#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
Unknown	0	genome.wustl.edu	37	Unknown	0	0	+	IGR	SNP	T	T	C			TCGA-AB-2916-03A-01W-0732-08	TCGA-AB-2916-11A-01W-0732-08	T	T	T	C	T	T	Verified	Invalid:failed_liftOver	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	40754d09-f57c-442e-bb13-35f5793c381a	4f994b34-a13a-4755-b0d4-2847b1c41e25	g.chrUnknown:0T>C								None (None upstream) : None (None downstream)																								0.0																																						dbGAP											0			MT																																								14767	SO:0001628	intergenic_variant	0																															Unknown.37:g.0T>C		Somatic	3010	0.72	22		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	14767	1372	11.00	171		Missense_Mutation	SNP	HMMPfam_Cytochrom_B_N,HMMPfam_Cytochrom_B_C,superfamily_Cytochrome_b/b6_C,superfamily_Transmembr_di-haem_cytochrome	p.I7T		37	c.20		MT																																																																																			-	superfamily_Transmembr_di-haem_cytochrome	0	0					MT-CYB			T			14767	+1	no_stop_codon:bad_bp_length_for_coding_region	ENST00000361789	ensembl	human	known	54_36p	missense	SNP	NULL	C
CD1B	910	genome.wustl.edu	37	1	158300845	158300845	+	Silent	SNP	C	C	T			TCGA-AB-2916-03A-01W-0732-08	TCGA-AB-2916-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	40754d09-f57c-442e-bb13-35f5793c381a	4f994b34-a13a-4755-b0d4-2847b1c41e25	g.chr1:158300845C>T	ENST00000368168.3	-	2	176	c.69G>A	c.(67-69)caG>caA	p.Q23Q		NM_001764.2	NP_001755.1	P29016	CD1B_HUMAN	CD1b molecule	23					antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	cell surface (GO:0009986)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)				breast(2)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	30	all_hematologic(112;0.0378)					AGGTCGGCCCCTGGAAGGCTG	0.443																																						dbGAP											0			1											170.0	169.0	170.0					1																	158300845		2203	4300	6503	156567469	SO:0001819	synonymous_variant	0			M28826	CCDS1176.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158485	ENSG00000158485		"""CD molecules"", ""Immunoglobulin superfamily / C1-set domain containing"""	1635	protein-coding gene	gene with protein product		188360	"""CD1B antigen, b polypeptide"", ""CD1b antigen"""	CD1		2447586	Standard	NM_001764		Approved		uc001frx.3	P29016	OTTHUMG00000017513	ENST00000368168.3:c.69G>A	1.37:g.158300845C>T		Somatic	296	2.31	7		0	0.00	0	WXS	Illumina HiSeq	Phase_IV	156567469	148	35.47	83	Q5TDK9|Q5TDL0|Q9UMM2	Silent	SNP	HMMPfam_MHC_I,HMMPfam_C1-set,HMMSmart_SM00407,superfamily_MHC antigen-recognition domain,superfamily_Immunoglobulin	p.Q23	ENST00000368168.3	37	c.69	CCDS1176.1	1																																																																																			-	NULL		0.443	CD1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CD1B	protein_coding	OTTHUMT00000046350.2	C	NM_001764		156567469	-1	no_errors	NM_001764.2	genbank	human	reviewed	54_36p	silent	SNP	0.003	T
OR2T10	127069	genome.wustl.edu	37	1	248756299	248756299	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AB-2916-03A-01W-0732-08	TCGA-AB-2916-11A-01W-0732-08	G	G	G	T	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	40754d09-f57c-442e-bb13-35f5793c381a	4f994b34-a13a-4755-b0d4-2847b1c41e25	g.chr1:248756299G>T	ENST00000330500.2	-	1	801	c.771C>A	c.(769-771)taC>taA	p.Y257*	Y_RNA_ENST00000364732.1_RNA	NM_001004693.1	NP_001004693.1	Q8NGZ9	O2T10_HUMAN	olfactory receptor, family 2, subfamily T, member 10	257						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(17)|skin(3)|upper_aerodigestive_tract(1)	26	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GCATGTAGTTGTAAATAGCAG	0.448																																						dbGAP											0			1											65.0	68.0	67.0					1																	248756299		2049	4237	6286	246822922	SO:0001587	stop_gained	0				CCDS31121.1	1q44	2012-08-09			ENSG00000184022	ENSG00000184022		"""GPCR / Class A : Olfactory receptors"""	19573	protein-coding gene	gene with protein product							Standard	NM_001004693		Approved		uc010pzn.2	Q8NGZ9	OTTHUMG00000040388	ENST00000330500.2:c.771C>A	1.37:g.248756299G>T	ENSP00000329210:p.Tyr257*	Somatic	107	2.73	3		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	246822922	153	38.00	95	B2RNK7	Nonsense_Mutation	SNP	HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_Family A G protein-coupled receptor-like	p.Y257*	ENST00000330500.2	37	c.771	CCDS31121.1	1	.	