#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_NormalRefReads_WU	i_NormalVAF_WU	i_NormalVarReads_WU	i_ORegAnno_bin	i_RNARefReads_WU	i_RNAVAF_WU	i_RNAVarReads_WU	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
EPHA10	284656	genome.wustl.edu	37	1	38227576	38227576	+	Silent	SNP	G	G	A			TCGA-AB-2827-03B-01W-0728-08	TCGA-AB-2827-11B-01W-0728-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	1a21f77d-2ab7-4b5a-b91a-2f561a459dd1	bf713301-022e-480e-8c3a-5c04981f30de	g.chr1:38227576G>A	ENST00000373048.4	-	3	350	c.351C>T	c.(349-351)ggC>ggT	p.G117G	EPHA10_ENST00000319637.6_Silent_p.G117G|EPHA10_ENST00000427468.2_Silent_p.G117G	NM_001099439.1	NP_001092909.1	Q5JZY3	EPHAA_HUMAN	EPH receptor A10	117	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				ephrin receptor signaling pathway (GO:0048013)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane-ephrin receptor activity (GO:0005005)			NS(2)|breast(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(13)|prostate(3)|skin(8)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				TACCCGCGGCGCCAGGGATGC	0.662																																						dbGAP											0			1											91.0	94.0	93.0					1																	38227576		2203	4300	6503	38000163	SO:0001819	synonymous_variant	0			AK090974	CCDS425.1, CCDS41305.1	1p34.3	2013-02-11			ENSG00000183317	ENSG00000183317		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	19987	protein-coding gene	gene with protein product		611123				12477932	Standard	NM_001099439		Approved	FLJ16103, FLJ33655	uc009vvi.3	Q5JZY3	OTTHUMG00000004325	ENST00000373048.4:c.351C>T	1.37:g.38227576G>A		187	1.06	2		NA	NA	NA	38000163	52	13.11	8	A4FU89|J3KPB5|Q6NW42	Silent	SNP	HMMPfam_Ephrin_lbd,HMMSmart_SM00615,HMMPfam_Pkinase_Tyr,HMMSmart_SM00219,PatternScan_RECEPTOR_TYR_KIN_V_1,PatternScan_RECEPTOR_TYR_KIN_V_2,HMMPfam_SAM_1,HMMSmart_SM00454,HMMSmart_SM00220,HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III,superfamily_Galactose-binding domain-like,superfamily_SAM/Pointed domain,superfamily_Protein kinase-like (PK-like),PatternScan_EGF_2	p.G117	ENST00000373048.4	37	c.351	CCDS41305.1	1																																																																																			-	HMMPfam_Ephrin_lbd,HMMSmart_SM00615,superfamily_Galactose-binding domain-like		0.662	EPHA10-003	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	EPHA10	protein_coding	OTTHUMT00000012497.2	G	NM_173641		38000163	-1	no_errors	NM_001099439.1	genbank	human	validated	54_36p	silent	SNP	0.531	A
SELENBP1	8991	genome.wustl.edu	37	1	151337703	151337703	+	Missense_Mutation	SNP	C	C	T	rs72710112	byFrequency	TCGA-AB-2827-03B-01W-0728-08	TCGA-AB-2827-11B-01W-0728-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	1a21f77d-2ab7-4b5a-b91a-2f561a459dd1	bf713301-022e-480e-8c3a-5c04981f30de	g.chr1:151337703C>T	ENST00000368868.5	-	10	1190	c.1099G>A	c.(1099-1101)Gag>Aag	p.E367K	SELENBP1_ENST00000435071.1_Missense_Mutation_p.E303K|SELENBP1_ENST00000426705.2_Missense_Mutation_p.E409K|SELENBP1_ENST00000473693.1_5'Flank|SELENBP1_ENST00000447402.3_Missense_Mutation_p.E305K	NM_003944.3	NP_003935.2	Q13228	SBP1_HUMAN	selenium binding protein 1	367					protein transport (GO:0015031)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	selenium binding (GO:0008430)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(11)|prostate(1)|urinary_tract(1)	20	Lung SC(34;0.00471)|Ovarian(49;0.00871)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			TTTAGTTCCTCGTCCTCCAGC	0.577													G|||	51	0.0101837	0.0166	0.0086	5008	,	,		20479	0.0		0.0169	False		,,,				2504	0.0061					dbGAP											0			1						G	LYS/GLU	65,4341		0,65,2138	53.0	53.0	53.0		1099	1.5	1.0	1	dbSNP_130	53	104,8496		1,102,4197	yes	missense	SELENBP1	NM_003944.2	56	1,167,6335	TT,TC,CC		1.2093,1.4753,1.2994	benign	367/473	151337703	169,12837	2203	4300	6503	149604327	SO:0001583	missense	0			U29091	CCDS995.1, CCDS58027.1, CCDS60266.1	1q21.3	2014-05-19			ENSG00000143416	ENSG00000143416			10719	protein-coding gene	gene with protein product		604188				9027582	Standard	NM_003944		Approved	hSP56, hSBP, LPSB	uc010pcy.3	Q13228	OTTHUMG00000012498	ENST00000368868.5:c.1099G>A	1.37:g.151337703C>T	ENSP00000357861:p.Glu367Lys	16	5.88	1		NA	NA	NA	149604327	113	44.98	94	A6NML9|A6PVW9|B2RDR3|B4DKP6|B4E1F3|Q49AQ8|Q96GX7	Missense_Mutation	SNP	HMMPfam_SBP56,superfamily_Cyt_cd1_haem_C	p.E367K	ENST00000368868.5	37	c.1099	CCDS995.1	1	30	0.013736263736263736	11	0.022357723577235773	6	0.016574585635359115	0	0.0	13	0.017150395778364115	G	10.74	1.434871	0.25813	0.014753	0.012093	ENSG00000143416	ENST00000368868;ENST00000447402;ENST00000435071	.	