008752	T	0.16428	0.0395	M	0.62723	1.935	0.43390	D	0.995509	D;D;D	0.69078	0.997;0.983;0.99	D;P;P	0.67231	0.95;0.81;0.827	T	0.01225	-1.1413	10	0.33141	T	0.24	.	10.1288	0.42665	0.0725:0.2552:0.6723:0.0	.	1540;1548;1548	B2RWN4;Q96RT7;Q96RT7-3	.;GCP6_HUMAN;.	K	1548;234	ENSP00000248846:T1548K;ENSP00000405979:T234K	ENSP00000248846:T1548K	T	-	2	0	TUBGCP6	48999437	1.000000	0.71417	0.666000	0.29783	0.006000	0.05464	4.532000	0.60608	0.513000	0.28278	0.591000	0.81541	ACG			0.662	TUBGCP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000075004.3		NM_020461	
FBXL2	25827	mdanderson.org	37	3	33416789	33416789	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr3:33416789G>T	ENST00000484457.1	+	10	758	c.667G>T	c.(667-669)Gat>Tat	p.D223Y	FBXL2_ENST00000283627.6_3'UTR|FBXL2_ENST00000446237.3_5'UTR|FBXL2_ENST00000507198.1_Missense_Mutation_p.D155Y|FBXL2_ENST00000542085.1_5'UTR|FBXL2_ENST00000538892.1_Missense_Mutation_p.D155Y|FBXL2_ENST00000538181.1_Missense_Mutation_p.D139Y	NM_012157.3	NP_036289.3			F-box and leucine-rich repeat protein 2											endometrium(2)|kidney(1)|large_intestine(7)|lung(3)|prostate(1)|urinary_tract(1)	15						GCGTATCACGGATGAAGGTGT	0.517																																					p.D223Y													.	.			0			c.G667T												127.0	124.0	125.0					3																	33416789		2203	4300	6503	SO:0001583	missense	25827	exon10			ATCACGGATGAAG	AF174589	CCDS2658.1, CCDS54560.1	3p22.3	2011-06-09			ENSG00000153558	ENSG00000153558		"""F-boxes / Leucine-rich repeats"""	13598	protein-coding gene	gene with protein product		605652				10508920, 10531035	Standard	NM_012157		Approved	FBL2, FBL3	uc003cfp.3	Q9UKC9	OTTHUMG00000130745	ENST00000484457.1:c.667G>T	3.37:g.33416789G>T	ENSP00000417601:p.Asp223Tyr		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	58	0.05	3	NM_012157	0		0		Missense_Mutation	SNP	ENST00000484457.1	37	CCDS2658.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.369148	0.82463	.	.	ENSG00000153558	ENST00000484457;ENST00000538892;ENST00000538181;ENST00000507198	T;T;T;T	0.13901	2.55;2.77;2.77;2.77	4.99	4.99	0.66335	.	0.100830	0.64402	D	0.000003	T	0.54447	0.1859	H	0.97707	4.06	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.998	T	0.71797	-0.4484	10	0.87932	D	0	.	17.4115	0.87487	0.0:0.0:1.0:0.0	.	139;118;223	B4E1B8;B4DMM3;Q9UKC9	.;.;FBXL2_HUMAN	Y	223;155;139;155	ENSP00000417601:D223Y;ENSP00000441228:D155Y;ENSP00000440794:D139Y;ENSP00000426163:D155Y	ENSP00000417601:D223Y	D	+	1	0	FBXL2	33391793	1.000000	0.71417	0.861000	0.33841	0.698000	0.40448	9.371000	0.97162	2.718000	0.92993	0.644000	0.83932	GAT			0.517	FBXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000253245.2		NM_012157	
STAB1	23166	mdanderson.org	37	3	52542370	52542370	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr3:52542370G>T	ENST00000321725.6	+	21	2306	c.2230G>T	c.(2230-2232)Ggc>Tgc	p.G744C		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	744	EGF-like 5. {ECO:0000255|PROSITE- ProRule:PRU00076, ECO:0000305}.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|oxidation-reduction process (GO:0055114)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|protein disulfide oxidoreductase activity (GO:0015035)|scavenger receptor activity (GO:0005044)			breast(4)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(13)|liver(1)|lung(27)|ovary(1)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	76				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		CTATGGCAAAGGCAATGTGAG	0.572																																					p.G744C													.	.			0			c.G2230T												84.0	76.0	79.0					3																	52542370		2203	4300	6503	SO:0001583	missense	23166	exon21			GGCAAAGGCAATG	AJ275213	CCDS33768.1	3p21.31	2008-07-18			ENSG00000010327	ENSG00000010327			18628	protein-coding gene	gene with protein product	"""MS-1 antigen"", ""fasciclin egf-like, laminin-type egf-like, and link domain-containing scavenger receptor-1"", ""common lymphatic endothelial and vascular endothelial receptor-1"""	608560				11829752, 12077138	Standard	XM_005264973		Approved	KIAA0246, STAB-1, FEEL-1, CLEVER-1, FELE-1, FEX1	uc003dej.3	Q9NY15	OTTHUMG00000158574	ENST00000321725.6:c.2230G>T	3.37:g.52542370G>T	ENSP00000312946:p.Gly744Cys		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	50	0.06	3	NM_015136	16	0.00	0	A7E297|Q8IUH0|Q8IUH1|Q93072	Missense_Mutation	SNP	ENST00000321725.6	37	CCDS33768.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.033821	0.93575	.	.	ENSG00000010327	ENST00000321725	D	0.90844	-2.74	5.71	5.71	0.89125	Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.96225	0.8769	M	0.89030	3	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96554	0.9410	10	0.87932	D	0	.	18.6215	0.91322	0.0:0.0:1.0:0.0	.	744;744	Q9NY15;Q9NY15-2	STAB1_HUMAN;.	C	744	ENSP00000312946:G744C	ENSP00000312946:G744C	G	+	1	0	STAB1	52517410	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	8.201000	0.89735	2.697000	0.92050	0.563000	0.77884	GGC			0.572	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000351380.2		NM_015136	
PBRM1	55193	broad.mit.edu	37	3	52677350	52677350	+	Silent	SNP	G	G	T			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr3:52677350G>T	ENST00000296302.7	-	9	910	c.909C>A	c.(907-909)tcC>tcA	p.S303S	PBRM1_ENST00000409767.1_Silent_p.S303S|PBRM1_ENST00000410007.1_Silent_p.S303S|PBRM1_ENST00000337303.4_Silent_p.S303S|PBRM1_ENST00000409057.1_Silent_p.S303S|PBRM1_ENST00000356770.4_Intron|PBRM1_ENST00000409114.3_Silent_p.S303S|PBRM1_ENST00000394830.3_Silent_p.S303S			Q86U86	PB1_HUMAN	polybromo 1	303					chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		CAGCCAAGTTGGATGGAGTCC	0.433			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""																																p.S303S				Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1	1252		0			c.C909A												119.0	116.0	117.0					3																	52677350		2203	4300	6503	SO:0001819	synonymous_variant	55193	exon10			CAAGTTGGATGGA	BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.909C>A	3.37:g.52677350G>T			Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	126	0.03	4	NM_018313	25	0.00	0	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Silent	SNP	ENST00000296302.7	37																																																																																						0.433	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		OTTHUMT00000327232.1		NM_018165	
