#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_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_NormalRefReads_WU	i_NormalVAF_WU	i_NormalVarReads_WU	i_ORegAnno_bin	i_RNARefReads_WU	i_RNAVAF_WU	i_RNAVarReads_WU	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_Start_position_hg18	i_TumorRefReads_WU	i_TumorVAF_WU	i_TumorVarReads_WU	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	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_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
USP9X	8239	genome.wustl.edu	37	X	41010296	41010296	+	Silent	SNP	G	G	A			TCGA-AB-3001-03A-01D-0739-09	TCGA-AB-3001-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	1ab338ac-7a1e-4796-9464-d0e3218050ea	89734d2a-e63f-4255-8f4a-223187fa0daf	g.chrX:41010296G>A	ENST00000324545.8	+	13	2382	c.1749G>A	c.(1747-1749)gcG>gcA	p.A583A	USP9X_ENST00000378308.2_Silent_p.A583A	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	583					axon extension (GO:0048675)|BMP signaling pathway (GO:0030509)|cerebellar cortex structural organization (GO:0021698)|chromosome segregation (GO:0007059)|female gamete generation (GO:0007292)|gene expression (GO:0010467)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|post-embryonic development (GO:0009791)|protein deubiquitination (GO:0016579)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)	co-SMAD binding (GO:0070410)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)	p.A576A(1)		NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87						TTGGTGAAGCGCCTCAAAATT	0.318													G|||	1	0.000264901	0.0008	0.0	3775	,	,		10461	0.0		0.0	False		,,,				2504	0.0				Ovarian(172;1807 2695 35459 49286)	dbGAP											1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	X											38.0	34.0	35.0					X																	41010296		2120	4244	6364	40895240	SO:0001819	synonymous_variant	0			X98296	CCDS43930.1, CCDS55403.1	Xp11.4	2010-08-03	2006-02-14		ENSG00000124486	ENSG00000124486		"""Ubiquitin-specific peptidases"""	12632	protein-coding gene	gene with protein product		300072	"""ubiquitin specific protease 9, X chromosome (fat facets-like Drosophila)"", ""ubiquitin specific protease 9, X-linked (fat facets-like, Drosophila)"", ""ubiquitin specific peptidase 9, X-linked (fat facets-like, Drosophila)"""			8922996	Standard	NM_001039590		Approved	DFFRX, FAF	uc004dfb.3	Q93008	OTTHUMG00000021367	ENST00000324545.8:c.1749G>A	X.37:g.41010296G>A		Somatic	703	0.14	1		58	0.00	0	WXS	Illumina HiSeq	Phase_IV	40895240	326	26.91	120	O75550|Q8WWT3|Q8WX12	Silent	SNP	HMMPfam_UCH,PatternScan_UCH_2_1,PatternScan_UCH_2_2,superfamily_Cysteine proteinases	p.A583	ENST00000324545.8	37	c.1749	CCDS43930.1	X																																																																																			-	NULL		0.318	USP9X-003	KNOWN	basic|CCDS	protein_coding	USP9X	protein_coding	OTTHUMT00000056250.4	G	NM_004652		40895240	+1	no_errors	NM_001039590.2	genbank	human	reviewed	54_36p	silent	SNP	0.996	A
AFF2	2334	genome.wustl.edu	37	X	147891443	147891443	+	Splice_Site	SNP	G	G	A	rs368578550		TCGA-AB-3001-03A-01D-0739-09	TCGA-AB-3001-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	1ab338ac-7a1e-4796-9464-d0e3218050ea	89734d2a-e63f-4255-8f4a-223187fa0daf	g.chrX:147891443G>A	ENST00000370460.2	+	4	1564	c.1085G>A	c.(1084-1086)cGg>cAg	p.R362Q	AFF2_ENST00000370457.5_Splice_Site_p.R358Q|AFF2_ENST00000370458.1_Splice_Site_p.R358Q|AFF2_ENST00000286437.5_Splice_Site_p.R32Q|AFF2_ENST00000342251.3_Splice_Site_p.R358Q	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	362					brain development (GO:0007420)|learning or memory (GO:0007611)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)	G-quadruplex RNA binding (GO:0002151)	p.R362Q(1)		breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	109	Acute lymphoblastic leukemia(192;6.56e-05)					GAAATCTTGCGGGTGAGTTTA	0.338																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	X						G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	1,3834		0,0,1,1632,570	202.0	173.0	183.0		1073,1073,1085,1073,95,1085	5.0	1.0	X		183	0,6728		0,0,0,2428,1872	no	missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice	AFF2	