#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_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_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ENSG_ID	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_Ens_Gene	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GMAF	i_HGNC	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_Mutation_Status	i_Normal_Alt_Count	i_Normal_Ref_Count	i_Normal_VAF	i_ORegAnno_bin	i_PurityEst	i_RNA_Tum_Ref_count	i_RNA_Tum_VAF	i_RNA_Tum_Var_count	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_Tier	i_Tumor_Alt_Count	i_Tumor_Ref_Count	i_Tumor_VAF	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_WGS_Norm_Ref_count	i_WGS_Norm_VAF	i_WGS_Norm_Var_count	i_WGS_Tum_Ref_count	i_WGS_Tum_VAF	i_WGS_Tum_Var_count	i_all_domains	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	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_deletion_substructures	i_domain	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_name	i_gene_type	i_havana_transcript	i_reference	i_refseq_mrna_id	i_rs_id	i_secondary_variant_classification	i_stop	i_strand	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_type	i_ucsc_cons	i_variant
ETV3	2117	genome.wustl.edu	37	1	157105270	157105270	+	Missense_Mutation	SNP	C	C	T			TCGA-DX-A1L4-01A-12D-A26G-09	TCGA-DX-A1L4-10A-01D-A26G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c1aa1b8-f02c-43e7-a410-cc0344f0107e	6c11585a-6ac8-4f59-90c4-cae54eb89e0e	g.chr1:157105270C>T	ENST00000368192.4	-	3	341	c.277G>A	c.(277-279)Gcc>Acc	p.A93T	ETV3_ENST00000460850.1_5'UTR|ETV3_ENST00000326786.4_Missense_Mutation_p.A93T	NM_001145312.1	NP_001138784.1	P41162	ETV3_HUMAN	ets variant 3	93					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|prostate(2)	9	Hepatocellular(266;0.158)	Prostate(1639;0.174)				TACCTGAGGGCCCGGCTCAGC	0.468																																																	0								ENSG00000117036						62.0	63.0	63.0					1																	157105270		2203	4300	6503	ETV3	SO:0001583	missense	0			-	HGNC	BC022868	CCDS1164.1, CCDS44250.1	1q21-q23	2008-09-12	2008-09-12		ENSG00000117036	ENSG00000117036			3492	protein-coding gene	gene with protein product		164873	"""ets variant gene 3, ETS family transcriptional repressor"", ""ets variant gene 3"""			8020980	Standard	NM_005240		Approved	PE-1	uc001fqr.2	P41162	OTTHUMG00000034298	ENST00000368192.4:c.277G>A	1.37:g.157105270C>T	ENSP00000357175:p.Ala93Thr	Somatic	0	62	0.00		0.5469949440746017	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	11	104	9.57	B4E3M7|Q8TAC8|Q9BX30	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Ets_dom,smart_Ets_dom,pfscan_Ets_dom,prints_Ets_dom	p.A93T	ENST00000368192.4	37	c.277	CCDS44250.1	1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.830626	0.91036	.	.	ENSG00000117036	ENST00000368192;ENST00000326786	T;T	0.71817	-0.6;-0.6	5.47	5.47	0.80525	Winged helix-turn-helix transcription repressor DNA-binding (1);Ets (5);	0.000000	0.64402	D	0.000001	D	0.85784	0.5777	M	0.90309	3.105	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.88370	0.2994	10	0.87932	D	0	.	18.0939	0.89482	0.0:1.0:0.0:0.0	.	93;93	P41162-2;P41162	.;ETV3_HUMAN	T	93	ENSP00000357175:A93T;ENSP00000327316:A93T	ENSP00000327316:A93T	A	-	1	0	ETV3	155371894	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.768000	0.85345	2.566000	0.86566	0.655000	0.94253	GCC	-	pfam_Ets_dom,smart_Ets_dom,pfscan_Ets_dom,prints_Ets_dom		0.468	ETV3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	ETV3	protein_coding	OTTHUMT00000082843.2	C	NM_005240	-		157105270	-1	no_errors	ENST00000368192	ensembl	human	known	74_37	missense	SNP	1.000	T
ADAM21P1	145241	genome.wustl.edu	37	14	70713951	70713951	+	RNA	SNP	G	G	A	rs202183568		TCGA-DX-A1L4-01A-12D-A26G-09	TCGA-DX-A1L4-10A-01D-A26G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c1aa1b8-f02c-43e7-a410-cc0344f0107e	6c11585a-6ac8-4f59-90c4-cae54eb89e0e	g.chr14:70713951G>A	ENST00000530196.1	-	0	567					NR_003951.1				ADAM metallopeptidase domain 21 pseudogene 1																		TCAATTTCATGAGTGAGGCCG	0.438																																																	0								ENSG00000235812																																			ADAM21P1			0			-	HGNC			14q24.2	2014-03-25	2010-01-12	2010-01-12	ENSG00000235812	ENSG00000235812			19822	pseudogene	pseudogene			"""a disintegrin and metalloproteinase domain 21 pseudogene"", ""ADAM metallopeptidase domain 21 pseudogene"""	ADAM21P			Standard	NR_003951		Approved		uc010ttg.2		OTTHUMG00000166565		14.37:g.70713951G>A		Somatic	0	28	0.00		0.5469949440746017	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	7	50	12.28		RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000530196.1	37	NULL		14																																																																																			-	-		0.438	ADAM21P1-002	KNOWN	basic	processed_transcript	ADAM21P1	pseudogene	OTTHUMT00000390451.1	G	NG_002467	rs202183568		70713951	-1	no_errors	ENST00000530196	ensembl	human	known	74_37	rna	SNP	0.732	A
MT-ND2	4536	genome.wustl.edu	37	M	2226	2226	+	5'Flank	SNP	T	T	C			TCGA-DX-A1L4-01A-12D-A26G-09	TCGA-DX-A1L4-10A-01D-A26G-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c1aa1b8-f02c-43e7-a410-cc0344f0107e	6c11585a-6ac8-4f59-90c4-cae54eb89e0e	g.chrM:2226T>C	ENST00000361453.3	+	0	0				MT-ND1_ENST00000361390.2_5'Flank|MT-TI_ENST00000387365.1_RNA|MT-RNR2_ENST00000387347.2_RNA|MT-TF_ENST00000387314.1_RNA|MT-RNR1_ENST00000389680.2_RNA|MT-TV_ENST00000387342.1_RNA|MT-TQ_ENST00000387372.1_RNA|MT-TL1_ENST00000386347.1_RNA|MT-TM_ENST00000387377.1_RNA			P03891	NU2M_HUMAN	mitochondrially encoded NADH dehydrogenase 2						cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|reactive oxygen species metabolic process (GO:0072593)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|lung(1)	3						ACACCCACTACCTAAAAAATC	0.363																																																	0								ENSG00000210082																																			MT-RNR2	SO:0001631	upstream_gene_variant	0			-	HGNC			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198763	ENSG00000198763	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7456	protein-coding gene	gene with protein product	"""complex I ND2 subunit"", ""NADH-ubiquinone oxidoreductase chain 2"""	516001	"""NADH dehydrogenase 2"""	MTND2			Standard			Approved	ND2, NAD2		P03891			M.37:g.2226T>C	Exception_encountered	Somatic	0	49	0.00		0.5469949440746017	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	8	75	9.64	Q34769|Q9TGI0|Q9TGI1|Q9TGI2|Q9TGI3|Q9TGI4	RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000361453.3	37	NULL		MT																																																																																			-	-		0.363	MT-ND2-201	KNOWN	basic|appris_principal	protein_coding	MT-RNR2	protein_coding		T	YP_003024027	-		2226	+1	no_errors	ENST00000387347	ensembl	human	known	74_37	rna	SNP	NULL	C
TTC23	64927	genome.wustl.edu	37	15	99759242	99759242	+	Missense_Mutation	SNP	G	G	T			TCGA-DX-A1L4-01A-12D-A26G-09	TCGA-DX-A1L4-10A-01D-A26G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c1aa1b8-f02c-43e7-a410-cc0344f0107e	6c11585a-6ac8-4f59-90c4-cae54eb89e0e	g.chr15:99759242G>T	ENST00000394132.2	-	7	1133	c.316C>A	c.(316-318)Caa>Aaa	p.Q106K	TTC23_ENST00000394129.2_Missense_Mutation_p.Q106K|TTC23_ENST00000558613.1_Missense_Mutation_p.Q106K|TTC23_ENST00000394136.1_Missense_Mutation_p.Q106K|TTC23_ENST00000394135.3_Missense_Mutation_p.Q106K|TTC23_ENST00000394130.1_Missense_Mutation_p.Q106K|TTC23_ENST00000558663.1_Missense_Mutation_p.Q106K|TTC23_ENST00000262074.4_Missense_Mutation_p.Q106K			Q5W5X9	TTC23_HUMAN	tetratricopeptide repeat domain 23	106										endometrium(2)|large_intestine(3)|lung(9)|urinary_tract(2)	16	all_cancers(4;1.49e-13)|Lung NSC(78;0.000545)|all_lung(78;0.00121)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		all cancers(5;8.11e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00215)			TGTTTTGCTTGCAGTGACAGT	0.423																																																	0								ENSG00000103852						210.0	201.0	204.0					15																	99759242		2197	4297	6494	TTC23	SO:0001583	missense	0			-	HGNC		CCDS10379.2	15q26.3	2013-01-11			ENSG00000103852	ENSG00000103852		"""Tetratricopeptide (TTC) repeat domain containing"""	25730	protein-coding gene	gene with protein product						12477932	Standard	NM_001288615		Approved	FLJ12572, HCC-8	uc002bux.3	Q5W5X9	OTTHUMG00000147344	ENST00000394132.2:c.316C>A	15.37:g.99759242G>T	ENSP00000377690:p.Gln106Lys	Somatic	0	18	0.00		0.5469949440746017	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	15	46	24.59	A8K6M5|Q53HK0|Q96BC9|Q9H8W9|Q9H9S7	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	smart_TPR_repeat	p.Q106K	ENST00000394132.2	37	c.316	CCDS10379.2	15	.	.	.	.	.	.	.	.	.	.	G	16.42	3.118126	0.56505	.	.	ENSG00000103852	ENST00000394132;ENST00000394136;ENST00000262074;ENST00000394135;ENST00000394130;ENST00000394129	T;T;T;T;T;T	0.46063	0.88;0.88;0.88;0.88;0.88;0.88	5.02	5.02	0.67125	Tetratricopeptide-like helical (1);	0.152963	0.44483	D	0.000460	T	0.41328	0.1154	M	0.83483	2.645	0.38641	D	0.951616	P;P	0.39282	0.573;0.666	B;B	0.32677	0.15;0.125	T	0.46190	-0.9209	10	0.11794	T	0.64	-18.6369	13.7281	0.62769	0.0:0.0:1.0:0.0	.	106;106	Q5W5X9-2;Q5W5X9	.;TTC23_HUMAN	K	106	ENSP00000377690:Q106K;ENSP00000377693:Q106K;ENSP00000262074:Q106K;ENSP00000377692:Q106K;ENSP00000377688:Q106K;ENSP00000457901:Q106K	ENSP00000262074:Q106K	Q	-	1	0	TTC23	97576765	1.000000	0.71417	0.998000	0.56505	0.973000	0.67179	5.456000	0.66665	2.618000	0.88619	0.655000	0.94253	CAA	-	smart_TPR_repeat		0.423	TTC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TTC23	protein_coding	OTTHUMT00000303953.2	G	NM_022905	-		99759242	-1	no_errors	ENST00000262074	ensembl	human	known	74_37	missense	SNP	0.998	T