DHFRL1	200895	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	3	93779801	93779803	+	In_Frame_Del	DEL	CTT	CTT	-	rs141897370	byFrequency	TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	CTT	CTT					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr3:93779801_93779803delCTT	ENST00000394221.2	-	2	1002_1004	c.553_555delAAG	c.(553-555)aagdel	p.K185del	DHFRL1_ENST00000481631.1_Intron|NSUN3_ENST00000314622.4_5'Flank|DHFRL1_ENST00000314636.2_In_Frame_Del_p.K185del	NM_001195643.1	NP_001182572.1	Q86XF0	DYRL1_HUMAN	dihydrofolate reductase-like 1	185	DHFR. {ECO:0000255|PROSITE- ProRule:PRU00660}.				glycine biosynthetic process (GO:0006545)|nucleotide biosynthetic process (GO:0009165)|one-carbon metabolic process (GO:0006730)|tetrahydrofolate biosynthetic process (GO:0046654)|tetrahydrofolate metabolic process (GO:0046653)|thymidine biosynthetic process (GO:0046105)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	dihydrofolate reductase activity (GO:0004146)|mRNA binding (GO:0003729)|NADP binding (GO:0050661)			kidney(1)|large_intestine(2)|lung(3)|skin(1)|stomach(1)	8						ATTAATCATCCTTCTCACATACT	0.379																																					p.185_186del													.	DHFRL1	25		0			c.554_556del																																									SO:0001651	inframe_deletion	200895	exon2			ATCATCCTTCTCA	AL832912	CCDS2926.1	3q11.2	2005-08-16	2005-02-07		ENSG00000178700	ENSG00000178700			27309	protein-coding gene	gene with protein product			"""dihydrofolate reductase pseudogene 4"""	DHFRP4		12477932	Standard	NM_001195643		Approved	FLJ16119	uc003drj.3	Q86XF0	OTTHUMG00000159014	ENST00000394221.2:c.553_555delAAG	3.37:g.93779801_93779803delCTT	ENSP00000377768:p.Lys185del		Somatic	98	0	0		WXS	Illumina HiSeq	.	94	0.11	10	NM_001195643	2	0.00	0	D3DN30|Q6P4I9	In_Frame_Del	DEL	ENST00000394221.2	37	CCDS2926.1																																																																																					0.379	DHFRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000352910.1		NM_176815	
SLC1A3	6507	mdanderson.org	37	5	36677031	36677031	+	Missense_Mutation	SNP	C	C	T			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr5:36677031C>T	ENST00000265113.4	+	6	1081	c.605C>T	c.(604-606)cCc>cTc	p.P202L	SLC1A3_ENST00000381918.3_Missense_Mutation_p.P202L|CTD-2353F22.1_ENST00000510740.1_RNA	NM_004172.4	NP_004163.3	P43003	EAA1_HUMAN	solute carrier family 1 (glial high affinity glutamate transporter), member 3	202					auditory behavior (GO:0031223)|cell morphogenesis involved in neuron differentiation (GO:0048667)|cranial nerve development (GO:0021545)|D-aspartate import (GO:0070779)|gamma-aminobutyric acid biosynthetic process (GO:0009449)|glutamate biosynthetic process (GO:0006537)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|neuromuscular process controlling balance (GO:0050885)|neurotransmitter uptake (GO:0001504)|positive regulation of synaptic transmission (GO:0050806)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|response to light stimulus (GO:0009416)|response to wounding (GO:0009611)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell projection (GO:0042995)|cell surface (GO:0009986)|fibril (GO:0043205)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	glutamate binding (GO:0016595)|high-affinity glutamate transmembrane transporter activity (GO:0005314)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(23)|skin(1)	41	all_lung(31;0.000245)		Epithelial(62;0.0444)|Lung(74;0.111)|all cancers(62;0.128)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TTTAAAGTGCCCATCCAGGCC	0.398																																					p.P202L													.	.			0			c.C605T												62.0	58.0	59.0					5																	36677031		2203	4300	6503	SO:0001583	missense	6507	exon6			AAGTGCCCATCCA		CCDS3919.1, CCDS54844.1	5p13	2013-05-22			ENSG00000079215	ENSG00000079215		"""Solute carriers"""	10941	protein-coding gene	gene with protein product	"""glutamate transporter variant EAAT1ex9skip"""	600111				7521911, 7698014	Standard	NM_004172		Approved	EAAT1, GLAST, EA6	uc003jkj.4	P43003	OTTHUMG00000090793	ENST00000265113.4:c.605C>T	5.37:g.36677031C>T	ENSP00000265113:p.Pro202Leu		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	61	0.05	3	NM_004172	9	0.00	0	B2R5T3|Q4JCQ8	Missense_Mutation	SNP	ENST00000265113.4	37	CCDS3919.1	.	.	.	.	.	.	.	.	.	.	C	13.56	2.274111	0.40194	.	.	ENSG00000079215	ENST00000265113;ENST00000427100;ENST00000381918	T;T	0.55760	0.51;0.5	6.02	6.02	0.97574	.	0.363870	0.34268	N	0.004114	T	0.45677	0.1354	L	0.41492	1.28	0.49389	D	0.99978	B;B	0.02656	0.0;0.0	B;B	0.08055	0.001;0.003	T	0.21177	-1.0253	10	0.30854	T	0.27	-20.1443	15.8536	0.78956	0.1963:0.8037:0.0:0.0	.	202;202	Q4JCQ8;P43003	.;EAA1_HUMAN	L	202;150;202	ENSP00000265113:P202L;ENSP00000371343:P202L	ENSP00000265113:P202L	P	+	2	0	SLC1A3	36712788	0.597000	0.26874	0.997000	0.53966	0.542000	0.35054	1.144000	0.31565	2.865000	0.98341	0.655000	0.94253	CCC			0.398	SLC1A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000207579.2		NM_004172	
CCDC152	100129792	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	5	42799496	42799496	+	Missense_Mutation	SNP	G	G	C			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr5:42799496G>C	ENST00000361970.5	+	8	665	c.578G>C	c.(577-579)aGa>aCa	p.R193T	CCDC152_ENST00000388827.4_Missense_Mutation_p.R137T|SEPP1_ENST00000509276.1_5'Flank	NM_001134848.1	NP_001128320.1	Q4G0S7	CC152_HUMAN	coiled-coil domain containing 152	193										endometrium(1)	1						AAACTAGCAAGAGTTCAGACT	0.313																																					p.R193T													.	.			0			c.G578C												119.0	106.0	110.0					5																	42799496		692	1585	2277	SO:0001583	missense	100129792	exon8			TAGCAAGAGTTCA		CCDS47203.1	5p12	2008-07-14			ENSG00000198865	ENSG00000198865			34438	protein-coding gene	gene with protein product							Standard	NM_001134848		Approved	LOC100129792	uc003jmx.3	Q4G0S7	OTTHUMG00000162141	ENST00000361970.5:c.578G>C	5.37:g.42799496G>C	ENSP00000354888:p.Arg193Thr		Somatic	198	0	0		WXS	Illumina HiSeq	.	145	0.18	26	NM_001134848	20	0.30	6	B3KXI4|B4E0P7|Q5BLP6	Missense_Mutation	SNP	ENST00000361970.5	37	CCDS47203.1	.	.	.	.	.	.	.	.	.	.	G	14.59	2.581409	0.46006	.	.	ENSG00000198865	ENST00000361970;ENST00000388827	T;T	0.50813	0.73;0.79	5.23	3.36	0.38483	.	0.119183	0.56097	D	0.000033	T	0.49745	0.1575	M	0.61703	1.905	0.37070	D	0.89849	P;P	0.44429	0.763;0.835	B;P	0.47645	0.288;0.553	T	0.55630	-0.8111	10	0.59425	D	0.04	-2.9826	8.3347	0.32208	0.1974:0.0:0.8026:0.0	.	137;193	B4E0P7;Q4G0S7	.;CC152_HUMAN	T	193;137	ENSP00000354888:R193T;ENSP00000373479:R137T	ENSP00000354888:R193T	R	+	2	0	CCDC152	42835253	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	1.392000	0.34486	0.505000	0.28104	-0.345000	0.07892	AGA			0.313	CCDC152-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000367497.1		XM_001717416	