.	.	4.59	1.53	0.23141	.	0.335079	0.30850	N	0.008752	T	0.03915	0.0110	N	0.04043	-0.29	0.18873	N	0.999988	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.08055	0.001;0.001;0.001;0.003	T	0.45175	-0.9279	9	0.07482	T	0.82	6.8005	8.4162	0.32672	0.0:0.2361:0.4133:0.3506	.	305;220;303;367	B4E1F3;B4DPI7;Q13228-2;Q13228	.;.;.;SBP1_HUMAN	K	367;305;303	.	ENSP00000357861:E367K	E	-	1	0	SELENBP1	149604327	1.000000	0.71417	0.983000	0.44433	0.471000	0.32888	0.932000	0.28884	0.554000	0.29061	-0.120000	0.15030	GAG	-	HMMPfam_SBP56,superfamily_Cyt_cd1_haem_C		0.577	SELENBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SELENBP1	protein_coding	OTTHUMT00000034904.4	C			149604327	-1	no_errors	NM_003944.2	genbank	human	reviewed	54_36p	missense	SNP	0.978	T
PPIC	5480	genome.wustl.edu	37	5	122361517	122361517	+	Missense_Mutation	SNP	C	C	T	rs143084462	byFrequency	TCGA-AB-2827-03B-01W-0728-08	TCGA-AB-2827-11B-01W-0728-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	1a21f77d-2ab7-4b5a-b91a-2f561a459dd1	bf713301-022e-480e-8c3a-5c04981f30de	g.chr5:122361517C>T	ENST00000306442.4	-	4	587	c.472G>A	c.(472-474)Ggc>Agc	p.G158S		NM_000943.4	NP_000934.1	P45877	PPIC_HUMAN	peptidylprolyl isomerase C (cyclophilin C)	158	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				protein folding (GO:0006457)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	6		all_cancers(142;0.0168)|Prostate(80;0.0322)|Lung NSC(810;0.102)|all_lung(232;0.163)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	OV - Ovarian serous cystadenocarcinoma(64;0.000331)|Epithelial(69;0.000553)|all cancers(49;0.00505)	L-Proline(DB00172)	ACATGTTTGCCGTCCAACCAG	0.438													C|||	6	0.00119808	0.0	0.0043	5008	,	,		19469	0.0		0.003	False		,,,				2504	0.0				Ovarian(99;690 1502 20765 45543 49568)	dbGAP											0			5						C	SER/GLY	12,4394	17.9+/-39.9	0,12,2191	81.0	70.0	74.0		472	5.7	1.0	5	dbSNP_134	74	56,8544	35.3+/-89.8	0,56,4244	yes	missense	PPIC	NM_000943.4	56	0,68,6435	TT,TC,CC		0.6512,0.2724,0.5228	probably-damaging	158/213	122361517	68,12938	2203	4300	6503	122389416	SO:0001583	missense	0			S71018	CCDS4133.1	5q23.2	2008-02-05			ENSG00000168938	ENSG00000168938	5.2.1.8		9256	protein-coding gene	gene with protein product		123842				1383094, 8031755	Standard	NM_000943		Approved	CYPC	uc003kth.3	P45877	OTTHUMG00000128921	ENST00000306442.4:c.472G>A	5.37:g.122361517C>T	ENSP00000303057:p.Gly158Ser	58	9.38	6		NA	NA	NA	122389416	91	35.21	50	A4LBB5	Missense_Mutation	SNP	HMMPfam_Pro_isomerase,PatternScan_CSA_PPIASE_1,superfamily_Cyclophilin-like	p.G158S	ENST00000306442.4	37	c.472	CCDS4133.1	5	5	0.0022893772893772895	0	0.0	3	0.008287292817679558	0	0.0	2	0.002638522427440633	C	35	5.509631	0.96386	0.002724	0.006512	ENSG00000168938	ENST00000306442	T	0.43294	0.95	5.65	5.65	0.86999	Peptidyl-prolyl cis-trans isomerase, cyclophilin-type (4);Cyclophilin-like (1);	0.000000	0.85682	D	0.000000	T	0.64821	0.2633	M	0.87900	2.915	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.72874	-0.4160	10	0.87932	D	0	.	19.9142	0.97043	0.0:1.0:0.0:0.0	.	158	P45877	PPIC_HUMAN	S	158	ENSP00000303057:G158S	ENSP00000303057:G158S	G	-	1	0	PPIC	122389416	1.000000	0.71417	0.998000	0.56505	0.975000	0.68041	4.537000	0.60643	2.941000	0.99782	0.655000	0.94253	GGC	-	HMMPfam_Pro_isomerase,superfamily_Cyclophilin-like		0.438	PPIC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PPIC	protein_coding	OTTHUMT00000250898.2	C	NM_000943		122389416	-1	no_errors	NM_000943.4	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
ATXN7L1	222255	genome.wustl.edu	37	7	105278946	105278946	+	Missense_Mutation	SNP	C	C	G			TCGA-AB-2827-03B-01W-0728-08	TCGA-AB-2827-11B-01W-0728-08	C	C	C	G	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	1a21f77d-2ab7-4b5a-b91a-2f561a459dd1	bf713301-022e-480e-8c3a-5c04981f30de	g.chr7:105278946C>G	ENST00000419735.3	-	7	1101	c.1056G>C	c.(1054-1056)gaG>gaC	p.E352D	ATXN7L1_ENST00000477775.1_Missense_Mutation_p.E228D|ATXN7L1_ENST00000472910.1_5'UTR	NM_020725.1	NP_065776.1	Q9ULK2	AT7L1_HUMAN	ataxin 7-like 1	352										endometrium(1)|large_intestine(4)|lung(5)	10						TCAGGAGATGCTCTTTATCTT	0.522																																						dbGAP											0			7											123.0	107.0	112.0					7																	105278946		692	1591	2283	105066182	SO:0001583	missense	0			AB033044	CCDS34727.1, CCDS47682.1, CCDS47683.1	7q22.1	2007-11-13			ENSG00000146776	ENSG00000146776			22210	protein-coding gene	gene with protein product			"""ataxin 7-like 4"""	ATXN7L4		15115762	Standard	NM_152749		Approved	KIAA1218, MGC33190	uc003vde.2	Q9ULK2	OTTHUMG00000157521	ENST00000419735.3:c.1056G>C	7.37:g.105278946C>G	ENSP00000410759:p.Glu352Asp	21	0.00	0		NA	NA	NA	105066182	99	44.75	81	A4D0Q2|B4DTS1|Q8N2T0	Missense_Mutation	SNP	HMMPfam_SCA7	p.E355D	ENST00000419735.3	37	c.1065	CCDS47682.1	7	.	