MIR548I2	100302277	genome.wustl.edu	37	4	9557816	9557821	+	RNA	DEL	AGAAGG	AGAAGG	-	rs111482845	byFrequency	TCGA-DX-A1L4-01A-12D-A26G-09	TCGA-DX-A1L4-10A-01D-A26G-09	AGAAGG	AGAAGG					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c1aa1b8-f02c-43e7-a410-cc0344f0107e	6c11585a-6ac8-4f59-90c4-cae54eb89e0e	g.chr4:9557816_9557821delAGAAGG	ENST00000408348.1	-	0	116_121					NR_031688.1				microRNA 548i-2																		GAACTTTGTTAGAAGGAGAAAAGATA	0.379														1768	0.353035	0.5711	0.3055	5008	,	,		20513	0.2956		0.2883	False		,,,				2504	0.2178																0								ENSG00000221275			1316,1898		338,640,629						0.1	0.0		dbSNP_132	163	1423,5627		193,1037,2295	no	intergenic				531,1677,2924	A1A1,A1R,RR		20.1844,40.9459,26.6855				2739,7525				MIR548I2			0				HGNC			4p16.1	2011-09-12		2008-12-18	ENSG00000221275	ENSG00000221275		"""ncRNAs / Micro RNAs"""	35353	non-coding RNA	RNA, micro				MIRN548I2			Standard	NR_031688		Approved	hsa-mir-548i-2	uc021xlt.1				4.37:g.9557816_9557821delAGAAGG		Somatic	NA	NA	NA		0.5469949440746017	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA		RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000408348.1	37	NULL		4																																																																																			-	-		0.379	MIR548I2-201	KNOWN	basic	miRNA	MIR548I2	miRNA		AGAAGG	NR_031688			9557821	-1	no_errors	ENST00000408348	ensembl	human	known	74_37	rna	DEL	0.009:0.010:0.011:0.017:0.022:0.026	-
ALOX12B	242	genome.wustl.edu	37	17	7989357	7989357	+	Missense_Mutation	SNP	G	G	A			TCGA-DX-A1L4-01A-12D-A26G-09	TCGA-DX-A1L4-10A-01D-A26G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c1aa1b8-f02c-43e7-a410-cc0344f0107e	6c11585a-6ac8-4f59-90c4-cae54eb89e0e	g.chr17:7989357G>A	ENST00000319144.4	-	2	589	c.329C>T	c.(328-330)aCc>aTc	p.T110I	MIR4314_ENST00000583321.1_RNA	NM_001139.2	NP_001130.1	O75342	LX12B_HUMAN	arachidonate 12-lipoxygenase, 12R type	110	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				arachidonic acid metabolic process (GO:0019369)|ceramide biosynthetic process (GO:0046513)|establishment of skin barrier (GO:0061436)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipoxygenase pathway (GO:0019372)|oxidation-reduction process (GO:0055114)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mucus secretion (GO:0070257)|protein lipidation (GO:0006497)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytosol (GO:0005829)	arachidonate 12-lipoxygenase activity (GO:0004052)|iron ion binding (GO:0005506)|linoleate 9S-lipoxygenase activity (GO:1990136)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|stomach(1)	16						GAGTGCCAGGGTCTCGTAGCC	0.612										Multiple Myeloma(8;0.094)																																							0								ENSG00000179477						106.0	92.0	97.0					17																	7989357		2203	4300	6503	ALOX12B	SO:0001583	missense	0			-	HGNC	AF038461	CCDS11129.1	17p13.1	2008-03-18			ENSG00000179477	ENSG00000179477	1.13.11.-	"""Arachidonate lipoxygenases"""	430	protein-coding gene	gene with protein product		603741				9618483	Standard	NM_001139		Approved	12R-LOX	uc002gjy.1	O75342	OTTHUMG00000108180	ENST00000319144.4:c.329C>T	17.37:g.7989357G>A	ENSP00000315167:p.Thr110Ile	Somatic	0	26	0.00		0.5469949440746017	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	52	8.77		Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_LipOase_C,pfam_PLAT/LH2_dom,superfamily_LipOase_C,superfamily_Lipase_LipOase,smart_PLAT/LH2_dom,pfscan_PLAT/LH2_dom,prints_LipOase_C,prints_LipOase_mml	p.T110I	ENST00000319144.4	37	c.329	CCDS11129.1	17	.	.	.	.	.	.	.	.	.	.	G	17.31	3.356299	0.61293	.	.	ENSG00000179477	ENST00000319144	T	0.77877	-1.13	4.63	4.63	0.57726	Lipoxygenase, C-terminal (1);Lipoxygenase, LH2 (4);Lipase/lipooxygenase, PLAT/LH2 (1);	0.331430	0.36815	N	0.002385	T	0.77232	0.4100	L	0.49455	1.56	0.36952	D	0.892912	P	0.46859	0.885	P	0.48089	0.566	T	0.79794	-0.1653	10	0.33940	T	0.23	-37.0103	14.56	0.68128	0.0:0.0:1.0:0.0	.	110	O75342	LX12B_HUMAN	I	110	ENSP00000315167:T110I	ENSP00000315167:T110I	T	-	2	0	ALOX12B	7930082	0.987000	0.35691	0.996000	0.52242	0.989000	0.77384	2.736000	0.47385	2.416000	0.81992	0.555000	0.69702	ACC	-	pfam_PLAT/LH2_dom,superfamily_LipOase_C,superfamily_Lipase_LipOase,smart_PLAT/LH2_dom,pfscan_PLAT/LH2_dom		0.612	ALOX12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ALOX12B	protein_coding	OTTHUMT00000226984.3	G		-		7989357	-1	no_errors	ENST00000319144	ensembl	human	known	74_37	missense	SNP	0.921	A
ADTRP	84830	genome.wustl.edu	37	6	11714728	11714728	+	Missense_Mutation	SNP	G	G	A			TCGA-DX-A1L4-01A-12D-A26G-09	TCGA-DX-A1L4-10A-01D-A26G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c1aa1b8-f02c-43e7-a410-cc0344f0107e	6c11585a-6ac8-4f59-90c4-cae54eb89e0e	g.chr6:11714728G>A	ENST00000414691.3	-	6	1086	c.676C>T	c.(676-678)Cgg>Tgg	p.R226W	ADTRP_ENST00000229583.5_Missense_Mutation_p.R244W|ADTRP_ENST00000514824.1_5'UTR	NM_032744.3	NP_116133.1	Q96IZ2	ADTRP_HUMAN	androgen-dependent TFPI-regulating protein	226						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)											CTCTTCTTCCGTGGCTGCCTC	0.413																																																	0								ENSG00000111863						144.0	138.0	140.0					6																	11714728		2203	4300	6503	ADTRP	SO:0001583	missense	0			-	HGNC	AJ420520	CCDS4521.1, CCDS47374.1	6p24.1	2012-01-30	2012-01-27	2012-01-27	ENSG00000111863	ENSG00000111863			21214	protein-coding gene	gene with protein product	"""androgen-induced 1-like"""	614348	"""chromosome 6 open reading frame 105"""	C6orf105		21868574	Standard	NM_032744		Approved	dJ413H6.1, AIG1L	uc011dip.2	Q96IZ2	OTTHUMG00000014260	ENST00000414691.3:c.676C>T	6.37:g.11714728G>A	ENSP00000404416:p.Arg226Trp	Somatic	0	77	0.00		0.5469949440746017	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	13	111	10.48	B2R7T9|B4DV39|Q5THW1	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Far-17a_AIG1	p.R244W	ENST00000414691.3	37	c.730	CCDS4521.1	6	.	.	.	.	.	.	.	.	.	.	G	19.48	3.835963	0.71373	.	.	ENSG00000111863	ENST00000414691;ENST00000229583	T;T	0.33216	1.43;1.42	6.15	-2.23	0.06930	.	.	.	.	.	T	0.12347	0.0300	L	0.53249	1.67	0.18873	N	0.999987	D;B	0.60160	0.987;0.005	P;B	0.46825	0.528;0.001	T	0.07385	-1.0775	9	0.66056	D	0.02	.	1.3421	0.02156	0.2376:0.0981:0.2128:0.4515	.	244;226	Q96IZ2-2;Q96IZ2	.;ADTRP_HUMAN	W	226;244	ENSP00000404416:R226W;ENSP00000229583:R244W	ENSP00000229583:R244W	R	-	1	2	C6orf105	11822714	0.000000	0.05858	0.000000	0.03702	0.624000	0.37722	-0.905000	0.04075	-0.388000	0.07797	-0.148000	0.13756	CGG	-	NULL		0.413	ADTRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ADTRP	protein_coding	OTTHUMT00000039864.3	G	NM_032744	-		11714728	-1	no_errors	ENST00000229583	ensembl	human	known	74_37	missense	SNP	0.000	A
LOC101927209	101927209	genome.wustl.edu	37	1	142620676	142620678	+	lincRNA	DEL	ATA	ATA	-	rs375376320		TCGA-DX-A1L4-01A-12D-A26G-09	TCGA-DX-A1L4-10A-01D-A26G-09	ATA	ATA					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c1aa1b8-f02c-43e7-a410-cc0344f0107e	6c11585a-6ac8-4f59-90c4-cae54eb89e0e	g.chr1:142620676_142620678delATA	ENST00000610091.1	-	0	6805_6807				RP11-417J8.3_ENST00000426408.1_lincRNA																							TAGTGAACTTATAATGTTTCTTT	0.217																																																	0								ENSG00000203849																																			RP11-417J8.6			0				Clone_based_vega_gene																													1.37:g.142620676_142620678delATA		Somatic	0	19	0.00		0.5469949440746017	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	18	14.29		RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000610091.1	37	NULL		1																																																																																			-	-		0.217	RP11-417J8.6-001	KNOWN	basic	lincRNA	ENSG00000203849	lincRNA	OTTHUMT00000037265.2	ATA				142620678	-1	no_errors	ENST00000369381	ensembl	human	known	74_37	rna	DEL	0.222:0.217:0.212	-
NAGPA	51172	genome.wustl.edu	37	16	5077858	5077858	+	Missense_Mutation	SNP	T	T	C			TCGA-DX-A1L4-01A-12D-A26G-09	TCGA-DX-A1L4-10A-01D-A26G-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c1aa1b8-f02c-43e7-a410-cc0344f0107e	6c11585a-6ac8-4f59-90c4-cae54eb89e0e	g.chr16:5077858T>C	ENST00000312251.3	-	7	1182	c.1163A>G	c.(1162-1164)aAc>aGc	p.N388S	NAGPA_ENST00000381955.3_Missense_Mutation_p.N388S|RP11-165E7.1_ENST00000588778.1_RNA	NM_016256.3	NP_057340.2	Q9UK23	NAGPA_HUMAN	N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase	388	EGF-like. {ECO:0000255|PROSITE- ProRule:PRU00076}.				carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|lysosome organization (GO:0007040)|protein glycosylation (GO:0006486)|protein targeting to lysosome (GO:0006622)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase activity (GO:0003944)			endometrium(4)|large_intestine(4)|lung(3)|urinary_tract(1)	12					N-Acetyl-D-glucosamine(DB00141)	TTCACTGCAGTTGGACCCGGT	0.687																																																	0								ENSG00000103174						13.0	14.0	14.0					16																	5077858		2149	4221	6370	NAGPA	SO:0001583	missense	0			-	HGNC	AF187072	CCDS10527.1	16p13.3	2008-02-05			ENSG00000103174	ENSG00000103174	3.1.4.45		17378	protein-coding gene	gene with protein product		607985				10551838, 12058031	Standard	NM_016256		Approved	APAA, UCE	uc002cyg.3	Q9UK23	OTTHUMG00000090515	ENST00000312251.3:c.1163A>G	16.37:g.5077858T>C	ENSP00000310998:p.Asn388Ser	Somatic	0	113	0.00		0.5469949440746017	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	12	133	8.28	B2RAS1|Q96EJ8	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_DUF2233,pfscan_EG-like_dom	p.N388S	ENST00000312251.3	37	c.1163	CCDS10527.1	16	.	.	.	.	.	.	.	.	.	.	T	13.98	2.399650	0.42512	.	.	ENSG00000103174	ENST00000312251;ENST00000381955	T;T	0.11169	2.8;2.8	4.57	2.18	0.27775	Epidermal growth factor-like (1);EGF-like region, conserved site (1);Epidermal growth factor-like, type 3 (1);	0.230900	0.42821	D	0.000644	T	0.08447	0.0210	L	0.44542	1.39	0.36927	D	0.891678	P	0.40144	0.704	B	0.36534	0.227	T	0.22173	-1.0224	10	0.56958	D	0.05	-19.4836	6.0465	0.19762	0.0:0.0861:0.1628:0.7511	.	388	Q9UK23	NAGPA_HUMAN	S	388	ENSP00000310998:N388S;ENSP00000371381:N388S	ENSP00000310998:N388S	N	-	2	0	NAGPA	5017859	1.000000	0.71417	1.000000	0.80357	0.753000	0.42808	1.531000	0.36018	0.612000	0.30071	0.459000	0.35465	AAC	-	pfscan_EG-like_dom		0.687	NAGPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NAGPA	protein_coding	OTTHUMT00000207003.1	T	NM_016256	-		5077858	-1	no_errors	ENST00000312251	ensembl	human	known	74_37	missense	SNP	0.999	C
