#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
ATP6AP2	10159	genome.wustl.edu	37	X	40456845	40456845	+	Missense_Mutation	SNP	C	C	T	rs146371390	byFrequency	TCGA-AB-2978-03A-01D-0739-09	TCGA-AB-2978-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	960efb3b-7c3b-42ec-8f29-011d13493c69	be9d0262-d1fa-48c4-bba6-0d5415fb9b52	g.chrX:40456845C>T	ENST00000378438.4	+	5	621	c.463C>T	c.(463-465)Cgt>Tgt	p.R155C	ATP6AP2_ENST00000535539.1_Missense_Mutation_p.R123C|ATP6AP2_ENST00000535777.1_Intron|ATP6AP2_ENST00000544975.1_Missense_Mutation_p.R79C|ATP6AP2_ENST00000486558.1_3'UTR	NM_005765.2	NP_005756.2	O75787	RENR_HUMAN	ATPase, H+ transporting, lysosomal accessory protein 2	155					angiotensin maturation (GO:0002003)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|eye pigmentation (GO:0048069)|head morphogenesis (GO:0060323)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of Wnt signaling pathway (GO:0030177)|proteolysis (GO:0006508)|regulation of MAPK cascade (GO:0043408)|rostrocaudal neural tube patterning (GO:0021903)	cell body (GO:0044297)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	aspartic-type endopeptidase activity (GO:0004190)|receptor activity (GO:0004872)	p.R155C(1)		endometrium(1)|large_intestine(1)|lung(2)	4						GCGCCAGCTCCGTAATCGCCT	0.403																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	X						C	CYS/ARG	2,3833		0,2,1630,571	97.0	88.0	91.0		463	5.4	0.9	X	dbSNP_134	91	0,6728		0,0,2428,1872	no	missense	ATP6AP2	NM_005765.2	180	0,2,4058,2443	TT,TC,CC,C		0.0,0.0522,0.0189	probably-damaging	155/351	40456845	2,10561	2203	4300	6503	40341789	SO:0001583	missense	0			AF248966	CCDS14252.1	Xp11.4	2014-06-17	2003-08-28	2003-08-29	ENSG00000182220	ENSG00000182220			18305	protein-coding gene	gene with protein product	"""prorenin receptor"", ""renin receptor"""	300556	"""ATPase, H+ transporting, lysosomal interacting protein 2"""	ATP6IP2		9556572, 11590366	Standard	NM_005765		Approved	M8-9, APT6M8-9, ATP6M8-9, PRR, RENR	uc004det.3	O75787	OTTHUMG00000024103	ENST00000378438.4:c.463C>T	X.37:g.40456845C>T	ENSP00000367697:p.Arg155Cys	810	3.57	30		130	0.00	0	40341789	36	26.53	13	B7Z9I3|Q5QTQ7|Q6T7F5|Q8NBP3|Q8NG15|Q96FV6|Q96LB5|Q9H2P8|Q9UG89	Missense_Mutation	SNP	HMMPfam_Renin_r	p.R155C	ENST00000378438.4	37	c.463	CCDS14252.1	X	.	.	.	.	.	.	.	.	.	.	C	25.7	4.663339	0.88251	5.22E-4	0.0	ENSG00000182220	ENST00000535539;ENST00000378438;ENST00000436783;ENST00000544975	T;T;T;T	0.51071	1.44;1.4;0.72;1.39	5.39	5.39	0.77823	.	0.045227	0.85682	D	0.000000	T	0.65407	0.2688	M	0.68317	2.08	0.80722	D	1	D;D;D	0.89917	1.0;0.996;0.993	P;P;P	0.60609	0.877;0.487;0.53	T	0.67015	-0.5777	10	0.52906	T	0.07	-10.3144	18.482	0.90815	0.0:1.0:0.0:0.0	.	123;79;155	B7Z9I3;B7Z413;O75787	.;.;RENR_HUMAN	C	123;155;155;79	ENSP00000438415:R123C;ENSP00000367697:R155C;ENSP00000403969:R155C;ENSP00000440459:R79C	ENSP00000367697:R155C	R	+	1	0	ATP6AP2	40341789	1.000000	0.71417	0.937000	0.37676	0.908000	0.53690	7.232000	0.78116	2.393000	0.81446	0.513000	0.50165	CGT	-	NULL		0.403	ATP6AP2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	ATP6AP2	protein_coding	OTTHUMT00000060679.1	C	NM_005765		40341789	+1	no_errors	NM_005765.2	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
SYTL4	94121	genome.wustl.edu	37	X	99936232	99936232	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2978-03A-01D-0739-09	TCGA-AB-2978-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	960efb3b-7c3b-42ec-8f29-011d13493c69	be9d0262-d1fa-48c4-bba6-0d5415fb9b52	g.chrX:99936232C>T	ENST00000372989.1	-	16	1881	c.1550G>A	c.(1549-1551)cGg>cAg	p.R517Q	SYTL4_ENST00000276141.6_Missense_Mutation_p.R517Q|SYTL4_ENST00000263033.5_Missense_Mutation_p.R517Q|SYTL4_ENST00000454200.2_Missense_Mutation_p.R519Q|SYTL4_ENST00000491602.1_5'Flank|SYTL4_ENST00000455616.1_Missense_Mutation_p.R517Q	NM_080737.2	NP_542775.2	Q96C24	SYTL4_HUMAN	synaptotagmin-like 4	517	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|multivesicular body sorting pathway (GO:0071985)|negative regulation of insulin secretion (GO:0046676)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endosome (GO:0005768)|extrinsic component of membrane (GO:0019898)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|synaptic vesicle (GO:0008021)	neurexin family protein binding (GO:0042043)|phospholipid binding (GO:0005543)|transporter activity (GO:0005215)|zinc ion binding (GO:0008270)	p.R517Q(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(2)	27					"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	ACTCTTTTTCCGGTCACCTCC	0.512																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	X											60.0	54.0	56.0					X																	99936232		2203	4300	6503	99822888	SO:0001583	missense	0				CCDS14472.1	Xq21.33	2008-07-31	2008-07-31		ENSG00000102362	ENSG00000102362			15588	protein-coding gene	gene with protein product	"""granuphilin-a"", ""exophilin-2"""	300723					Standard	NM_080737		Approved		uc010nnc.3	Q96C24	OTTHUMG00000022004	ENST00000372989.1:c.1550G>A	X.37:g.99936232C>T	ENSP00000362080:p.Arg517Gln	640	0.31	2		2	0.00	0	99822888	105	32.69	51	Q5H9J3|Q5JPG8|Q8N9P4|Q9H4R0|Q9H4R1	Missense_Mutation	SNP	HMMPfam_C2,HMMSmart_SM00239,HMMPfam_RPH3A_effector,superfamily_C2 domain (Calcium/lipid-binding domain CaLB),superfamily_FYVE/PHD zinc finger	p.R517Q	ENST00000372989.1	37	c.1550	CCDS14472.1	X	.	.	.	.	.	.	.	.	.	.	C	9.565	1.119573	0.20877	.	.	ENSG00000102362	ENST00000372989;ENST00000455616;ENST00000454200;ENST00000276141;ENST00000263033	T;T;T;T;T	0.20738	2.05;2.05;2.05;2.05;2.05	4.98	2.12	0.27331	C2 calcium/lipid-binding domain, CaLB (1);	0.439888	0.23896	N	0.043482	T	0.15912	0.0383	L	0.47716	1.5	0.28354	N	0.920789	B	0.09022	0.002	B	0.06405	0.002	T	0.12293	-1.0553	9	.	.	.	-3.1743	7.6911	0.28569	0.1355:0.7082:0.0:0.1563	.	517	Q96C24	SYTL4_HUMAN	Q	517;517;519;517;517	ENSP00000362080:R517Q;ENSP00000390252:R517Q;ENSP00000403556:R519Q;ENSP00000276141:R517Q;ENSP00000263033:R517Q	.	R	-	2	0	SYTL4	99822888	0.897000	0.30589	1.000000	0.80357	0.994000	0.84299	1.214000	0.32419	1.096000	0.41439	0.468000	0.43344	CGG	-	superfamily_C2 domain (Calcium/lipid-binding domain CaLB)		0.512	SYTL4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	SYTL4	protein_coding	OTTHUMT00000057488.1	C	NM_080737		99822888	-1	no_errors	NM_080737.1	genbank	human	validated	54_36p	missense	SNP	0.989	T