.	.	.	.	.	.	.	.	.	C	16.03	3.007332	0.54361	.	.	ENSG00000146776	ENST00000419735;ENST00000477775;ENST00000472195	T;T;T	0.16073	2.38;2.37;2.37	5.49	3.69	0.42338	.	0.000000	0.64402	D	0.000006	T	0.21921	0.0528	N	0.22421	0.69	0.80722	D	1	D;B;D	0.58268	0.982;0.244;0.982	D;B;P	0.67548	0.952;0.097;0.622	T	0.03008	-1.1083	10	0.21540	T	0.41	.	9.5849	0.39510	0.0:0.7864:0.0:0.2136	.	136;228;352	A4D0Q3;Q9ULK2-3;Q9ULK2	.;.;AT7L1_HUMAN	D	352;228;228	ENSP00000410759:E352D;ENSP00000418476:E228D;ENSP00000419566:E228D	ENSP00000410759:E352D	E	-	3	2	ATXN7L1	105066182	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.437000	0.44828	0.814000	0.34374	0.655000	0.94253	GAG	-	NULL		0.522	ATXN7L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	ATXN7L1	protein_coding	OTTHUMT00000349037.2	C			105066182	-1	no_start_codon	ENST00000297416	ensembl	human	known	54_36p	missense	SNP	1.000	G
MYC	4609	genome.wustl.edu	37	8	128750684	128750684	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2827-03B-01W-0728-08	TCGA-AB-2827-11B-01W-0728-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	1a21f77d-2ab7-4b5a-b91a-2f561a459dd1	bf713301-022e-480e-8c3a-5c04981f30de	g.chr8:128750684C>T	ENST00000259523.6	+	2	1381	c.176C>T	c.(175-177)cCg>cTg	p.P59L	MYC_ENST00000524013.1_Missense_Mutation_p.P73L|MYC_ENST00000377970.2_Missense_Mutation_p.P74L			P01106	MYC_HUMAN	v-myc avian myelocytomatosis viral oncogene homolog	59			P -> A (in a Burkitt lymphoma sample). {ECO:0000269|PubMed:8220424}.		branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|cell cycle arrest (GO:0007050)|cellular iron ion homeostasis (GO:0006879)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|chromosome organization (GO:0051276)|energy reserve metabolic process (GO:0006112)|fibroblast apoptotic process (GO:0044346)|gene expression (GO:0010467)|MAPK cascade (GO:0000165)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell division (GO:0051782)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of monocyte differentiation (GO:0045656)|negative regulation of stress-activated MAPK cascade (GO:0032873)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|oxygen transport (GO:0015671)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of metanephric cap mesenchymal cell proliferation (GO:0090096)|positive regulation of response to DNA damage stimulus (GO:2001022)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression (GO:0010468)|regulation of telomere maintenance (GO:0032204)|response to drug (GO:0042493)|response to gamma radiation (GO:0010332)|response to growth factor (GO:0070848)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|protein complex binding (GO:0032403)|repressing transcription factor binding (GO:0070491)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|lung(7)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	16	all_cancers(1;6.19e-134)|all_epithelial(1;1.75e-119)|all_lung(1;5.66e-51)|Breast(1;1.08e-22)|all_neural(1;4.45e-21)|Medulloblastoma(1;1.88e-20)|Colorectal(1;1.92e-09)|Lung SC(1;4.52e-07)|Ovarian(5;0.000122)|Esophageal squamous(12;0.000995)|Renal(1;0.0921)|Hepatocellular(40;0.108)|Myeloproliferative disorder(2;0.135)|Melanoma(291;0.185)	Myeloproliferative disorder(644;0.0255)|Ovarian(118;0.0654)|Breast(495;0.212)|Acute lymphoblastic leukemia(644;0.22)	Epithelial(1;1.63e-94)|all cancers(1;5.82e-87)|OV - Ovarian serous cystadenocarcinoma(1;2.12e-71)|BRCA - Breast invasive adenocarcinoma(1;4.3e-14)|Lung(2;0.000381)|Colorectal(2;0.0102)|LUAD - Lung adenocarcinoma(14;0.0172)|READ - Rectum adenocarcinoma(2;0.0723)|LUSC - Lung squamous cell carcinoma(258;0.151)	KIRC - Kidney renal clear cell carcinoma(542;0.248)	Nadroparin(DB08813)	CTGCCCACCCCGCCCCTGTCC	0.677		3	"""A, T"""	"""IGK@, BCL5, BCL7A , BTG1, TRA@, IGH@"""	"""Burkitt lymphoma,  amplified in other cancers, B-CLL"""						OREG0018982	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										dbGAP		Dom	yes		8	8q24.12-q24.13	4609	v-myc myelocytomatosis viral oncogene homolog (avian)		"""L, E"""	0			8											16.0	19.0	18.0					8																	128750684		2203	4299	6502	128819866	SO:0001583	missense	0				CCDS6359.2	8q24	2013-07-09	2013-07-09		ENSG00000136997	ENSG00000136997		"""Basic helix-loop-helix proteins"""	7553	protein-coding gene	gene with protein product		190080					Standard	NM_002467		Approved	c-Myc, bHLHe39, MYCC	uc003ysi.3	P01106	OTTHUMG00000128475	ENST00000259523.6:c.176C>T	8.37:g.128750684C>T	ENSP00000259523:p.Pro59Leu	80	0.00	0	1567	NA	NA	NA	128819866	56	16.18	11	A8WFE7|P01107|Q14026	Missense_Mutation	SNP	HMMPfam_HLH,HMMSmart_SM00353,HMMPfam_Myc-LZ,superfamily_HLH helix-loop-helix DNA-binding domain,HMMPfam_Myc_N	p.P74L	ENST00000259523.6	37	c.221		8	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.09|16.09	3.025619|3.025619	0.54683|0.54683	.