CDC7	8317	genome.wustl.edu	37	1	91977217	91977217	+	Silent	SNP	T	T	A			TCGA-DX-A1L4-01A-12D-A26G-09	TCGA-DX-A1L4-10A-01D-A26G-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c1aa1b8-f02c-43e7-a410-cc0344f0107e	6c11585a-6ac8-4f59-90c4-cae54eb89e0e	g.chr1:91977217T>A	ENST00000428239.1	+	5	658	c.399T>A	c.(397-399)gcT>gcA	p.A133A	CDC7_ENST00000430031.2_Silent_p.A105A|CDC7_ENST00000234626.6_Silent_p.A133A	NM_001134420.1	NP_001127892.1	O00311	CDC7_HUMAN	cell division cycle 7	133	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle phase transition (GO:0044770)|cell division (GO:0051301)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|stomach(2)	23		all_lung(203;0.0165)|Lung NSC(277;0.0562)		all cancers(265;0.00108)|Epithelial(280;0.0184)|KIRC - Kidney renal clear cell carcinoma(1967;0.124)		TAGTTATTGCTATGCCATATC	0.313																																																	0								ENSG00000097046						205.0	206.0	206.0					1																	91977217		2203	4300	6503	CDC7	SO:0001819	synonymous_variant	0			-	HGNC	AF015592	CCDS734.1	1p22	2013-01-17	2013-01-17	2003-07-23	ENSG00000097046	ENSG00000097046			1745	protein-coding gene	gene with protein product		603311	"""CDC7 (cell division cycle 7, S. cerevisiae, homolog)-like 1"", ""CDC7 cell division cycle 7 (S. cerevisiae)"", ""cell division cycle 7 (S. cerevisiae)"", ""cell division cycle 7 homolog (S. cerevisiae)"""	CDC7L1		9405610, 9250678	Standard	NM_003503		Approved	Hsk1, huCdc7, HsCdc7	uc001dof.3	O00311	OTTHUMG00000047810	ENST00000428239.1:c.399T>A	1.37:g.91977217T>A		Somatic	0	43	0.00		0.5469949440746017	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	10	91	9.90	D3DT31|O00558|Q5T5U5	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_Prot_kinase_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_dom	p.A133	ENST00000428239.1	37	c.399	CCDS734.1	1																																																																																			-	pfam_Prot_kinase_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_dom		0.313	CDC7-201	KNOWN	basic|appris_principal|CCDS	protein_coding	CDC7	protein_coding	OTTHUMT00000027928.1	T	NM_003503	-		91977217	+1	no_errors	ENST00000234626	ensembl	human	known	74_37	silent	SNP	0.984	A
KRTAP4-1	85285	genome.wustl.edu	37	17	39340970	39340970	+	Missense_Mutation	SNP	C	C	T			TCGA-DX-A1L4-01A-12D-A26G-09	TCGA-DX-A1L4-10A-01D-A26G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c1aa1b8-f02c-43e7-a410-cc0344f0107e	6c11585a-6ac8-4f59-90c4-cae54eb89e0e	g.chr17:39340970C>T	ENST00000398472.1	-	1	624	c.137G>A	c.(136-138)cGc>cAc	p.R46H				Q9BYQ7	KRA41_HUMAN	keratin associated protein 4-1	46	18 X 5 AA repeats of C-C-[GRQC]-[SPT]- [VSTL].					keratin filament (GO:0045095)				kidney(1)|large_intestine(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	5		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			GCAGGATGGGCGGCAGCAGCT	0.642																																																	0								ENSG00000198443						29.0	33.0	32.0					17																	39340970		2175	4287	6462	KRTAP4-1	SO:0001583	missense	0			-	HGNC	AC006070		17q21.2	2013-06-25			ENSG00000198443	ENSG00000198443		"""Keratin associated proteins"""	18907	protein-coding gene	gene with protein product			"""keratin associated protein 4-10"""	KRTAP4-10		11279113	Standard	NM_033060		Approved	KAP4.1, KAP4.10	uc002hwe.4	Q9BYQ7	OTTHUMG00000132081	ENST00000398472.1:c.137G>A	17.37:g.39340970C>T	ENSP00000381489:p.Arg46His	Somatic	0	114	0.00		0.5469949440746017	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	22	181	10.84	A8MWS7|Q3SYF2	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Keratin-assoc	p.R46H	ENST00000398472.1	37	c.137		17	.	.	.	.	.	.	.	.	.	.	C	11.65	1.700421	0.30142	.	.	ENSG00000244537;ENSG00000198443;ENSG00000198443	ENST00000458321;ENST00000398472;ENST00000334190	T	0.01484	4.84	4.81	0.21	0.15231	.	.	.	.	.	T	0.01489	0.0048	.	.	.	0.23845	N	0.996687	B	0.19073	0.033	B	0.19946	0.027	T	0.49153	-0.8969	8	0.66056	D	0.02	.	0.8855	0.01243	0.1649:0.3987:0.1603:0.2762	.	46	Q9BYQ7	KRA41_HUMAN	H	42;46;46	ENSP00000381489:R46H	ENSP00000335483:R46H	R	-	2	0	KRTAP4-2;KRTAP4-1	36594496	0.000000	0.05858	0.055000	0.19348	0.003000	0.03518	-0.027000	0.12371	0.097000	0.17492	-0.894000	0.02916	CGC	-	pfam_Keratin-assoc		0.642	KRTAP4-1-001	KNOWN	basic|appris_principal	protein_coding	KRTAP4-1	protein_coding	OTTHUMT00000255108.1	C	NM_033060	-		39340970	-1	no_errors	ENST00000398472	ensembl	human	known	74_37	missense	SNP	0.712	T
TRAF7	84231	genome.wustl.edu	37	16	2225556	2225556	+	Missense_Mutation	SNP	A	A	G			TCGA-DX-A1L4-01A-12D-A26G-09	TCGA-DX-A1L4-10A-01D-A26G-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c1aa1b8-f02c-43e7-a410-cc0344f0107e	6c11585a-6ac8-4f59-90c4-cae54eb89e0e	g.chr16:2225556A>G	ENST00000326181.6	+	17	1691	c.1559A>G	c.(1558-1560)aAc>aGc	p.N520S		NM_032271.2	NP_115647.2	Q6Q0C0	TRAF7_HUMAN	TNF receptor-associated factor 7, E3 ubiquitin protein ligase	520					activation of MAPKKK activity (GO:0000185)|apoptotic process (GO:0006915)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of MAPK cascade (GO:0043410)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasmic vesicle (GO:0031410)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	23						ACAGGCCTCAACCACTGGGTG	0.642																																																	0								ENSG00000131653						78.0	77.0	77.0					16																	2225556		2198	4300	6498	TRAF7	SO:0001583	missense	0			-	HGNC	AL136921	CCDS10461.1	16p13.3	2013-01-10	2012-02-23	2004-06-04	ENSG00000131653	ENSG00000131653		"""RING-type (C3HC4) zinc fingers"", ""WD repeat domain containing"""	20456	protein-coding gene	gene with protein product		606692	"""ring finger and WD repeat domain 1"", ""TNF receptor-associated factor 7"""	RFWD1		11230166, 15001576	Standard	NM_032271		Approved	RNF119, DKFZp586I021, MGC7807	uc002cow.3	Q6Q0C0	OTTHUMG00000128826	ENST00000326181.6:c.1559A>G	16.37:g.2225556A>G	ENSP00000318944:p.Asn520Ser	Somatic	0	13	0.00		0.5469949440746017	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	6	17	26.09	Q9H073	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_WD40_repeat,superfamily_WD40_repeat_dom,superfamily_TRAF-like,smart_Znf_RING,smart_WD40_repeat,pfscan_Znf_RING,pfscan_Znf_TRAF,pfscan_WD40_repeat,pfscan_WD40_repeat_dom,prints_G-protein_beta_WD-40_rep	p.N520S	ENST00000326181.6	37	c.1559	CCDS10461.1	16	.	.	.	.	.	.	.	.	.	.	A	21.0	4.075103	0.76415	.	.	ENSG00000131653	ENST00000326181	T	0.58652	0.32	4.49	4.49	0.54785	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.66733	0.2819	L	0.47078	1.49	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.61787	-0.6991	10	0.19590	T	0.45	-55.8238	13.3899	0.60818	1.0:0.0:0.0:0.0	.	520	Q6Q0C0	TRAF7_HUMAN	S	520	ENSP00000318944:N520S	ENSP00000318944:N520S	N	+	2	0	TRAF7	2165557	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.237000	0.89807	2.026000	0.59711	0.459000	0.35465	AAC	-	pfam_WD40_repeat,superfamily_WD40_repeat_dom,smart_WD40_repeat,pfscan_WD40_repeat_dom		0.642	TRAF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TRAF7	protein_coding	OTTHUMT00000250762.1	A	NM_032271	-		2225556	+1	no_errors	ENST00000326181	ensembl	human	known	74_37	missense	SNP	1.000	G
SRPX	8406	genome.wustl.edu	37	X	38079976	38079978	+	In_Frame_Del	DEL	GCA	GCA	-	rs35523939|rs72249350|rs139109693		TCGA-DX-A1L4-01A-12D-A26G-09	TCGA-DX-A1L4-10A-01D-A26G-09	GCA	GCA					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c1aa1b8-f02c-43e7-a410-cc0344f0107e	6c11585a-6ac8-4f59-90c4-cae54eb89e0e	g.chrX:38079976_38079978delGCA	ENST00000378533.3	-	1	174_176	c.68_70delTGC	c.(67-72)ctgcgc>cgc	p.L23del	RP13-43E11.1_ENST00000423919.1_RNA|SRPX_ENST00000544439.1_In_Frame_Del_p.L23del|SRPX_ENST00000343800.6_Intron|SRPX_ENST00000538295.1_In_Frame_Del_p.L23del|SRPX_ENST00000432886.2_In_Frame_Del_p.L23del|TM4SF2_ENST00000465127.1_Intron	NM_006307.4	NP_006298.1	P78539	SRPX_HUMAN	sushi-repeat containing protein, X-linked	23			Missing. {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:8634709, ECO:0000269|PubMed:9162095}.		autophagy (GO:0006914)|cell adhesion (GO:0007155)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|phagolysosome assembly (GO:0001845)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|response to endoplasmic reticulum stress (GO:0034976)	autophagic vacuole (GO:0005776)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)		p.L23delL(2)		autonomic_ganglia(1)|breast(2)|endometrium(5)|large_intestine(5)|lung(10)|prostate(2)	25						GGCGGGACGCgcagcagcagcag	0.729											OREG0019726	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		636	0.168477	0.1657	0.1398	3775	,	,		8591	0.0129		0.2028	False		,,,				2504	0.1053																2	Deletion - In frame(2)	prostate(2)						ENSG00000101955																																			SRPX	SO:0001651	inframe_deletion	0				HGNC	U78093	CCDS14245.1, CCDS55400.1, CCDS55401.1, CCDS55402.1	Xp21.1	2011-01-25	2011-01-25		ENSG00000101955	ENSG00000101955			11309	protein-coding gene	gene with protein product		300187	"""sushi-repeat-containing protein, X chromosome"", ""sushi-repeat-containing protein, X-linked"""			8634708, 8634709	Standard	NM_006307		Approved	ETX1	uc004ddy.2	P78539	OTTHUMG00000021362	ENST00000378533.3:c.68_70delTGC	X.37:g.38079985_38079987delGCA	ENSP00000367794:p.Leu23del	Somatic	0	10	0.00	875	0.5469949440746017	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	2	20	9.09	A8K065|B3KWP8|B4DDB8|B4DQH5|F5H4D7|G3V1L0|Q4VX66|Q99652|Q99913	In_Frame_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_Hyalin,pfam_Sushi_SCR_CCP,superfamily_Sushi_SCR_CCP,smart_Sushi_SCR_CCP,pfscan_Hyalin,pfscan_Sushi_SCR_CCP	p.L23in_frame_del	ENST00000378533.3	37	c.70_68	CCDS14245.1	X																																																																																			-	NULL		0.729	SRPX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	SRPX	protein_coding	OTTHUMT00000056243.1	GCA	NM_006307			38079978	-1	no_errors	ENST00000378533	ensembl	human	known	74_37	in_frame_del	DEL	0.000:0.001:0.002	-