STAG2	10735	genome.wustl.edu	37	X	123220476	123220476	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AB-2978-03A-01D-0739-09	TCGA-AB-2978-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	960efb3b-7c3b-42ec-8f29-011d13493c69	be9d0262-d1fa-48c4-bba6-0d5415fb9b52	g.chrX:123220476C>T	ENST00000371160.1	+	30	3423	c.3133C>T	c.(3133-3135)Cga>Tga	p.R1045*	STAG2_ENST00000371145.3_Nonsense_Mutation_p.R1045*|STAG2_ENST00000354548.5_Nonsense_Mutation_p.R976*|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000218089.9_Nonsense_Mutation_p.R1045*|STAG2_ENST00000371157.3_Nonsense_Mutation_p.R1045*|STAG2_ENST00000371144.3_Nonsense_Mutation_p.R1045*	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	1045					meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)	p.R1045*(1)		breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						GATGTCTTACCGAAATTCTTT	0.433																																						dbGAP											1	Substitution - Nonsense(1)	haematopoietic_and_lymphoid_tissue(1)	X											190.0	157.0	168.0					X																	123220476		2203	4300	6503	123048157	SO:0001587	stop_gained	0			Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.3133C>T	X.37:g.123220476C>T	ENSP00000360202:p.Arg1045*	989	1.40	14		6	62.50	10	123048157	145	20.33	37	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Nonsense_Mutation	SNP	HMMPfam_STAG,superfamily_ARM-type_fold	p.R1045*	ENST00000371160.1	37	c.3133	CCDS14607.1	X	.	.	.	.	.	.	.	.	.	.	C	43	10.078881	0.99332	.	.	ENSG00000101972	ENST00000218089;ENST00000354548;ENST00000371160;ENST00000371157;ENST00000371145;ENST00000371144	.	.	.	5.22	0.396	0.16309	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.0759	15.262	0.73631	0.6782:0.3218:0.0:0.0	.	.	.	.	X	1045;976;1045;1045;1045;1045	.	ENSP00000218089:R1045X	R	+	1	2	STAG2	123048157	1.000000	0.71417	0.999000	0.59377	0.987000	0.75469	1.174000	0.31932	0.105000	0.17753	-0.364000	0.07487	CGA	-	superfamily_ARM-type_fold		0.433	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	STAG2	protein_coding	OTTHUMT00000156159.2	C	NM_006603		123048157	+1	no_errors	NM_001042749.1	genbank	human	validated	54_36p	nonsense	SNP	1.000	T
PRKAA2	5563	genome.wustl.edu	37	1	57161723	57161723	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AB-2978-03A-01D-0739-09	TCGA-AB-2978-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	960efb3b-7c3b-42ec-8f29-011d13493c69	be9d0262-d1fa-48c4-bba6-0d5415fb9b52	g.chr1:57161723C>T	ENST00000371244.4	+	6	745	c.679C>T	c.(679-681)Cga>Tga	p.R227*		NM_006252.3	NP_006243.2	P54646	AAPK2_HUMAN	protein kinase, AMP-activated, alpha 2 catalytic subunit	227	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				autophagy (GO:0006914)|carnitine shuttle (GO:0006853)|cell cycle arrest (GO:0007050)|cellular lipid metabolic process (GO:0044255)|cellular response to glucose starvation (GO:0042149)|cellular response to nutrient levels (GO:0031669)|cholesterol biosynthetic process (GO:0006695)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid homeostasis (GO:0055089)|glucose homeostasis (GO:0042593)|insulin receptor signaling pathway (GO:0008286)|lipid biosynthetic process (GO:0008610)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|positive regulation of glycolytic process (GO:0045821)|protein phosphorylation (GO:0006468)|regulation of circadian rhythm (GO:0042752)|regulation of energy homeostasis (GO:2000505)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	[acetyl-CoA carboxylase] kinase activity (GO:0050405)|[hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity (GO:0047322)|AMP-activated protein kinase activity (GO:0004679)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|histone serine kinase activity (GO:0035174)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)	p.R227*(1)		breast(6)|endometrium(1)|large_intestine(6)|lung(7)|ovary(1)|prostate(1)|stomach(1)	23					Acetylsalicylic acid(DB00945)	TAAGAAGATCCGAGGGGGTGT	0.443																																						dbGAP											1	Substitution - Nonsense(1)	haematopoietic_and_lymphoid_tissue(1)	1											293.0	291.0	292.0					1																	57161723		2203	4300	6503	56934311	SO:0001587	stop_gained	0			BC069823	CCDS605.1	1p31	2011-08-25			ENSG00000162409	ENSG00000162409			9377	protein-coding gene	gene with protein product		600497		PRKAA		7959015	Standard	NM_006252		Approved	AMPK, AMPKa2	uc001cyk.4	P54646	OTTHUMG00000008282	ENST00000371244.4:c.679C>T	1.37:g.57161723C>T	ENSP00000360290:p.Arg227*	838	2.90	25		NA	NA	NA	56934311	194	49.74	192	Q9H1E8|Q9UD43	Nonsense_Mutation	SNP	HMMSmart_S_TKc,PatternScan_PROTEIN_KINASE_ST,superfamily_Kinase_like,PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase	p.R227*	ENST00000371244.4	37	c.679	CCDS605.1	1	.	.	.	.	.	.	.	.	.	.	C	37	6.041286	0.97226	.	.	ENSG00000162409	ENST00000371244	.	.	.	5.98	3.94	0.45596	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	-8.9339	14.1147	0.65146	0.4497:0.5503:0.0:0.0	.	.	.	.	X	227	.	ENSP00000360290:R227X	R	+	1	2	PRKAA2	56934311	0.284000	0.24287	1.000000	0.80357	0.947000	0.59692	0.095000	0.15127	1.361000	0.45981	0.655000	0.94253	CGA	-	HMMSmart_S_TKc,superfamily_Kinase_like,HMMPfam_Pkinase		0.443	PRKAA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PRKAA2	protein_coding	OTTHUMT00000022753.2	C	NM_006252		56934311	+1	no_errors	NM_006252.3	genbank	human	validated	54_36p	nonsense	SNP	1.000	T