ZSWIM6	57688	mdanderson.org	37	5	60628422	60628422	+	Missense_Mutation	SNP	G	G	A			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr5:60628422G>A	ENST00000252744.5	+	1	323	c.323G>A	c.(322-324)cGc>cAc	p.R108H		NM_020928.1	NP_065979.1	Q9HCJ5	ZSWM6_HUMAN	zinc finger, SWIM-type containing 6	108	Gly-rich.				neuron projection morphogenesis (GO:0048812)|regulation of neuron migration (GO:2001222)		zinc ion binding (GO:0008270)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)	8						GTGCAGCGCCGCATAGTCTAT	0.706																																					p.R108H													.	.			0			c.G323A												5.0	10.0	8.0					5																	60628422		670	1558	2228	SO:0001583	missense	57688	exon1			AGCGCCGCATAGT	BC039438	CCDS47215.1	5q12.1	2011-03-17			ENSG00000130449	ENSG00000130449		"""Zinc fingers, SWIM-type"""	29316	protein-coding gene	gene with protein product		615951				10997877, 16427614	Standard	NM_020928		Approved	KIAA1577	uc003jsr.3	Q9HCJ5	OTTHUMG00000162388	ENST00000252744.5:c.323G>A	5.37:g.60628422G>A	ENSP00000252744:p.Arg108His		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	58	0.05	3	NM_020928	0		0		Missense_Mutation	SNP	ENST00000252744.5	37	CCDS47215.1	.	.	.	.	.	.	.	.	.	.	G	13.15	2.149934	0.37923	.	.	ENSG00000130449	ENST00000252744	T	0.54071	0.59	1.79	1.79	0.24919	.	.	.	.	.	T	0.69691	0.3139	M	0.77103	2.36	0.33744	D	0.619751	D	0.71674	0.998	D	0.78314	0.991	T	0.78016	-0.2369	9	0.87932	D	0	.	11.0937	0.48132	0.0:0.0:1.0:0.0	.	108	Q9HCJ5	ZSWM6_HUMAN	H	108	ENSP00000252744:R108H	ENSP00000252744:R108H	R	+	2	0	ZSWIM6	60664179	1.000000	0.71417	1.000000	0.80357	0.120000	0.20174	6.597000	0.74118	0.802000	0.34089	0.186000	0.17326	CGC			0.706	ZSWIM6-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000368710.1		NM_020928	
NSD1	64324	broad.mit.edu	37	5	176638303	176638303	+	Missense_Mutation	SNP	A	A	G			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr5:176638303A>G	ENST00000439151.2	+	5	2948	c.2903A>G	c.(2902-2904)aAg>aGg	p.K968R	NSD1_ENST00000347982.4_Missense_Mutation_p.K699R|NSD1_ENST00000361032.4_Missense_Mutation_p.K865R|NSD1_ENST00000354179.4_Missense_Mutation_p.K699R	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	968					gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		TCAGAGAAAAAGGGAGATGGC	0.517			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																											p.K968R				Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	NSD1_ENST00000439151,colon,carcinoma,0,2	NSD1	416	2	0			c.A2903G												65.0	66.0	66.0					5																	176638303		2203	4300	6503	SO:0001583	missense	64324	exon5	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	AGAAAAAGGGAGA	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	14234	protein-coding gene	gene with protein product		606681	"""Sotos syndrome"""	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.2903A>G	5.37:g.176638303A>G	ENSP00000395929:p.Lys968Arg		Somatic	223	0.0044843049	1		WXS	Illumina HiSeq	Phase_I	210	0.01	3	NM_022455	40	0.00	0	Q96PD8|Q96RN7	Missense_Mutation	SNP	ENST00000439151.2	37	CCDS4412.1	.	.	.	.	.	.	.	.	.	.	A	0.034	-1.316745	0.01331	.	.	ENSG00000165671	ENST00000354179;ENST00000439151;ENST00000347982;ENST00000361032	D;D;D;D	0.93133	-3.07;-3.07;-3.07;-3.17	4.83	-1.98	0.07480	.	0.630400	0.15556	N	0.256168	T	0.78266	0.4256	N	0.03608	-0.345	0.09310	N	1	B;B;B	0.19817	0.039;0.039;0.023	B;B;B	0.18871	0.023;0.023;0.006	T	0.68074	-0.5505	9	.	.	.	.	5.4943	0.16793	0.5017:0.1509:0.3473:0.0	.	699;865;968	Q96L73-2;Q96L73-3;Q96L73	.;.;NSD1_HUMAN	R	699;968;699;865	ENSP00000346111:K699R;ENSP00000395929:K968R;ENSP00000343209:K699R;ENSP00000354310:K865R	.	K	+	2	0	NSD1	176570909	0.976000	0.34144	0.030000	0.17652	0.107000	0.19398	0.281000	0.18810	-0.407000	0.07576	-0.250000	0.11733	AAG			0.517	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000253412.2		NM_172349	
HIST1H3C	8352	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	6	26045698	26045698	+	Silent	SNP	G	G	A			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr6:26045698G>A	ENST00000540144.1	+	1	60	c.60G>A	c.(58-60)caG>caA	p.Q20Q	HIST1H2BB_ENST00000357905.2_5'Flank	NM_003531.2	NP_003522.1	P68431	H31_HUMAN	histone cluster 1, H3c	20					blood coagulation (GO:0007596)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|regulation of gene silencing (GO:0060968)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|ovary(1)|skin(1)	8						CGCGCAAGCAGCTTGCTACTA	0.587																																					p.Q20Q													.	.			0			c.G60A												40.0	43.0	42.0					6																	26045698		2203	4300	6503	SO:0001819	synonymous_variant	8352	exon1			CAAGCAGCTTGCT	X57128	CCDS4576.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000196532	ENSG00000278272		"""Histones / Replication-dependent"""	4768	protein-coding gene	gene with protein product		602812	"""H3 histone family, member C"", ""histone 1, H3c"""	H3FC		8227173, 9119399, 12408966	Standard	NM_003531		Approved	H3/c, H3.1	uc003nfv.3	P68431	OTTHUMG00000014416	ENST00000540144.1:c.60G>A	6.37:g.26045698G>A			Somatic	103	0	0		WXS	Illumina HiSeq	.	165	0.20	33	NM_003531	27	0.30	8	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Silent	SNP	ENST00000540144.1	37	CCDS4576.1																																																																																					0.587	HIST1H3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000040078.1		NM_003531	
BTN2A3P	54718	hgsc.bcm.edu;broad.mit.edu	37	6	26422353	26422353	+	RNA	SNP	C	C	T	rs571530750	byFrequency	TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr6:26422353C>T	ENST00000466808.2	+	0	7							Q96KV6	BT2A3_HUMAN	butyrophilin, subfamily 2, member A3, pseudogene							integral component of membrane (GO:0016021)		p.P3S(2)									GCTCATGGAACCAGCTGCTGC	0.622													C|||	7	0.00139776	0.0023	0.0	5008	,	,		16376	0.001		0.0	False		,,,				2504	0.0031				.													BTN2A3,NS,carcinoma,0,9	BTN2A3	0	9	2	Substitution - Missense(2)	endometrium(1)|kidney(1)	.																																											54718	.			ATGGAACCAGCTG	AL021917		6p22.1	2014-01-14	2011-09-06	2011-09-06	ENSG00000124549	ENSG00000124549		"""Butyrophilins"""	13229	pseudogene	pseudogene		613592	"""butyrophilin, subfamily 2, member A3"""	BTN2A3			Standard	NR_027795		Approved	BTN2.3	uc011dkl.1	Q96KV6	OTTHUMG00000014453		6.37:g.26422353C>T			Somatic	47	0	0		WXS	Illumina HiSeq	.	73	0.07	5	.	3	0.00	0	A6NEF4	RNA	SNP	ENST00000466808.2	37																																																																																						0.622	BTN2A3P-001	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000040118.4		NR_027795	