TRPM1	4308	genome.wustl.edu	37	15	31294794	31294797	+	Frame_Shift_Del	DEL	TTCT	TTCT	-			TCGA-DX-A1L4-01A-12D-A26G-09	TCGA-DX-A1L4-10A-01D-A26G-09	TTCT	TTCT					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c1aa1b8-f02c-43e7-a410-cc0344f0107e	6c11585a-6ac8-4f59-90c4-cae54eb89e0e	g.chr15:31294794_31294797delTTCT	ENST00000256552.6	-	28	4253_4256	c.4106_4109delAGAA	c.(4105-4110)aagaacfs	p.KN1369fs	RP11-348B17.1_ENST00000561299.1_RNA|TRPM1_ENST00000397795.2_Frame_Shift_Del_p.KN1347fs|TRPM1_ENST00000542188.1_Frame_Shift_Del_p.KN1386fs	NM_001252024.1	NP_001238953.1			transient receptor potential cation channel, subfamily M, member 1											NS(2)|breast(3)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(15)|lung(48)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(3)	99		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		CTCTTCAGCGTTCTTTAAGTCATC	0.426																																																	0								ENSG00000134160																																			TRPM1	SO:0001589	frameshift_variant	0				HGNC	AF071787	CCDS10024.2, CCDS58345.1, CCDS58346.1, CCDS58347.1	15q13.3	2014-01-28		2002-01-18	ENSG00000134160	ENSG00000134160		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	7146	protein-coding gene	gene with protein product		603576	"""melastatin 1"""	MLSN1		9806836, 9537257, 16382100	Standard	NM_001252020		Approved	LTRPC1, CSNB1C	uc021sia.1	Q7Z4N2	OTTHUMG00000129267	ENST00000256552.6:c.4106_4109delAGAA	15.37:g.31294794_31294797delTTCT	ENSP00000256552:p.Lys1369fs	Somatic	0	34	0.00		0.5469949440746017	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	6	36	14.29		Frame_Shift_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_Ion_trans_dom	p.K1386fs	ENST00000256552.6	37	c.4160_4157	CCDS58346.1	15																																																																																			-	NULL		0.426	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	TRPM1	protein_coding	OTTHUMT00000417166.2	TTCT	NM_002420			31294797	-1	no_errors	ENST00000542188	ensembl	human	known	74_37	frame_shift_del	DEL	0.000:0.000:0.002:0.002	-
SLC22A18	5002	genome.wustl.edu	37	11	2938206	2938206	+	Intron	SNP	A	A	G	rs370251197|rs372861149|rs551444699	byFrequency	TCGA-DX-A1L4-01A-12D-A26G-09	TCGA-DX-A1L4-10A-01D-A26G-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c1aa1b8-f02c-43e7-a410-cc0344f0107e	6c11585a-6ac8-4f59-90c4-cae54eb89e0e	g.chr11:2938206A>G	ENST00000380574.1	+	6	1086				SLC22A18_ENST00000347936.2_Intron|SLC22A18_ENST00000441077.1_Intron|SLC22A18_ENST00000449793.2_Intron|SLC22A18_ENST00000312221.5_Intron			Q96BI1	S22AI_HUMAN	solute carrier family 22, member 18						drug transmembrane transport (GO:0006855)|drug transport (GO:0015893)|excretion (GO:0007588)|organic cation transport (GO:0015695)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	drug transmembrane transporter activity (GO:0015238)|symporter activity (GO:0015293)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(2)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	8		all_epithelial(84;0.000124)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)|all_lung(207;0.198)		BRCA - Breast invasive adenocarcinoma(625;0.00256)|LUSC - Lung squamous cell carcinoma(625;0.192)		GAGAGGCAGGAAGGCCCAGAC	0.652													G|||	210	0.0419329	0.0045	0.0288	5008	,	,		16134	0.0685		0.0368	False		,,,				2504	0.0798																0								ENSG00000110628																																			SLC22A18	SO:0001627	intron_variant	0			-	HGNC	AF028738	CCDS7740.1	11p15.5	2013-05-22	2008-01-11	2004-01-21	ENSG00000110628	ENSG00000110628		"""Solute carriers"""	10964	protein-coding gene	gene with protein product		602631	"""solute carrier family 22 (organic cation transporter), member 1-like"""	ORCTL2, BWSCR1A, IMPT1, SLC22A1L		9499412, 9520460	Standard	NM_183233		Approved	BWR1A, TSSC5, ITM	uc001lwx.3	Q96BI1	OTTHUMG00000010037	ENST00000380574.1:c.655+236A>G	11.37:g.2938206A>G		Somatic	0	40	0.00		0.5469949440746017	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	11	83	11.70	O14906|O43562|O60485|O60680|Q7LDS5|Q7LGF7	RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000380574.1	37	NULL	CCDS7740.1	11																																																																																			-	-		0.652	SLC22A18-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	SLC22A18	protein_coding	OTTHUMT00000027770.1	A	NM_183233	-		2938206	+1	no_errors	ENST00000449603	ensembl	human	known	74_37	rna	SNP	0.008	G
STAB2	55576	genome.wustl.edu	37	12	104092880	104092880	+	Missense_Mutation	SNP	G	G	A			TCGA-DX-A1L4-01A-12D-A26G-09	TCGA-DX-A1L4-10A-01D-A26G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c1aa1b8-f02c-43e7-a410-cc0344f0107e	6c11585a-6ac8-4f59-90c4-cae54eb89e0e	g.chr12:104092880G>A	ENST00000388887.2	+	34	3793	c.3589G>A	c.(3589-3591)Gac>Aac	p.D1197N		NM_017564.9	NP_060034.9			stabilin 2											NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						CCAGGAGGAGGACGTCCTCCG	0.502																																																	0								ENSG00000136011						131.0	106.0	114.0					12																	104092880		2203	4300	6503	STAB2	SO:0001583	missense	0			-	HGNC	AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"""hyaluronic acid receptor for endocytosis"""	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.3589G>A	12.37:g.104092880G>A	ENSP00000373539:p.Asp1197Asn	Somatic	0	36	0.00		0.5469949440746017	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	326	77	80.89		Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_FAS1_domain,pfam_Link,superfamily_C-type_lectin_fold,superfamily_FAS1_domain,superfamily_Growth_fac_rcpt_N_dom,smart_EG-like_dom,smart_EGF_laminin,smart_EGF-like_Ca-bd_dom,smart_FAS1_domain,smart_Link,pfscan_EG-like_dom,pfscan_FAS1_domain,pfscan_Link	p.D1197N	ENST00000388887.2	37	c.3589	CCDS31888.1	12	.	.	.	.	.	.	.	.	.	.	G	13.99	2.401898	0.42613	.	.	ENSG00000136011	ENST00000388887	D	0.90004	-2.6	5.45	3.28	0.37604	FAS1 domain (5);Growth factor, receptor (1);	0.162209	0.52532	D	0.000063	T	0.79275	0.4418	N	0.13327	0.33	0.09310	N	1	B	0.29162	0.235	B	0.32465	0.146	T	0.67162	-0.5740	10	0.25106	T	0.35	.	11.8506	0.52410	0.213:0.0:0.787:0.0	.	1197	Q8WWQ8	STAB2_HUMAN	N	1197	ENSP00000373539:D1197N	ENSP00000373539:D1197N	D	+	1	0	STAB2	102617010	0.998000	0.40836	0.291000	0.24904	0.400000	0.30750	2.652000	0.46682	1.305000	0.44909	0.561000	0.74099	GAC	-	pfam_FAS1_domain,superfamily_FAS1_domain,superfamily_Growth_fac_rcpt_N_dom,smart_FAS1_domain,pfscan_FAS1_domain		0.502	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	STAB2	protein_coding	OTTHUMT00000407089.1	G		-		104092880	+1	no_errors	ENST00000388887	ensembl	human	known	74_37	missense	SNP	0.018	A
RP11-566K19.3	0	genome.wustl.edu	37	15	22752707	22752715	+	RNA	DEL	CTCTCCTCC	CTCTCCTCC	-	rs147037053	byFrequency	TCGA-DX-A1L4-01A-12D-A26G-09	TCGA-DX-A1L4-10A-01D-A26G-09	CTCTCCTCC	CTCTCCTCC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c1aa1b8-f02c-43e7-a410-cc0344f0107e	6c11585a-6ac8-4f59-90c4-cae54eb89e0e	g.chr15:22752707_22752715delCTCTCCTCC	ENST00000560026.1	-	0	360_368																											AAAGCGTAGGCTCTCCTCCAGGAGGCTCT	0.44														392	0.0782748	0.1135	0.0663	5008	,	,		16614	0.0437		0.0537	False		,,,				2504	0.1002																0								ENSG00000259596																																			RP11-566K19.3			0				Clone_based_vega_gene																													15.37:g.22752707_22752715delCTCTCCTCC		Somatic	NA	NA	NA		0.5469949440746017	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA		RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000560026.1	37	NULL		15																																																																																			-	-		0.440	RP11-566K19.3-001	KNOWN	non_canonical_polymorphism|basic|readthrough_transcript	processed_transcript	ENSG00000259596	processed_transcript	OTTHUMT00000415617.1	CTCTCCTCC				22752715	-1	no_errors	ENST00000560026	ensembl	human	known	74_37	rna	DEL	0.054:0.077:0.097:0.114:0.128:0.140:0.150:0.157:0.163	-
PDLIM3	27295	genome.wustl.edu	37	4	186427772	186427772	+	Missense_Mutation	SNP	C	C	T	rs143121072		TCGA-DX-A1L4-01A-12D-A26G-09	TCGA-DX-A1L4-10A-01D-A26G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c1aa1b8-f02c-43e7-a410-cc0344f0107e	6c11585a-6ac8-4f59-90c4-cae54eb89e0e	g.chr4:186427772C>T	ENST00000284770.5	-	6	770	c.697G>A	c.(697-699)Gtg>Atg	p.V233M	PDLIM3_ENST00000284771.6_Missense_Mutation_p.V185M|PDLIM3_ENST00000284767.5_3'UTR	NM_014476.5	NP_055291.2	Q53GG5	PDLI3_HUMAN	PDZ and LIM domain 3	233					actin filament organization (GO:0007015)|heart development (GO:0007507)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	structural constituent of muscle (GO:0008307)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(1)|lung(5)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	17		all_lung(41;1.03e-13)|Lung NSC(41;2.49e-13)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.00996)|Colorectal(36;0.0161)|all_hematologic(60;0.0592)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.4e-10)|BRCA - Breast invasive adenocarcinoma(30;8.64e-05)|GBM - Glioblastoma multiforme(59;0.000167)|STAD - Stomach adenocarcinoma(60;0.000828)|LUSC - Lung squamous cell carcinoma(40;0.00984)|COAD - Colon adenocarcinoma(29;0.0115)|READ - Rectum adenocarcinoma(43;0.171)		ATCCGGTACACGTCCGACTCG	0.647																																																	0								ENSG00000154553						64.0	57.0	59.0					4																	186427772		2203	4300	6503	PDLIM3	SO:0001583	missense	0			-	HGNC	AF002280	CCDS3844.1, CCDS47172.1, CCDS75218.1, CCDS75219.1	4q35	2014-09-17			ENSG00000154553	ENSG00000154553			20767	protein-coding gene	gene with protein product		605889				10063829, 8828038	Standard	NM_014476		Approved	ALP	uc003ixw.4	Q53GG5	OTTHUMG00000160412	ENST00000284770.5:c.697G>A	4.37:g.186427772C>T	ENSP00000284770:p.Val233Met	Somatic	0	38	0.00		0.5469949440746017	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	17	85	16.67	B2R866|O43590|O60439|O60440|Q8N6Y6|Q9BVP4	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_PDZ,pfam_Znf_LIM,superfamily_PDZ,smart_PDZ,smart_ZASP,smart_Znf_LIM,pfscan_Znf_LIM,pfscan_PDZ	p.V233M	ENST00000284770.5	37	c.697	CCDS3844.1	4	.	.	.	.	.	.	.	.	.	.	C	27.0	4.791460	0.90367	.	.	ENSG00000154553	ENST00000284770;ENST00000284771	T;T	0.51325	0.71;1.52	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.75117	0.3806	M	0.87547	2.89	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.995	T	0.78630	-0.2129	10	0.87932	D	0	-22.9268	19.9991	0.97403	0.0:1.0:0.0:0.0	.	185;233	Q53GG5-2;Q53GG5	.;PDLI3_HUMAN	M	233;185	ENSP00000284770:V233M;ENSP00000284771:V185M	ENSP00000284770:V233M	V	-	1	0	PDLIM3	186664766	1.000000	0.71417	0.970000	0.41538	0.504000	0.33889	7.818000	0.86416	2.724000	0.93272	0.655000	0.94253	GTG	-	NULL		0.647	PDLIM3-001	KNOWN	basic|CCDS	protein_coding	PDLIM3	protein_coding	OTTHUMT00000360499.2	C	NM_014476	-		186427772	-1	no_errors	ENST00000284770	ensembl	human	known	74_37	missense	SNP	1.000	T