NRAS	4893	genome.wustl.edu	37	1	115256529	115256529	+	Missense_Mutation	SNP	T	T	G	rs11554290	byFrequency	TCGA-AB-2978-03A-01D-0739-09	TCGA-AB-2978-11A-01D-0739-09	T	T	T	G	T	T	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	960efb3b-7c3b-42ec-8f29-011d13493c69	be9d0262-d1fa-48c4-bba6-0d5415fb9b52	g.chr1:115256529T>G	ENST00000369535.4	-	3	435	c.182A>C	c.(181-183)cAa>cCa	p.Q61P		NM_002524.4	NP_002515.1	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	61			Q -> K (in CMNS and NCMS; somatic mutation). {ECO:0000269|PubMed:23392294}.|Q -> R (in CMNS, NCMS and KNEN; also found in lung carcinoma cell and melanoma; dbSNP:rs11554290). {ECO:0000269|PubMed:18633438, ECO:0000269|PubMed:22499344, ECO:0000269|PubMed:23392294, ECO:0000269|PubMed:3276402}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of skeletal muscle tissue development (GO:0048642)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|small GTPase mediated signal transduction (GO:0007264)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.Q61R(817)|p.Q61L(175)|p.Q61P(23)|p.Q61K(1)		NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		GTACTCTTCTTGTCCAGCTGT	0.458	Q61L(C3A_LIVER)|Q61L(HEPG2_LIVER)|Q61L(HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(IPC298_SKIN)|Q61L(KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(MELJUSO_SKIN)|Q61L(MHHES1_BONE)|Q61L(MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61P(TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(HT1197_URINARY_TRACT)|Q61R(KMS27_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(KU1919_URINARY_TRACT)|Q61R(NCIH2347_LUNG)|Q61R(ONS76_CENTRAL_NERVOUS_SYSTEM)|Q61R(SKMEL2_SKIN)|Q61R(SW1271_LUNG)|Q61R(TT2609C02_THYROID)	50	Mis		"""melanoma, MM, AML, thyroid"""				Noonan syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)																												dbGAP		Dom	yes		1	1p13.2	4893	neuroblastoma RAS viral (v-ras) oncogene homolog		"""L, E"""	1016	Substitution - Missense(1016)	skin(466)|thyroid(279)|haematopoietic_and_lymphoid_tissue(124)|NS(50)|large_intestine(27)|lung(17)|urinary_tract(11)|adrenal_gland(7)|liver(7)|breast(7)|soft_tissue(4)|testis(3)|endometrium(3)|ovary(3)|central_nervous_system(2)|pancreas(2)|eye(1)|prostate(1)|meninges(1)|autonomic_ganglia(1)	1											180.0	156.0	164.0					1																	115256529		2203	4300	6503	115058052	SO:0001583	missense	0	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	BC005219	CCDS877.1	1p13.2	2014-09-17			ENSG00000213281	ENSG00000213281			7989	protein-coding gene	gene with protein product		164790					Standard	NM_002524		Approved	N-ras	uc009wgu.3	P01111	OTTHUMG00000012059	ENST00000369535.4:c.182A>C	1.37:g.115256529T>G	ENSP00000358548:p.Gln61Pro	749	1.19	9		23	39.47	15	115058052	69	25.00	23	Q14971|Q15104|Q15282	Missense_Mutation	SNP	HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases	p.Q61P	ENST00000369535.4	37	c.182	CCDS877.1	1	.	.	.	.	.	.	.	.	.	.	T	20.0	3.930531	0.73327	.	.	ENSG00000213281	ENST00000369535	D	0.84146	-1.81	5.08	5.08	0.68730	Small GTP-binding protein domain (1);	0.000000	0.53938	U	0.000043	D	0.92708	0.7682	H	0.97806	4.08	0.80722	D	1	B	0.29253	0.239	P	0.45681	0.49	D	0.93564	0.6898	10	0.87932	D	0	.	15.0132	0.71565	0.0:0.0:0.0:1.0	.	61	P01111	RASN_HUMAN	P	61	ENSP00000358548:Q61P	ENSP00000358548:Q61P	Q	-	2	0	NRAS	115058052	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.761000	0.85260	2.120000	0.65058	0.533000	0.62120	CAA	-	HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases		0.458	NRAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NRAS	protein_coding	OTTHUMT00000033395.2	T	NM_002524		115058052	-1	no_errors	NM_002524.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	G
TET2	54790	genome.wustl.edu	37	4	106196213	106196213	+	Nonsense_Mutation	SNP	C	C	T	rs370735654		TCGA-AB-2978-03A-01D-0739-09	TCGA-AB-2978-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	960efb3b-7c3b-42ec-8f29-011d13493c69	be9d0262-d1fa-48c4-bba6-0d5415fb9b52	g.chr4:106196213C>T	ENST00000540549.1	+	11	5406	c.4546C>T	c.(4546-4548)Cga>Tga	p.R1516*	TET2_ENST00000513237.1_Nonsense_Mutation_p.R1537*|TET2_ENST00000545826.1_3'UTR|TET2_ENST00000380013.4_Nonsense_Mutation_p.R1516*			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	1516					5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)	p.R1516*(8)		NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		AGAACTTTTGCGACTTTCAGG	0.502			"""Mis N, F"""		MDS																																	dbGAP		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	8	Substitution - Nonsense(8)	haematopoietic_and_lymphoid_tissue(8)	4						C	stop/ARG	0,1384		0,0,692	29.0	36.0	34.0		4546	3.4	0.0	4		34	1,3181		0,1,1590	no	stop-gained	TET2	NM_001127208.2		0,1,2282	TT,TC,CC		0.0314,0.0,0.0219		1516/2003	106196213	1,4565	692	1591	2283	106415662	SO:0001587	stop_gained	0			AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"""KIAA1546"", ""tet oncogene family member 2"""	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	ENST00000540549.1:c.4546C>T	4.37:g.106196213C>T	ENSP00000442788:p.Arg1516*	881	3.72	34		12	55.56	15	106415662	360	40.79	248	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Nonsense_Mutation	SNP	NULL	p.R318*	ENST00000540549.1	37	c.952	CCDS47120.1	4	.	.	.	.	.	.	.	.	.	.	C	49	15.416196	0.99833	0.0	3.14E-4	ENSG00000168769	ENST00000540549;ENST00000513237;ENST00000380013	.	.	.	5.12	3.36	0.38483	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.2977	8.2504	0.31715	0.1552:0.7658:0.0:0.0791	.	.	.	.	X	1516;1537;1516	.	ENSP00000369351:R1516X	R	+	1	2	TET2	106415662	1.000000	0.71417	0.008000	0.14137	0.980000	0.70556	2.624000	0.46444	0.533000	0.28675	0.580000	0.79431	CGA	-	NULL		0.502	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	TET2	protein_coding	OTTHUMT00000253952.2	C	NM_017628		106415662	+1	no_start_codon	ENST00000265149	ensembl	human	known	54_36p	nonsense	SNP	0.992	T