PSORS1C1	170679	mdanderson.org	37	6	31084507	31084507	+	Intron	SNP	G	G	T			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr6:31084507G>T	ENST00000259881.9	+	1	61				CDSN_ENST00000376288.2_Silent_p.G295G|PSORS1C1_ENST00000467107.1_3'UTR	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1											kidney(1)|ovary(2)|prostate(1)|skin(1)	5						CCACCTCGTAGCCACCATAGG	0.552																																					p.G295G													.	.			0			c.C885A												35.0	34.0	34.0					6																	31084507		1928	3845	5773	SO:0001627	intron_variant	1041	exon2			CTCGTAGCCACCA	AB031479	CCDS34390.1	6p21.3	2014-01-28	2003-06-12		ENSG00000204540	ENSG00000204540			17202	protein-coding gene	gene with protein product		613525	"""chromosome 6 open reading frame 16"""	C6orf16			Standard	NM_014068		Approved	SEEK1	uc003nsl.2	Q9UIG5	OTTHUMG00000031077	ENST00000259881.9:c.-229+1839G>T	6.37:g.31084507G>T			Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	49	0.06	3	NM_001264	0		0	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Silent	SNP	ENST00000259881.9	37	CCDS34390.1																																																																																					0.552	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000076110.3		NM_014068	
HLA-DQB2	3120	ucsc.edu	37	6	32726742	32726742	+	Silent	SNP	A	A	G			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr6:32726742A>G	ENST00000437316.2	-	3	594	c.531T>C	c.(529-531)aaT>aaC	p.N177N	HLA-DQB2_ENST00000435145.2_Silent_p.N177N|HLA-DQB2_ENST00000411527.1_Silent_p.N177N			P05538	DQB2_HUMAN	major histocompatibility complex, class II, DQ beta 2	181	Beta-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|B cell affinity maturation (GO:0002344)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of alpha-beta T cell activation (GO:0046635)|positive regulation of antigen processing and presentation (GO:0002579)|positive regulation of T-helper 1 type immune response (GO:0002827)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|early endosome (GO:0005769)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|external side of plasma membrane (GO:0009897)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)|toxic substance binding (GO:0015643)			endometrium(1)|kidney(1)|lung(1)|prostate(2)	5						TCCAGTCACCATTCCTAATGA	0.557																																					p.N177N													.	HLA-DQB2	22		0			c.T531C																																									SO:0001819	synonymous_variant	3120	exon3			GTCACCATTCCTA	M83890	CCDS56419.1	6p21.3	2013-01-11			ENSG00000232629	ENSG00000232629		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4945	protein-coding gene	gene with protein product		615161		HLA-DXB		2564844	Standard	NM_001198858		Approved		uc003oby.4	P05538	OTTHUMG00000031125	ENST00000437316.2:c.531T>C	6.37:g.32726742A>G			Somatic	136	0	0		RNA-Seq	Illumina HiSeq		163	0.01	2	NM_001198858	94	0.29	27	A6NIA5|Q29826|Q29870|Q29871|Q29872|Q29873|Q5SR06	Silent	SNP	ENST00000437316.2	37		.	.	.	.	.	.	.	.	.	.	G	0.461	-0.889297	0.02511	.	.	ENSG00000232629	ENST00000427449	.	.	.	3.43	-3.02	0.05446	.	.	.	.	.	T	0.38161	0.1030	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43556	-0.9384	4	.	.	.	.	9.7489	0.40464	0.6427:0.0:0.3573:0.0	rs17850864	.	.	.	T	176	.	.	M	-	2	0	HLA-DQB2	32834720	0.113000	0.22115	0.969000	0.41365	0.044000	0.14063	-0.735000	0.04888	-1.104000	0.03015	-1.383000	0.01170	ATG			0.557	HLA-DQB2-003	KNOWN	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000076216.2	rescued with RNA-seq		
CUL9	23113	mdanderson.org	37	6	43153342	43153342	+	Silent	SNP	G	G	T			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr6:43153342G>T	ENST00000252050.4	+	3	828	c.744G>T	c.(742-744)ctG>ctT	p.L248L	CUL9_ENST00000372647.2_Silent_p.L248L|CUL9_ENST00000354495.3_Silent_p.L248L	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	248					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						GCATTCATCTGCCTCAGGTAC	0.473																																					p.L248L													.	.			0			c.G744T												105.0	81.0	89.0					6																	43153342		2203	4300	6503	SO:0001819	synonymous_variant	23113	exon3			TCATCTGCCTCAG	AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"""parkin-like cytoplasmic p53 binding protein"", ""p53-associated parkin-like cytoplasmic protein"""	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.744G>T	6.37:g.43153342G>T			Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	32	0.09	3	NM_015089	6	0.00	0	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Silent	SNP	ENST00000252050.4	37	CCDS4890.1																																																																																					0.473	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000040582.2		NM_015089	
POPDC3	64208	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	6	105609640	105609640	+	Missense_Mutation	SNP	C	C	T	rs567589295		TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr6:105609640C>T	ENST00000254765.3	-	2	423	c.145G>A	c.(145-147)Ggg>Agg	p.G49R	POPDC3_ENST00000474760.1_Intron|BVES-AS1_ENST00000369120.2_RNA|BVES-AS1_ENST00000369122.3_RNA|BVES-AS1_ENST00000580511.1_RNA|BVES-AS1_ENST00000580854.1_RNA	NM_022361.4	NP_071756.2	Q9HBV1	POPD3_HUMAN	popeye domain containing 3	49					regulation of membrane potential (GO:0042391)	integral component of membrane (GO:0016021)				NS(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(2)|skin(3)|urinary_tract(1)	26		all_cancers(87;4.87e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0157)|Colorectal(196;0.202)|Lung NSC(302;0.238)				TAAAGGAGCCCGAAGAATCCA	0.473													C|||	1	0.000199681	0.0	0.0	5008	,	,		17819	0.0		0.0	False		,,,				2504	0.001				p.G49R													.	.			0			c.G145A												80.0	91.0	87.0					6																	105609640		2203	4300	6503	SO:0001583	missense	64208	exon2			GGAGCCCGAAGAA	BC022323	CCDS5052.1	6q21	2003-06-12			ENSG00000132429	ENSG00000132429			17649	protein-coding gene	gene with protein product		605824				10882522	Standard	NM_022361		Approved	POP3, MGC22671, bA355M14.1	uc003prb.3	Q9HBV1	OTTHUMG00000015293	ENST00000254765.3:c.145G>A	6.37:g.105609640C>T	ENSP00000254765:p.Gly49Arg		Somatic	147	0	0		WXS	Illumina HiSeq	.	157	0.13	21	NM_022361	0		0	B2RA98|Q5T3Y8|Q8TBW6	Missense_Mutation	SNP	ENST00000254765.3	37	CCDS5052.1	.	.	.	.	.	.	.	.	.	.	C	32	5.109286	0.94292	.	.	ENSG00000132429	ENST00000254765	T	0.42900	0.96	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.64283	0.2584	M	0.81112	2.525	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.67409	-0.5678	10	0.72032	D	0.01	-1.7788	19.867	0.96808	0.0:1.0:0.0:0.0	.	49	Q9HBV1	POPD3_HUMAN	R	49	ENSP00000254765:G49R	ENSP00000254765:G49R	G	-	1	0	POPDC3	105716333	1.000000	0.71417	0.989000	0.46669	0.993000	0.82548	7.818000	0.86416	2.704000	0.92352	0.655000	0.94253	GGG			0.473	POPDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000041651.1		NM_022361	