KLHL18	23276	genome.wustl.edu	37	3	47385390	47385390	+	Missense_Mutation	SNP	G	G	A			TCGA-DX-A1L4-01A-12D-A26G-09	TCGA-DX-A1L4-10A-01D-A26G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c1aa1b8-f02c-43e7-a410-cc0344f0107e	6c11585a-6ac8-4f59-90c4-cae54eb89e0e	g.chr3:47385390G>A	ENST00000232766.5	+	10	1704	c.1684G>A	c.(1684-1686)Gga>Aga	p.G562R	KLHL18_ENST00000455924.2_Missense_Mutation_p.G450R	NM_025010.4	NP_079286.2	O94889	KLH18_HUMAN	kelch-like family member 18	562										endometrium(2)|kidney(1)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	21		Acute lymphoblastic leukemia(5;0.164)		BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00645)|Kidney(197;0.00741)		GTGCCATGAGGGAGGGGTCGG	0.582																																																	0								ENSG00000114648						98.0	96.0	96.0					3																	47385390		2203	4300	6503	KLHL18	SO:0001583	missense	0			-	HGNC	AB018338	CCDS33749.1	3p21	2013-01-30	2013-01-30		ENSG00000114648	ENSG00000114648		"""Kelch-like"", ""BTB/POZ domain containing"""	29120	protein-coding gene	gene with protein product			"""kelch-like 18 (Drosophila)"""			9872452	Standard	NM_025010		Approved	KIAA0795, FLJ13703	uc003crd.3	O94889	OTTHUMG00000156522	ENST00000232766.5:c.1684G>A	3.37:g.47385390G>A	ENSP00000232766:p.Gly562Arg	Somatic	0	12	0.00		0.5469949440746017	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	7	37	15.91	A8K612|Q7Z3E8|Q8N125	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Kelch_1,pfam_Kelch_2,pfam_BACK,pfam_BTB_POZ,superfamily_BTB/POZ_fold,smart_BTB/POZ-like,smart_BACK,smart_Kelch_1,pirsf_Kelch-like_gigaxonin,pfscan_BTB/POZ-like	p.G562R	ENST00000232766.5	37	c.1684	CCDS33749.1	3	.	.	.	.	.	.	.	.	.	.	G	25.2	4.615040	0.87359	.	.	ENSG00000114648	ENST00000232766;ENST00000455924	T;T	0.74842	-0.73;-0.88	5.15	4.28	0.50868	Galactose oxidase, beta-propeller (1);	0.000000	0.85682	D	0.000000	D	0.82504	0.5051	M	0.62154	1.92	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80801	-0.1220	10	0.31617	T	0.26	.	12.7299	0.57193	0.0784:0.0:0.9216:0.0	.	562	O94889	KLH18_HUMAN	R	562;450	ENSP00000232766:G562R;ENSP00000405585:G450R	ENSP00000232766:G562R	G	+	1	0	KLHL18	47360394	1.000000	0.71417	0.977000	0.42913	0.978000	0.69477	9.587000	0.98229	1.412000	0.46977	0.561000	0.74099	GGA	-	smart_Kelch_1,pirsf_Kelch-like_gigaxonin		0.582	KLHL18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KLHL18	protein_coding	OTTHUMT00000344493.1	G	NM_025010	-		47385390	+1	no_errors	ENST00000232766	ensembl	human	known	74_37	missense	SNP	1.000	A
NPVF	64111	genome.wustl.edu	37	7	25266594	25266594	+	Missense_Mutation	SNP	C	C	A			TCGA-DX-A1L4-01A-12D-A26G-09	TCGA-DX-A1L4-10A-01D-A26G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c1aa1b8-f02c-43e7-a410-cc0344f0107e	6c11585a-6ac8-4f59-90c4-cae54eb89e0e	g.chr7:25266594C>A	ENST00000222674.2	-	2	236	c.190G>T	c.(190-192)Gat>Tat	p.D64Y		NM_022150.3	NP_071433	Q9HCQ7	NPVF_HUMAN	neuropeptide VF precursor	64					negative regulation of gonadotropin secretion (GO:0032277)|neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)				cervix(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|urinary_tract(1)	15						GGTCCCCAATCTTTTAATTCC	0.378																																																	0								ENSG00000105954						106.0	112.0	110.0					7																	25266594		2203	4300	6503	NPVF	SO:0001583	missense	0			-	HGNC	AB040290	CCDS5395.1	7p21-p15	2013-02-28	2006-10-06	2006-10-06	ENSG00000105954	ENSG00000105954		"""Endogenous ligands"""	13782	protein-coding gene	gene with protein product	"""RFamide-related peptide precursor"", ""FMRFamide-related peptide precursor"""		"""chromosome 7 open reading frame 9"""	C7orf9		11951088, 11173868	Standard	NM_022150		Approved	RFRP	uc003sxo.3	Q9HCQ7	OTTHUMG00000128509	ENST00000222674.2:c.190G>T	7.37:g.25266594C>A	ENSP00000222674:p.Asp64Tyr	Somatic	0	47	0.00		0.5469949440746017	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	11	75	12.79	A4D164|Q7LE27|Q96PI9	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	NULL	p.D64Y	ENST00000222674.2	37	c.190	CCDS5395.1	7	.	.	.	.	.	.	.	.	.	.	C	14.08	2.430040	0.43122	.	.	ENSG00000105954	ENST00000222674	T	0.27720	1.65	5.67	4.75	0.60458	.	0.088198	0.48767	D	0.000177	T	0.50684	0.1630	L	0.52905	1.665	0.44539	D	0.997491	D	0.89917	1.0	D	0.77004	0.989	T	0.49862	-0.8894	10	0.87932	D	0	-8.435	15.664	0.77213	0.0:0.8642:0.1358:0.0	.	64	Q9HCQ7	RFRP_HUMAN	Y	64	ENSP00000222674:D64Y	ENSP00000222674:D64Y	D	-	1	0	NPVF	25233119	1.000000	0.71417	1.000000	0.80357	0.653000	0.38743	1.850000	0.39328	2.836000	0.97738	0.655000	0.94253	GAT	-	NULL		0.378	NPVF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NPVF	protein_coding	OTTHUMT00000250315.1	C	NM_022150	-		25266594	-1	no_errors	ENST00000222674	ensembl	human	known	74_37	missense	SNP	1.000	A
ULK4P2	100288380	genome.wustl.edu	37	15	30888946	30888946	+	RNA	SNP	T	T	A	rs71478486	byFrequency	TCGA-DX-A1L4-01A-12D-A26G-09	TCGA-DX-A1L4-10A-01D-A26G-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c1aa1b8-f02c-43e7-a410-cc0344f0107e	6c11585a-6ac8-4f59-90c4-cae54eb89e0e	g.chr15:30888946T>A	ENST00000569682.1	+	0	252									ULK4 pseudogene 2																		GTTGAGGTAATGTCTTTTATG	0.403													t|||	1784	0.35623	0.5741	0.3357	5008	,	,		18580	0.1498		0.339	False		,,,				2504	0.3067																0								ENSG00000260128																																			ULK4P2			0			-	HGNC			15q13.2	2013-09-12	2013-09-12	2011-11-25	ENSG00000260128	ENSG00000260128			15776	pseudogene	pseudogene			"""family with sequence similarity 7, member A2"", ""unc-51-like kinase 4 (C. elegans) pseudogene 2"""	FAM7A2		11829490	Standard	NR_027470		Approved	D-X			OTTHUMG00000175653		15.37:g.30888946T>A		Somatic	0	28	0.00		0.5469949440746017	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	7	53	11.67		RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000569682.1	37	NULL		15																																																																																			-	-		0.403	ULK4P2-002	PUTATIVE	basic	processed_transcript	ULK4P2	pseudogene	OTTHUMT00000430722.1	T		rs201386313		30888946	+1	no_errors	ENST00000566793	ensembl	human	putative	74_37	rna	SNP	0.164	A
LRRC75A	388341	genome.wustl.edu	37	17	16344167	16344167	+	IGR	DEL	A	A	-	rs112317984|rs555182592	byFrequency	TCGA-DX-A1L4-01A-12D-A26G-09	TCGA-DX-A1L4-10A-01D-A26G-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c1aa1b8-f02c-43e7-a410-cc0344f0107e	6c11585a-6ac8-4f59-90c4-cae54eb89e0e	g.chr17:16344167delA	ENST00000409083.3	-	0	2656				C17orf76-AS1_ENST00000484836.1_RNA|C17orf76-AS1_ENST00000365172.1_RNA|C17orf76-AS1_ENST00000391079.1_RNA|C17orf76-AS1_ENST00000581718.1_RNA|C17orf76-AS1_ENST00000477249.2_RNA|C17orf76-AS1_ENST00000481898.1_RNA|C17orf76-AS1_ENST00000460249.1_RNA|C17orf76-AS1_ENST00000475947.2_RNA|C17orf76-AS1_ENST00000487066.1_RNA|C17orf76-AS1_ENST00000582911.1_RNA|C17orf76-AS1_ENST00000578380.2_RNA|C17orf76-AS1_ENST00000483140.1_RNA|C17orf76-AS1_ENST00000472367.1_RNA|C17orf76-AS1_ENST00000581913.1_RNA|C17orf76-AS1_ENST00000481027.1_RNA|C17orf76-AS1_ENST00000475953.1_RNA|C17orf76-AS1_ENST00000584926.1_RNA|C17orf76-AS1_ENST00000480811.1_RNA|RP11-138I1.3_ENST00000585048.1_lincRNA|C17orf76-AS1_ENST00000580180.1_RNA|C17orf76-AS1_ENST00000478103.2_RNA|C17orf76-AS1_ENST00000584141.1_RNA|C17orf76-AS1_ENST00000384229.1_RNA|C17orf76-AS1_ENST00000580770.1_RNA|C17orf76-AS1_ENST00000584177.1_RNA|C17orf76-AS1_ENST00000579473.1_RNA|C17orf76-AS1_ENST00000470491.2_RNA|C17orf76-AS1_ENST00000491009.1_RNA|C17orf76-AS1_ENST00000492250.1_RNA|C17orf76-AS1_ENST00000583400.2_RNA	NM_207387.3	NP_997270.2														lung(1)	1						actccatctcaaaaaaaaaaa	0.413																																																	0								ENSG00000266651																																			RP11-138I1.3	SO:0001628	intergenic_variant	0				Clone_based_vega_gene																													17.37:g.16344167delA		Somatic	0	9	0.00		0.5469949440746017	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	10	23.08		RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000409083.3	37	NULL	CCDS11178.2	17																																																																																			-	-		0.413	FAM211A-001	NOVEL	basic|exp_conf|CCDS	protein_coding	ENSG00000266651	protein_coding	OTTHUMT00000130461.2	A				16344167	-1	no_errors	ENST00000585048	ensembl	human	known	74_37	rna	DEL	0.000	-