HOOK3	84376	genome.wustl.edu	37	8	42823287	42823287	+	Missense_Mutation	SNP	C	C	G			TCGA-AB-2978-03A-01D-0739-09	TCGA-AB-2978-11A-01D-0739-09	C	C	C	G	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	960efb3b-7c3b-42ec-8f29-011d13493c69	be9d0262-d1fa-48c4-bba6-0d5415fb9b52	g.chr8:42823287C>G	ENST00000307602.4	+	11	1252	c.1052C>G	c.(1051-1053)aCt>aGt	p.T351S		NM_032410.3	NP_115786.1	Q86VS8	HOOK3_HUMAN	hook microtubule-tethering protein 3	351					cytoplasmic microtubule organization (GO:0031122)|early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|Golgi localization (GO:0051645)|interkinetic nuclear migration (GO:0022027)|lysosome organization (GO:0007040)|microtubule anchoring at centrosome (GO:0034454)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|protein localization to centrosome (GO:0071539)|protein transport (GO:0015031)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|FHF complex (GO:0070695)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule organizing center (GO:0005815)|pericentriolar material (GO:0000242)	identical protein binding (GO:0042802)|microtubule binding (GO:0008017)	p.T351S(1)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	31	Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.000105)|Lung NSC(58;0.000419)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.048)|LUSC - Lung squamous cell carcinoma(45;0.114)			ATGCAGAATACTGTCAGTCTA	0.403			T	RET	papillary thyroid																																	dbGAP		Dom	yes		8	8p11.21	84376	hook homolog 3		E	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	8											91.0	89.0	90.0					8																	42823287		2203	4300	6503	42942444	SO:0001583	missense	0			AK090540	CCDS6139.1	8p11.21	2013-08-21	2013-08-21		ENSG00000168172	ENSG00000168172			23576	protein-coding gene	gene with protein product		607825	"""hook homolog 3 (Drosophila)"""			9927460	Standard	NM_032410		Approved	HK3	uc003xpr.3	Q86VS8	OTTHUMG00000165278	ENST00000307602.4:c.1052C>G	8.37:g.42823287C>G	ENSP00000305699:p.Thr351Ser	758	4.17	33		15	46.43	13	42942444	65	42.98	49	D3DSY8|Q8NBH0|Q9BY13	Missense_Mutation	SNP	HMMPfam_HOOK	p.T351S	ENST00000307602.4	37	c.1052	CCDS6139.1	8	.	.	.	.	.	.	.	.	.	.	C	17.18	3.323183	0.60634	.	.	ENSG00000168172	ENST00000307602	T	0.20738	2.05	5.37	5.37	0.77165	.	0.145358	0.64402	D	0.000012	T	0.39332	0.1074	L	0.55103	1.725	0.41085	D	0.985559	D;P	0.69078	0.997;0.664	D;P	0.70487	0.969;0.527	T	0.07558	-1.0766	10	0.08599	T	0.76	-18.8514	19.0793	0.93175	0.0:1.0:0.0:0.0	.	351;351	Q2VJ45;Q86VS8	.;HOOK3_HUMAN	S	351	ENSP00000305699:T351S	ENSP00000305699:T351S	T	+	2	0	HOOK3	42942444	1.000000	0.71417	0.998000	0.56505	0.801000	0.45260	4.961000	0.63681	2.649000	0.89929	0.655000	0.94253	ACT	-	HMMPfam_HOOK		0.403	HOOK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HOOK3	protein_coding	OTTHUMT00000383172.2	C	NM_032410		42942444	+1	no_errors	NM_032410.3	genbank	human	validated	54_36p	missense	SNP	1.000	G
PXDNL	137902	genome.wustl.edu	37	8	52321633	52321633	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2978-03A-01D-0739-09	TCGA-AB-2978-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	960efb3b-7c3b-42ec-8f29-011d13493c69	be9d0262-d1fa-48c4-bba6-0d5415fb9b52	g.chr8:52321633C>T	ENST00000356297.4	-	17	2651	c.2551G>A	c.(2551-2553)Gac>Aac	p.D851N	PXDNL_ENST00000543296.1_Missense_Mutation_p.D851N	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	851					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)	p.D50N(1)		NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				CCCCGGGGGTCGGCGTGCCGG	0.697																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	8											17.0	22.0	20.0					8																	52321633		2036	4167	6203	52484186	SO:0001583	missense	0				CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"""Immunoglobulin superfamily / I-set domain containing"""	26359	protein-coding gene	gene with protein product	"""polysomal ribonuclease 1 homolog (Xenopus)"""	615904	"""peroxidasin homolog-like (Drosophila)"""			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.2551G>A	8.37:g.52321633C>T	ENSP00000348645:p.Asp851Asn	249	1.58	4		NA	NA	NA	52484186	40	34.43	21	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	HMMPfam_LRRCT,HMMSmart_SM00082,HMMPfam_VWC,HMMSmart_SM00214,PatternScan_VWFC_1,HMMPfam_LRR_1,HMMPfam_An_peroxidase,HMMSmart_SM00369,HMMSmart_SM00408,HMMSmart_SM00409,superfamily_Heme-dependent peroxidases,HMMPfam_I-set,superfamily_Immunoglobulin,superfamily_L domain-like	p.D851N	ENST00000356297.4	37	c.2551	CCDS47855.1	8	.	.	.	.	.	.	.	.	.	.	C	17.20	3.328598	0.60743	.	.	ENSG00000147485	ENST00000356297;ENST00000543296	D;D	0.85171	-1.95;-1.95	3.25	2.34	0.29019	.	0.545329	0.16040	N	0.232480	D	0.91331	0.7266	H	0.96943	3.91	0.29509	N	0.854321	P	0.47762	0.9	P	0.47673	0.554	D	0.87267	0.2283	10	0.66056	D	0.02	.	11.1673	0.48550	0.0:0.8874:0.0:0.1126	.	851	A1KZ92	PXDNL_HUMAN	N	851	ENSP00000348645:D851N;ENSP00000444865:D851N	ENSP00000348645:D851N	D	-	1	0	PXDNL	52484186	1.000000	0.71417	0.002000	0.10522	0.001000	0.01503	4.937000	0.63513	0.065000	0.16485	-0.942000	0.02676	GAC	-	HMMPfam_An_peroxidase,superfamily_Heme-dependent peroxidases		0.697	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	PXDNL	protein_coding	OTTHUMT00000377905.1	C	NM_144651		52484186	-1	no_errors	NM_144651.4	genbank	human	validated	54_36p	missense	SNP	0.996	T
OR51L1	119682	genome.wustl.edu	37	11	5020927	5020927	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2978-03A-01D-0739-09	TCGA-AB-2978-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	960efb3b-7c3b-42ec-8f29-011d13493c69	be9d0262-d1fa-48c4-bba6-0d5415fb9b52	g.chr11:5020927G>A	ENST00000321543.1	+	1	715	c.715G>A	c.(715-717)Gca>Aca	p.A239T		NM_001004755.1	NP_001004755.1	Q8NGJ5	O51L1_HUMAN	olfactory receptor, family 51, subfamily L, member 1	239						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A239T(1)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(19)|skin(2)|stomach(1)	31		Medulloblastoma(188;0.0061)|all_neural(188;0.0479)|Breast(177;0.086)		Epithelial(150;1.75e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		GCAGCTAAAGGCACTCAACAC	0.433																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	11											242.0	210.0	221.0					11																	5020927		2201	4298	6499	4977503	SO:0001583	missense	0			AB065799	CCDS31369.1	11p15.4	2012-08-09			ENSG00000176798	ENSG00000176798		"""GPCR / Class A : Olfactory receptors"""	14759	protein-coding gene	gene with protein product							Standard	NM_001004755		Approved		uc010qyu.2	Q8NGJ5	OTTHUMG00000066605	ENST00000321543.1:c.715G>A	11.37:g.5020927G>A	ENSP00000322156:p.Ala239Thr	902	3.74	35		NA	NA	NA	4977503	210	28.08	82	Q6IFE5	Missense_Mutation	SNP	HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321	p.A239T	ENST00000321543.1	37	c.715	CCDS31369.1	11	.	.	.	.	.	.	.	.	.	.	G	19.36	3.811892	0.70797	.	.	ENSG00000176798	ENST00000321543	T	0.00357	7.89	5.43	4.49	0.54785	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42420	D	0.000718	T	0.00496	0.0016	M	0.74546	2.27	0.27858	N	0.940493	P	0.45715	0.865	P	0.49421	0.61	T	0.52343	-0.8588	10	0.46703	T	0.11	.	13.53	0.61617	0.0775:0.0:0.9225:0.0	.	239	Q8NGJ5	O51L1_HUMAN	T	239	ENSP00000322156:A239T	ENSP00000322156:A239T	A	+	1	0	OR51L1	4977503	0.994000	0.37717	1.000000	0.80357	0.855000	0.48748	2.402000	0.44521	2.822000	0.97130	0.650000	0.86243	GCA	-	HMMPfam_7tm_1,superfamily_SSF81321		0.433	OR51L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR51L1	protein_coding	OTTHUMT00000142812.1	G	NM_001004755		4977503	+1	no_errors	NM_001004755.1	genbank	human	provisional	54_36p	missense	SNP	0.995	A