.	.	.	.	.	.	.	.	.	.	6.558	0.471301	0.12461	.	.	ENSG00000184022	ENST00000330500	.	.	.	2.35	-0.0136	0.13983	.	.	.	.	.	.	.	.	.	.	.	0.47153	D	0.999331	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.784	0.18322	0.4898:0.0:0.5102:0.0	.	.	.	.	X	257	.	ENSP00000329210:Y257X	Y	-	3	2	OR2T10	246822922	0.000000	0.05858	0.021000	0.16686	0.006000	0.05464	-0.193000	0.09573	0.180000	0.19960	0.447000	0.29281	TAC	-	HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like		0.448	OR2T10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR2T10	protein_coding	OTTHUMT00000097139.1	G	NM_001004693		246822922	-1	no_errors	NM_001004693.1	genbank	human	provisional	54_36p	nonsense	SNP	0.000	T
DNMT3A	1788	genome.wustl.edu	37	2	25457243	25457243	+	Missense_Mutation	SNP	G	G	A	rs377577594		TCGA-AB-2916-03A-01W-0732-08	TCGA-AB-2916-11A-01W-0732-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	40754d09-f57c-442e-bb13-35f5793c381a	4f994b34-a13a-4755-b0d4-2847b1c41e25	g.chr2:25457243G>A	ENST00000264709.3	-	23	2981	c.2644C>T	c.(2644-2646)Cgc>Tgc	p.R882C	DNMT3A_ENST00000321117.5_Missense_Mutation_p.R882C|DNMT3A_ENST00000380746.4_Missense_Mutation_p.R693C|DNMT3A_ENST00000474887.1_5'Flank|DNMT3A_ENST00000402667.1_Missense_Mutation_p.R659C	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	882	SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.		R -> C (in a patient with chronic myelomonocytic leukemia; somatic mutation). {ECO:0000269|PubMed:21828135}.|R -> H (in a patient with chronic myelomonocytic leukemia; somatic mutation). {ECO:0000269|PubMed:21828135}.|R -> P (in a patient with chronic myelomonocytic leukemia; somatic mutation). {ECO:0000269|PubMed:21828135}.		C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)	p.R882C(93)|p.R882S(8)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTCGCCAAGCGGCTCATGTTG	0.597			"""Mis, F, N, S"""		AML																																	dbGAP		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	101	Substitution - Missense(101)	haematopoietic_and_lymphoid_tissue(101)	2						G	CYS/ARG,CYS/ARG,CYS/ARG	0,4406		0,0,2203	55.0	50.0	52.0		2644,2077,2644	5.7	1.0	2		52	4,8596		0,4,4296	no	missense,missense,missense	DNMT3A	NM_022552.3,NM_153759.2,NM_175629.1	180,180,180	0,4,6499	AA,AG,GG		0.0465,0.0,0.0308	probably-damaging,probably-damaging,probably-damaging	882/913,693/724,882/913	25457243	4,13002	2203	4300	6503	25310747	SO:0001583	missense	0				CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.2644C>T	2.37:g.25457243G>A	ENSP00000264709:p.Arg882Cys	Somatic	93	1.06	1		16	34.62	9	WXS	Illumina HiSeq	Phase_IV	25310747	64	30.11	28	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Missense_Mutation	SNP	HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT	p.R882C	ENST00000264709.3	37	c.2644	CCDS33157.1	2	.	.	.	.	.	.	.	.	.	.	G	22.0	4.224411	0.79576	0.0	4.65E-4	ENSG00000119772	ENST00000380746;ENST00000321117;ENST00000264709;ENST00000402667	D;D;D;D	0.97186	-4.28;-4.28;-4.28;-4.28	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	D	0.98538	0.9512	M	0.87180	2.865	0.80722	D	1	D;D	0.89917	1.0;1.0	D;P	0.65573	0.936;0.685	D	0.99425	1.0934	10	0.87932	D	0	-8.768	18.4404	0.90665	0.0:0.0:1.0:0.0	.	882;693	Q9Y6K1;E9PEB8	DNM3A_HUMAN;.	C	693;882;882;659	ENSP00000370122:R693C;ENSP00000324375:R882C;ENSP00000264709:R882C;ENSP00000384237:R659C	ENSP00000264709:R882C	R	-	1	0	DNMT3A	25310747	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.864000	0.99589	2.698000	0.92095	0.561000	0.74099	CGC	-	superfamily_S-adenosyl-L-methionine-dependent methyltransferases		0.597	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	DNMT3A	protein_coding	OTTHUMT00000211587.1	G	NM_022552		25310747	-1	no_errors	NM_022552.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