|.	.|.	ENSG00000136997|ENSG00000136997	ENST00000259523;ENST00000517291;ENST00000377970;ENST00000524013;ENST00000454617|ENST00000520751	T;T;T;T|.	0.40756|.	1.02;1.02;1.02;1.02|.	4.78|4.78	4.78|4.78	0.61160|0.61160	Transcription regulator Myc, N-terminal (1);|.	0.049059|.	0.85682|.	D|.	0.000000|.	D|D	0.83124|0.83124	0.5186|0.5186	M|M	0.87456|0.87456	2.885|2.885	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.87578|.	0.998|.	D|D	0.86425|0.86425	0.1757|0.1757	10|6	0.87932|0.87932	D|D	0|0	-28.4733|-28.4733	17.3275|17.3275	0.87253|0.87253	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	59|.	P01106|.	MYC_HUMAN|.	L|C	59;73;74;73;40|48	ENSP00000259523:P59L;ENSP00000429441:P73L;ENSP00000367207:P74L;ENSP00000430235:P73L|.	ENSP00000259523:P59L|ENSP00000430226:R48C	P|R	+|+	2|1	0|0	MYC|MYC	128819866|128819866	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	7.536000|7.536000	0.82023|0.82023	2.654000|2.654000	0.90174|0.90174	0.561000|0.561000	0.74099|0.74099	CCG|CGC	-	HMMPfam_Myc_N		0.677	MYC-002	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	MYC	protein_coding	OTTHUMT00000250278.1	C			128819866	+1	no_errors	NM_002467.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
KANK1	23189	genome.wustl.edu	37	9	711981	711981	+	Silent	SNP	C	C	G			TCGA-AB-2827-03B-01W-0728-08	TCGA-AB-2827-11B-01W-0728-08	C	C	C	G	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	1a21f77d-2ab7-4b5a-b91a-2f561a459dd1	bf713301-022e-480e-8c3a-5c04981f30de	g.chr9:711981C>G	ENST00000382303.1	+	7	1867	c.1215C>G	c.(1213-1215)gcC>gcG	p.A405A	KANK1_ENST00000382293.3_Silent_p.A247A|KANK1_ENST00000382297.2_Silent_p.A405A|KANK1_ENST00000489369.1_3'UTR	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	405	Interaction with KIF21A.				negative regulation of actin filament polymerization (GO:0030837)|negative regulation of cell migration (GO:0030336)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of lamellipodium morphogenesis (GO:2000393)|negative regulation of neuron projection development (GO:0010977)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of wound healing (GO:0090303)|regulation of establishment of cell polarity (GO:2000114)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	beta-catenin binding (GO:0008013)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|stomach(4)|upper_aerodigestive_tract(1)	43		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)		CTGTGGGTGCCGAGGAGAACA	0.562																																						dbGAP											0			9											94.0	73.0	80.0					9																	711981		2203	4300	6503	701981	SO:0001819	synonymous_variant	0			AL833161	CCDS6441.1, CCDS34976.1	9p24.3	2013-01-10	2008-01-29	2008-01-29	ENSG00000107104	ENSG00000107104		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	19309	protein-coding gene	gene with protein product		607704	"""ankyrin repeat domain 15"""	ANKRD15		12133830, 17996375, 19554261	Standard	NM_015158		Approved	KIAA0172, KANK	uc003zgn.2	Q14678	OTTHUMG00000019434	ENST00000382303.1:c.1215C>G	9.37:g.711981C>G		48	0.00	0		NA	NA	NA	701981	97	18.55	23	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Silent	SNP	HMMPfam_Ank,HMMSmart_ANK,superfamily_ANK	p.A405	ENST00000382303.1	37	c.1215	CCDS34976.1	9																																																																																			-	superfamily_ANK		0.562	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KANK1	protein_coding	OTTHUMT00000051484.2	C	NM_015158		701981	+1	no_errors	NM_015158.2	genbank	human	reviewed	54_36p	silent	SNP	0.883	G