NM_001169122.1,NM_001169123.1,NM_001169124.1,NM_001169125.1,NM_001170628.1,NM_002025.3	43,43,43,43,43,43	0,0,1,4060,2442	AA,AG,A,GG,G		0.0,0.0261,0.0095	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	358/1277,358/1302,362/1277,358/1273,32/953,362/1312	147891443	1,10562	2203	4300	6503	147699135	SO:0001630	splice_region_variant	0			U48436	CCDS14684.1, CCDS55521.1, CCDS76040.1	Xq28	2008-02-05	2005-06-27	2005-06-27	ENSG00000155966	ENSG00000155966			3776	protein-coding gene	gene with protein product		300806	"""fragile X mental retardation 2"""	FMR2			Standard	NM_002025		Approved	FRAXE	uc004fcp.3	P51816	OTTHUMG00000022613	ENST00000370460.2:c.1086+1G>A	X.37:g.147891443G>A		Somatic	1422	0.49	7		252	0.00	0	WXS	Illumina HiSeq	Phase_IV	147699135	387	23.82	121	A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Missense_Mutation	SNP	HMMPfam_AF-4	p.R362Q	ENST00000370460.2	37	c.1085	CCDS14684.1	X	.	.	.	.	.	.	.	.	.	.	G	25.2	4.616088	0.87359	2.61E-4	0.0	ENSG00000155966	ENST00000370460;ENST00000370457;ENST00000342251;ENST00000370458;ENST00000286437	T;T;T;T;T	0.68025	-0.3;-0.3;-0.3;-0.3;0.02	5.87	5.01	0.66863	.	0.141084	0.45606	D	0.000353	T	0.74966	0.3786	L	0.39245	1.2	0.42575	D	0.993197	B;B;B;B;B;B;D	0.89917	0.04;0.032;0.032;0.032;0.032;0.04;1.0	B;B;B;B;B;B;D	0.81914	0.028;0.016;0.016;0.016;0.016;0.028;0.995	T	0.77351	-0.2620	10	0.66056	D	0.02	.	14.2101	0.65759	0.0731:0.0:0.9269:0.0	.	32;362;358;358;358;362;358	B4DXD5;P51816-6;P51816-3;P51816-2;P51816-5;P51816;P51816-4	.;.;.;.;.;AFF2_HUMAN;.	Q	362;358;358;358;32	ENSP00000359489:R362Q;ENSP00000359486:R358Q;ENSP00000345459:R358Q;ENSP00000359487:R358Q;ENSP00000286437:R32Q	ENSP00000286437:R32Q	R	+	2	0	AFF2	147699135	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	6.877000	0.75562	1.247000	0.43917	-0.191000	0.12829	CGG	-	HMMPfam_AF-4		0.338	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	AFF2	protein_coding	OTTHUMT00000058673.2	G	NM_002025	Missense_Mutation	147699135	+1	no_errors	NM_002025.2	genbank	human	validated	54_36p	missense	SNP	1.000	A
CACNA1E	777	genome.wustl.edu	37	1	181754552	181754552	+	Missense_Mutation	SNP	C	C	G			TCGA-AB-3001-03A-01D-0739-09	TCGA-AB-3001-11A-01D-0739-09	C	C	C	G	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	1ab338ac-7a1e-4796-9464-d0e3218050ea	89734d2a-e63f-4255-8f4a-223187fa0daf	g.chr1:181754552C>G	ENST00000367573.2	+	42	5677	c.5677C>G	c.(5677-5679)Cag>Gag	p.Q1893E	CACNA1E_ENST00000360108.3_Missense_Mutation_p.Q1874E|CACNA1E_ENST00000367570.1_Missense_Mutation_p.Q1893E|CACNA1E_ENST00000357570.5_Missense_Mutation_p.Q1844E|CACNA1E_ENST00000526775.1_Missense_Mutation_p.Q1874E|CACNA1E_ENST00000367567.4_Missense_Mutation_p.Q1500E|CACNA1E_ENST00000358338.5_Missense_Mutation_p.Q1825E	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1893					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)	p.Q1893E(1)		NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						GCTGGAGGAACAGGTGAAAGT	0.537																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	1											59.0	61.0	60.0					1																	181754552		2131	4248	6379	180021175	SO:0001583	missense	0			AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.5677C>G	1.37:g.181754552C>G	ENSP00000356545:p.Gln1893Glu	Somatic	1466	0.41	6		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	180021175	878	30.04	377	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	HMMPfam_Ion_trans,HMMPfam_Ca_chan_IQ,superfamily_Voltage-gated potassium channels	p.Q1893E	ENST00000367573.2	37	c.5677	CCDS55664.1	1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.538974	0.85917	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	T;T;T;T;T;T;T	0.63255	-0.03;-0.03;-0.03;-0.03;-0.03;-0.03;-0.03	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.74512	0.3726	L	0.47716	1.5	0.80722	D	1	P;D	0.58268	0.831;0.982	B;D	0.70227	0.319;0.968	T	0.71978	-0.4429	10	0.41790	T	0.15	.	19.3614	0.94440	0.0:1.0:0.0:0.0	.	1874;1893	Q15878-2;Q15878-3	.;.	E	1893;1874;1844;1825;1500;1874;1893	ENSP00000356542:Q1893E;ENSP00000434814:Q1874E;ENSP00000350183:Q1844E;ENSP00000351101:Q1825E;ENSP00000356539:Q1500E;ENSP00000353222:Q1874E;ENSP00000356545:Q1893E	ENSP00000350183:Q1844E	Q	+	1	0	CACNA1E	180021175	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.338000	0.79269	2.735000	0.93741	0.655000	0.94253	CAG	-	HMMPfam_Ca_chan_IQ		0.537	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	CACNA1E	protein_coding	OTTHUMT00000090793.2	C	NM_000721		180021175	+1	no_errors	NM_000721.2	genbank	human	reviewed	54_36p	missense	SNP	1.000	G