STK39	27347	genome.wustl.edu	37	2	168997252	168997252	+	Silent	SNP	C	C	T			TCGA-AB-2916-03A-01W-0732-08	TCGA-AB-2916-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	40754d09-f57c-442e-bb13-35f5793c381a	4f994b34-a13a-4755-b0d4-2847b1c41e25	g.chr2:168997252C>T	ENST00000355999.4	-	6	1350	c.645G>A	c.(643-645)gcG>gcA	p.A215A		NM_013233.2	NP_037365.2	Q9UEW8	STK39_HUMAN	serine threonine kinase 39	215	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular hypotonic response (GO:0071476)|intracellular signal transduction (GO:0035556)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of rubidium ion transmembrane transporter activity (GO:2000687)|negative regulation of rubidium ion transport (GO:2000681)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of potassium ion transport (GO:0043268)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|response to stress (GO:0006950)|signal transduction by phosphorylation (GO:0023014)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(3)|prostate(2)|skin(2)	13						TTGCTAGGAACGCACTTACCC	0.368																																						dbGAP											0			2											80.0	82.0	82.0					2																	168997252		2040	4232	6272	168705498	SO:0001819	synonymous_variant	0			AF099989	CCDS42770.1	2q24.3	2010-06-25	2010-06-25		ENSG00000198648	ENSG00000198648			17717	protein-coding gene	gene with protein product	"""STE20/SPS1 homolog (yeast)"""	607648				10980603	Standard	NM_013233		Approved	DCHT, SPAK	uc002uea.3	Q9UEW8	OTTHUMG00000133745	ENST00000355999.4:c.645G>A	2.37:g.168997252C>T		Somatic	108	0.00	0		15	57.14	20	WXS	Illumina HiSeq	Phase_IV	168705498	138	35.81	77	O14774|Q53S90|Q53SL7|Q53SS1|Q9UER4|X5D9C8	Silent	SNP	HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like),PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase	p.A215	ENST00000355999.4	37	c.645	CCDS42770.1	2																																																																																			-	HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase		0.368	STK39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	STK39	protein_coding	OTTHUMT00000258112.2	C	NM_013233		168705498	-1	no_errors	NM_013233.2	genbank	human	reviewed	54_36p	silent	SNP	0.986	T
BTD	686	genome.wustl.edu	37	3	15686426	15686426	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2916-03A-01W-0732-08	TCGA-AB-2916-11A-01W-0732-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	40754d09-f57c-442e-bb13-35f5793c381a	4f994b34-a13a-4755-b0d4-2847b1c41e25	g.chr3:15686426G>A	ENST00000303498.5	+	4	1172	c.1063G>A	c.(1063-1065)Gac>Aac	p.D355N	BTD_ENST00000383778.4_Missense_Mutation_p.D335N|BTD_ENST00000449107.1_Missense_Mutation_p.D357N|BTD_ENST00000437172.1_Missense_Mutation_p.D357N	NM_000060.2|NM_001281723.1	NP_000051.1|NP_001268652.1	P43251	BTD_HUMAN	biotinidase	355	CN hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00054}.				biotin metabolic process (GO:0006768)|central nervous system development (GO:0007417)|epidermis development (GO:0008544)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical part of cell (GO:0045177)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|nucleolus (GO:0005730)|perikaryon (GO:0043204)	biotin carboxylase activity (GO:0004075)|biotinidase activity (GO:0047708)			breast(2)|endometrium(3)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	18						AGGTGAAACGGACCCATCCCA	0.463																																						dbGAP											0			3											74.0	75.0	74.0					3																	15686426		2203	4300	6503	15661430	SO:0001583	missense	0			AF018631	CCDS2628.1, CCDS63563.1, CCDS63564.1, CCDS63565.1	3p25	2007-03-26			ENSG00000169814	ENSG00000169814	3.5.1.12		1122	protein-coding gene	gene with protein product		609019				8001986	Standard	NM_001281723		Approved		uc003cah.3	P43251	OTTHUMG00000129861	ENST00000303498.5:c.1063G>A	3.37:g.15686426G>A	ENSP00000306477:p.Asp355Asn	Somatic	97	2.02	2		15	25.00	5	WXS	Illumina HiSeq	Phase_IV	15661430	105	36.31	61	A6NHF2|B2R865|B4DFX1|B4DLJ9|B7Z7C9|F8W1Q3|Q96EM9	Missense_Mutation	SNP	HMMPfam_CN_hydrolase,superfamily_Carbon-nitrogen hydrolase	p.D355N	ENST00000303498.5	37	c.1063	CCDS2628.1	3	.	.	.	.	.	.	.	.	.	.	G	9.153	1.016812	0.19355	.	.	ENSG00000169814	ENST00000449107;ENST00000303498;ENST00000437172;ENST00000383778	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	5.58	2.7	0.31948	Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase (1);	0.485202	0.20970	N	0.082408	T	0.69006	0.3063	N	0.08118	0	0.09310	N	1	B;B;B	0.25235	0.121;0.121;0.121	B;B;B	0.19391	0.025;0.025;0.025	T	0.54702	-0.8254	10	0.15066	T	0.55	-29.2067	7.2111	0.25935	0.132:0.0:0.6313:0.2367	.	357;357;355	A6NHF2;B4DLJ9;P43251	.;.;BTD_HUMAN	N	357;355;357;335	ENSP00000388212:D357N;ENSP00000306477:D355N;ENSP00000400995:D357N;ENSP00000373288:D335N	ENSP00000306477:D355N	D	+	1	0	BTD	15661430	0.004000	0.15560	0.318000	0.25279	0.795000	0.44927	0.564000	0.23563	0.718000	0.32166	0.561000	0.74099	GAC	-	NULL		0.463	BTD-001	KNOWN	basic|CCDS	protein_coding	BTD	protein_coding	OTTHUMT00000252103.2	G	NM_000060		15661430	+1	no_errors	NM_000060.2	genbank	human	reviewed	54_36p	missense	SNP	0.003	A