TMCO3	55002	genome.wustl.edu	37	13	114193794	114193794	+	Silent	SNP	C	C	T			TCGA-AB-2827-03B-01W-0728-08	TCGA-AB-2827-11B-01W-0728-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	1a21f77d-2ab7-4b5a-b91a-2f561a459dd1	bf713301-022e-480e-8c3a-5c04981f30de	g.chr13:114193794C>T	ENST00000434316.2	+	10	2021	c.1662C>T	c.(1660-1662)ttC>ttT	p.F554F	TMCO3_ENST00000375391.1_Intron	NM_017905.4	NP_060375.4	Q6UWJ1	TMCO3_HUMAN	transmembrane and coiled-coil domains 3	554						integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)			NS(1)|endometrium(4)|large_intestine(9)|liver(1)|lung(8)|prostate(1)|stomach(1)	25	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0145)|all_epithelial(44;0.00286)|all_lung(25;0.0273)|Breast(118;0.0411)|Lung NSC(25;0.0983)	all cancers(43;0.0317)			TCCGCGACTTCCTGGCCATCG	0.522																																						dbGAP											0			13											83.0	80.0	81.0					13																	114193794		2203	4300	6503	113241795	SO:0001819	synonymous_variant	0			BC012564	CCDS9537.1	13q34	2008-02-05	2005-07-22	2005-07-22	ENSG00000150403	ENSG00000150403			20329	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 11"""	C13orf11			Standard	NM_017905		Approved	FLJ20623	uc001vtu.4	Q6UWJ1	OTTHUMG00000017389	ENST00000434316.2:c.1662C>T	13.37:g.114193794C>T		121	0.00	0		NA	NA	NA	113241795	127	39.44	84	Q5JSB1|Q6NUN1|Q8NG29|Q8TCI6|Q96EA6|Q9NWT2	Silent	SNP	HMMPfam_Na_H_Exchanger	p.F554	ENST00000434316.2	37	c.1662	CCDS9537.1	13																																																																																			-	HMMPfam_Na_H_Exchanger		0.522	TMCO3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	TMCO3	protein_coding	OTTHUMT00000045931.3	C	NM_017905		113241795	+1	no_errors	NM_017905.4	genbank	human	validated	54_36p	silent	SNP	0.996	T
SPESP1	246777	genome.wustl.edu	37	15	69238661	69238661	+	Missense_Mutation	SNP	G	G	A	rs371688614		TCGA-AB-2827-03B-01W-0728-08	TCGA-AB-2827-11B-01W-0728-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	1a21f77d-2ab7-4b5a-b91a-2f561a459dd1	bf713301-022e-480e-8c3a-5c04981f30de	g.chr15:69238661G>A	ENST00000310673.3	+	2	942	c.788G>A	c.(787-789)cGa>cAa	p.R263Q	NOX5_ENST00000455873.3_Intron|RP11-809H16.2_ENST00000557966.1_RNA|NOX5_ENST00000260364.5_Intron|NOX5_ENST00000448182.3_Intron	NM_145658.3	NP_663633.1	Q6UW49	SPESP_HUMAN	sperm equatorial segment protein 1	263				R -> P (in Ref. 1; AAM69364). {ECO:0000305}.	acrosome reaction (GO:0007340)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organismal development (GO:0007275)	acrosomal vesicle (GO:0001669)				breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(11)|prostate(1)|skin(1)|urinary_tract(1)	19						CACCTAAAACGAAGCCTTGCT	0.373																																						dbGAP											0			15						G	GLN/ARG,	0,4400		0,0,2200	59.0	60.0	60.0		788,	2.2	0.7	15		60	1,8595	1.2+/-3.3	0,1,4297	no	missense,intron	NOX5,SPESP1	NM_145658.3,NM_001184780.1	43,	0,1,6497	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,	263/351,	69238661	1,12995	2200	4298	6498	67025715	SO:0001583	missense	0			AF275321	CCDS10230.1	15q22.31	2011-04-15				ENSG00000258484			15570	protein-coding gene	gene with protein product		609399				12773409	Standard	NM_145658		Approved	SP-ESP	uc002arn.2	Q6UW49		ENST00000310673.3:c.788G>A	15.37:g.69238661G>A	ENSP00000312284:p.Arg263Gln	6	0.00	0		NA	NA	NA	67025715	134	20.00	34	Q8NG22|Q8WVH8	Missense_Mutation	SNP	NULL	p.R263Q	ENST00000310673.3	37	c.788	CCDS10230.1	15	.	.	.	.	.	.	.	.	.	.	G	14.67	2.606177	0.46527	0.0	1.16E-4	ENSG00000258484	ENST00000310673	T	0.24723	1.84	5.28	2.24	0.28232	.	0.225081	0.22654	N	0.057288	T	0.17408	0.0418	L	0.34521	1.04	0.22787	N	0.99873	D	0.55172	0.97	B	0.43754	0.43	T	0.10917	-1.0609	10	0.59425	D	0.04	-5.4787	4.5682	0.12196	0.1953:0.1834:0.6212:0.0	.	263	Q6UW49	SPESP_HUMAN	Q	263	ENSP00000312284:R263Q	ENSP00000312284:R263Q	R	+	2	0	SPESP1	67025715	0.960000	0.32886	0.710000	0.30468	0.163000	0.22366	1.605000	0.36815	1.366000	0.46076	0.655000	0.94253	CGA	-	NULL		0.373	SPESP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SPESP1	protein_coding	OTTHUMT00000257125.1	G	NM_145658		67025715	+1	no_errors	NM_145658.2	genbank	human	provisional	54_36p	missense	SNP	0.090	A
FAM65A	79567	genome.wustl.edu	37	16	67573989	67573989	+	Missense_Mutation	SNP	C	C	T	rs374336975		TCGA-AB-2827-03B-01W-0728-08	TCGA-AB-2827-11B-01W-0728-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	1a21f77d-2ab7-4b5a-b91a-2f561a459dd1	bf713301-022e-480e-8c3a-5c04981f30de	g.chr16:67573989C>T	ENST00000379312.3	+	7	581	c.460C>T	c.