SPATS2L	26010	genome.wustl.edu	37	2	201337597	201337597	+	Missense_Mutation	SNP	G	G	T			TCGA-AB-3001-03A-01D-0739-09	TCGA-AB-3001-11A-01D-0739-09	G	G	G	T	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	1ab338ac-7a1e-4796-9464-d0e3218050ea	89734d2a-e63f-4255-8f4a-223187fa0daf	g.chr2:201337597G>T	ENST00000358677.5	+	12	1350	c.1103G>T	c.(1102-1104)aGc>aTc	p.S368I	SPATS2L_ENST00000409988.3_Missense_Mutation_p.S368I|SPATS2L_ENST00000460095.1_3'UTR|SPATS2L_ENST00000451764.2_Missense_Mutation_p.S368I|SPATS2L_ENST00000360760.5_Missense_Mutation_p.S299I|SPATS2L_ENST00000409385.1_Missense_Mutation_p.S308I|SPATS2L_ENST00000409140.3_Missense_Mutation_p.S368I|SPATS2L_ENST00000409755.3_Missense_Mutation_p.S398I|SPATS2L_ENST00000409718.1_Missense_Mutation_p.S368I|SPATS2L_ENST00000409151.1_Missense_Mutation_p.S376I	NM_001282735.1|NM_001282743.1|NM_001282744.1|NM_015535.2	NP_001269664.1|NP_001269672.1|NP_001269673.1|NP_056350.2	Q9NUQ6	SPS2L_HUMAN	spermatogenesis associated, serine-rich 2-like	368						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|protein complex (GO:0043234)	poly(A) RNA binding (GO:0044822)	p.S398I(1)		endometrium(1)|kidney(1)|lung(4)|ovary(2)|pancreas(1)|prostate(1)	10						ACTCCCTGCAGCTCCCTGCTG	0.483																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	2											87.0	92.0	91.0					2																	201337597		1999	4180	6179	201045842	SO:0001583	missense	0			AF193059	CCDS46483.1, CCDS46484.1, CCDS74621.1, CCDS74622.1	2q33.1	2009-06-12			ENSG00000196141	ENSG00000196141			24574	protein-coding gene	gene with protein product	"""DNA polymerase transactivated protein 6"""	613817				11230166	Standard	NM_001100422		Approved	DNAPTP6	uc002uvr.4	Q9NUQ6	OTTHUMG00000154589	ENST00000358677.5:c.1103G>T	2.37:g.201337597G>T	ENSP00000351503:p.Ser368Ile	Somatic	980	0.20	2		8	20.00	2	WXS	Illumina HiSeq	Phase_IV	201045842	514	18.02	113	A8K381|B4DRE6|B4DT67|B7WNZ7|Q53T22|Q8WV53|Q8WYG1|Q9NTW4	Missense_Mutation	SNP	HMMPfam_DUF1387	p.S368I	ENST00000358677.5	37	c.1103	CCDS46483.1	2	.	.	.	.	.	.	.	.	.	.	G	18.65	3.668970	0.67814	.	.	ENSG00000196141	ENST00000409718;ENST00000358677;ENST00000409988;ENST00000409385;ENST00000451764;ENST00000360760;ENST00000409140;ENST00000409755;ENST00000409151	.	.	.	5.39	3.54	0.40534	.	0.212211	0.42964	D	0.000624	T	0.58935	0.2157	L	0.54323	1.7	0.38400	D	0.945639	P;B;B	0.38677	0.642;0.402;0.188	B;B;B	0.43445	0.42;0.2;0.17	T	0.65311	-0.6199	9	0.66056	D	0.02	-14.2592	14.469	0.67504	0.0:0.2782:0.7218:0.0	.	398;299;368	B4DT67;Q9NUQ6-2;Q9NUQ6	.;.;SPS2L_HUMAN	I	368;368;368;308;368;299;368;398;376	.	ENSP00000351503:S368I	S	+	2	0	SPATS2L	201045842	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	0.813000	0.27225	0.779000	0.33543	0.655000	0.94253	AGC	-	HMMPfam_DUF1387		0.483	SPATS2L-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	LOC26010	protein_coding	OTTHUMT00000336208.3	G	NM_015535		201045842	+1	no_errors	NM_001100422.1	genbank	human	validated	54_36p	missense	SNP	1.000	T
SI	6476	genome.wustl.edu	37	3	164730805	164730805	+	Missense_Mutation	SNP	G	G	T			TCGA-AB-3001-03A-01D-0739-09	TCGA-AB-3001-11A-01D-0739-09	G	G	G	T	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	1ab338ac-7a1e-4796-9464-d0e3218050ea	89734d2a-e63f-4255-8f4a-223187fa0daf	g.chr3:164730805G>T	ENST00000264382.3	-	34	4087	c.4025C>A	c.