STC2	8614	genome.wustl.edu	37	5	172745042	172745042	+	Silent	SNP	G	G	A			TCGA-AB-2916-03A-01W-0732-08	TCGA-AB-2916-11A-01W-0732-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	40754d09-f57c-442e-bb13-35f5793c381a	4f994b34-a13a-4755-b0d4-2847b1c41e25	g.chr5:172745042G>A	ENST00000265087.4	-	4	2026	c.717C>T	c.(715-717)caC>caT	p.H239H	STC2_ENST00000520593.1_5'Flank	NM_003714.2	NP_003705.1	O76061	STC2_HUMAN	stanniocalcin 2	239					cellular calcium ion homeostasis (GO:0006874)|cellular response to hypoxia (GO:0071456)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of gene expression (GO:0010629)|negative regulation of multicellular organism growth (GO:0040015)|regulation of hormone biosynthetic process (GO:0046885)|regulation of store-operated calcium entry (GO:2001256)|response to oxidative stress (GO:0006979)|response to peptide hormone (GO:0043434)|response to vitamin D (GO:0033280)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|heme binding (GO:0020037)|protein homodimerization activity (GO:0042803)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(3)	25	Renal(175;0.000159)|Lung NSC(126;0.00229)|all_lung(126;0.004)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|Ovarian(839;0.223)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			CTGCTTCCCCGTGGTGGGCCC	0.667																																						dbGAP											0			5											62.0	63.0	62.0					5																	172745042		2203	4300	6503	172677648	SO:0001819	synonymous_variant	0			AB012664	CCDS4388.1	5q35.2	2004-05-17			ENSG00000113739	ENSG00000113739			11374	protein-coding gene	gene with protein product		603665				9723890, 9753616	Standard	NM_003714		Approved	STC-2	uc003mco.1	O76061	OTTHUMG00000130542	ENST00000265087.4:c.717C>T	5.37:g.172745042G>A		Somatic	38	2.56	1		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	172677648	24	43.18	19		Silent	SNP	HMMPfam_Stanniocalcin	p.H239	ENST00000265087.4	37	c.717	CCDS4388.1	5																																																																																			-	HMMPfam_Stanniocalcin		0.667	STC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	STC2	protein_coding	OTTHUMT00000252965.1	G	NM_003714		172677648	-1	no_errors	NM_003714.2	genbank	human	reviewed	54_36p	silent	SNP	0.003	A
MYB	4602	genome.wustl.edu	37	6	135510959	135510959	+	Missense_Mutation	SNP	T	T	C			TCGA-AB-2916-03A-01W-0732-08	TCGA-AB-2916-11A-01W-0732-08	T	T	T	C	T	T	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	40754d09-f57c-442e-bb13-35f5793c381a	4f994b34-a13a-4755-b0d4-2847b1c41e25	g.chr6:135510959T>C	ENST00000367814.4	+	4	430	c.244T>C	c.(244-246)Tgg>Cgg	p.W82R	MYB_ENST00000533624.1_Missense_Mutation_p.W82R|MYB_ENST00000341911.5_Missense_Mutation_p.W82R|MYB_ENST00000420123.2_Missense_Mutation_p.W58R|MYB_ENST00000525369.1_Missense_Mutation_p.W82R|MYB_ENST00000534044.1_Missense_Mutation_p.W82R|MYB_ENST00000528774.1_Missense_Mutation_p.W82R|MYB_ENST00000442647.2_Missense_Mutation_p.W82R|MYB_ENST00000316528.8_Missense_Mutation_p.W82R|MYB_ENST00000534121.1_Missense_Mutation_p.W82R|MYB_ENST00000531845.1_3'UTR|MYB_ENST00000527615.1_Missense_Mutation_p.W82R	NM_001161659.1|NM_005375.2	NP_001155131.1|NP_005366.2	P10242	MYB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog	82	HTH myb-type 1. {ECO:0000255|PROSITE- ProRule:PRU00625}.				