INTS4L2	644619	broad.mit.edu	37	7	65150814	65150815	+	RNA	INS	-	-	C	rs376935907		TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr7:65150814_65150815insC	ENST00000430126.2	+	0	757							Q2T9F4	IN4L2_HUMAN	integrator complex subunit 4-like 2																		TCTTCATCCCTCACCCCCCCCC	0.46																																					.													.	.			0			.																																											0	.			CATCCCTCACCCC	BC111554		7q11.21	2013-03-26			ENSG00000232270	ENSG00000273024			22351	other	unknown							Standard	NR_027392		Approved	MGC133166	uc003tue.2	Q2T9F4	OTTHUMG00000156558		7.37:g.65150815_65150815dupC			Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	90	0.09	8	.	0		0		RNA	INS	ENST00000430126.2	37																																																																																						0.460	INTS4L2-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000345545.2		NR_027392	
SEMA3E	9723	broad.mit.edu	37	7	83277770	83277770	+	Missense_Mutation	SNP	T	T	G	rs544498058	byFrequency	TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr7:83277770T>G	ENST00000307792.3	-	1	556	c.89A>C	c.(88-90)cAc>cCc	p.H30P		NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	30					axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell-matrix adhesion (GO:0001953)|patterning of blood vessels (GO:0001569)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell shape (GO:0008360)|semaphorin-plexin signaling pathway (GO:0071526)|sprouting angiogenesis (GO:0002040)|synapse organization (GO:0050808)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(19)|ovary(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	51		Medulloblastoma(109;0.109)				TAACCGGGGGTGGGTAGTATC	0.433													T|||	23	0.00459265	0.0008	0.0086	5008	,	,		14469	0.0069		0.007	False		,,,				2504	0.002				p.H30P													.	SEMA3E	125		0			c.A89C												107.0	91.0	97.0					7																	83277770		2203	4300	6503	SO:0001583	missense	9723	exon1			CGGGGGTGGGTAG	AB002329	CCDS34674.1, CCDS55121.1	7q21.11	2013-01-11			ENSG00000170381	ENSG00000170381		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10727	protein-coding gene	gene with protein product	"""M-sema H"""	608166		SEMAH		9205841, 9515811	Standard	NM_012431		Approved	M-SemaK, KIAA0331, coll-5	uc003uhy.2	O15041	OTTHUMG00000154693	ENST00000307792.3:c.89A>C	7.37:g.83277770T>G	ENSP00000303212:p.His30Pro		Somatic	145	0.1379310345	20		WXS	Illumina HiSeq	Phase_I	296	0.16	47	NM_012431	0		0	B4E1P1|Q75M94|Q75M97	Missense_Mutation	SNP	ENST00000307792.3	37	CCDS34674.1	.	.	.	.	.	.	.	.	.	.	T	5.742	0.321430	0.10845	.	.	ENSG00000170381	ENST00000307792;ENST00000541514	T	0.20881	2.04	4.27	4.27	0.50696	Semaphorin/CD100 antigen (1);	0.523883	0.19399	N	0.115209	T	0.14442	0.0349	N	0.19112	0.55	0.58432	D	0.999997	B	0.22604	0.072	B	0.28232	0.087	T	0.09596	-1.0667	10	0.23891	T	0.37	.	11.2518	0.49031	0.0:0.0:0.0:1.0	.	30	O15041	SEM3E_HUMAN	P	30	ENSP00000303212:H30P	ENSP00000303212:H30P	H	-	2	0	SEMA3E	83115706	0.649000	0.27322	0.266000	0.24541	0.932000	0.56968	1.588000	0.36633	1.777000	0.52277	0.533000	0.62120	CAC			0.433	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000336606.1		NM_012431	
EPHB4	2050	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	7	100419938	100419938	+	Missense_Mutation	SNP	A	A	C			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr7:100419938A>C	ENST00000358173.3	-	4	1231	c.763T>G	c.(763-765)Tgt>Ggt	p.C255G	EPHB4_ENST00000360620.3_Missense_Mutation_p.C255G|EPHB4_ENST00000477446.1_5'UTR|RN7SL750P_ENST00000582814.1_RNA	NM_004444.4	NP_004435.3	P54760	EPHB4_HUMAN	EPH receptor B4	255	Cys-rich.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|ephrin receptor signaling pathway (GO:0048013)|heart morphogenesis (GO:0003007)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(3)	47	Lung NSC(181;0.041)|all_lung(186;0.0581)					CCCGGAGCACAGCTGCAGCCC	0.682																																					p.C255G	GBM(200;2113 3072 25865 52728)												.	.			0			c.T763G												12.0	11.0	11.0					7																	100419938		2187	4268	6455	SO:0001583	missense	2050	exon4			GAGCACAGCTGCA	AY056047	CCDS5706.1	7q22	2013-02-11	2004-10-28		ENSG00000196411	ENSG00000196411		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3395	protein-coding gene	gene with protein product		600011	"""EphB4"""	HTK		8188704	Standard	NM_004444		Approved	Tyro11	uc003uwn.1	P54760	OTTHUMG00000157040	ENST00000358173.3:c.763T>G	7.37:g.100419938A>C	ENSP00000350896:p.Cys255Gly		Somatic	47	0	0		WXS	Illumina HiSeq	.	126	0.12	15	NM_004444	656	0.28	181	B5A970|B5A971|B5A972|Q7Z635|Q9BTA5|Q9BXP0	Missense_Mutation	SNP	ENST00000358173.3	37	CCDS5706.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.083169	0.76642	.	.	ENSG00000196411	ENST00000360620;ENST00000358173	D;D	0.99824	-6.96;-6.96	5.62	5.62	0.85841	Tyrosine-protein kinase, receptor class V, conserved site (1);	0.000000	0.64402	D	0.000014	D	0.99829	0.9923	M	0.89353	3.025	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;1.0	D;D;D;D;D	0.91635	0.997;0.999;0.997;0.991;0.998	D	0.96716	0.9529	10	0.87932	D	0	.	13.7571	0.62943	1.0:0.0:0.0:0.0	.	255;255;255;255;255	B5A972;B5A971;B5A970;Q96L35;P54760	.;.;.;.;EPHB4_HUMAN	G	255	ENSP00000353833:C255G;ENSP00000350896:C255G	ENSP00000350896:C255G	C	-	1	0	EPHB4	100257874	1.000000	0.71417	0.994000	0.49952	0.704000	0.40688	6.203000	0.72137	2.138000	0.66242	0.459000	0.35465	TGT			0.682	EPHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000347222.1		NM_004444	
PRSS3P2	154754	broad.mit.edu	37	7	142482025	142482025	+	RNA	DEL	A	A	-	rs370076329		TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr7:142482025delA	ENST00000603901.1	+	0	591					NR_001296.3		Q8NHM4	TRY6_HUMAN	protease, serine, 3 pseudogene 2						endothelial cell migration (GO:0043542)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)										TGCAGTGCCCACATGGAGAAG	0.572																																					.													.	.			0			.																																											0	.			GTGCCCACATGGA			7q34	2012-03-06			ENSG00000250606	ENSG00000275896			43788	pseudogene	pseudogene	"""trypsinogen C"""						Standard	NR_001296		Approved	TRY6	uc011ksq.2	Q8NHM4	OTTHUMG00000158904		7.37:g.142482025delA			Somatic	31	0.064516129	2		WXS	Illumina HiSeq	Phase_I	43	0.33	14	.	0		0		RNA	DEL	ENST00000603901.1	37																																																																																						0.572	PRSS3P2-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000470000.1		NR_001296	