(4024-4026)aCa>aAa	p.T1342K		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	1342	Sucrase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	brush border (GO:0005903)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|oligo-1,6-glucosidase activity (GO:0004574)|sucrose alpha-glucosidase activity (GO:0004575)	p.T1342K(1)		NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)|Scopolamine(DB00747)	TTTATCTATTGTTATGTTGGG	0.338										HNSCC(35;0.089)																												dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	3											124.0	122.0	123.0					3																	164730805		2203	4300	6503	166213499	SO:0001583	missense	0			X63597	CCDS3196.1	3q25.2-q26.2	2004-04-06	2004-04-06		ENSG00000090402	ENSG00000090402	3.2.1.10		10856	protein-coding gene	gene with protein product	"""Oligosaccharide alpha-1,6-glucosidase"""	609845	"""sucrase-isomaltase"""			2962903, 1353958	Standard	NM_001041		Approved		uc003fei.3	P14410	OTTHUMG00000158065	ENST00000264382.3:c.4025C>A	3.37:g.164730805G>T	ENSP00000264382:p.Thr1342Lys	Somatic	987	0.40	4		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	166213499	510	30.80	227	A2RUC3|Q1JQ80|Q1RMC2	Missense_Mutation	SNP	HMMPfam_Glyco_hydro_31,PatternScan_GLYCOSYL_HYDROL_F31_1,PatternScan_GLYCOSYL_HYDROL_F31_2,HMMPfam_Trefoil,HMMSmart_SM00018,superfamily_Trefoil,superfamily_(Trans)glycosidases,PatternScan_P_TREFOIL	p.T1342K	ENST00000264382.3	37	c.4025	CCDS3196.1	3	.	.	.	.	.	.	.	.	.	.	G	16.51	3.143941	0.57044	.	.	ENSG00000090402	ENST00000264382	D	0.88664	-2.41	4.35	4.35	0.52113	Glycoside hydrolase, superfamily (1);	0.252260	0.38548	N	0.001645	D	0.90906	0.7142	M	0.64404	1.975	0.38371	D	0.944881	P	0.50819	0.939	P	0.56788	0.806	D	0.91868	0.5505	10	0.56958	D	0.05	.	10.3626	0.44003	0.0915:0.0:0.9085:0.0	.	1342	P14410	SUIS_HUMAN	K	1342	ENSP00000264382:T1342K	ENSP00000264382:T1342K	T	-	2	0	SI	166213499	0.949000	0.32298	0.975000	0.42487	0.399000	0.30720	1.931000	0.40134	2.210000	0.71456	0.585000	0.79938	ACA	-	HMMPfam_Glyco_hydro_31,superfamily_(Trans)glycosidases		0.338	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SI	protein_coding	OTTHUMT00000350116.1	G	NM_001041		166213499	-1	no_errors	NM_001041.2	genbank	human	validated	54_36p	missense	SNP	0.808	T
SIMC1	375484	genome.wustl.edu	37	5	175717167	175717167	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-3001-03A-01D-0739-09	TCGA-AB-3001-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	1ab338ac-7a1e-4796-9464-d0e3218050ea	89734d2a-e63f-4255-8f4a-223187fa0daf	g.chr5:175717167C>T	ENST00000443967.1	+	4	990	c.583C>T	c.(583-585)Cgc>Tgc	p.R195C	SIMC1_ENST00000429602.2_Missense_Mutation_p.R214C|SIMC1_ENST00000341199.6_Intron|SIMC1_ENST00000430704.2_Intron|SIMC1_ENST00000503595.1_3'UTR			Q8NDZ2	SIMC1_HUMAN	SUMO-interacting motifs containing 1	195	Pro-rich.						SUMO polymer binding (GO:0032184)	p.R195C(1)									AGATGTATCTCGCCCACCACA	0.582																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	5											88.0	66.0	73.0					5																	175717167		2203	4299	6502	175649773	SO:0001583	missense	0			BC037298	CCDS4398.2	5q35.2	2013-08-14	2012-11-14	2012-11-14	ENSG00000170085	ENSG00000170085			24779	protein-coding gene	gene with protein product	"""oocyte maturation associated 1"", ""platform element for inhibition of autolytic degradation"""		"""chromosome 5 open reading frame 25"""	C5orf25		23086935, 23707407	Standard	NM_198567		Approved	FLJ44216, OOMA1, PLEIAD	uc003mds.4	Q8NDZ2	OTTHUMG00000130663	ENST00000443967.1:c.583C>T	5.37:g.175717167C>T	ENSP00000406571:p.Arg195Cys	Somatic	2500	0.52	13		6	73.91	17	WXS	Illumina HiSeq	Phase_IV	175649773	693	30.53	305	J3KQQ8|Q6NXN8|Q6ZTU4|Q8IZ15	Missense_Mutation	SNP	NULL	p.R195C	ENST00000443967.1	37	c.583		5	.	.	.	.	.	.	.	.	.	.	C	8.804	0.933541	0.18206	.	.	ENSG00000170085	ENST00000443967;ENST00000429602;ENST00000377277	T;T	0.28454	2.37;1.61	4.46	1.84	0.25277	.	1.206680	0.05750	N	0.602987	T	0.21468	0.0517	.	.	.	0.28075	N	0.932434	B;B	0.06786	0.001;0.0	B;B	0.01281	0.0;0.0	T	0.26395	-1.0104	9	0.44086	T	0.13	-4.4541	4.7063	0.12851	0.0:0.1108:0.1918:0.6974	.	214;195	B4DRM7;Q8NDZ2	.;CE025_HUMAN	C	195;214;106	ENSP00000406571:R195C;ENSP00000410552:R214C	ENSP00000366489:R106C	R	+	1	0	C5orf25	175649773	0.997000	0.39634	0.958000	0.39756	0.386000	0.30323	0.784000	0.26816	0.683000	0.31428	-0.331000	0.08364	CGC	-	NULL		0.582	SIMC1-001	KNOWN	basic	protein_coding	C5orf25	protein_coding	OTTHUMT00000253155.2	C	NM_198567		175649773	+1	no_errors	NM_198567.4	genbank	human	validated	54_36p	missense	SNP	0.021	T