B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|chromatin remodeling (GO:0006338)|embryonic digestive tract development (GO:0048566)|G1/S transition of mitotic cell cycle (GO:0000082)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 methylation (GO:0051574)|positive regulation of T-helper cell differentiation (GO:0045624)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|thymus development (GO:0048538)	nuclear matrix (GO:0016363)	chromatin binding (GO:0003682)|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)			breast(4)|endometrium(1)|kidney(2)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	28	all_epithelial(2;0.109)|Breast(56;0.158)|Colorectal(23;0.221)	Lung NSC(302;3.08e-05)|Ovarian(999;0.208)		OV - Ovarian serous cystadenocarcinoma(155;0.0079)|GBM - Glioblastoma multiforme(68;0.0117)		CCAGCACCGATGGCAGAAAGT	0.393			T	NFIB	adenoid cystic carcinoma																																	dbGAP		Dom	yes		6	6q22-23	4602	v-myb myeloblastosis viral oncogene homolog		E	0			6											115.0	125.0	122.0					6																	135510959		2203	4300	6503	135552652	SO:0001583	missense	0				CCDS5174.1, CCDS47481.1, CCDS47482.1, CCDS55058.1, CCDS55059.1, CCDS55060.1, CCDS55061.1, CCDS55062.1	6q22-q23	2013-07-09	2013-07-09		ENSG00000118513	ENSG00000118513			7545	protein-coding gene	gene with protein product		189990				17599807	Standard	NM_001130172		Approved	c-myb	uc003qfh.3	P10242	OTTHUMG00000015629	ENST00000367814.4:c.244T>C	6.37:g.135510959T>C	ENSP00000356788:p.Trp82Arg	Somatic	94	0.00	0		52	20.00	13	WXS	Illumina HiSeq	Phase_IV	135552652	119	10.45	14	E9PI07|E9PLZ5|E9PNA4|E9PNL6|E9PRS2|P78391|P78392|P78525|P78526|Q14023|Q14024|Q708E4|Q708E7|Q9UE83	Missense_Mutation	SNP	HMMSmart_SM00717,superfamily_Homeodomain-like,HMMPfam_Wos2,HMMPfam_Myb_DNA-binding,HMMPfam_Cmyb_C	p.W82R	ENST00000367814.4	37	c.244	CCDS5174.1	6	.	.	.	.	.	.	.	.	.	.	T	23.5	4.420635	0.83559	.	.	ENSG00000118513	ENST00000341911;ENST00000442647;ENST00000316528;ENST00000237302;ENST00000367814;ENST00000527615;ENST00000420123;ENST00000525369;ENST00000528774;ENST00000534121;ENST00000534044;ENST00000533624;ENST00000430686	T;T;T;T;T;T;T;T;T;T;T	0.57107	2.0;1.58;1.53;1.59;0.75;1.29;2.0;2.03;1.19;1.63;0.42	5.91	5.91	0.95273	Transcription regulator HTH, Myb-type, DNA-binding (1);Myb, DNA-binding (1);SANT domain, DNA binding (1);Homeodomain-related (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.82545	0.5060	H	0.99261	4.49	0.80722	D	1	D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;0.997;1.0;1.0	D;D;D;D;D;D;D;D;D	0.97110	1.0;0.999;0.999;1.0;1.0;1.0;0.989;1.0;1.0	D	0.90196	0.4253	10	0.87932	D	0	-5.65	16.3486	0.83191	0.0:0.0:0.0:1.0	.	82;82;82;82;82;82;82;82;82	E9PI07;E9PLZ5;P10242-2;E9PNL6;E9PRS2;E9PNA4;P10242-4;P10242;Q708E1	.;.;.;.;.;.;.;MYB_HUMAN;.	R	82;82;82;82;82;82;58;82;82;82;82;82;36	ENSP00000339992:W82R;ENSP00000410825:W82R;ENSP00000326328:W82R;ENSP00000356788:W82R;ENSP00000433227:W82R;ENSP00000435938:W82R;ENSP00000434723:W82R;ENSP00000432851:W82R;ENSP00000435055:W82R;ENSP00000436605:W82R;ENSP00000390460:W36R	ENSP00000237302:W82R	W	+	1	0	MYB	135552652	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.040000	0.89188	2.259000	0.74868	0.528000	0.53228	TGG	-	HMMSmart_SM00717,superfamily_Homeodomain-like,HMMPfam_Myb_DNA-binding		0.393	MYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	MYB	protein_coding	OTTHUMT00000042347.4	T			135552652	+1	no_errors	NM_005375.1	genbank	human	validated	54_36p	missense	SNP	1.000	C
AC004899.1	0	genome.wustl.edu	37	7	48887396	48887396	+	5'UTR	SNP	G	G	T			TCGA-AB-2916-03A-01W-0732-08	TCGA-AB-2916-11A-01W-0732-08	G	G	G	T	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	40754d09-f57c-442e-bb13-35f5793c381a	4f994b34-a13a-4755-b0d4-2847b1c41e25	g.chr7:48887396G>T	ENST00000596947.1	+	0	35																											TAAACCATTTGCCAGATTGAG	0.338																																						dbGAP											0			7																																								48857942	SO:0001623	5_prime_UTR_variant	0																														ENST00000596947.1:c.-105G>T	7.37:g.48887396G>T		Somatic	72	1.37	1		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	48857942	141	21.55	39		RNA	SNP	-	NULL	ENST00000596947.1	37	NULL		7																																																																																			-	-		0.338	AC004899.1-201	KNOWN	basic|appris_principal	protein_coding	LOC100131447	protein_coding		G			48857942	-1	pseudogene	XR_036885.1	genbank	human	model	54_36p	rna	SNP	1.000	T