(460-462)Cgg>Tgg	p.R154W	FAM65A_ENST00000540839.3_Missense_Mutation_p.R170W|CTD-2012K14.2_ENST00000567122.1_RNA|FAM65A_ENST00000428437.2_Missense_Mutation_p.R164W|FAM65A_ENST00000042381.4_Missense_Mutation_p.R150W|CTD-2012K14.3_ENST00000563083.1_RNA|FAM65A_ENST00000422602.2_Missense_Mutation_p.R170W|FAM65A_ENST00000566522.1_3'UTR|CTD-2012K14.4_ENST00000564717.1_RNA	NM_001193522.1|NM_024519.3	NP_001180451.1|NP_078795.2	Q6ZS17	FA65A_HUMAN	family with sequence similarity 65, member A	154						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(12)|lung(12)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	39		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0474)|Epithelial(162;0.117)		CTGTGTCCAGCGGCGTCTCCG	0.627																																						dbGAP											0			16						C	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	0,4396		0,0,2198	112.0	109.0	110.0		460,508,490,448	4.2	1.0	16		110	3,8597	3.0+/-9.4	0,3,4297	no	missense,missense,missense,missense	FAM65A	NM_001193522.1,NM_001193523.1,NM_001193524.1,NM_024519.3	101,101,101,101	0,3,6495	TT,TC,CC		0.0349,0.0,0.0231	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	154/1224,170/1240,164/1234,150/1220	67573989	3,12993	2198	4300	6498	66131490	SO:0001583	missense	0			AK127792	CCDS10840.1, CCDS54026.1, CCDS54027.1, CCDS54028.1	16q22.1	2008-02-05			ENSG00000039523	ENSG00000039523			25836	protein-coding gene	gene with protein product						11572484	Standard	NM_001193522		Approved	FLJ13725	uc010vjp.2	Q6ZS17	OTTHUMG00000137536	ENST00000379312.3:c.460C>T	16.37:g.67573989C>T	ENSP00000368614:p.Arg154Trp	99	6.60	7		NA	NA	NA	66131490	192	46.45	170	B4DEQ9|B4DIM2|E9PBS3|Q4G0A4|Q7Z5R7|Q8NDA4|Q96J39|Q96PV8|Q9H8D9	Missense_Mutation	SNP	superfamily_ARM-type_fold	p.R150W	ENST00000379312.3	37	c.448	CCDS54028.1	16	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.3|25.3	4.623546|4.623546	0.87460|0.87460	0.0|0.0	3.49E-4|3.49E-4	ENSG00000039523|ENSG00000039523	ENST00000428437|ENST00000379312;ENST00000042381;ENST00000422602;ENST00000540839	.|T;T;T	.|0.02085	.|4.46;4.46;4.46	5.22|5.22	4.24|4.24	0.50183|0.50183	.|.	.|0.112822	.|0.64402	.|D	.|0.000017	T|T	0.08358|0.08358	0.0208|0.0208	L|L	0.43152|0.43152	1.355|1.355	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0	.|D;D;D;D	.|0.85130	.|0.997;0.997;0.997;0.997	T|T	0.13415|0.13415	-1.0510|-1.0510	5|10	.|0.51188	.|T	.|0.08	-7.4684|-7.4684	14.8567|14.8567	0.70344|0.70344	0.1449:0.8551:0.0:0.0|0.1449:0.8551:0.0:0.0	.|.	.|164;170;154;170	.|B4DIM2;E9PBS3;Q6ZS17;B4DEQ9	.|.;.;FA65A_HUMAN;.	V|W	144|154;150;170;164	.|ENSP00000368614:R154W;ENSP00000042381:R150W;ENSP00000400099:R170W	.|ENSP00000042381:R150W	A|R	+|+	2|1	0|2	FAM65A|FAM65A	66131490|66131490	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	1.202000|1.202000	0.32271|0.32271	1.142000|1.142000	0.42291|0.42291	0.484000|0.484000	0.47621|0.47621	GCG|CGG	-	NULL		0.627	FAM65A-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	FAM65A	protein_coding	OTTHUMT00000268866.3	C	NM_024519		66131490	+1	no_errors	NM_024519.2	genbank	human	validated	54_36p	missense	SNP	1.000	T
RNF157	114804	genome.wustl.edu	37	17	74158051	74158051	+	Silent	SNP	G	G	A			TCGA-AB-2827-03B-01W-0728-08	TCGA-AB-2827-11B-01W-0728-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	1a21f77d-2ab7-4b5a-b91a-2f561a459dd1	bf713301-022e-480e-8c3a-5c04981f30de	g.chr17:74158051G>A	ENST00000269391.6	-	10	957	c.825C>T	c.(823-825)gcC>gcT	p.A275A	RNF157_ENST00000319945.6_Silent_p.A275A	NM_052916.2	NP_443148.1	Q96PX1	RN157_HUMAN	ring finger protein 157	275							zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	25			LUSC - Lung squamous cell carcinoma(166;0.187)			CCACACACTCGGCACTGTTAT	0.547																																					GBM(186;507 2120 27388 27773 52994)	dbGAP											0			17											134.0	98.0	110.0					17																	74158051		2203	4300	6503	71669646	SO:0001819	synonymous_variant	0			AK091467	CCDS32740.1	17q25.3	2004-02-27			ENSG00000141576	ENSG00000141576		"""RING-type (C3HC4) zinc fingers"""	29402	protein-coding gene	gene with protein product						11572484	Standard	NM_052916		Approved	KIAA1917	uc002jqz.3	Q96PX1	OTTHUMG00000132627	ENST00000269391.6:c.825C>T	17.37:g.74158051G>A		38	0.00	0		NA	NA	NA	71669646	86	29.27	36	Q8NB72|Q96N56	Silent	SNP	HMMSmart_SM00184,HMMPfam_zf-C3HC4,superfamily_RING/U-box	p.A275	ENST00000269391.6	37	c.825	CCDS32740.1	17																																																																																			-	superfamily_RING/U-box		0.547	RNF157-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RNF157	protein_coding	OTTHUMT00000255874.2	G	XM_290732		71669646	-1	no_errors	NM_052916.2	genbank	human	validated	54_36p	silent	SNP	0.627	A