OR5M1	390168	genome.wustl.edu	37	11	56380881	56380881	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2978-03A-01D-0739-09	TCGA-AB-2978-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	960efb3b-7c3b-42ec-8f29-011d13493c69	be9d0262-d1fa-48c4-bba6-0d5415fb9b52	g.chr11:56380881G>A	ENST00000526538.1	-	1	97	c.98C>T	c.(97-99)gCg>gTg	p.A33V		NM_001004740.1	NP_001004740.1	Q8NGP8	OR5M1_HUMAN	olfactory receptor, family 5, subfamily M, member 1	33						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A33V(1)		central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(7)|upper_aerodigestive_tract(1)	12						TAGGTAGATCGCAAGGAATAC	0.493																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	11											176.0	168.0	171.0					11																	56380881		1974	4152	6126	56137457	SO:0001583	missense	0			AB065742	CCDS53631.1	11q11	2012-08-09				ENSG00000255012		"""GPCR / Class A : Olfactory receptors"""	8352	protein-coding gene	gene with protein product							Standard	NM_001004740		Approved	OST050	uc001nja.1	Q8NGP8		ENST00000526538.1:c.98C>T	11.37:g.56380881G>A	ENSP00000435416:p.Ala33Val	811	1.10	9		NA	NA	NA	56137457	114	24.50	37	Q6IF60|Q96RB6	Missense_Mutation	SNP	HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321	p.A33V	ENST00000526538.1	37	c.98	CCDS53631.1	11	.	.	.	.	.	.	.	.	.	.	G	0.007	-1.989048	0.00439	.	.	ENSG00000255012	ENST00000526538	T	0.01304	5.03	3.71	-4.71	0.03279	.	0.706820	0.11479	N	0.559933	T	0.00412	0.0013	N	0.00538	-1.39	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.42732	-0.9434	10	0.05436	T	0.98	-10.9499	6.0199	0.19623	0.4171:0.3321:0.2509:0.0	.	33	Q8NGP8	OR5M1_HUMAN	V	33	ENSP00000435416:A33V	ENSP00000435416:A33V	A	-	2	0	OR5M1	56137457	0.000000	0.05858	0.132000	0.22025	0.255000	0.26057	0.093000	0.15086	-0.690000	0.05142	-1.819000	0.00600	GCG	-	superfamily_SSF81321		0.493	OR5M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR5M1	protein_coding	OTTHUMT00000391610.1	G	NM_001004740		56137457	-1	no_errors	NM_001004740.1	genbank	human	provisional	54_36p	missense	SNP	0.053	A
CBL	867	genome.wustl.edu	37	11	119168130	119168130	+	Silent	SNP	G	G	A	rs143840974	byFrequency	TCGA-AB-2978-03A-01D-0739-09	TCGA-AB-2978-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	960efb3b-7c3b-42ec-8f29-011d13493c69	be9d0262-d1fa-48c4-bba6-0d5415fb9b52	g.chr11:119168130G>A	ENST00000264033.4	+	14	2566	c.2190G>A	c.(2188-2190)acG>acA	p.T730T		NM_005188.3	NP_005179.2	P22681	CBL_HUMAN	Cbl proto-oncogene, E3 ubiquitin protein ligase	730	Asp/Glu-rich (acidic).|Interaction with CD2AP.				cell surface receptor signaling pathway (GO:0007166)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|flotillin complex (GO:0016600)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ephrin receptor binding (GO:0046875)|ligase activity (GO:0016874)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SH3 domain binding (GO:0017124)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.T730T(1)		breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(194)|kidney(3)|large_intestine(9)|lung(30)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	251		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784)		ATAGCTGTACGTATGAAGCAA	0.393			"""T, Mis S, O"""	MLL	"""AML, JMML, MDS"""				Noonan syndrome;CBL gene-associated Juvenile Myelomonocytic Leukemia and Developmental Anomalies																													dbGAP		"""Dom, Rec"""	yes		11	11q23.3	867	Cas-Br-M (murine) ecotropic retroviral transforming		L	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	11											117.0	106.0	110.0					11																	119168130		2199	4295	6494	118673340	SO:0001819	synonymous_variant	0	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CBL-associated JMML	X57110	CCDS8418.1	11q23.3	2014-09-17	2012-02-23		ENSG00000110395	ENSG00000110395		"""RING-type (C3HC4) zinc fingers"""	1541	protein-coding gene	gene with protein product	"""oncogene CBL2"""	165360	"""Cas-Br-M (murine) ecotropic retroviral transforming sequence"""	CBL2		2013228	Standard	NM_005188		Approved	RNF55, c-Cbl	uc001pwe.4	P22681	OTTHUMG00000166170	ENST00000264033.4:c.2190G>A	11.37:g.119168130G>A		528	2.04	11		17	34.62	9	118673340	90	28.00	35	A3KMP8	Silent	SNP	HMMPfam_UBA,HMMSmart_RING,HMMPfam_Cbl_N,superfamily_Adaptor_Cbl_N,HMMPfam_Cbl_N2,HMMPfam_Cbl_N3,HMMSmart_UBA,PatternScan_ZF_RING_1,HMMPfam_zf-C3HC4,superfamily_SSF47473,superfamily_SSF55550,superfamily_SSF57850	p.T730	ENST00000264033.4	37	c.2190	CCDS8418.1	11																																																																																			-	NULL		0.393	CBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CBL	protein_coding	OTTHUMT00000388219.4	G	NM_005188		118673340	+1	no_errors	NM_005188.2	genbank	human	reviewed	54_36p	silent	SNP	0.666	A