MFHAS1	9258	broad.mit.edu	37	8	8749216	8749216	+	Silent	SNP	A	A	G			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr8:8749216A>G	ENST00000276282.6	-	1	1939	c.1353T>C	c.(1351-1353)ccT>ccC	p.P451P		NM_004225.2	NP_004216.2	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified sequence 1	451	Roc. {ECO:0000255|PROSITE- ProRule:PRU00758}.									endometrium(1)|kidney(3)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|stomach(1)	21		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.124)		TCACAGGGGGAGGTGACGGTG	0.612																																					p.P451P	Melanoma(103;1201 2045 17515 28966)												.	MFHAS1	58		0			c.T1353C												67.0	58.0	61.0					8																	8749216		2203	4300	6503	SO:0001819	synonymous_variant	9258	exon1			AGGGGGAGGTGAC	AB016816	CCDS34844.1	8p23.1	2014-03-07			ENSG00000147324	ENSG00000147324			16982	protein-coding gene	gene with protein product	"""leucine rich repeat containing 65"", ""malignant fibrous histiocytoma-amplified sequences with leucine-rich tandem repeats 1"""	605352				9973190	Standard	NM_004225		Approved	MASL1, LRRC65	uc003wsj.1	Q9Y4C4	OTTHUMG00000163676	ENST00000276282.6:c.1353T>C	8.37:g.8749216A>G			Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	91	0.03	3	NM_004225	19	0.00	0	Q96CI0	Silent	SNP	ENST00000276282.6	37	CCDS34844.1																																																																																					0.612	MFHAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000374724.2		NM_004225	
PCMTD1	115294	mdanderson.org	37	8	52733270	52733270	+	Missense_Mutation	SNP	C	C	T			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr8:52733270C>T	ENST00000360540.5	-	7	1121	c.715G>A	c.(715-717)Gct>Act	p.A239T	PCMTD1_ENST00000522514.1_Missense_Mutation_p.A239T|PCMTD1_ENST00000519559.1_5'UTR|PCMTD1_ENST00000544451.1_Missense_Mutation_p.A163T	NM_052937.2	NP_443169.2	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	239						cytoplasm (GO:0005737)	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719)			NS(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(17)|prostate(2)|skin(8)|soft_tissue(1)	37		Lung NSC(129;0.0795)|all_lung(136;0.144)				TTCCTGACAGCACAGGGAGCT	0.343																																					p.A239T													.	.			0			c.G715A												24.0	23.0	23.0					8																	52733270		2195	4278	6473	SO:0001583	missense	115294	exon6			TGACAGCACAGGG		CCDS6148.1, CCDS69480.1	8q11.23	2010-08-05			ENSG00000168300	ENSG00000168300			30483	protein-coding gene	gene with protein product							Standard	XM_005251146		Approved	FLJ10883	uc003xqx.4	Q96MG8	OTTHUMG00000164246	ENST00000360540.5:c.715G>A	8.37:g.52733270C>T	ENSP00000353739:p.Ala239Thr		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	78	0.06	5	NM_052937	41	0.00	0	Q96FK9	Missense_Mutation	SNP	ENST00000360540.5	37	CCDS6148.1	.	.	.	.	.	.	.	.	.	.	C	11.42	1.634291	0.29068	.	.	ENSG00000168300	ENST00000360540;ENST00000544451;ENST00000522514	T;T;T	0.37752	1.18;1.18;1.18	5.77	5.77	0.91146	.	0.108661	0.64402	D	0.000005	T	0.21718	0.0523	N	0.17474	0.49	0.39279	D	0.964533	B;B;B	0.28419	0.001;0.211;0.0	B;B;B	0.22601	0.001;0.04;0.001	T	0.12734	-1.0536	10	0.16420	T	0.52	-25.2146	13.44	0.61108	0.274:0.726:0.0:0.0	.	109;163;239	B4E2B4;F5H1M8;Q96MG8	.;.;PCMD1_HUMAN	T	239;163;239	ENSP00000353739:A239T;ENSP00000444026:A163T;ENSP00000428099:A239T	ENSP00000353739:A239T	A	-	1	0	PCMTD1	52895823	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	1.730000	0.38125	2.722000	0.93159	0.655000	0.94253	GCT			0.343	PCMTD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000377909.2		NM_052937	
COL22A1	169044	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	8	139629170	139629170	+	Missense_Mutation	SNP	G	G	A			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr8:139629170G>A	ENST00000303045.6	-	54	4303	c.3857C>T	c.(3856-3858)gCa>gTa	p.A1286V	COL22A1_ENST00000341807.4_5'UTR|COL22A1_ENST00000435777.1_Missense_Mutation_p.A1266V	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	1286	Collagen-like 12.|Gly-rich.|Pro-rich.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			GGGACCGGGTGCACCAGAATC	0.577										HNSCC(7;0.00092)																											p.A1286V													COL22A1,right_upper_lobe,carcinoma,-1,1	COL22A1	-1	1	0			c.C3857T												74.0	74.0	74.0					8																	139629170		2203	4300	6503	SO:0001583	missense	169044	exon54			CCGGGTGCACCAG	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"""Collagens"""	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.3857C>T	8.37:g.139629170G>A	ENSP00000303153:p.Ala1286Val		Somatic	88	0	0		WXS	Illumina HiSeq	.	91	0.19	17	NM_152888	48	0.27	13	B7ZMH0|C9K0G4|Q8IVT9	Missense_Mutation	SNP	ENST00000303045.6	37	CCDS6376.1	.	.	.	.	.	.	.	.	.	.	G	0.421	-0.908530	0.02434	.	.	ENSG00000169436	ENST00000303045;ENST00000435777;ENST00000545577	D;D	0.94376	-3.24;-3.41	4.35	1.59	0.23543	.	0.825040	0.10255	N	0.696678	D	0.83519	0.5272	N	0.12182	0.205	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.10450	0.003;0.005	T	0.70684	-0.4804	10	0.30854	T	0.27	.	3.9494	0.09363	0.1965:0.0:0.6166:0.1869	.	1266;1286	Q8NFW1-2;Q8NFW1	.;COMA1_HUMAN	V	1286;1266;979	ENSP00000303153:A1286V;ENSP00000387655:A1266V	ENSP00000303153:A1286V	A	-	2	0	COL22A1	139698352	0.061000	0.20836	0.000000	0.03702	0.131000	0.20780	1.014000	0.29950	0.359000	0.24239	0.555000	0.69702	GCA			0.577	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000315905.2		XM_291257	
FAM214B	80256	hgsc.bcm.edu	37	9	35106621	35106621	+	Missense_Mutation	SNP	G	G	A	rs373199885	byFrequency	TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr9:35106621G>A	ENST00000378561.1	-	4	4028	c.973C>T	c.(973-975)Cgg>Tgg	p.R325W	FAM214B_ENST00000603301.1_Missense_Mutation_p.R325W|FAM214B_ENST00000378566.1_Missense_Mutation_p.R20W|FAM214B_ENST00000605244.1_Missense_Mutation_p.R325W|FAM214B_ENST00000378554.2_Missense_Mutation_p.R325W|FAM214B_ENST00000488109.2_Missense_Mutation_p.R325W|FAM214B_ENST00000605392.1_5'Flank|FAM214B_ENST00000322813.5_Missense_Mutation_p.R325W|FAM214B_ENST00000378557.1_Missense_Mutation_p.R325W			Q7L5A3	F214B_HUMAN	family with sequence similarity 214, member B	325						nucleus (GO:0005634)											GGCCCCTTCCGGAGGCTTCGA	0.627													G|||	5	0.000998403	0.0038	0.0	5008	,	,		16749	0.0		0.0	False		,,,				2504	0.0				p.R325W													KIAA1539,NS,carcinoma,+1,1	KIAA1539	1	1	0			c.C973T							G	TRP/ARG	1,4335		0,1,2167	8.0	10.0	10.0		973	5.4	1.0	9		10	0,8490		0,0,4245	no	missense	KIAA1539	NM_025182.2	101	0,1,6412	AA,AG,GG		0.0,0.0231,0.0078	probably-damaging	325/539	35106621	1,12825	2168	4245	6413	SO:0001583	missense	80256	exon5			CCTTCCGGAGGCT	AB040972	CCDS6578.1	9p13.2	2011-12-01	2011-12-01	2011-12-01	ENSG00000005238	ENSG00000005238			25666	protein-coding gene	gene with protein product			"""KIAA1539"""	KIAA1539		10819331	Standard	NM_025182		Approved	FLJ11560, bA182N22.6	uc003zwo.3	Q7L5A3	OTTHUMG00000019847	ENST00000378561.1:c.973C>T	9.37:g.35106621G>A	ENSP00000367823:p.Arg325Trp		Somatic	42	0	0		WXS	Illumina HiSeq	.	66	0.05	3	NM_025182	102	0.00	0	B1AML4|B1AML5|D3DRN5|O60377|Q9BQ60|Q9HAI9|Q9P1Y9	Missense_Mutation	SNP	ENST00000378561.1	37	CCDS6578.1	.	.	.	.	.	.	.	.	.	.	G	18.69	3.678139	0.68042	2.31E-4	0.0	ENSG00000005238	ENST00000378566;ENST00000322813;ENST00000378561;ENST00000378557;ENST00000378554	.	.	.	5.37	5.37	0.77165	.	0.126735	0.53938	D	0.000044	T	0.48624	0.1510	L	0.42245	1.32	0.46798	D	0.999203	D	0.60575	0.988	B	0.42386	0.386	T	0.55289	-0.8164	9	0.72032	D	0.01	-21.604	16.6599	0.85238	0.0:0.0:1.0:0.0	.	325	Q7L5A3	K1539_HUMAN	W	20;325;325;325;325	.	ENSP00000319897:R325W	R	-	1	2	KIAA1539	35096621	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.221000	0.51215	2.808000	0.96608	0.650000	0.86243	CGG			0.627	FAM214B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000052261.1		NM_025182	