USP36	57602	genome.wustl.edu	37	17	76825031	76825031	+	Silent	SNP	G	G	A			TCGA-AB-2827-03B-01W-0728-08	TCGA-AB-2827-11B-01W-0728-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	1a21f77d-2ab7-4b5a-b91a-2f561a459dd1	bf713301-022e-480e-8c3a-5c04981f30de	g.chr17:76825031G>A	ENST00000542802.3	-	5	977	c.534C>T	c.(532-534)ttC>ttT	p.F178F	USP36_ENST00000589424.1_Silent_p.F178F|USP36_ENST00000312010.6_Silent_p.F178F|USP36_ENST00000590546.2_Silent_p.F178F			Q9P275	UBP36_HUMAN	ubiquitin specific peptidase 36	178	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|ubiquitin-specific protease activity (GO:0004843)	p.F178F(2)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	34			BRCA - Breast invasive adenocarcinoma(99;0.000842)|OV - Ovarian serous cystadenocarcinoma(97;0.151)			CGCTGTTGGCGAAGGCCTGGA	0.463																																						dbGAP											2	Substitution - coding silent(2)	breast(2)	17											76.0	71.0	73.0					17																	76825031		2203	4300	6503	74336626	SO:0001819	synonymous_variant	0			AB040886	CCDS32755.1	17q25.3	2008-02-05	2005-08-08			ENSG00000055483		"""Ubiquitin-specific peptidases"""	20062	protein-coding gene	gene with protein product		612543	"""ubiquitin specific protease 36"""			12838346	Standard	NM_025090		Approved	KIAA1453, FLJ12851	uc002jvz.1	Q9P275		ENST00000542802.3:c.534C>T	17.37:g.76825031G>A		18	0.00	0		NA	NA	NA	74336626	95	44.19	76	Q05C98|Q05DD0|Q6IQ38|Q8NDM8|Q9NVC8	Silent	SNP	HMMPfam_UCH,PatternScan_IG_MHC,PatternScan_UCH_2_1,PatternScan_UCH_2_2,superfamily_SSF54001	p.F178	ENST00000542802.3	37	c.534	CCDS32755.1	17																																																																																			-	HMMPfam_UCH,superfamily_SSF54001		0.463	USP36-003	KNOWN	basic|appris_principal|CCDS	protein_coding	USP36	protein_coding	OTTHUMT00000437472.3	G	NM_025090		74336626	-1	no_errors	NM_025090.3	genbank	human	validated	54_36p	silent	SNP	0.979	A
TEX19	400629	genome.wustl.edu	37	17	80320077	80320077	+	Silent	SNP	C	C	G	rs11557867	byFrequency	TCGA-AB-2827-03B-01W-0728-08	TCGA-AB-2827-11B-01W-0728-08	C	C	C	G	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	1a21f77d-2ab7-4b5a-b91a-2f561a459dd1	bf713301-022e-480e-8c3a-5c04981f30de	g.chr17:80320077C>G	ENST00000333437.4	+	2	361	c.51C>G	c.(49-51)ctC>ctG	p.L17L		NM_207459.3	NP_997342.1	Q8NA77	TEX19_HUMAN	testis expressed 19	17					cell differentiation (GO:0030154)|meiotic nuclear division (GO:0007126)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)				breast(1)|endometrium(1)|kidney(1)|lung(2)|upper_aerodigestive_tract(1)	6						TGTCCTACCTCTACGCCTCCT	0.552													.|||	111	0.0221645	0.0257	0.0418	5008	,	,		22512	0.0		0.0378	False		,,,				2504	0.0102					dbGAP											0			17						C		179,4227	117.5+/-155.4	5,169,2029	180.0	155.0	163.0		51	-1.9	0.0	17	dbSNP_120	163	374,8226	122.2+/-181.2	11,352,3937	no	coding-synonymous	TEX19	NM_207459.3		16,521,5966	GG,GC,CC		4.3488,4.0626,4.2519		17/165	80320077	553,12453	2203	4300	6503	77913366	SO:0001819	synonymous_variant	0			BC016939	CCDS11809.1	17q25.3	2009-04-14			ENSG00000182459	ENSG00000182459			33802	protein-coding gene	gene with protein product		615647					Standard	NM_207459		Approved	FLJ35767	uc002keq.3	Q8NA77	OTTHUMG00000132857	ENST00000333437.4:c.51C>G	17.37:g.80320077C>G		61	1.61	1		NA	NA	NA	77913366	14	30.00	6		Silent	SNP	NULL	p.L17	ENST00000333437.4	37	c.51	CCDS11809.1	17																																																																																			-	NULL		0.552	TEX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FLJ35767	protein_coding	OTTHUMT00000256331.1	C	NM_207459		77913366	+1	no_errors	NM_207459.1	genbank	human	predicted	54_36p	silent	SNP	0.000	G
PLA2G4C	8605	genome.wustl.edu	37	19	48607930	48607930	+	Missense_Mutation	SNP	C	C	G			TCGA-AB-2827-03B-01W-0728-08	TCGA-AB-2827-11B-01W-0728-08	C	C	C	G	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	1a21f77d-2ab7-4b5a-b91a-2f561a459dd1	bf713301-022e-480e-8c3a-5c04981f30de	g.chr19:48607930C>G	ENST00000599921.1	-	4	529	c.172G>C	c.(172-174)Gcc>Ccc	p.A58P	PLA2G4C_ENST00000413144.2_Missense_Mutation_p.A58P|PLA2G4C_ENST00000354276.3_Missense_Mutation_p.A58P|PLA2G4C_ENST00000599111.1_Missense_Mutation_p.A68P			Q9UP65	PA24C_HUMAN	phospholipase A2, group IVC (cytosolic, calcium-independent)	58	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				arachidonic acid metabolic process (GO:0019369)|glycerophospholipid biosynthetic process (GO:0046474)|glycerophospholipid catabolic process (GO:0046475)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|parturition (GO:0007567)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	calcium-independent phospholipase A2 activity (GO:0047499)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(12)|lung(13)|ovary(2)|prostate(1)|skin(3)	38		all_cancers(25;2.84e-05)|all_lung(116;4.62e-05)|Lung NSC(112;7.61e-05)|all_epithelial(76;0.000192)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;8.09e-05)|all cancers(93;0.000517)|Epithelial(262;0.0135)|GBM - Glioblastoma multiforme(486;0.0717)		CCAAGGCAGGCAATGTGAGCC	0.567																																						dbGAP											0			19											97.0	84.0	88.0					19																	48607930		2203	4300	6503	53299742	SO:0001583	missense	0			AF065214	CCDS12710.1, CCDS54286.1, CCDS59403.1	19q13.3	2008-09-19					3.1.1.4		9037	protein-coding gene	gene with protein product		603602				9705332	Standard	NM_003706		Approved	cPLA2-gamma	uc002phx.3	Q9UP65		ENST00000599921.1:c.172G>C	19.37:g.48607930C>G	ENSP00000469473:p.Ala58Pro	30	3.23	1		NA	NA	NA	53299742	57	47.75	53	B2RB71|B4DI40|O75457|Q6IBI8|Q9UG68	Missense_Mutation	SNP	HMMPfam_PLA2_B,HMMSmart_PLAc,superfamily_Acyl_Trfase/lysoPlipase	p.A58P	ENST00000599921.1	37	c.172	CCDS12710.1	19	.	