MON2	23041	genome.wustl.edu	37	12	62949949	62949949	+	Missense_Mutation	SNP	G	G	A			TCGA-DX-A1L4-01A-12D-A26G-09	TCGA-DX-A1L4-10A-01D-A26G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c1aa1b8-f02c-43e7-a410-cc0344f0107e	6c11585a-6ac8-4f59-90c4-cae54eb89e0e	g.chr12:62949949G>A	ENST00000393632.2	+	25	3777	c.3386G>A	c.(3385-3387)aGa>aAa	p.R1129K	MON2_ENST00000393629.2_Missense_Mutation_p.R1129K|MON2_ENST00000552738.1_Missense_Mutation_p.R1106K|MON2_ENST00000393630.3_Missense_Mutation_p.R1130K|MON2_ENST00000280379.6_Missense_Mutation_p.R1130K|MON2_ENST00000546600.1_Missense_Mutation_p.R1129K	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	1129					actin cytoskeleton organization (GO:0030036)|Golgi to endosome transport (GO:0006895)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(15)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	57			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		TTCAACACTAGAAGATATTTG	0.373																																																	0								ENSG00000061987						71.0	67.0	68.0					12																	62949949		2203	4300	6503	MON2	SO:0001583	missense	0			-	HGNC		CCDS31849.1, CCDS61175.1, CCDS61177.1, CCDS61178.1	12q14.1	2014-08-12	2006-04-04		ENSG00000061987	ENSG00000061987			29177	protein-coding gene	gene with protein product			"""MON2 homolog (yeast)"""			16301316, 24285343	Standard	NM_015026		Approved	KIAA1040	uc001sre.3	Q7Z3U7	OTTHUMG00000169992	ENST00000393632.2:c.3386G>A	12.37:g.62949949G>A	ENSP00000377252:p.Arg1129Lys	Somatic	0	14	0.00		0.5469949440746017	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	68	34	66.67	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_DUF1981_Sec7_assoc,superfamily_ARM-type_fold	p.R1130K	ENST00000393632.2	37	c.3389	CCDS31849.1	12	.	.	.	.	.	.	.	.	.	.	G	10.39	1.336872	0.24253	.	.	ENSG00000061987	ENST00000393632;ENST00000393630;ENST00000280379;ENST00000546600;ENST00000552738;ENST00000393629	T;T;T;T;T;T	0.70516	-0.49;-0.49;-0.49;-0.49;-0.49;-0.49	4.66	4.66	0.58398	.	0.000000	0.85682	D	0.000000	T	0.42539	0.1207	N	0.01048	-1.04	0.58432	D	0.999997	B;B;B;B	0.17852	0.004;0.014;0.008;0.024	B;B;B;B	0.20955	0.014;0.025;0.032;0.025	T	0.43845	-0.9366	9	.	.	.	-13.2598	17.895	0.88885	0.0:0.0:1.0:0.0	.	1129;1106;1129;1129	B9EGP5;F8VWA6;F8W1Z6;Q7Z3U7-4	.;.;.;.	K	1129;1130;1130;1129;1106;1129	ENSP00000377252:R1129K;ENSP00000377250:R1130K;ENSP00000280379:R1130K;ENSP00000447407:R1129K;ENSP00000449215:R1106K;ENSP00000377249:R1129K	.	R	+	2	0	MON2	61236216	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	9.536000	0.98067	2.305000	0.77605	0.462000	0.41574	AGA	-	superfamily_ARM-type_fold		0.373	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MON2	protein_coding	OTTHUMT00000406767.3	G	NM_015026	-		62949949	+1	no_errors	ENST00000393630	ensembl	human	known	74_37	missense	SNP	1.000	A
ZDHHC11B	653082	genome.wustl.edu	37	5	741736	741736	+	Missense_Mutation	SNP	G	G	T	rs61128505	byFrequency	TCGA-DX-A1L4-01A-12D-A26G-09	TCGA-DX-A1L4-10A-01D-A26G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c1aa1b8-f02c-43e7-a410-cc0344f0107e	6c11585a-6ac8-4f59-90c4-cae54eb89e0e	g.chr5:741736G>T	ENST00000382776.4	-	7	907	c.908C>A	c.(907-909)gCt>gAt	p.A303D	ZDHHC11_ENST00000424784.2_Intron|ZDHHC11B_ENST00000508859.2_Missense_Mutation_p.A314D			P0C7U3	ZH11B_HUMAN	zinc finger, DHHC-type containing 11B	303						integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			lung(3)|stomach(1)	4						CAGGGCGCCAGCTCCTTGCTG	0.438													.|||	4531	0.904752	0.972	0.9063	5008	,	,		21891	0.9702		0.8429	False		,,,				2504	0.8088																0								ENSG00000206077																																			ZDHHC11B	SO:0001583	missense	0			-	HGNC			5p15.33	2007-01-29				ENSG00000206077		"""Zinc fingers, DHHC-type"""	32962	protein-coding gene	gene with protein product							Standard	XM_003118532		Approved			P0C7U3		ENST00000382776.4:c.908C>A	5.37:g.741736G>T	ENSP00000445280:p.Ala303Asp	Somatic	0	25	0.00		0.5469949440746017	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	7	32	17.95	A6NHR3	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Znf_DHHC_palmitoyltrfase,pfscan_Znf_DHHC_palmitoyltrfase	p.A303D	ENST00000382776.4	37	c.908		5	.	.	.	.	.	.	.	.	.	.	t	0.021	-1.422845	0.01126	.	.	ENSG00000206077	ENST00000508859;ENST00000382776	T;T	0.28895	1.59;1.6	2.29	-3.8	0.04307	.	.	.	.	.	T	0.15132	0.0365	.	.	.	0.58432	P	1.999999999946489E-6	.	.	.	.	.	.	T	0.22312	-1.0220	5	0.29301	T	0.29	.	0.2495	0.00203	0.3527:0.2495:0.1642:0.2335	rs61128505	.	.	.	D	314;303	ENSP00000442373:A314D;ENSP00000445280:A303D	ENSP00000445280:A303D	A	-	2	0	ZDHHC11B	794736	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.473000	0.00988	-1.527000	0.01758	-1.667000	0.00748	GCT	-	NULL		0.438	ZDHHC11B-201	KNOWN	basic|appris_candidate	protein_coding	ZDHHC11B	protein_coding		G	XM_926053	rs61128505		741736	-1	no_errors	ENST00000382776	ensembl	human	known	74_37	missense	SNP	0.000	T
PCOLCE2	26577	genome.wustl.edu	37	3	142607822	142607823	+	5'UTR	INS	-	-	GCTCACACTGGCAGCAGCGCTG			TCGA-DX-A1L4-01A-12D-A26G-09	TCGA-DX-A1L4-10A-01D-A26G-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c1aa1b8-f02c-43e7-a410-cc0344f0107e	6c11585a-6ac8-4f59-90c4-cae54eb89e0e	g.chr3:142607822_142607823insGCTCACACTGGCAGCAGCGCTG	ENST00000295992.3	-	0	222_223				PCOLCE2_ENST00000485766.1_5'Flank|PCOLCE2_ENST00000461818.1_5'UTR	NM_013363.3	NP_037495.1	Q9UKZ9	PCOC2_HUMAN	procollagen C-endopeptidase enhancer 2						positive regulation of peptidase activity (GO:0010952)	extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|peptidase activator activity (GO:0016504)			NS(1)|endometrium(1)|large_intestine(11)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	32						CTCACACCGCCGCTCACACTGG	0.772																																																	0								ENSG00000163710																																			PCOLCE2	SO:0001623	5_prime_UTR_variant	0				HGNC	AF098269	CCDS3127.1	3q21-q24	2008-07-18			ENSG00000163710	ENSG00000163710			8739	protein-coding gene	gene with protein product		607064				10873381	Standard	NM_013363		Approved	PCPE2	uc003evd.3	Q9UKZ9	OTTHUMG00000159312	ENST00000295992.3:c.-85->CAGCGCTGCTGCCAGTGTGAGC	3.37:g.142607822_142607823insGCTCACACTGGCAGCAGCGCTG		Somatic	NA	NA	NA		0.5469949440746017	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	B2RCH9|D3DNG4|Q9BRH3	RNA	INS	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000295992.3	37	NULL	CCDS3127.1	3																																																																																			-	-		0.772	PCOLCE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PCOLCE2	protein_coding	OTTHUMT00000354509.1	-	NM_013363			142607823	-1	no_errors	ENST00000461818	ensembl	human	known	74_37	rna	INS	0.000:0.000	GCTCACACTGGCAGCAGCGCTG
PLEKHG2	64857	genome.wustl.edu	37	19	39911414	39911414	+	Silent	SNP	C	C	T			TCGA-DX-A1L4-01A-12D-A26G-09	TCGA-DX-A1L4-10A-01D-A26G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c1aa1b8-f02c-43e7-a410-cc0344f0107e	6c11585a-6ac8-4f59-90c4-cae54eb89e0e	g.chr19:39911414C>T	ENST00000409794.3	+	13	2171	c.1321C>T	c.(1321-1323)Cta>Tta	p.L441L	PLEKHG2_ENST00000425673.1_Silent_p.L441L|PLEKHG2_ENST00000378550.1_Silent_p.L441L|PLEKHG2_ENST00000409797.2_Silent_p.L441L|PLEKHG2_ENST00000458508.2_Silent_p.L382L	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	441					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|pancreas(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	40	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			TAAGCCTGTCCTAGAGCCCCT	0.547																																																	0								ENSG00000090924						78.0	88.0	85.0					19																	39911414		2203	4300	6503	PLEKHG2	SO:0001819	synonymous_variant	0			-	HGNC	AK024429	CCDS33022.2	19q13.2	2013-01-11			ENSG00000090924	ENSG00000090924		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	29515	protein-coding gene	gene with protein product		611893				11839748, 18045877	Standard	NM_022835		Approved	CLG, FLJ00018, ARHGEF42	uc010xuz.2	Q9H7P9	OTTHUMG00000152570	ENST00000409794.3:c.1321C>T	19.37:g.39911414C>T		Somatic	0	33	0.00		0.5469949440746017	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	36	12.20	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_DH-domain,superfamily_DH-domain,smart_DH-domain,smart_Pleckstrin_homology,pfscan_Pleckstrin_homology,pfscan_DH-domain	p.L441	ENST00000409794.3	37	c.1321	CCDS33022.2	19																																																																																			-	NULL		0.547	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PLEKHG2	protein_coding	OTTHUMT00000326802.1	C	NM_022835	-		39911414	+1	no_errors	ENST00000409794	ensembl	human	known	74_37	silent	SNP	0.984	T
HEG1	57493	genome.wustl.edu	37	3	124732419	124732419	+	Silent	SNP	A	A	G	rs202026679|rs540539937|rs376430192		TCGA-DX-A1L4-01A-12D-A26G-09	TCGA-DX-A1L4-10A-01D-A26G-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c1aa1b8-f02c-43e7-a410-cc0344f0107e	6c11585a-6ac8-4f59-90c4-cae54eb89e0e	g.chr3:124732419A>G	ENST00000311127.4	-	6	2071	c.2004T>C	c.(2002-2004)tcT>tcC	p.S668S	HEG1_ENST00000477536.1_5'UTR	NM_020733.1	NP_065784.1	Q9ULI3	HEG1_HUMAN	heart development protein with EGF-like domains 1	668	Ser-rich.				cardiac atrium morphogenesis (GO:0003209)|cell-cell junction assembly (GO:0007043)|endothelial cell morphogenesis (GO:0001886)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|lymph circulation (GO:0003017)|lymph vessel development (GO:0001945)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|post-embryonic development (GO:0009791)|regulation of body fluid levels (GO:0050878)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)|ventricular septum development (GO:0003281)	cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(24)|ovary(2)|urinary_tract(4)	47						aagaagaagaagaggaggagg	0.488																																																	0								ENSG00000173706						51.0	56.0	55.0					3																	124732419		2137	4243	6380	HEG1	SO:0001819	synonymous_variant	0			-	HGNC	AK074987	CCDS46898.1	3q21.2	2013-03-08	2013-03-08		ENSG00000173706	ENSG00000173706			29227	protein-coding gene	gene with protein product	"""heart of glass"""	614182	"""HEG homolog 1 (zebrafish)"""			10574462, 19151727, 23007647	Standard	NM_020733		Approved	KIAA1237, HEG	uc003ehs.4	Q9ULI3	OTTHUMG00000159486	ENST00000311127.4:c.2004T>C	3.37:g.124732419A>G		Somatic	0	16	0.00		0.5469949440746017	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	8	36	18.18	Q6NX66|Q8NC40|Q9BSV0	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_EG-like_dom,pfam_EGF-like_Ca-bd_dom,smart_EGF-like_Ca-bd_dom,smart_EG-like_dom,pfscan_EG-like_dom	p.S668	ENST00000311127.4	37	c.2004	CCDS46898.1	3																																																																																			-	NULL		0.488	HEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HEG1	protein_coding	OTTHUMT00000355732.2	A	XM_087386	rs202026679		124732419	-1	no_errors	ENST00000311127	ensembl	human	known	74_37	silent	SNP	0.028	G