RASSF9	9182	genome.wustl.edu	37	12	86199196	86199196	+	Missense_Mutation	SNP	G	G	T			TCGA-AB-2978-03A-01D-0739-09	TCGA-AB-2978-11A-01D-0739-09	G	G	G	T	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	960efb3b-7c3b-42ec-8f29-011d13493c69	be9d0262-d1fa-48c4-bba6-0d5415fb9b52	g.chr12:86199196G>T	ENST00000361228.3	-	2	960	c.592C>A	c.(592-594)Cat>Aat	p.H198N		NM_005447.3	NP_005438.2	O75901	RASF9_HUMAN	Ras association (RalGDS/AF-6) domain family (N-terminal) member 9	198					endosomal transport (GO:0016197)|protein targeting (GO:0006605)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|trans-Golgi network transport vesicle membrane (GO:0012510)	transporter activity (GO:0005215)	p.H198N(1)		endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						ACTTGCTGATGAATAGTATGG	0.378																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	12											150.0	140.0	143.0					12																	86199196		1840	4100	5940	84723327	SO:0001583	missense	0				CCDS44950.1	12q21.31	2008-02-22	2008-02-22	2008-02-22		ENSG00000198774			15739	protein-coding gene	gene with protein product		610383	"""peptidylglycine alpha-amidating monooxygenase COOH-terminal interactor"""	PAMCI		9837933, 18272789	Standard	NM_005447		Approved	P-CIP1	uc001taf.1	O75901	OTTHUMG00000169831	ENST00000361228.3:c.592C>A	12.37:g.86199196G>T	ENSP00000354884:p.His198Asn	535	0.74	4		NA	NA	NA	84723327	110	22.54	32	B3KMQ4|Q8N5U8	Missense_Mutation	SNP	HMMSmart_SM00314	p.H198N	ENST00000361228.3	37	c.592	CCDS44950.1	12	.	.	.	.	.	.	.	.	.	.	G	11.12	1.543760	0.27563	.	.	ENSG00000198774	ENST00000361228	T	0.42900	0.96	4.9	3.06	0.35304	.	0.368487	0.28052	N	0.016788	T	0.34395	0.0896	L	0.44542	1.39	0.33295	D	0.564031	B	0.06786	0.001	B	0.06405	0.002	T	0.38286	-0.9668	10	0.30854	T	0.27	-16.6722	13.078	0.59097	0.0:0.0:0.5779:0.4221	.	198	O75901	RASF9_HUMAN	N	198	ENSP00000354884:H198N	ENSP00000354884:H198N	H	-	1	0	RASSF9	84723327	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	3.208000	0.51114	0.591000	0.29711	-0.133000	0.14855	CAT	-	NULL		0.378	RASSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RASSF9	protein_coding	OTTHUMT00000406109.1	G			84723327	-1	no_errors	NM_005447.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
DOCK9	23348	genome.wustl.edu	37	13	99457268	99457268	+	Missense_Mutation	SNP	G	G	A	rs373489385		TCGA-AB-2978-03A-01D-0739-09	TCGA-AB-2978-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	960efb3b-7c3b-42ec-8f29-011d13493c69	be9d0262-d1fa-48c4-bba6-0d5415fb9b52	g.chr13:99457268G>A	ENST00000376460.1	-	52	5832	c.5752C>T	c.(5752-5754)Cgc>Tgc	p.R1918C	DOCK9_ENST00000339416.2_Missense_Mutation_p.R1905C	NM_001130048.1|NM_015296.2	NP_001123520.1|NP_056111.1	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9	1919	DHR-2.				blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R1919C(1)		breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(18)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					AGGATGGTGCGCCGTTTGCAC	0.587																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	13						G	CYS/ARG,CYS/ARG	0,4044		0,0,2022	71.0	74.0	73.0		5752,5755	4.3	1.0	13		73	1,8361		0,1,4180	no	missense,missense	DOCK9	NM_001130048.1,NM_015296.2	180,180	0,1,6202	AA,AG,GG		0.012,0.0,0.0081	probably-damaging,probably-damaging	1918/2069,1919/2070	99457268	1,12405	2022	4181	6203	98255269	SO:0001583	missense	0			AF527605	CCDS45062.1	13q32.3	2013-01-10			ENSG00000088387	ENSG00000088387		"""Pleckstrin homology (PH) domain containing"""	14132	protein-coding gene	gene with protein product	"""zizimin1"""	607325				12172552, 12432077	Standard	NM_015296		Approved	KIAA1058, ZIZ1	uc001vnt.2	Q9BZ29	OTTHUMG00000017260	ENST00000376460.1:c.5752C>T	13.37:g.99457268G>A	ENSP00000365643:p.Arg1918Cys	531	4.49	25		1	0.00	0	98255269	85	37.50	51	B3KX25|E9PFM9|Q5JUD4|Q5JUD6|Q5T2Q1|Q5TAN8|Q9BZ25|Q9BZ26|Q9BZ27|Q9BZ28|Q9UPU4	Missense_Mutation	SNP	HMMPfam_PH,HMMSmart_SM00233,HMMPfam_Ded_cyto,superfamily_PH domain-like	p.R1919C	ENST00000376460.1	37	c.5755	CCDS45062.1	13	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.6|21.6	4.169088|4.169088	0.78339|0.78339	0.0|0.0	1.2E-4|1.2E-4	ENSG00000088387|ENSG00000088387	ENST00000400228|ENST00000376460;ENST00000357329;ENST00000376455;ENST00000400235;ENST00000428223;ENST00000400220;ENST00000339416;ENST00000376453	.|T;T	.|0.25579	.|1.79;1.79	5.2|5.2	4.33|4.33	0.51752|0.51752	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.59609|0.59609	0.2206|0.2206	M|M	0.91196|0.91196	3.185|3.185	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D;D	.|0.85130	.|0.993;0.987;0.992;0.995;0.997;0.977	T|T	0.71303|0.71303	-0.4633|-0.4633	5|10	.|0.87932	.|D	.|0	.|.	15.2509|15.2509	0.73545|0.73545	0.0:0.0:0.8585:0.1415|0.0:0.0:0.8585:0.1415	.|.	.|624;537;1918;1919;574;536	.|B7Z6H5;B7Z2J2;Q9BZ29-5;Q9BZ29;B7Z6G9;F5H1Q4	.|.;.;.;DOCK9_HUMAN;.;.	V|C	480|1918;1919;1911;1896;1918;826;1905;536	.|ENSP00000365643:R1918C;ENSP00000341086:R1905C	.|ENSP00000341086:R1905C	A|R	-|-	2|1	0|0	DOCK9|DOCK9	98255269|98255269	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	3.336000|3.336000	0.52113|0.52113	1.285000|1.285000	0.44548|0.44548	0.655000|0.655000	0.94253|0.94253	GCG|CGC	-	HMMPfam_Ded_cyto		0.587	DOCK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DOCK9	protein_coding	OTTHUMT00000045566.1	G	NM_015296		98255269	-1	no_errors	NM_015296.1	genbank	human	validated	54_36p	missense	SNP	1.000	A
Unknown	0	genome.wustl.edu	37	14	20228603	20228603	+	IGR	SNP	G	G	A			TCGA-AB-2978-03A-01D-0739-09	TCGA-AB-2978-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	960efb3b-7c3b-42ec-8f29-011d13493c69	be9d0262-d1fa-48c4-bba6-0d5415fb9b52	g.chr14:20228603G>A								OR4Q3 (12075 upstream) : snoU13 (3462 downstream)																							GTTGGTAGTTGCCAACAGTGG	0.438																																						dbGAP											0			14																																								19298443	SO:0001628	intergenic_variant	0																															14.37:g.20228603G>A		743	2.23	17		NA	NA	NA	19298443	129	22.29	37		Missense_Mutation	SNP	HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321	p.A179T		37	c.535		14																																																																																			-	HMMPfam_7tm_1,superfamily_SSF81321	0	0.438					OR4H12P			G			19298443	+1	no_errors	ENST00000316004	ensembl	human	known	54_36p	missense	SNP	0.012	A