RUFY1	80230	genome.wustl.edu	37	5	179025796	179025796	+	Missense_Mutation	SNP	C	C	G			TCGA-AB-3001-03A-01D-0739-09	TCGA-AB-3001-11A-01D-0739-09	C	C	C	G	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	1ab338ac-7a1e-4796-9464-d0e3218050ea	89734d2a-e63f-4255-8f4a-223187fa0daf	g.chr5:179025796C>G	ENST00000319449.4	+	14	1747	c.1735C>G	c.(1735-1737)Ctg>Gtg	p.L579V	RUFY1_ENST00000393438.2_Missense_Mutation_p.L471V|RUFY1_ENST00000377001.2_3'UTR|RUFY1_ENST00000437570.2_Missense_Mutation_p.L471V|RP11-1379J22.2_ENST00000500262.1_RNA	NM_025158.4	NP_079434.3	Q96T51	RUFY1_HUMAN	RUN and FYVE domain containing 1	579					endocytosis (GO:0006897)|regulation of endocytosis (GO:0030100)	cytoplasm (GO:0005737)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	lipid binding (GO:0008289)|protein transporter activity (GO:0008565)|zinc ion binding (GO:0008270)	p.L471V(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	26	all_cancers(89;0.00018)|all_epithelial(37;8.37e-05)|Renal(175;0.000159)|Lung NSC(126;0.00108)|all_lung(126;0.00195)	all_cancers(40;0.0322)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CAGGATGGAGCTGCAACAAGT	0.527										HNSCC(44;0.11)																												dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	5											110.0	106.0	108.0					5																	179025796		2203	4300	6503	178958402	SO:0001583	missense	0			AF361055	CCDS4445.2, CCDS34312.1	5q35.3	2008-02-05			ENSG00000176783	ENSG00000176783		"""Zinc fingers, FYVE domain containing"""	19760	protein-coding gene	gene with protein product		610327				11877430	Standard	NM_001040451		Approved	FLJ22251, ZFYVE12, RABIP4	uc003mka.2	Q96T51	OTTHUMG00000130913	ENST00000319449.4:c.1735C>G	5.37:g.179025796C>G	ENSP00000325594:p.Leu579Val	Somatic	752	0.66	5		44	22.81	13	WXS	Illumina HiSeq	Phase_IV	178958402	678	18.68	156	Q59FF3|Q71S93|Q9H6I3	Missense_Mutation	SNP	HMMPfam_FYVE,HMMSmart_SM00064,HMMPfam_RUN,HMMSmart_SM00593,superfamily_FYVE/PHD zinc finger	p.L579V	ENST00000319449.4	37	c.1735	CCDS4445.2	5	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.852|9.852	1.193863|1.193863	0.22037|0.22037	.|.	.|.	ENSG00000176783|ENSG00000176783	ENST00000502434|ENST00000319449;ENST00000437570;ENST00000393438;ENST00000360569	.|T;T;T	.|0.55052	.|0.54;0.58;0.58	4.98|4.98	1.74|1.74	0.24563|0.24563	.|.	.|0.000000	.|0.64402	.|D	.|0.000002	T|T	0.51075|0.51075	0.1653|0.1653	M|M	0.78637|0.78637	2.42|2.42	0.80722|0.80722	D|D	1|1	.|B	.|0.28378	.|0.209	.|B	.|0.32393	.|0.145	T|T	0.47497|0.47497	-0.9113|-0.9113	5|10	.|0.37606	.|T	.|0.19	-9.1946|-9.1946	8.8794|8.8794	0.35365|0.35365	0.0:0.5889:0.0:0.4111|0.0:0.5889:0.0:0.4111	.|.	.|579	.|Q96T51	.|RUFY1_HUMAN	G|V	256|579;471;471;181	.|ENSP00000325594:L579V;ENSP00000390025:L471V;ENSP00000377087:L471V	.|ENSP00000325594:L579V	A|L	+|+	2|1	0|2	RUFY1|RUFY1	178958402|178958402	0.998000|0.998000	0.40836|0.40836	0.678000|0.678000	0.29963|0.29963	0.139000|0.139000	0.21198|0.21198	0.580000|0.580000	0.23803|0.23803	0.516000|0.516000	0.28340|0.28340	0.561000|0.561000	0.74099|0.74099	GCT|CTG	-	NULL		0.527	RUFY1-001	KNOWN	basic|CCDS	protein_coding	RUFY1	protein_coding	OTTHUMT00000253505.2	C	NM_001040451		178958402	+1	no_errors	NM_025158.1	genbank	human	validated	54_36p	missense	SNP	1.000	G
HIVEP1	3096	genome.wustl.edu	37	6	12122529	12122529	+	Missense_Mutation	SNP	T	T	C			TCGA-AB-3001-03A-01D-0739-09	TCGA-AB-3001-11A-01D-0739-09	T	T	T	C	T	T	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	1ab338ac-7a1e-4796-9464-d0e3218050ea	89734d2a-e63f-4255-8f4a-223187fa0daf	g.chr6:12122529T>C	ENST00000379388.2	+	4	2833	c.2501T>C	c.(2500-2502)tTa>tCa	p.L834S		NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	834					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L834S(1)		NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				CTTGACTGTTTACCTATCACA	0.418																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	6											151.0	140.0	143.0					6																	12122529		1894	4128	6022	12230515	SO:0001583	missense	0			J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"""Zinc fingers, C2H2-type"""	4920	protein-coding gene	gene with protein product		194540	"""human immunodeficiency virus type I enhancer-binding protein 1"", ""zinc finger protein 40"""	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.2501T>C	6.37:g.12122529T>C	ENSP00000368698:p.Leu834Ser	Somatic	1407	0.21	3		1	66.67	2	WXS	Illumina HiSeq	Phase_IV	12230515	233	31.67	108	B2RTU3|Q14122|Q5MPB1|Q5VW60	Missense_Mutation	SNP	HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers	p.L834S	ENST00000379388.2	37	c.2501	CCDS43426.1	6	.	