SPATA31D5P	347127	broad.mit.edu	37	9	84530744	84530744	+	RNA	SNP	T	T	C			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr9:84530744T>C	ENST00000527857.1	+	0	766					NR_026851.1				SPATA31 subfamily D, member 5, pseudogene																		CCCTCTCCCCTTTTCCCACCG	0.542																																					.													.	.			0			.																																											0	.			CTCCCCTTTTCCC			9q21.32	2012-10-12	2012-10-12	2012-10-12	ENSG00000240632	ENSG00000240632			38602	pseudogene	pseudogene			"""family with sequence similarity 75, member D5"", ""family with sequence similarity 75, member D5, pseudogene"""	FAM75D5			Standard	NR_026851		Approved	FLJ43950, FAM75D5P	uc011lst.2		OTTHUMG00000020087		9.37:g.84530744T>C			Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	158	0.02	3	.	0		0		RNA	SNP	ENST00000527857.1	37																																																																																						0.542	SPATA31D5P-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000052810.2		NR_026851	
ODF2	4957	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	9	131262420	131262420	+	Silent	SNP	C	C	T			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr9:131262420C>T	ENST00000434106.3	+	21	2739	c.2376C>T	c.(2374-2376)agC>agT	p.S792S	ODF2_ENST00000372807.5_Silent_p.S787S|ODF2_ENST00000604420.1_Silent_p.S792S|ODF2_ENST00000444119.2_Silent_p.S768S|ODF2_ENST00000393527.3_Silent_p.S768S|ODF2_ENST00000351030.3_Silent_p.S787S	NM_153433.1	NP_702911.1	Q5BJF6	ODFP2_HUMAN	outer dense fiber of sperm tails 2	792					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|regulation of cilium assembly (GO:1902017)|spermatid development (GO:0007286)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)|primary cilium (GO:0072372)	Rab GTPase binding (GO:0017137)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(7)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	37						CCAACCGCAGCATGCAGAACT	0.577																																					p.S856S													.	.			0			c.C2568T												218.0	173.0	188.0					9																	131262420		2203	4300	6503	SO:0001819	synonymous_variant	4957	exon21			CCGCAGCATGCAG	AF012549	CCDS6902.1, CCDS56585.1, CCDS56586.1, CCDS56587.1, CCDS56588.1, CCDS56589.1, CCDS56590.1	9q34	2010-04-23	2002-10-21		ENSG00000136811	ENSG00000136811			8114	protein-coding gene	gene with protein product	"""cancer/testis antigen 134"""	602015	"""outer dense fibre of sperm tails 2"""			9045620, 10072582	Standard	NM_153435		Approved	ODF84, CT134	uc004bvc.3	Q5BJF6	OTTHUMG00000020748	ENST00000434106.3:c.2376C>T	9.37:g.131262420C>T			Somatic	84	0	0		WXS	Illumina HiSeq	.	119	0.31	37	NM_153435	130	0.55	72	B1AND3|B4DRK4|B4DX73|B4DZ02|E7EWL2|F5H6J4|O14721|O60631|Q1W2J6|Q6UN26|Q7Z5I6|Q96FN2	Silent	SNP	ENST00000434106.3	37	CCDS56588.1																																																																																					0.577	ODF2-011	KNOWN	basic|CCDS	protein_coding	protein_coding		OTTHUMT00000054449.3			
IER5L	389792	mdanderson.org	37	9	131939453	131939453	+	Silent	SNP	G	G	T			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chr9:131939453G>T	ENST00000372491.2	-	1	1087	c.879C>A	c.(877-879)ggC>ggA	p.G293G	RP11-247A12.8_ENST00000599172.2_RNA|RP11-247A12.2_ENST00000372490.3_RNA	NM_203434.2	NP_982258.2	Q5T953	IER5L_HUMAN	immediate early response 5-like	293													Ovarian(14;0.0448)|Medulloblastoma(224;0.235)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0178)		CGGACGCCAGGCCCGGTCCCG	0.716																																					p.G293G													.	.			0			c.C879A												11.0	14.0	13.0					9																	131939453		1883	4035	5918	SO:0001819	synonymous_variant	389792	exon1			CGCCAGGCCCGGT	BC013070	CCDS43888.1	9q34.11	2013-09-20			ENSG00000188483	ENSG00000188483			23679	protein-coding gene	gene with protein product							Standard	NM_203434		Approved	bA247A12.2	uc010myt.1	Q5T953	OTTHUMG00000020773	ENST00000372491.2:c.879C>A	9.37:g.131939453G>T			Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	43	0.07	3	NM_203434	18	0.00	0	Q6P3E2	Silent	SNP	ENST00000372491.2	37	CCDS43888.1																																																																																					0.716	IER5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000054556.2			
MT-CO1	4512	broad.mit.edu	37	M	5989	5989	+	Missense_Mutation	SNP	T	T	C			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chrM:5989T>C	ENST00000361624.2	+	1	86	c.86T>C	c.(85-87)cTa>cCa	p.L29P	MT-ATP6_ENST00000361899.2_5'Flank|MT-TM_ENST00000387377.1_RNA|MT-TY_ENST00000387409.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-TL1_ENST00000386347.1_RNA|MT-TD_ENST00000387419.1_RNA|MT-CO2_ENST00000361739.1_5'Flank|MT-ATP8_ENST00000361851.1_5'Flank|MT-RNR2_ENST00000387347.2_RNA|MT-TS1_ENST00000387416.2_RNA|MT-TI_ENST00000387365.1_RNA|MT-TA_ENST00000387392.1_RNA|MT-TC_ENST00000387405.1_RNA|MT-TW_ENST00000387382.1_RNA|MT-TQ_ENST00000387372.1_RNA|MT-TN_ENST00000387400.1_RNA			P00395	COX1_HUMAN	mitochondrially encoded cytochrome c oxidase I	29					aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidative phosphorylation (GO:0006119)|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 IV (GO:0005751)|respiratory chain complex IV (GO:0045277)	cytochrome-c oxidase activity (GO:0004129)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(4)|endometrium(25)|kidney(19)|lung(3)|prostate(3)	54						AGCTGGAGTCCTAGGCACAGC	0.517																																					p.L29P													.	.			0			c.T86C																																									SO:0001583	missense	4512	exon1			GAGTCCTAGGCAC			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198804	ENSG00000198804		"""Mitochondrial respiratory chain complex / Complex IV"""	7419	protein-coding gene	gene with protein product		516030	"""cytochrome c oxidase I"""	MTCO1		7219534	Standard			Approved	COX1, COI		P00395		ENST00000361624.2:c.86T>C	M.37:g.5989T>C	ENSP00000354499:p.Leu29Pro		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	45	0.07	3	ENST00000361624	0		0	Q34770	Missense_Mutation	SNP	ENST00000361624.2	37																																																																																						0.517	MT-CO1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				YP_003024028	