DNAH9	1770	genome.wustl.edu	37	17	11642257	11642257	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2978-03A-01D-0739-09	TCGA-AB-2978-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	960efb3b-7c3b-42ec-8f29-011d13493c69	be9d0262-d1fa-48c4-bba6-0d5415fb9b52	g.chr17:11642257G>A	ENST00000262442.4	+	29	5943	c.5875G>A	c.(5875-5877)Gag>Aag	p.E1959K	DNAH9_ENST00000454412.2_Missense_Mutation_p.E1959K|AC005701.1_ENST00000584990.1_RNA	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	1959	AAA 1. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.E1959K(1)		NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		CCTTGGGGAGGAGATCAGCCT	0.483																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	17											125.0	111.0	116.0					17																	11642257		2203	4300	6503	11582982	SO:0001583	missense	0			U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.5875G>A	17.37:g.11642257G>A	ENSP00000262442:p.Glu1959Lys	814	2.28	19		NA	NA	NA	11582982	190	46.78	167	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	HMMSmart_SM00382,HMMPfam_Dynein_heavy,PatternScan_CPSASE_2,HMMPfam_AAA_5,HMMPfam_DHC_N1,HMMPfam_DHC_N2,superfamily_Spectrin repeat,superfamily_P-loop containing nucleoside triphosphate hydrolases	p.E1959K	ENST00000262442.4	37	c.5875	CCDS11160.1	17	.	.	.	.	.	.	.	.	.	.	G	13.01	2.110479	0.37242	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.39997	1.05;1.05	5.84	5.84	0.93424	ATPase, AAA+ type, core (1);	0.211058	0.39615	N	0.001308	T	0.44477	0.1295	L	0.55481	1.735	0.80722	D	1	B	0.20052	0.041	B	0.27608	0.081	T	0.25222	-1.0138	10	0.21540	T	0.41	.	20.1392	0.98050	0.0:0.0:1.0:0.0	.	1959	Q9NYC9	DYH9_HUMAN	K	1959;1959;541	ENSP00000262442:E1959K;ENSP00000414874:E1959K	ENSP00000262442:E1959K	E	+	1	0	DNAH9	11582982	1.000000	0.71417	1.000000	0.80357	0.367000	0.29736	4.774000	0.62339	2.751000	0.94390	0.591000	0.81541	GAG	-	HMMSmart_SM00382,superfamily_P-loop containing nucleoside triphosphate hydrolases		0.483	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DNAH9	protein_coding	OTTHUMT00000252756.2	G	NM_001372		11582982	+1	no_errors	NM_001372.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
U2AF1L4	199746	genome.wustl.edu	37	19	36234765	36234765	+	Silent	SNP	G	G	T	rs576356371		TCGA-AB-2978-03A-01D-0739-09	TCGA-AB-2978-11A-01D-0739-09	G	G	G	T	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	960efb3b-7c3b-42ec-8f29-011d13493c69	be9d0262-d1fa-48c4-bba6-0d5415fb9b52	g.chr19:36234765G>T	ENST00000412391.2	-	7	536	c.523C>A	c.(523-525)Cgg>Agg	p.R175R	U2AF1L4_ENST00000378975.3_Silent_p.R136R|IGFLR1_ENST00000344990.3_5'Flank|U2AF1L4_ENST00000588100.1_5'Flank|IGFLR1_ENST00000592537.1_5'Flank|IGFLR1_ENST00000246532.1_5'Flank|U2AF1L4_ENST00000292879.5_Nonsense_Mutation_p.C116*|AD000671.6_ENST00000589807.1_3'UTR|IGFLR1_ENST00000592889.1_5'Flank|PSENEN_ENST00000591949.1_5'Flank|AC002398.9_ENST00000591613.2_5'Flank|PSENEN_ENST00000587708.2_5'Flank|PSENEN_ENST00000222266.2_5'Flank|IGFLR1_ENST00000588992.1_5'Flank			Q8WU68	U2AF4_HUMAN	U2 small nuclear RNA auxiliary factor 1-like 4	175					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	spliceosomal complex (GO:0005681)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.C116*(1)|p.R136R(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)	8	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GAAATGGGCCGCAGATGCATG	0.582													G|||	1	0.000199681	0.0	0.0014	5008	,	,		16220	0.0		0.0	False		,,,				2504	0.0					dbGAP											2	Substitution - Nonsense(1)|Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(2)	19											53.0	52.0	52.0					19																	36234765		2203	4300	6503	40926605	SO:0001819	synonymous_variant	0			BC021186, AY569437	CCDS12473.1, CCDS42551.1	19q13.13	2013-02-12	2006-04-12	2006-04-12		ENSG00000161265		"""RNA binding motif (RRM) containing"""	23020	protein-coding gene	gene with protein product		601080	"""U2(RNU2) small nuclear RNA auxiliary factor 1-like 3"", ""U2 small nuclear RNA auxiliary factor 1-like 3"""	U2AF1L3		8586425, 11739736	Standard	NM_001040425		Approved	MGC33901, U2af26	uc002obf.3	Q8WU68		ENST00000412391.2:c.523C>A	19.37:g.36234765G>T		309	3.13	10		3	62.50	5	40926605	49	37.97	30	A6NKI8|Q56UU3	Nonsense_Mutation	SNP	HMMPfam_zf-CCCH,HMMSmart_RRM_1,superfamily_SSF54928	p.C116*	ENST00000412391.2	37	c.348		19	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.71|13.71	2.317127|2.317127	0.40996|0.40996	.|.	.|.	ENSG00000161265|ENSG00000161265	ENST00000392196|ENST00000292879	.|.	.|.	.|.	5.43|5.43	0.941|0.941	0.19519|0.19519	.|.	.|1.906560	.|0.02393	.|N	.|0.079938	T|.	0.09818|.	0.0241|.	.|.	.|.	.|.	0.09310|0.09310	N|N	0.999999|0.999999	B|.	0.23735|.	0.09|.	B|.	0.17433|.	0.018|.	T|.	0.30995|.	-0.9959|.	7|.	0.87932|0.02654	D|T	0|1	-6.7426|-6.7426	1.3922|1.3922	0.02253|0.02253	0.2444:0.1472:0.4567:0.1518|0.2444:0.1472:0.4567:0.1518	.|.	56|.	B4E1T9|.	.|.	E|X	56|116	.|.	ENSP00000376034:A56E|ENSP00000292879:C116X	A|C	-|-	2|3	0|2	U2AF1L4|U2AF1L4	40926605|40926605	0.341000|0.341000	0.24801|0.24801	0.001000|0.001000	0.08648|0.08648	0.007000|0.007000	0.05969|0.05969	1.902000|1.902000	0.39848|0.39848	0.127000|0.127000	0.18452|0.18452	-0.176000|-0.176000	0.13171|0.13171	GCG|TGC	-	NULL		0.582	U2AF1L4-201	KNOWN	basic|appris_principal	protein_coding	U2AF1L4	protein_coding		G	NM_144987		40926605	-1	no_errors	NM_144987.1	genbank	human	validated	54_36p	nonsense	SNP	0.996	T
CEACAM19	56971	genome.wustl.edu	37	19	45184539	45184539	+	Silent	SNP	C	C	A			TCGA-AB-2978-03A-01D-0739-09	TCGA-AB-2978-11A-01D-0739-09	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	960efb3b-7c3b-42ec-8f29-011d13493c69	be9d0262-d1fa-48c4-bba6-0d5415fb9b52	g.chr19:45184539C>A	ENST00000403660.3	+	6	957	c.747C>A	c.(745-747)ctC>ctA	p.L249L	CTB-171A8.1_ENST00000590796.1_RNA|CEACAM19_ENST00000358777.4_Silent_p.L249L|CEACAM19_ENST00000480278.1_3'UTR			Q7Z692	CEA19_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 19	249						integral component of membrane (GO:0016021)		p.L249L(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)	11	Lung NSC(12;0.00308)|all_lung(12;0.00806)	Prostate(69;0.0376)				CTCCAGTCCTCCTGGTGTCCC	0.592																																						dbGAP											1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	19											110.0	89.0	96.0					19																	45184539		2203	4300	6503	49876379	SO:0001819	synonymous_variant	0			AF406955	CCDS12641.1, CCDS46108.1	19q13.31	2013-01-11			ENSG00000186567	ENSG00000186567		"""Immunoglobulin superfamily / V-set domain containing"""	31951	protein-coding gene	gene with protein product		606691					Standard	NM_020219		Approved	CEAL1	uc002ozo.4	Q7Z692	OTTHUMG00000151528	ENST00000403660.3:c.747C>A	19.37:g.45184539C>A		729	3.18	24		2	60.00	3	49876379	59	39.80	39	Q5XJ15|Q7Z693	Silent	SNP	superfamily_Immunoglobulin	p.L249	ENST00000403660.3	37	c.747	CCDS12641.1	19																																																																																			-	NULL		0.592	CEACAM19-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	CEACAM19	protein_coding	OTTHUMT00000323022.1	C	NM_020219		49876379	+1	no_errors	NM_020219.1	genbank	human	validated	54_36p	silent	SNP	0.676	A