.	.	.	.	.	.	.	.	.	C	18.73	3.686828	0.68157	.	.	ENSG00000105499	ENST00000354276;ENST00000413144	T;T	0.05717	3.4;3.4	3.37	3.37	0.38596	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (3);	0.270973	0.29609	N	0.011675	T	0.25382	0.0617	M	0.85945	2.785	0.35746	D	0.819049	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.996;0.999	T	0.34477	-0.9827	10	0.66056	D	0.02	-17.0088	10.6005	0.45365	0.0:1.0:0.0:0.0	.	68;58;58	B4DI40;Q8WWC5;Q9UP65	.;.;PA24C_HUMAN	P	58	ENSP00000346228:A58P;ENSP00000400036:A58P	ENSP00000346228:A58P	A	-	1	0	PLA2G4C	53299742	0.982000	0.34865	0.986000	0.45419	0.922000	0.55478	2.098000	0.41757	1.590000	0.49995	0.404000	0.27445	GCC	-	HMMPfam_PLA2_B,HMMSmart_PLAc,superfamily_Acyl_Trfase/lysoPlipase		0.567	PLA2G4C-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	PLA2G4C	protein_coding	OTTHUMT00000465551.1	C			53299742	-1	no_errors	NM_003706.1	genbank	human	provisional	54_36p	missense	SNP	0.980	G
MTMR3	8897	genome.wustl.edu	37	22	30398934	30398934	+	Missense_Mutation	SNP	G	G	C			TCGA-AB-2827-03B-01W-0728-08	TCGA-AB-2827-11B-01W-0728-08	G	G	G	C	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	1a21f77d-2ab7-4b5a-b91a-2f561a459dd1	bf713301-022e-480e-8c3a-5c04981f30de	g.chr22:30398934G>C	ENST00000401950.2	+	9	965	c.623G>C	c.(622-624)aGt>aCt	p.S208T	MTMR3_ENST00000406629.1_Missense_Mutation_p.S208T|MTMR3_ENST00000351488.3_Missense_Mutation_p.S208T|MTMR3_ENST00000323630.5_Missense_Mutation_p.S72T|MTMR3_ENST00000333027.3_Missense_Mutation_p.S208T	NM_021090.3	NP_066576.1	Q13615	MTMR3_HUMAN	myotubularin related protein 3	208	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|large_intestine(3)|ovary(2)|skin(8)|upper_aerodigestive_tract(1)	17			OV - Ovarian serous cystadenocarcinoma(5;0.00204)|Epithelial(10;0.06)|all cancers(5;0.107)			GAACTGGAAAGTGTATCAAGT	0.507																																						dbGAP											0			22											119.0	106.0	111.0					22																	30398934		2203	4300	6503	28728934	SO:0001583	missense	0			U58034	CCDS13870.1, CCDS13871.1, CCDS46682.1	22q12.2	2011-06-09			ENSG00000100330	ENSG00000100330		"""Zinc fingers, FYVE domain containing"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7451	protein-coding gene	gene with protein product		603558				8640223, 9736772	Standard	NM_153050		Approved	KIAA0371, ZFYVE10, FYVE-DSP1	uc003agv.4	Q13615	OTTHUMG00000151278	ENST00000401950.2:c.623G>C	22.37:g.30398934G>C	ENSP00000384651:p.Ser208Thr	41	0.00	0		NA	NA	NA	28728934	113	41.92	83	A5PL26|A7MD32|Q9NYN5|Q9NYN6|Q9UDX6|Q9UEG3	Missense_Mutation	SNP	HMMPfam_FYVE,HMMSmart_SM00064,HMMSmart_SM00404,HMMPfam_Myotub-related,superfamily_FYVE/PHD zinc finger,PatternScan_TYR_PHOSPHATASE_1,superfamily_PH domain-like,superfamily_(Phosphotyrosine protein) phosphatases II	p.S208T	ENST00000401950.2	37	c.623	CCDS13870.1	22	.	.	.	.	.	.	.	.	.	.	G	15.78	2.935151	0.52866	.	.	ENSG00000100330	ENST00000401950;ENST00000333027;ENST00000323630;ENST00000351488;ENST00000406629	D;D;D;D;D	0.90133	-2.62;-2.62;-2.62;-2.62;-2.62	5.7	5.7	0.88788	Myotubularin phosphatase domain (1);Myotubularin-related (1);	0.077325	0.85682	D	0.000000	D	0.90448	0.7009	N	0.25286	0.73	0.53005	D	0.99996	D;B;D	0.58970	0.984;0.034;0.984	P;B;P	0.56042	0.79;0.18;0.79	D	0.91150	0.4952	10	0.54805	T	0.06	.	18.8247	0.92114	0.0:0.0:1.0:0.0	.	208;208;208	Q13615-3;Q13615;Q13615-2	.;MTMR3_HUMAN;.	T	208;208;72;208;208	ENSP00000384651:S208T;ENSP00000331649:S208T;ENSP00000318070:S72T;ENSP00000307271:S208T;ENSP00000384077:S208T	ENSP00000318070:S72T	S	+	2	0	MTMR3	28728934	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	3.652000	0.54439	2.694000	0.91930	0.467000	0.42956	AGT	-	HMMPfam_Myotub-related,superfamily_(Phosphotyrosine protein) phosphatases II		0.507	MTMR3-001	KNOWN	basic|CCDS	protein_coding	MTMR3	protein_coding	OTTHUMT00000322066.1	G	NM_021090		28728934	+1	no_errors	NM_021090.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	C