CSMD1	64478	genome.wustl.edu	37	8	2966162	2966162	+	Missense_Mutation	SNP	G	G	T			TCGA-AB-2916-03A-01W-0732-08	TCGA-AB-2916-11A-01W-0732-08	G	G	G	T	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	40754d09-f57c-442e-bb13-35f5793c381a	4f994b34-a13a-4755-b0d4-2847b1c41e25	g.chr8:2966162G>T	ENST00000520002.1	-	45	7275	c.6720C>A	c.(6718-6720)gaC>gaA	p.D2240E	CSMD1_ENST00000602723.1_Missense_Mutation_p.D2240E|CSMD1_ENST00000537824.1_Missense_Mutation_p.D2239E|CSMD1_ENST00000400186.3_Missense_Mutation_p.D2240E|CSMD1_ENST00000542608.1_Missense_Mutation_p.D2239E|CSMD1_ENST00000602557.1_Missense_Mutation_p.D2240E			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	2240	CUB 13. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		CATTTGAAAAGTCGCTGTGGA	0.488																																						dbGAP											0			8											86.0	85.0	85.0					8																	2966162		1927	4134	6061	2953569	SO:0001583	missense	0					8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14026	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 24"""	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.6720C>A	8.37:g.2966162G>T	ENSP00000430733:p.Asp2240Glu	Somatic	115	1.71	2		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	2953569	113	42.79	86	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	HMMPfam_Sushi,HMMSmart_SM00032,HMMPfam_CUB,HMMSmart_SM00042,superfamily_Spermadhesin CUB domain,superfamily_Complement control module/SCR domain	p.L2241I	ENST00000520002.1	37	c.6721		8	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.20|13.20	2.165047|2.165047	0.38217|0.38217	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608|ENST00000335551	T;T;T;T|.	0.67523|.	-0.27;-0.27;-0.27;-0.27|.	4.95|4.95	3.12|3.12	0.35913|0.35913	CUB (5);|.	0.153108|.	0.42821|.	D|.	0.000644|.	D|D	0.84306|0.84306	0.5443|0.5443	H|H	0.96547|0.96547	3.84|3.84	0.80722|0.80722	D|D	1|1	D;P;D|.	0.71674|.	0.997;0.742;0.998|.	D;P;D|.	0.85130|.	0.992;0.597;0.997|.	D|D	0.85321|0.85321	0.1084|0.1084	10|5	0.59425|.	D|.	0.04|.	.|.	9.1813|9.1813	0.37143|0.37143	0.3084:0.0:0.6916:0.0|0.3084:0.0:0.6916:0.0	.|.	2240;2240;2239|.	E5RIG2;Q96PZ7;F5H2I8|.	.;CSMD1_HUMAN;.|.	E|I	2240;2240;2101;2239;2239|1720	ENSP00000383047:D2240E;ENSP00000430733:D2240E;ENSP00000441462:D2239E;ENSP00000446243:D2239E|.	ENSP00000320445:D2101E|.	D|L	-|-	3|1	2|0	CSMD1|CSMD1	2953569|2953569	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.025000|0.025000	0.11179|0.11179	1.305000|1.305000	0.33493|0.33493	0.572000|0.572000	0.29383|0.29383	0.579000|0.579000	0.79373|0.79373	GAC|CTT	-	NULL		0.488	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	CSMD1	protein_coding	OTTHUMT00000374500.2	G	NM_033225		2953569	-1	pseudogene:no_stop_codon:bad_bp_length_for_coding_region	NM_033225.4	genbank	human	validated	54_36p	missense	SNP	1.000	T
ARL3	403	genome.wustl.edu	37	10	104449677	104449677	+	Missense_Mutation	SNP	G	G	T	rs201727171	byFrequency	TCGA-AB-2916-03A-01W-0732-08	TCGA-AB-2916-11A-01W-0732-08	G	G	G	T	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	40754d09-f57c-442e-bb13-35f5793c381a	4f994b34-a13a-4755-b0d4-2847b1c41e25	g.chr10:104449677G>T	ENST00000260746.5	-	4	419	c.288C>A	c.(286-288)gaC>gaA	p.D96E		NM_004311.3	NP_004302.1	P36405	ARL3_HUMAN	ADP-ribosylation factor-like 3	96					cilium morphogenesis (GO:0060271)|cytokinesis (GO:0000910)|intraciliary transport (GO:0042073)|kidney development (GO:0001822)|photoreceptor cell development (GO:0042461)|post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|primary cilium (GO:0072372)|spindle microtubule (GO:0005876)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|microtubule binding (GO:0008017)			large_intestine(2)	2		Colorectal(252;0.122)		Epithelial(162;4.88e-09)|all cancers(201;1.29e-07)|BRCA - Breast invasive adenocarcinoma(275;0.22)		ATCTTTTTCTGTCTGCACTGT	0.323																																						dbGAP											0			10											51.0	56.0	54.0					10																	104449677		2203	4298	6501	104439667	SO:0001583	missense	0			U07151	CCDS7538.1	10q23.3	2014-05-09			ENSG00000138175	ENSG00000138175		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	694	protein-coding gene	gene with protein product		604695				8034651, 10072593	Standard	NM_004311		Approved	ARFL3	uc001kwa.3	P36405	OTTHUMG00000018965	ENST00000260746.5:c.288C>A	10.37:g.104449677G>T	ENSP00000260746:p.Asp96Glu	Somatic	103	0.96	1		9	55.00	11	WXS	Illumina HiSeq	Phase_IV	104439667	103	36.20	59	B2R6C7|Q53X83|Q5JSM2	Missense_Mutation	SNP	HMMSmart_ARF,PatternScan_ARF,HMMPfam_Arf,superfamily_SSF52540	p.D96E	ENST00000260746.5	37	c.288	CCDS7538.1	10	.	.	.	.	.	.	.	.	.	.	G	21.8	4.206575	0.79127	.	