.	.	.	.	.	.	.	.	.	T	18.26	3.585644	0.66105	.	.	ENSG00000095951	ENST00000379388	T	0.11277	2.79	6.01	6.01	0.97437	.	0.000000	0.29133	N	0.013043	T	0.18341	0.0440	L	0.47190	1.495	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.01036	-1.1473	9	.	.	.	-16.096	16.5285	0.84344	0.0:0.0:0.0:1.0	.	834	P15822	ZEP1_HUMAN	S	834	ENSP00000368698:L834S	.	L	+	2	0	HIVEP1	12230515	1.000000	0.71417	0.750000	0.31169	0.992000	0.81027	8.040000	0.89188	2.307000	0.77673	0.528000	0.53228	TTA	-	NULL		0.418	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HIVEP1	protein_coding	OTTHUMT00000039870.2	T	NM_002114		12230515	+1	no_errors	NM_002114.2	genbank	human	validated	54_36p	missense	SNP	0.997	C
WAC	51322	genome.wustl.edu	37	10	28905292	28905292	+	Splice_Site	SNP	G	G	A			TCGA-AB-3001-03A-01D-0739-09	TCGA-AB-3001-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	1ab338ac-7a1e-4796-9464-d0e3218050ea	89734d2a-e63f-4255-8f4a-223187fa0daf	g.chr10:28905292G>A	ENST00000354911.4	+	12	1907		c.e12+1		WAC_ENST00000375664.4_Splice_Site|WAC_ENST00000375646.1_Splice_Site|WAC_ENST00000347934.4_Splice_Site	NM_016628.4	NP_057712.2	Q9BTA9	WAC_HUMAN	WW domain containing adaptor with coiled-coil						cellular response to DNA damage stimulus (GO:0006974)|G1 DNA damage checkpoint (GO:0044783)|histone H2B conserved C-terminal lysine ubiquitination (GO:0071894)|histone monoubiquitination (GO:0010390)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of macroautophagy (GO:0016239)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	chromatin binding (GO:0003682)|RNA polymerase II core binding (GO:0000993)	p.?(1)		NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|urinary_tract(1)	32						AGAGAAGCAGGTATGTTATGT	0.398																																						dbGAP											1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	10											69.0	60.0	63.0					10																	28905292		2203	4300	6503	28945298	SO:0001630	splice_region_variant	0			AK055852	CCDS7159.1, CCDS7160.1, CCDS7161.1	10p12.1	2007-05-17	2003-03-19		ENSG00000095787	ENSG00000095787			17327	protein-coding gene	gene with protein product		615049	"""WW domain-containing adaptor with coiled coil"""			11827461	Standard	NR_024557		Approved	Wwp4, FLJ31290, PRO1741, BM-016, MGC10753	uc001iuf.3	Q9BTA9	OTTHUMG00000017872	ENST00000354911.4:c.1746+1G>A	10.37:g.28905292G>A		Somatic	746	0.53	4		6	14.29	1	WXS	Illumina HiSeq	Phase_IV	28945298	685	30.67	303	A8K2A9|C9JBT9|D3DRW5|D3DRW6|D3DRW7|Q53EN9|Q5JU75|Q5JU77|Q5VXK0|Q5VXK2|Q8TCK1|Q96DP3|Q96FW6|Q96JI3	Splice_Site	SNP	-	e12+1	ENST00000354911.4	37	c.1746+1	CCDS7159.1	10	.	.	.	.	.	.	.	.	.	.	G	20.4	3.979753	0.74360	.	.	ENSG00000095787	ENST00000375664;ENST00000375646;ENST00000347934;ENST00000354911	.	.	.	5.12	5.12	0.69794	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.9354	0.92583	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	WAC	28945298	1.000000	0.71417	0.996000	0.52242	0.861000	0.49209	9.752000	0.98900	2.559000	0.86315	0.655000	0.94253	.	-	-		0.398	WAC-017	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	WAC	protein_coding	OTTHUMT00000047371.1	G	NM_100264	Intron	28945298	+1	no_errors	NM_016628.3	genbank	human	reviewed	54_36p	splice_site	SNP	1.000	A