ADAM21	8747	genome.wustl.edu	37	14	70924450	70924450	+	Silent	SNP	C	C	T	rs58247196		TCGA-DX-A1L4-01A-12D-A26G-09	TCGA-DX-A1L4-10A-01D-A26G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c1aa1b8-f02c-43e7-a410-cc0344f0107e	6c11585a-6ac8-4f59-90c4-cae54eb89e0e	g.chr14:70924450C>T	ENST00000603540.1	+	2	492	c.234C>T	c.(232-234)gtC>gtT	p.V78V	ADAM21_ENST00000267499.3_Silent_p.V78V|RP11-486O13.4_ENST00000556646.1_lincRNA	NM_003813.3	NP_003804.2	Q9UKJ8	ADA21_HUMAN	ADAM metallopeptidase domain 21	78					binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	axon (GO:0030424)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	31				all cancers(60;0.00326)|BRCA - Breast invasive adenocarcinoma(234;0.00646)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)		ATATGAGGGTCAAGAAGCTCT	0.512																																																	0								ENSG00000139985						105.0	108.0	107.0					14																	70924450		2203	4300	6503	ADAM21	SO:0001819	synonymous_variant	0			-	HGNC	AF029900	CCDS9804.1	14q24.1	2008-09-05	2005-08-18		ENSG00000139985	ENSG00000139985		"""ADAM metallopeptidase domain containing"""	200	protein-coding gene	gene with protein product		603713	"""a disintegrin and metalloproteinase domain 21"""			9469942	Standard	NM_003813		Approved	ADAM31	uc001xmd.3	Q9UKJ8		ENST00000603540.1:c.234C>T	14.37:g.70924450C>T		Somatic	0	24	0.00		0.5469949440746017	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	14	40	25.93	O43507|Q2VPC6|Q32MR0	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_Peptidase_M12B,pfam_ADAM_Cys-rich,pfam_Peptidase_M12B_N,pfam_Blood-coag_inhib_Disintegrin,superfamily_Blood-coag_inhib_Disintegrin,smart_Blood-coag_inhib_Disintegrin,smart_ADAM_Cys-rich,pfscan_Blood-coag_inhib_Disintegrin,pfscan_Peptidase_M12B,prints_Blood-coag_inhib_Disintegrin	p.V78	ENST00000603540.1	37	c.234	CCDS9804.1	14																																																																																			-	pfam_Peptidase_M12B_N		0.512	ADAM21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ADAM21	protein_coding	OTTHUMT00000413008.3	C		rs58247196		70924450	+1	no_errors	ENST00000267499	ensembl	human	known	74_37	silent	SNP	0.170	T
MYO7A	4647	genome.wustl.edu	37	11	76895771	76895792	+	Intron	DEL	GGAGGCGGGGACACCAGGGCCT	GGAGGCGGGGACACCAGGGCCT	-	rs111906251|rs143953991|rs78509218|rs111033223|rs369969967|rs12291062	byFrequency	TCGA-DX-A1L4-01A-12D-A26G-09	TCGA-DX-A1L4-10A-01D-A26G-09	GGAGGCGGGGACACCAGGGCCT	GGAGGCGGGGACACCAGGGCCT					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c1aa1b8-f02c-43e7-a410-cc0344f0107e	6c11585a-6ac8-4f59-90c4-cae54eb89e0e	g.chr11:76895771_76895792delGGAGGCGGGGACACCAGGGCCT	ENST00000409709.3	+	27	3775				MYO7A_ENST00000409893.1_Stop_Codon_Del|MYO7A_ENST00000409619.2_Intron|MYO7A_ENST00000458637.2_Intron	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA						actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						GTCAGTGCCGGGAGGCGGGGACACCAGGGCCTGAAAGTCTTT	0.599														2033	0.40595	0.466	0.4712	5008	,	,		20094	0.3194		0.4901	False		,,,				2504	0.2812																0								ENSG00000137474		,,	1379,2453		340,699,877					,,	-8.4	0.0		dbSNP_126	18	3099,4701		776,1547,1577	no	intron,frameshift,intron	MYO7A	NM_001127180.1,NM_001127179.2,NM_000260.3	,,	1116,2246,2454	A1A1,A1R,RR		39.7308,35.9864,38.4972	,,	,,		4478,7154				MYO7A	SO:0001627	intron_variant	0				HGNC	U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474		"""A-kinase anchor proteins"", ""Myosins / Myosin superfamily : Class VII"""	7606	protein-coding gene	gene with protein product		276903	"""myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))"""	USH1B, DFNB2, DFNA11		8884266	Standard	NM_000260		Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000409709.3:c.3503+11GGAGGCGGGGACACCAGGGCCT>-	11.37:g.76895771_76895792delGGAGGCGGGGACACCAGGGCCT		Somatic	NA	NA	NA		0.5469949440746017	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Frame_Shift_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_Myosin_head_motor_dom,pfam_IQ_motif_EF-hand-BS,superfamily_P-loop_NTPase,smart_Myosin_head_motor_dom,smart_IQ_motif_EF-hand-BS,smart_MyTH4_dom,prints_Myosin_head_motor_dom,pfscan_IQ_motif_EF-hand-BS,pfscan_MyTH4_dom	p.G1172fs	ENST00000409709.3	37	c.3514_3535	CCDS53683.1	11																																																																																			-	smart_MyTH4_dom,pfscan_MyTH4_dom		0.599	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	MYO7A	protein_coding	OTTHUMT00000328133.1	GGAGGCGGGGACACCAGGGCCT	NM_000260			76895792	+1	no_errors	ENST00000409893	ensembl	human	putative	74_37	frame_shift_del	DEL	0.000:0.000:0.001:0.001:0.004:0.000:0.000:0.000:0.000:0.000:0.000:0.000:0.000:0.000:0.000:0.000:0.011:0.011:0.009:0.051:0.048:0.007	-
CACNA1G	8913	genome.wustl.edu	37	17	48646553	48646553	+	Missense_Mutation	SNP	T	T	C			TCGA-DX-A1L4-01A-12D-A26G-09	TCGA-DX-A1L4-10A-01D-A26G-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c1aa1b8-f02c-43e7-a410-cc0344f0107e	6c11585a-6ac8-4f59-90c4-cae54eb89e0e	g.chr17:48646553T>C	ENST00000359106.5	+	3	382	c.382T>C	c.(382-384)Ttt>Ctt	p.F128L	CACNA1G_ENST00000510366.1_Missense_Mutation_p.F128L|CACNA1G_ENST00000507336.1_Missense_Mutation_p.F128L|CACNA1G_ENST00000514181.1_Missense_Mutation_p.F128L|CACNA1G_ENST00000515765.1_Missense_Mutation_p.F128L|CACNA1G_ENST00000352832.5_Missense_Mutation_p.F128L|CACNA1G_ENST00000514079.1_Missense_Mutation_p.F128L|CACNA1G_ENST00000507609.1_Missense_Mutation_p.F128L|CACNA1G_ENST00000513689.2_Missense_Mutation_p.F128L|CACNA1G_ENST00000502264.1_Missense_Mutation_p.F128L|CACNA1G_ENST00000442258.2_Missense_Mutation_p.F128L|CACNA1G_ENST00000507510.2_Missense_Mutation_p.F128L|CACNA1G_ENST00000354983.4_Missense_Mutation_p.F128L|CACNA1G_ENST00000416767.4_Missense_Mutation_p.F128L|CACNA1G_ENST00000515411.1_Missense_Mutation_p.F128L|CACNA1G_ENST00000514717.1_Missense_Mutation_p.F128L|CACNA1G_ENST00000503485.1_Missense_Mutation_p.F128L|CACNA1G_ENST00000510115.1_Missense_Mutation_p.F128L|CACNA1G_ENST00000512389.1_Missense_Mutation_p.F128L|CACNA1G_ENST00000505165.1_Missense_Mutation_p.F128L|CACNA1G_ENST00000360761.4_Missense_Mutation_p.F128L|CACNA1G_ENST00000513964.1_Missense_Mutation_p.F128L|CACNA1G_ENST00000429973.2_Missense_Mutation_p.F128L|CACNA1G_ENST00000515165.1_Missense_Mutation_p.F128L|CACNA1G_ENST00000507896.1_Missense_Mutation_p.F128L|CACNA1G_ENST00000358244.5_Missense_Mutation_p.F128L	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	128					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	CTTTGCCTTCTTTGCCGTGGA	0.517																																																	0								ENSG00000006283						141.0	131.0	134.0					17																	48646553		1985	4164	6149	CACNA1G	SO:0001583	missense	0			-	HGNC	AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.382T>C	17.37:g.48646553T>C	ENSP00000352011:p.Phe128Leu	Somatic	0	103	0.00		0.5469949440746017	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	16	155	9.36	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Ion_trans_dom,pfam_PKD1_2_channel,prints_VDCC_T_a1su,prints_VDCCAlpha1	p.F128L	ENST00000359106.5	37	c.382	CCDS45730.1	17	.	.	.	.	.	.	.	.	.	.	t	30	5.053072	0.93793	.	.	ENSG00000006283	ENST00000360761;ENST00000352832;ENST00000416767;ENST00000354983;ENST00000442258;ENST00000502264;ENST00000512389;ENST00000513964;ENST00000514717;ENST00000510366;ENST00000503485;ENST00000507510;ENST00000507336;ENST00000513689;ENST00000507609;ENST00000510115;ENST00000515165;ENST00000514181;ENST00000515765;ENST00000514079;ENST00000358244;ENST00000359106;ENST00000429973;ENST00000515411;ENST00000505165;ENST00000507896	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.98987	-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3	5.17	5.17	0.71159	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99576	0.9847	H	0.98027	4.13	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	0.988;0.997;0.999;0.983;0.999;0.995;0.991;0.999;0.991;1.0;0.999;1.0;1.0;0.999;0.995;0.971;0.989;0.999;0.999;1.0;0.985;1.0;0.999;1.0;0.997;0.987	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;P;D;D;D;D;D;D;D;D;P	0.91635	0.983;0.996;0.997;0.992;0.997;0.994;0.989;0.997;0.989;0.999;0.996;0.999;0.999;0.998;0.989;0.928;0.869;0.99;0.997;0.999;0.977;0.999;0.996;0.99;0.989;0.793	D	0.97737	1.0206	10	0.72032	D	0.01	.	15.0144	0.71573	0.0:0.0:0.0:1.0	.	128;128;128;128;128;128;128;128;128;128;128;128;128;128;128;128;128;128;128;128;128;128;128;128;128;128	Q19QZ5;Q19QZ1;Q19QZ4;Q19R07;Q19QY8;Q19R10;Q19QZ6;Q19QZ3;Q19R06;Q19R00;Q19R04;O43497-10;Q19QZ9;Q19QZ7;Q19R08;Q19QZ8;Q19R03;O43497-4;Q19R02;Q19R12;Q19R17;Q19R11;Q2TAC4;O43497;Q19R13;O43497-11	.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;CAC1G_HUMAN;.;.	L	128	ENSP00000353990:F128L;ENSP00000339302:F128L;ENSP00000392390:F128L;ENSP00000347078:F128L;ENSP00000409759:F128L;ENSP00000425522:F128L;ENSP00000426261:F128L;ENSP00000425451:F128L;ENSP00000422407:F128L;ENSP00000426814:F128L;ENSP00000427238:F128L;ENSP00000423112:F128L;ENSP00000420918:F128L;ENSP00000426172:F128L;ENSP00000423045:F128L;ENSP00000427173:F128L;ENSP00000426098:F128L;ENSP00000425698:F128L;ENSP00000426232:F128L;ENSP00000423317:F128L;ENSP00000350979:F128L;ENSP00000352011:F128L;ENSP00000414388:F128L;ENSP00000423155:F128L;ENSP00000422268:F128L;ENSP00000421518:F128L	ENSP00000339302:F128L	F	+	1	0	CACNA1G	46001552	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	8.026000	0.88783	1.959000	0.56917	0.334000	0.21626	TTT	-	pfam_Ion_trans_dom		0.517	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	CACNA1G	protein_coding	OTTHUMT00000367895.1	T	NM_018896	-		48646553	+1	no_errors	ENST00000359106	ensembl	human	known	74_37	missense	SNP	1.000	C