.	ENSG00000138175	ENST00000260746	D	0.83250	-1.7	5.78	4.88	0.63580	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.92844	0.7724	H	0.97465	4.01	0.80722	D	1	D	0.60160	0.987	P	0.59825	0.864	D	0.94257	0.7499	10	0.87932	D	0	-19.0957	11.479	0.50314	0.1554:0.0:0.8446:0.0	.	96	P36405	ARL3_HUMAN	E	96	ENSP00000260746:D96E	ENSP00000260746:D96E	D	-	3	2	ARL3	104439667	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	5.926000	0.70070	1.448000	0.47680	0.455000	0.32223	GAC	-	HMMSmart_ARF,HMMPfam_Arf,superfamily_SSF52540		0.323	ARL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ARL3	protein_coding	OTTHUMT00000050088.2	G	NM_004311		104439667	-1	no_errors	NM_004311.2	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
CFAP46	54777	genome.wustl.edu	37	10	134671121	134671121	+	Silent	SNP	G	G	A	rs149527720		TCGA-AB-2916-03A-01W-0732-08	TCGA-AB-2916-11A-01W-0732-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	40754d09-f57c-442e-bb13-35f5793c381a	4f994b34-a13a-4755-b0d4-2847b1c41e25	g.chr10:134671121G>A	ENST00000368586.5	-	39	5647	c.5547C>T	c.(5545-5547)agC>agT	p.S1849S	TTC40_ENST00000263170.5_Silent_p.S10S	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						GGCCCTGGACGCTGTGAAGCC	0.572																																						dbGAP											0			10						G		1,4405		0,1,2202	175.0	114.0	135.0		483	-4.4	0.0	10	dbSNP_134	135	0,8600		0,0,4300	no	coding-synonymous	C10orf92	NM_001200049.1		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		161/1028	134671121	1,13005	2203	4300	6503	134521111	SO:0001819	synonymous_variant	0																														ENST00000368586.5:c.5547C>T	10.37:g.134671121G>A		Somatic	34	2.78	1		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	134521111	8	65.22	15		Silent	SNP	NULL	p.S10	ENST00000368586.5	37	c.30	CCDS58101.1	10																																																																																			-	NULL		0.572	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	C10orf92	protein_coding	OTTHUMT00000051095.3	G			134521111	-1	no_errors	ENST00000263170	ensembl	human	known	54_36p	silent	SNP	0.001	A
KCNA4	3739	genome.wustl.edu	37	11	30033061	30033061	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2916-03A-01W-0732-08	TCGA-AB-2916-11A-01W-0732-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	40754d09-f57c-442e-bb13-35f5793c381a	4f994b34-a13a-4755-b0d4-2847b1c41e25	g.chr11:30033061G>A	ENST00000328224.6	-	2	2398	c.1165C>T	c.(1165-1167)Cgc>Tgc	p.R389C	KCNA4_ENST00000526518.1_5'Flank	NM_002233.3	NP_002224.1	P22459	KCNA4_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 4	389					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	potassium ion binding (GO:0030955)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(39)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	78					Dalfampridine(DB06637)	GCAAAGCAGCGAACCACAAAC	0.443																																						dbGAP											0			11											82.0	77.0	79.0					11																	30033061		2040	4231	6271	29989637	SO:0001583	missense	0			M55514	CCDS41629.1	11p14	2012-07-05	2002-07-10			ENSG00000182255		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6222	protein-coding gene	gene with protein product		176266	"""potassium voltage-gated channel, shaker-related subfamily, member 4-like"""	KCNA4L		2263489, 16382104	Standard	NM_002233		Approved	Kv1.4, HK1, HPCN2	uc001msk.3	P22459		ENST00000328224.6:c.1165C>T	11.37:g.30033061G>A	ENSP00000328511:p.Arg389Cys	Somatic	479	3.82	19		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	29989637	154	50.63	160		Missense_Mutation	SNP	HMMSmart_SM00225,HMMPfam_K_tetra,HMMPfam_Ion_trans,superfamily_POZ domain,HMMPfam_K_channel_TID,superfamily_Voltage-gated potassium channels	p.R389C	ENST00000328224.6	37	c.1165	CCDS41629.1	11	.	.	.	.	.	.	.	.	.	.	G	16.14	3.038625	0.55003	.	.	ENSG00000182255	ENST00000328224	D	0.98732	-5.1	5.3	5.3	0.74995	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99664	0.9875	H	0.99914	4.94	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96965	0.9704	10	0.87932	D	0	.	18.9734	0.92724	0.0:0.0:1.0:0.0	.	389	P22459	KCNA4_HUMAN	C	389	ENSP00000328511:R389C	ENSP00000328511:R389C	R	-	1	0	KCNA4	29989637	1.000000	0.71417	0.999000	0.59377	0.925000	0.55904	6.597000	0.74118	2.485000	0.83878	0.563000	0.77884	CGC	-	HMMPfam_Ion_trans,superfamily_Voltage-gated potassium channels		0.443	KCNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KCNA4	protein_coding	OTTHUMT00000388074.2	G	NM_002233		29989637	-1	no_errors	NM_002233.2	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