CCDC186	55088	genome.wustl.edu	37	10	115904370	115904370	+	Silent	SNP	G	G	A			TCGA-AB-3001-03A-01D-0739-09	TCGA-AB-3001-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	1ab338ac-7a1e-4796-9464-d0e3218050ea	89734d2a-e63f-4255-8f4a-223187fa0daf	g.chr10:115904370G>A	ENST00000369287.3	-	6	1373	c.1107C>T	c.(1105-1107)ggC>ggT	p.G369G	C10orf118_ENST00000543782.1_5'Flank	NM_018017.2	NP_060487.2	Q7Z3E2	CC186_HUMAN		369								p.G369G(1)		NS(1)|autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(9)|ovary(2)	24		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0161)|all cancers(201;0.0397)		TAGTCGTTTCGCCTTCCTAAA	0.303																																						dbGAP											1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	10											127.0	117.0	121.0					10																	115904370		2202	4298	6500	115894360	SO:0001819	synonymous_variant	0																														ENST00000369287.3:c.1107C>T	10.37:g.115904370G>A		Somatic	643	1.23	8		8	33.33	4	WXS	Illumina HiSeq	Phase_IV	115894360	92	18.58	21	Q2M2V6|Q3ZB81|Q6NS91|Q7RTP1|Q8N117|Q8N3G3|Q8N6C2|Q9NWA3	Silent	SNP	superfamily_Prefoldin	p.G369	ENST00000369287.3	37	c.1107	CCDS7587.1	10																																																																																			-	NULL		0.303	C10orf118-006	KNOWN	basic|appris_principal|CCDS	protein_coding	C10orf118	protein_coding	OTTHUMT00000050455.1	G			115894360	-1	no_errors	NM_018017.2	genbank	human	validated	54_36p	silent	SNP	0.950	A
LUZP2	338645	genome.wustl.edu	37	11	24759849	24759849	+	Splice_Site	SNP	G	G	C			TCGA-AB-3001-03A-01D-0739-09	TCGA-AB-3001-11A-01D-0739-09	G	G	G	C	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	1ab338ac-7a1e-4796-9464-d0e3218050ea	89734d2a-e63f-4255-8f4a-223187fa0daf	g.chr11:24759849G>C	ENST00000336930.6	+	4	399		c.e4+1		LUZP2_ENST00000531187.1_Splice_Site|LUZP2_ENST00000533227.1_Splice_Site			Q86TE4	LUZP2_HUMAN	leucine zipper protein 2							extracellular region (GO:0005576)		p.?(2)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(11)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	32						CCAGGCTACTGTAAGTGTGTT	0.368																																						dbGAP											2	Unknown(2)	haematopoietic_and_lymphoid_tissue(1)|lung(1)	11											81.0	83.0	83.0					11																	24759849		2203	4300	6503	24716425	SO:0001630	splice_region_variant	0			AL832641	CCDS31446.1, CCDS58128.1	11p14.3	2005-09-18			ENSG00000187398	ENSG00000187398			23206	protein-coding gene	gene with protein product		608178				12856284	Standard	NM_001009909		Approved		uc001mqs.3	Q86TE4	OTTHUMG00000166109	ENST00000336930.6:c.333+1G>C	11.37:g.24759849G>C		Somatic	1289	0.39	5		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	24716425	1226	17.26	256	A2RUB8|E9PN53|Q6UXE7|Q6ZS65	Splice_Site	SNP	-	e4+1	ENST00000336930.6	37	c.333+1	CCDS31446.1	11	.	.	.	.	.	.	.	.	.	.	G	21.3	4.128856	0.77549	.	.	ENSG00000187398	ENST00000336930;ENST00000529015;ENST00000533227	.	.	.	5.77	5.77	0.91146	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.4594	0.87616	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	LUZP2	24716425	1.000000	0.71417	1.000000	0.80357	0.878000	0.50629	7.689000	0.84165	2.725000	0.93324	0.655000	0.94253	.	-	-		0.368	LUZP2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	LUZP2	protein_coding	OTTHUMT00000387861.1	G	NM_001009909	Intron	24716425	+1	no_errors	NM_001009909.2	genbank	human	validated	54_36p	splice_site	SNP	0.994	C
LRIG3	121227	genome.wustl.edu	37	12	59279661	59279661	+	Missense_Mutation	SNP	C	C	T	rs371085189		TCGA-AB-3001-03A-01D-0739-09	TCGA-AB-3001-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	1ab338ac-7a1e-4796-9464-d0e3218050ea	89734d2a-e63f-4255-8f4a-223187fa0daf	g.chr12:59279661C>T	ENST00000320743.3	-	10	1482	c.1196G>A	c.(1195-1197)cGt>cAt	p.R399H	LRIG3_ENST00000379141.4_Missense_Mutation_p.R339H	NM_153377.4	NP_700356.2	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like domains 3	399					otolith morphogenesis (GO:0032474)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R399H(1)	LRIG3/ROS1(2)	breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(12)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48			GBM - Glioblastoma multiforme(1;1.17e-18)			AGTAATAGAACGGATCCGATT	0.373			T	ROS1	NSCLC																																	dbGAP		Dom	yes		12	12q14.1	121227	leucine-rich repeats and immunoglobulin-like domains 3		E	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	12						C	HIS/ARG,HIS/ARG	0,4406		0,0,2203	159.0	178.0	172.0		1016,1196	5.9	1.0	12		172	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	LRIG3	NM_001136051.1,NM_153377.3	29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	339/1060,399/1120	59279661	1,13005	2203	4300	6503	57565928	SO:0001583	missense	0			AY505340	CCDS8960.1, CCDS44933.1	12q13.2	