LINC00200	399706	genome.wustl.edu	37	10	1206620	1206676	+	lincRNA	DEL	CTGCTGGCTGGCACGTTCGCACGTGGCCATGTCAGCTCCAAGGAGGATGCTGACATC	CTGCTGGCTGGCACGTTCGCACGTGGCCATGTCAGCTCCAAGGAGGATGCTGACATC	-	rs577317299|rs372905850|rs576294471|rs539624301|rs556373839|rs185756919|rs112749382	byFrequency	TCGA-DX-A1L4-01A-12D-A26G-09	TCGA-DX-A1L4-10A-01D-A26G-09	CTGCTGGCTGGCACGTTCGCACGTGGCCATGTCAGCTCCAAGGAGGATGCTGACATC	CTGCTGGCTGGCACGTTCGCACGTGGCCATGTCAGCTCCAAGGAGGATGCTGACATC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c1aa1b8-f02c-43e7-a410-cc0344f0107e	6c11585a-6ac8-4f59-90c4-cae54eb89e0e	g.chr10:1206620_1206676delCTGCTGGCTGGCACGTTCGCACGTGGCCATGTCAGCTCCAAGGAGGATGCTGACATC	ENST00000425630.1	+	0	308					NR_015376.2				long intergenic non-protein coding RNA 200																		ATGCCGACTACTGCTGGCTGGCACGTTCGCACGTGGCCATGTCAGCTCCAAGGAGGATGCTGACATCCTGCTGGCTG	0.599																																																	0								ENSG00000229205																																			LINC00200			0				HGNC	AK097673		10p15.3	2012-10-12	2011-08-11	2011-08-11	ENSG00000229205	ENSG00000229205		"""Long non-coding RNAs"""	30974	non-coding RNA	RNA, long non-coding			"""chromosome 10 open reading frame 139"", ""non-protein coding RNA 200"""	C10orf139, NCRNA00200			Standard	NR_015376		Approved	FLJ40354	uc010qag.1		OTTHUMG00000017539		10.37:g.1206620_1206676delCTGCTGGCTGGCACGTTCGCACGTGGCCATGTCAGCTCCAAGGAGGATGCTGACATC		Somatic	NA	NA	NA		0.5469949440746017	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA		RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000425630.1	37	NULL		10																																																																																			-	-		0.599	LINC00200-001	KNOWN	basic	lincRNA	LINC00200	lincRNA	OTTHUMT00000046417.2	CTGCTGGCTGGCACGTTCGCACGTGGCCATGTCAGCTCCAAGGAGGATGCTGACATC	NR_015376			1206676	+1	no_errors	ENST00000583117	ensembl	human	known	74_37	rna	DEL	0.003:0.004:0.007:0.006:0.006:0.005:0.003:0.002:0.003:0.003:0.003:0.003:0.004:0.004:0.003:0.004:0.004:0.003:0.003:0.006:0.007:0.007:0.006:0.007:0.007:0.006:0.004:0.003:0.001:0.001:0.001:0.002:0.005:0.007:0.007:0.005:0.003:0.002:0.005:0.006:0.007:0.006:0.004:0.001:0.000:0.000:0.000:0.001:0.001:0.003:0.003:0.005:0.008:0.010:0.010:0.008:0.005	-
LOC728554	728554	genome.wustl.edu	37	5	177303235	177303259	+	RNA	DEL	TGGTGGTGGTACGTTGGTGGTACGT	TGGTGGTGGTACGTTGGTGGTACGT	-	rs144453903		TCGA-DX-A1L4-01A-12D-A26G-09	TCGA-DX-A1L4-10A-01D-A26G-09	TGGTGGTGGTACGTTGGTGGTACGT	TGGTGGTGGTACGTTGGTGGTACGT					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c1aa1b8-f02c-43e7-a410-cc0344f0107e	6c11585a-6ac8-4f59-90c4-cae54eb89e0e	g.chr5:177303235_177303259delTGGTGGTGGTACGTTGGTGGTACGT	ENST00000506672.1	+	0	339					NR_003615.2																						gtggtggtggtggtggtggtacgttggtggtacgttggtggtacg	0.556																																																	0								ENSG00000170089																																			RP11-423H2.1			0				Clone_based_vega_gene																													5.37:g.177303235_177303259delTGGTGGTGGTACGTTGGTGGTACGT		Somatic	NA	NA	NA		0.5469949440746017	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA		RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000506672.1	37	NULL		5																																																																																			-	-		0.556	RP11-423H2.1-002	KNOWN	basic	processed_transcript	LOC728554	pseudogene	OTTHUMT00000373226.1	TGGTGGTGGTACGTTGGTGGTACGT				177303259	+1	no_errors	ENST00000507037	ensembl	human	known	74_37	rna	DEL	0.014:0.010:0.008:0.007:0.002:0.001:0.000:0.000:0.000:0.000:0.000:0.000:0.000:0.001:0.001:0.000:0.001:0.001:0.002:0.001:0.001:0.001:0.001:0.004:0.002	-
ALG13	79868	genome.wustl.edu	37	X	111000722	111000722	+	Intron	DEL	T	T	-	rs75519151		TCGA-DX-A1L4-01A-12D-A26G-09	TCGA-DX-A1L4-10A-01D-A26G-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c1aa1b8-f02c-43e7-a410-cc0344f0107e	6c11585a-6ac8-4f59-90c4-cae54eb89e0e	g.chrX:111000722delT	ENST00000394780.3	+	26	2985				ALG13_ENST00000470971.1_Intron|ALG13_ENST00000251943.4_Intron	NM_001099922.2|NM_001257231.1	NP_001093392.1|NP_001244160.1	Q9NP73	ALG13_HUMAN	ALG13, UDP-N-acetylglucosaminyltransferase subunit						cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|lipid glycosylation (GO:0030259)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)	carbohydrate binding (GO:0030246)|cysteine-type peptidase activity (GO:0008234)|N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity (GO:0004577)|poly(A) RNA binding (GO:0044822)			endometrium(2)|lung(10)|skin(1)	13						CCAATTCTTATTTTTTTTTTT	0.338													|||unknown(HR)	783	0.207417	0.1831	0.1873	3775	,	,		11385	0.1478		0.1402	False		,,,				2504	0.1237																0								ENSG00000101901																																			ALG13	SO:0001627	intron_variant	0				HGNC	AF220051	CCDS14559.1, CCDS55477.1, CCDS59173.1, CCDS76011.1, CCDS76012.1, CCDS76013.1	Xq23	2014-02-24	2013-02-21	2006-11-07	ENSG00000101901	ENSG00000101901	2.4.1.141	"""Tudor domain containing"", ""OTU domain containing"""	30881	protein-coding gene	gene with protein product	"""tudor domain containing 13"", ""N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase"""	300776	"""glycosyltransferase 28 domain containing 1"", ""chromosome X open reading frame 45"", ""asparagine-linked glycosylation 13 homolog (S. cerevisiae)"""	GLT28D1, CXorf45		12477932	Standard	NM_018466		Approved	MDS031, YGL047W, FLJ23018, TDRD13	uc011msy.2	Q9NP73	OTTHUMG00000022209	ENST00000394780.3:c.2974-94T>-	X.37:g.111000722delT		Somatic	0	14	0.00		0.5469949440746017	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	40	9.09	B1AKD6|B1AKM1|B2R5L5|B7Z6J0|B7Z804|B7Z847|B7Z9A8|B7ZAJ1|B7ZB57|Q17RC3|Q5JXY9|Q9H5U8	RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000394780.3	37	NULL	CCDS55477.1	X																																																																																			-	-		0.338	ALG13-011	PUTATIVE	basic|appris_principal|CCDS	protein_coding	ALG13	protein_coding	OTTHUMT00000272895.1	T	NM_018466			111000722	+1	no_errors	ENST00000487243	ensembl	human	putative	74_37	rna	DEL	0.002	-
HLA-F	3134	genome.wustl.edu	37	6	29692901	29692901	+	Missense_Mutation	SNP	C	C	T			TCGA-DX-A1L4-01A-12D-A26G-09	TCGA-DX-A1L4-10A-01D-A26G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c1aa1b8-f02c-43e7-a410-cc0344f0107e	6c11585a-6ac8-4f59-90c4-cae54eb89e0e	g.chr6:29692901C>T	ENST00000376861.1	+	5	1088	c.704C>T	c.(703-705)aCg>aTg	p.T235M	HLA-F_ENST00000434407.2_Intron|HLA-F_ENST00000334668.4_Missense_Mutation_p.T235M|HLA-F_ENST00000440587.2_Missense_Mutation_p.T117M|HLA-F_ENST00000259951.7_Missense_Mutation_p.T235M			P30511	HLAF_HUMAN	major histocompatibility complex, class I, F	235	Alpha-3.|Ig-like C1-type.				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 exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)|TAP1 binding (GO:0046978)|TAP2 binding (GO:0046979)			cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	8						GCGGAGATCACGCTGACCTGG	0.627																																																	0								ENSG00000204642						54.0	50.0	51.0					6																	29692901		2203	4300	6503	HLA-F	SO:0001583	missense	0			-	HGNC	AY253269	CCDS43437.1, CCDS43438.1, CCDS43439.1	6p21.3	2013-01-11			ENSG00000204642	ENSG00000204642		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4963	protein-coding gene	gene with protein product		143110				1688605	Standard	NM_018950		Approved		uc003nno.4	P30511	OTTHUMG00000031156	ENST00000376861.1:c.704C>T	6.37:g.29692901C>T	ENSP00000366057:p.Thr235Met	Somatic	0	90	0.00		0.5469949440746017	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	26	144	15.20	Q5JQI8|Q5JQJ1|Q5SPT5|Q860R0|Q8MGQ1|Q8WLP5|Q95HC0|Q9TP68	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_MHC_I_a_a1/a2,pfam_Ig_C1-set,superfamily_MHC_I/II-like_Ag-recog,smart_Ig_C1-set,pfscan_Ig-like_dom,prints_MHC_I_a	p.T235M	ENST00000376861.1	37	c.704	CCDS43438.1	6	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	8.352|8.352	0.831018|0.831018	0.16820|0.16820	.|.	.|.	ENSG00000204642|ENSG00000204642	ENST00000429294|ENST00000376861;ENST00000449921;ENST00000334668;ENST00000259951;ENST00000399258;ENST00000440587	.|T;T;T;T	.|0.03181	.|4.02;4.02;4.02;4.02	1.92|1.92	1.92|1.92	0.25849|0.25849	.|Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	.|1.013100	.|0.07958	.|U	.|0.981985	T|T	0.03739|0.03739	0.0106|0.0106	M|M	0.83692|0.83692	2.655|2.655	0.19575|0.19575	N|N	0.999965|0.999965	.|P;D;D	.|0.89917	.|0.943;0.982;1.0	.|B;B;P	.|0.45913	.|0.276;0.274;0.497	T|T	0.38156|0.38156	-0.9674|-0.9674	5|10	.|0.87932	.|D	.|0	.|.	7.2321|7.2321	0.26049|0.26049	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|235;235;235	.|A8MVU7;P30511;P30511-3	.|.;HLAF_HUMAN;.	C|M	114|235;212;235;235;149;117	.|ENSP00000366057:T235M;ENSP00000334263:T235M;ENSP00000259951:T235M;ENSP00000404130:T117M	.|ENSP00000259951:T235M	R|T	+|+	1|2	0|0	HLA-F|HLA-F	29800880|29800880	0.000000|0.000000	0.05858|0.05858	0.719000|0.719000	0.30619|0.30619	0.313000|0.313000	0.28021|0.28021	-0.045000|-0.045000	0.12003|0.12003	1.046000|1.046000	0.40249|0.40249	0.436000|0.436000	0.28706|0.28706	CGC|ACG	-	pfam_Ig_C1-set,smart_Ig_C1-set,pfscan_Ig-like_dom		0.627	HLA-F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HLA-F	protein_coding	OTTHUMT00000195083.1	C	NM_018950	-		29692901	+1	no_errors	ENST00000259951	ensembl	human	known	74_37	missense	SNP	0.675	T