FRMPD4	9758	mdanderson.org	37	X	12734431	12734431	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chrX:12734431G>T	ENST00000380682.1	+	15	2359	c.1853G>T	c.(1852-1854)tGt>tTt	p.C618F		NM_014728.3	NP_055543.2	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	618					positive regulation of synapse structural plasticity (GO:0051835)	cytoskeleton (GO:0005856)|dendritic spine (GO:0043197)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			breast(1)|central_nervous_system(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)	22						GAGGCCCCCTGTGAGGCAGAC	0.532																																					p.C618F													.	.			0			c.G1853T												78.0	78.0	78.0					X																	12734431		2203	4300	6503	SO:0001583	missense	9758	exon15			CCCCCTGTGAGGC	AB002314	CCDS35201.1	Xp22.31	2006-02-09	2006-02-09	2006-02-09	ENSG00000169933	ENSG00000169933			29007	protein-coding gene	gene with protein product		300838	"""PDZ domain containing 10"""	PDZK10, PDZD10		9205841	Standard	NM_014728		Approved	KIAA0316	uc004cuz.2	Q14CM0	OTTHUMG00000021138	ENST00000380682.1:c.1853G>T	X.37:g.12734431G>T	ENSP00000370057:p.Cys618Phe		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	57	0.05	3	NM_014728	1	0.00	0	A8K0X9|O15032	Missense_Mutation	SNP	ENST00000380682.1	37	CCDS35201.1	.	.	.	.	.	.	.	.	.	.	G	12.16	1.854255	0.32791	.	.	ENSG00000169933	ENST00000380682;ENST00000429478;ENST00000304087	T	0.22134	1.97	5.86	4.99	0.66335	.	0.417032	0.28156	N	0.016382	T	0.17704	0.0425	L	0.60455	1.87	0.09310	N	1	P;P	0.46706	0.818;0.883	B;B	0.38655	0.232;0.278	T	0.35699	-0.9778	10	0.49607	T	0.09	.	4.0304	0.09706	0.2016:0.0:0.5987:0.1997	.	610;618	B7ZLE1;Q14CM0	.;FRPD4_HUMAN	F	618;609;607	ENSP00000370057:C618F	ENSP00000304583:C607F	C	+	2	0	FRMPD4	12644352	0.997000	0.39634	0.534000	0.28014	0.948000	0.59901	4.596000	0.61055	1.222000	0.43521	0.600000	0.82982	TGT			0.532	FRMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000055771.1		XM_045712	
SUPT20HL1	100130302	hgsc.bcm.edu	37	X	24382423	24382423	+	IGR	SNP	G	G	C			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chrX:24382423G>C								AC004552.1 (15400 upstream) : PDK3 (100914 downstream)																							tgctgctgctgctgctcctgc	0.617																																					p.A516P													.	.			0			c.G1546C																																									SO:0001628	intergenic_variant	100130302	exon1			GCTGCTGCTGCTC																													X.37:g.24382423G>C			Somatic	71	0	0		WXS	Illumina HiSeq	.	160	0.06	9	NM_001136234	0		0		Missense_Mutation	SNP		37																																																																																					0	0.617										
RGN	9104	mdanderson.org	37	X	46951545	46951545	+	Silent	SNP	G	G	T			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chrX:46951545G>T	ENST00000352078.4	+	6	1125	c.780G>T	c.(778-780)gtG>gtT	p.V260V	RGN_ENST00000336169.3_Silent_p.V260V|RGN_ENST00000397180.1_Silent_p.V260V|RGN_ENST00000457380.1_Silent_p.V188V	NM_004683.4	NP_004674.1	Q15493	RGN_HUMAN	regucalcin	260					cellular calcium ion homeostasis (GO:0006874)|L-ascorbic acid biosynthetic process (GO:0019853)|positive regulation of ATPase activity (GO:0032781)|regulation of calcium-mediated signaling (GO:0050848)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|enzyme regulator activity (GO:0030234)|gluconolactonase activity (GO:0004341)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(2)|skin(1)|urinary_tract(1)	9						AAATGTATGTGACCTGCGCCC	0.448																																					p.V260V													.	.			0			c.G780T												75.0	70.0	71.0					X																	46951545		2203	4300	6503	SO:0001819	synonymous_variant	9104	exon6			GTATGTGACCTGC	D31815	CCDS14272.1, CCDS75968.1	Xp11.3	2014-03-14	2013-04-26		ENSG00000130988	ENSG00000130988	3.1.1.17		9989	protein-coding gene	gene with protein product	"""senescence marker protein-30"", ""gluconolactonase"""	300212	"""regucalcin (senescence marker protein-30)"""			7548213	Standard	NM_152869		Approved	SMP30, RC	uc004dha.1	Q15493	OTTHUMG00000021435	ENST00000352078.4:c.780G>T	X.37:g.46951545G>T			Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	126	0.04	5	NM_004683	0		0	A4FTW1|A8K271|Q53FC9|Q5JRR5	Silent	SNP	ENST00000352078.4	37	CCDS14272.1																																																																																					0.448	RGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000056385.1		NM_004683	
AR	367	hgsc.bcm.edu	37	X	66765222	66765223	+	Missense_Mutation	DNP	GC	GC	AG			TCGA-2G-AAFH-01A-12D-A42Y-10	TCGA-2G-AAFH-10A-01D-A433-10	GC	GC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258cf1c4-41c5-4e54-ad57-0961483d99ba	bb501e72-c643-4afb-b1e8-56593b08cb2f	g.chrX:66765222_66765223GC>AG	ENST00000374690.3	+	1	758_759	c.234_235GC>AG	c.(232-237)caGCag>caAGag	p.Q79E	AR_ENST00000504326.1_Missense_Mutation_p.Q79E|AR_ENST00000513847.1_3'UTR|AR_ENST00000396044.3_Missense_Mutation_p.Q79E	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	78	Gln-rich.|Modulating.				androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|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)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	agcagcagcagcagcaagagac	0.653									Androgen Insensitivity Syndrome																												p.Q79E													.	.			0			c.C235G																																									SO:0001583	missense	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	GCAGCAGCAGCAA	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"""Nuclear hormone receptors"""	644	protein-coding gene	gene with protein product	"""testicular feminization"", ""Kennedy disease"""	313700	"""dihydrotestosterone receptor"", ""spinal and bulbar muscular atrophy"""	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	Exception_encountered	X.37:g.66765222_66765223delinsAG	ENSP00000363822:p.Gln79Glu		Somatic	107	0	0		WXS	Illumina HiSeq	.	145	0.06	8	NM_000044	0		0	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	DNP	ENST00000374690.3	37	CCDS14387.1																																																																																					0.653	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000057007.1		NM_000044	