2013-01-11				ENSG00000139263		"""Immunoglobulin superfamily / I-set domain containing"""	30991	protein-coding gene	gene with protein product		608870					Standard	NM_153377		Approved	FLJ90440, KIAA3016	uc001sqr.4	Q6UXM1	OTTHUMG00000169940	ENST00000320743.3:c.1196G>A	12.37:g.59279661C>T	ENSP00000326759:p.Arg399His	Somatic	798	0.75	6		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	57565928	198	29.79	84	Q6UXL7|Q8NC72	Missense_Mutation	SNP	HMMPfam_LRRCT,HMMSmart_SM00082,HMMPfam_LRR_1,HMMSmart_SM00369,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_I-set,HMMSmart_SM00365,superfamily_Immunoglobulin,superfamily_RNI-like	p.R399H	ENST00000320743.3	37	c.1196	CCDS8960.1	12	.	.	.	.	.	.	.	.	.	.	C	22.6	4.316532	0.81469	0.0	1.16E-4	ENSG00000139263	ENST00000379141;ENST00000320743	T;T	0.59224	0.28;0.28	5.93	5.93	0.95920	.	0.000000	0.30383	N	0.009750	T	0.66597	0.2805	L	0.37561	1.115	0.46113	D	0.998879	P;D	0.89917	0.718;1.0	B;D	0.71870	0.281;0.975	T	0.62483	-0.6845	9	.	.	.	.	15.7776	0.78236	0.0:0.8645:0.1355:0.0	.	339;399	Q6UXM1-2;Q6UXM1	.;LRIG3_HUMAN	H	339;399	ENSP00000368436:R339H;ENSP00000326759:R399H	.	R	-	2	0	LRIG3	57565928	0.997000	0.39634	0.999000	0.59377	0.504000	0.33889	1.898000	0.39809	2.805000	0.96524	0.655000	0.94253	CGT	-	HMMPfam_LRR_1,HMMSmart_SM00369,HMMSmart_SM00365,superfamily_RNI-like		0.373	LRIG3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	LRIG3	protein_coding	OTTHUMT00000406623.1	C	NM_153377		57565928	-1	no_errors	NM_153377.1	genbank	human	provisional	54_36p	missense	SNP	0.998	T
PRPF8	10594	genome.wustl.edu	37	17	1561947	1561947	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-3001-03A-01D-0739-09	TCGA-AB-3001-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	1ab338ac-7a1e-4796-9464-d0e3218050ea	89734d2a-e63f-4255-8f4a-223187fa0daf	g.chr17:1561947C>T	ENST00000572621.1	-	32	5514	c.5249G>A	c.(5248-5250)gGg>gAg	p.G1750E	PRPF8_ENST00000304992.6_Missense_Mutation_p.G1750E			Q6P2Q9	PRP8_HUMAN	pre-mRNA processing factor 8	1750	Involved in interaction with pre-mRNA 5' splice site.|Restriction endonuclease homology domain.				gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	poly(A) RNA binding (GO:0044822)|U5 snRNA binding (GO:0030623)|U6 snRNA binding (GO:0017070)	p.G1750E(1)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(13)|lung(24)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	77				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)		GAGCTGTAGCCCCTTGCGGAT	0.498																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	17											145.0	128.0	134.0					17																	1561947		2203	4300	6503	1508697	SO:0001583	missense	0			AB007510	CCDS11010.1	17p13.3	2013-07-16	2013-06-10		ENSG00000174231	ENSG00000174231			17340	protein-coding gene	gene with protein product		607300	"""PRP8 pre-mRNA processing factor 8 homolog (yeast)"", ""PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae)"""	RP13		11468273, 10411133	Standard	NM_006445		Approved	PRPC8, Prp8, hPrp8, SNRNP220	uc002fte.3	Q6P2Q9	OTTHUMG00000090553	ENST00000572621.1:c.5249G>A	17.37:g.1561947C>T	ENSP00000460348:p.Gly1750Glu	Somatic	1403	0.43	6		294	25.76	102	WXS	Illumina HiSeq	Phase_IV	1508697	394	19.43	95	O14547|O75965	Missense_Mutation	SNP	HMMPfam_Mov34,HMMSmart_SM00232,HMMPfam_PRO8NT,HMMPfam_PROCN,HMMPfam_PROCT,HMMPfam_U6-snRNA_bdg,HMMPfam_U5_2-snRNA_bdg,HMMPfam_RRM_4	p.G1750E	ENST00000572621.1	37	c.5249	CCDS11010.1	17	.	.	.	.	.	.	.	.	.	.	c	20.9	4.059972	0.76074	.	.	ENSG00000174231	ENST00000304992;ENST00000540177	T	0.80304	-1.36	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	D	0.90800	0.7111	M	0.92122	3.275	0.80722	D	1	P	0.46277	0.875	P	0.53689	0.732	D	0.91604	0.5297	10	0.59425	D	0.04	-16.9033	20.2946	0.98546	0.0:1.0:0.0:0.0	.	1750	Q6P2Q9	PRP8_HUMAN	E	1750;275	ENSP00000304350:G1750E	ENSP00000304350:G1750E	G	-	2	0	PRPF8	1508697	1.000000	0.71417	0.996000	0.52242	0.234000	0.25298	7.818000	0.86416	2.804000	0.96469	0.462000	0.41574	GGG	-	NULL		0.498	PRPF8-002	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	PRPF8	protein_coding	OTTHUMT00000438412.2	C			1508697	-1	no_errors	NM_006445.3	genbank	human	reviewed	54_36p	missense	SNP	0.997	T