RUNX1	861	genome.wustl.edu	37	21	36231783	36231783	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AB-2978-03A-01D-0739-09	TCGA-AB-2978-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	960efb3b-7c3b-42ec-8f29-011d13493c69	be9d0262-d1fa-48c4-bba6-0d5415fb9b52	g.chr21:36231783G>A	ENST00000344691.4	-	3	2097	c.520C>T	c.(520-522)Cga>Tga	p.R174*	RUNX1_ENST00000325074.5_Nonsense_Mutation_p.R189*|RUNX1_ENST00000437180.1_Nonsense_Mutation_p.R201*|RUNX1_ENST00000399240.1_Nonsense_Mutation_p.R174*|RUNX1_ENST00000486278.2_Nonsense_Mutation_p.R177*|RUNX1_ENST00000300305.3_Nonsense_Mutation_p.R201*|RUNX1_ENST00000358356.5_Nonsense_Mutation_p.R174*	NM_001001890.2	NP_001001890.1	Q01196	RUNX1_HUMAN	runt-related transcription factor 1	174	Interaction with DNA.|Runt. {ECO:0000255|PROSITE- ProRule:PRU00399}.		R -> Q (in FPDMM; impaired phosphorylation). {ECO:0000269|PubMed:10508512, ECO:0000269|PubMed:18695000}.		behavioral response to pain (GO:0048266)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system development (GO:0007417)|definitive hemopoiesis (GO:0060216)|embryonic hemopoiesis (GO:0035162)|hair follicle morphogenesis (GO:0031069)|hematopoietic stem cell proliferation (GO:0071425)|hemopoiesis (GO:0030097)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|myeloid cell differentiation (GO:0030099)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of granulocyte differentiation (GO:0030853)|peripheral nervous system neuron development (GO:0048935)|positive regulation of angiogenesis (GO:0045766)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of progesterone secretion (GO:2000872)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hair follicle cell proliferation (GO:0071336)|regulation of signal transduction (GO:0009966)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	basement membrane (GO:0005604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.R201*(5)|p.R201G(1)		breast(5)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(428)|large_intestine(3)|lung(6)|oesophagus(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	452						CGAGGTTCTCGGGGCCCATCC	0.552			T	"""RPL22, MDS1, EVI1, CBFA2T3, CBFA2T1, ETV6, LAF4"""	"""AML, preB- ALL, T-ALL"""																																	dbGAP		Dom	yes		21	21q22.3	861	runt-related transcription factor 1  (AML1)		L	6	Substitution - Nonsense(5)|Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(5)|large_intestine(1)	21	GRCh37	CM992141	RUNX1	M							274.0	240.0	251.0					21																	36231783		2203	4300	6503	35153653	SO:0001587	stop_gained	0			X79549	CCDS13639.1, CCDS42922.1, CCDS46646.1	21q22.3	2014-09-17	2008-07-29		ENSG00000159216	ENSG00000159216			10471	protein-coding gene	gene with protein product	"""aml1 oncogene"""	151385	"""acute myeloid leukemia 1"""	AML1, CBFA2		1427868, 7835892	Standard	NM_001001890		Approved	PEBP2A2, AMLCR1	uc010gmv.3	Q01196	OTTHUMG00000086299	ENST00000344691.4:c.520C>T	21.37:g.36231783G>A	ENSP00000340690:p.Arg174*	519	1.52	8		216	19.63	53	35153653	25	46.81	22	A8MV94|B2RMS4|D3DSG1|O60472|O60473|O76047|O76089|Q13081|Q13755|Q13756|Q13757|Q13758|Q13759|Q15341|Q15343|Q16122|Q16284|Q16285|Q16286|Q16346|Q16347|Q92479	Nonsense_Mutation	SNP	superfamily_p53-like transcription factors,HMMPfam_Runt,HMMPfam_RunxI	p.R201*	ENST00000344691.4	37	c.601	CCDS42922.1	21	.	.	.	.	.	.	.	.	.	.	G	40	8.081424	0.98643	.	.	ENSG00000159216	ENST00000344691;ENST00000300305;ENST00000437180;ENST00000325074;ENST00000399240;ENST00000399245;ENST00000358356;ENST00000399237;ENST00000486278	.	.	.	5.12	4.21	0.49690	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.7194	12.147	0.54028	0.0:0.0:0.8085:0.1914	.	.	.	.	X	174;201;201;189;174;177;174;189;177	.	ENSP00000300305:R201X	R	-	1	2	RUNX1	35153653	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.798000	0.47884	1.088000	0.41272	0.655000	0.94253	CGA	-	superfamily_p53-like transcription factors,HMMPfam_Runt		0.552	RUNX1-001	KNOWN	basic|CCDS	protein_coding	RUNX1	protein_coding	OTTHUMT00000194230.1	G			35153653	-1	no_errors	NM_001754.2	genbank	human	reviewed	54_36p	nonsense	SNP	1.000	A
TET2	54790	genome.wustl.edu	37	4	106183007	106183008	+	Splice_Site	INS	-	-	T			TCGA-AB-2978-03A-01D-0739-09	TCGA-AB-2978-11A-01D-0739-09	-	-	-	T	-	-	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	960efb3b-7c3b-42ec-8f29-011d13493c69	be9d0262-d1fa-48c4-bba6-0d5415fb9b52	g.chr4:106183007_106183008insT	ENST00000540549.1	+	8	4904		c.e8+2		TET2_ENST00000513237.1_Splice_Site|TET2_ENST00000545826.1_Splice_Site|TET2_ENST00000380013.4_Splice_Site			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2						5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)	p.?(2)		NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		AATAATCAGGTAAGTTTAAATA	0.302			"""Mis N, F"""		MDS																																	dbGAP		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	2	Unknown(2)	haematopoietic_and_lymphoid_tissue(2)	4																																								106402457	SO:0001630	splice_region_variant	0			AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"""KIAA1546"", ""tet oncogene family member 2"""	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	ENST00000540549.1:c.4044+2->T	4.37:g.106183007_106183007dupT		384	0.00	0		6	0.00	0	106402456	83	0.00	0	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Splice_Site	INS	-	e3+2	ENST00000540549.1	37	c.450+2_450+1	CCDS47120.1	4																																																																																			-	-		0.302	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	TET2	protein_coding	OTTHUMT00000253952.2	-	NM_017628	Intron	106402457	+1	no_start_codon	ENST00000265149	ensembl	human	known	54_36p	splice_site_ins	INS	1.000:0.991	T