TRIP4	9325	genome.wustl.edu	37	15	64686316	64686316	+	Splice_Site	SNP	T	T	C			TCGA-AB-2916-03A-01W-0732-08	TCGA-AB-2916-11A-01W-0732-08	T	T	T	C	T	T	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	40754d09-f57c-442e-bb13-35f5793c381a	4f994b34-a13a-4755-b0d4-2847b1c41e25	g.chr15:64686316T>C	ENST00000261884.3	+	2	331		c.e2+2		TRIP4_ENST00000559565.1_Splice_Site	NM_016213.4	NP_057297.2	Q15650	TRIP4_HUMAN	thyroid hormone receptor interactor 4						positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	21						AAAAAGATGGTAAGTTAATGT	0.313																																						dbGAP											0			15											67.0	67.0	67.0					15																	64686316		2203	4300	6503	62473369	SO:0001630	splice_region_variant	0			L40371	CCDS10194.1	15q22.1	2014-02-17			ENSG00000103671	ENSG00000103671		"""-"""	12310	protein-coding gene	gene with protein product	"""zinc finger, C2HC5-type"""	604501				7776974	Standard	NM_016213		Approved	HsT17391, ZC2HC5	uc002anm.3	Q15650	OTTHUMG00000133033	ENST00000261884.3:c.271+2T>C	15.37:g.64686316T>C		Somatic	128	1.53	2		0	100.00	7	WXS	Illumina HiSeq	Phase_IV	62473369	121	35.94	69	B2RAS0|Q96ED7|Q9UKH0	Splice_Site	SNP	-	e2+2	ENST00000261884.3	37	c.271+2	CCDS10194.1	15	.	.	.	.	.	.	.	.	.	.	T	18.61	3.660883	0.67700	.	.	ENSG00000103671	ENST00000261884	.	.	.	5.68	5.68	0.88126	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.8776	0.79178	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	TRIP4	62473369	1.000000	0.71417	1.000000	0.80357	0.869000	0.49853	4.390000	0.59646	2.289000	0.77006	0.533000	0.62120	.	-	-		0.313	TRIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TRIP4	protein_coding	OTTHUMT00000256635.2	T	NM_016213	Intron	62473369	+1	no_errors	NM_016213.3	genbank	human	validated	54_36p	splice_site	SNP	1.000	C
PHACTR1	221692	genome.wustl.edu	37	6	13206134	13206135	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AB-2916-03A-01W-0732-08	TCGA-AB-2916-11A-01W-0732-08	-	-	-	G	-	-	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	40754d09-f57c-442e-bb13-35f5793c381a	4f994b34-a13a-4755-b0d4-2847b1c41e25	g.chr6:13206134_13206135insG	ENST00000379350.1	+	7	881_882	c.752_753insG	c.(751-756)gtggggfs	p.VG251fs	PHACTR1_ENST00000457702.2_Frame_Shift_Ins_p.VG106fs|PHACTR1_ENST00000379345.2_Intron|PHACTR1_ENST00000332995.7_Frame_Shift_Ins_p.VG251fs			Q9C0D0	PHAR1_HUMAN	phosphatase and actin regulator 1	251					actin cytoskeleton reorganization (GO:0031532)|actomyosin structure organization (GO:0031032)|cell motility (GO:0048870)|stress fiber assembly (GO:0043149)	cell junction (GO:0030054)|cytosol (GO:0005829)|nucleus (GO:0005634)|synapse (GO:0045202)	actin binding (GO:0003779)|protein phosphatase inhibitor activity (GO:0004864)			breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	26	Breast(50;0.0427)|Ovarian(93;0.12)	all_hematologic(90;0.122)|Lung SC(78;0.195)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.239)			TGTATGCCCGTGGGGGGGCCAG	0.599																																						dbGAP											0			6																																								13314114	SO:0001589	frameshift_variant	0			AB051520	CCDS75401.1	6p23	2013-01-24	2004-05-20	2004-05-21	ENSG00000112137	ENSG00000112137		"""Phosphatase and actin regulators"""	20990	protein-coding gene	gene with protein product		608723	"""RPEL repeat containing 1"""	RPEL1		11214970, 15107502	Standard	NM_030948		Approved	KIAA1733, dJ257A7.2	uc010jpc.3	Q9C0D0	OTTHUMG00000014270	ENST00000379350.1:c.759dupG	6.37:g.13206141_13206141dupG	ENSP00000368655:p.Val251fs	Somatic	12	0.00	0		2	0.00	0	WXS	Illumina HiSeq	Phase_IV	13314113	45	8.16	4	A8K1V2|Q3MJ93|Q5JSJ2	Frame_Shift_Ins	INS	HMMPfam_RPEL,HMMSmart_SM00707	p.P254fs	ENST00000379350.1	37	c.752_753		6																																																																																			-	NULL		0.599	PHACTR1-001	KNOWN	basic|appris_candidate_longest	protein_coding	PHACTR1	protein_coding	OTTHUMT00000039876.1	-	XM_166420		13314114	+1	no_errors	NM_030948.1	genbank	human	validated	54_36p	frame_shift_ins	INS	0.638:0.521	G
