#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_CAF	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_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_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_ORegAnno_bin	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_normal_ref_reads	i_normal_ref_reads_val	i_normal_vaf	i_normal_vaf_val	i_normal_var_reads	i_normal_var_reads_val	i_reference	i_refseq_mrna_id	i_rsID	i_rsID_ref_var_alleles	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_tumor_ref_reads	i_tumor_ref_reads_val	i_tumor_vaf	i_tumor_vaf_val	i_tumor_var_reads	i_tumor_var_reads_val	i_type	i_ucsc_cons	i_variant
ZNF645	158506	genome.wustl.edu	37	X	22291397	22291397	+	Missense_Mutation	SNP	C	C	T			TCGA-ZT-A8OM-01A-11D-A428-09	TCGA-ZT-A8OM-10A-01D-A42B-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	0679e9b5-d798-4515-b290-39f2800eb027	0fe4d4c7-74a4-4caa-81c4-434984fd134a	g.chrX:22291397C>T	ENST00000323684.1	+	1	333	c.289C>T	c.(289-291)Cgt>Tgt	p.R97C		NM_152577.3	NP_689790.1	Q8N7E2	ZN645_HUMAN	zinc finger protein 645	97	HYB domain.				protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(4)|large_intestine(8)|lung(9)|ovary(2)|pancreas(1)|skin(1)|urinary_tract(1)	27						TCCGCGCTGTCGTTATCCTGT	0.398																																							0											0													80.0	68.0	72.0					X																	22291397		2203	4300	6503	SO:0001583	missense	0			AK098601	CCDS14205.1	Xp22.11	2014-01-21			ENSG00000175809	ENSG00000175809			26371	protein-coding gene	gene with protein product							Standard	NM_152577		Approved	FLJ25735, HAKAIL, CT138	uc004dai.2	Q8N7E2	OTTHUMG00000021242	ENST00000323684.1:c.289C>T	X.37:g.22291397C>T	ENSP00000323348:p.Arg97Cys		A0AV29|A0AV31|E3SBK4|Q6DJY9	Missense_Mutation	SNP	pfscan_Znf_RING,pfscan_Znf_C2H2	p.R97C	ENST00000323684.1	37	c.289	CCDS14205.1	X	.	.	.	.	.	.	.	.	.	.	C	10.58	1.390926	0.25118	.	.	ENSG00000175809	ENST00000323684	T	0.32988	1.43	3.27	-5.15	0.02866	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (1);	0.446073	0.22889	U	0.054412	T	0.12178	0.0296	N	0.14661	0.345	0.09310	N	1	P	0.49358	0.923	B	0.38712	0.28	T	0.27905	-1.0060	10	0.59425	D	0.04	.	7.1993	0.25871	0.3607:0.1434:0.4959:0.0	.	97	Q8N7E2	ZN645_HUMAN	C	97	ENSP00000323348:R97C	ENSP00000323348:R97C	R	+	1	0	ZNF645	22201318	0.968000	0.33430	0.000000	0.03702	0.028000	0.11728	0.302000	0.19192	-1.443000	0.01953	-0.576000	0.04144	CGT	0	pfscan_Znf_RING		0.398	ZNF645-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ZNF645	protein_coding	OTTHUMT00000056037.1	29	184	0	0.00	0	0	C	NM_152577	0	0		22291397	1	no_errors	ENST00000323684	ensembl	human	known	74_37	missense	55	164	8.33	6.78	5	12	SNP	0.051	T
VWA5B1	127731	genome.wustl.edu	37	1	20669080	20669080	+	Missense_Mutation	SNP	C	C	G			TCGA-ZT-A8OM-01A-11D-A428-09	TCGA-ZT-A8OM-10A-01D-A42B-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	0679e9b5-d798-4515-b290-39f2800eb027	0fe4d4c7-74a4-4caa-81c4-434984fd134a	g.chr1:20669080C>G	ENST00000375079.2	+	15	2485	c.2289C>G	c.(2287-2289)gaC>gaG	p.D763E	VWA5B1_ENST00000375083.4_Missense_Mutation_p.D763E|VWA5B1_ENST00000525343.1_3'UTR|VWA5B1_ENST00000289815.8_Missense_Mutation_p.D763E	NM_001039500.2	NP_001034589.2	Q5TIE3	VW5B1_HUMAN	von Willebrand factor A domain containing 5B1	763						extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(3)|kidney(1)|prostate(1)|skin(1)	7						GGACTTCTGACAGCCGAAGCC	0.637																																							0											0													35.0	37.0	37.0					1																	20669080		692	1591	2283	SO:0001583	missense	0			AK125833, AK057346		1p36.12	2014-02-12			ENSG00000158816	ENSG00000158816			26538	protein-coding gene	gene with protein product							Standard	NM_001039500		Approved	FLJ32784	uc009vps.2	Q5TIE3	OTTHUMG00000002835	ENST00000375079.2:c.2289C>G	1.37:g.20669080C>G	ENSP00000364220:p.Asp763Glu		A4IF35|A4IF36|Q3ZCM4|Q6ZUB4|Q96M71	Missense_Mutation	SNP	pfam_VWF_A,smart_VWF_A,pfscan_VWF_A	p.D763E	ENST00000375079.2	37	c.2289		1	.	.	.	.	.	.	.	.	.	.	C	8.136	0.784229	0.16189	.	.	ENSG00000158816	ENST00000375089;ENST00000289815;ENST00000375083;ENST00000375079	T;T;T	0.12361	2.69;2.69;2.69	4.35	4.35	0.52113	.	0.496209	0.21161	N	0.079147	T	0.07593	0.0191	N	0.19112	0.55	0.58432	D	0.999997	B;B;B	0.30281	0.001;0.073;0.275	B;B;B	0.27796	0.002;0.059;0.083	T	0.06463	-1.0825	10	0.02654	T	1	-1.5409	13.0665	0.59036	0.0:1.0:0.0:0.0	.	763;763;763	Q5TIE3;Q5TIE3-5;Q5TIE3-2	VW5B1_HUMAN;.;.	E	763	ENSP00000289815:D763E;ENSP00000364224:D763E;ENSP00000364220:D763E	ENSP00000289815:D763E	D	+	3	2	VWA5B1	20541667	0.002000	0.14202	0.026000	0.17262	0.122000	0.20287	0.460000	0.21924	2.366000	0.80165	0.416000	0.27883	GAC	0	NULL		0.637	VWA5B1-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	VWA5B1	protein_coding	OTTHUMT00000007945.4	51	93	0	0.00	0	0	C	XM_001722222	0	0		20669080	1	no_errors	ENST00000289815	ensembl	human	known	74_37	missense	53	87	7.02	10.10	4	10	SNP	0.179	G
MROH9	80133	genome.wustl.edu	37	1	170985470	170985470	+	Missense_Mutation	SNP	T	T	C			TCGA-ZT-A8OM-01A-11D-A428-09	TCGA-ZT-A8OM-10A-01D-A42B-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	0679e9b5-d798-4515-b290-39f2800eb027	0fe4d4c7-74a4-4caa-81c4-434984fd134a	g.chr1:170985470T>C	ENST00000367759.4	+	17	2055	c.1901T>C	c.(1900-1902)aTg>aCg	p.M634T		NM_001163629.1	NP_001157101.1	Q5TGP6	MROH9_HUMAN	maestro heat-like repeat family member 9	0																	TGTACTCTGATGGATCATGTG	0.433																																							0											0													146.0	117.0	126.0					1																	170985470		692	1591	2283	SO:0001583	missense	0			AK027203	CCDS41436.1, CCDS53429.1	1q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000117501	ENSG00000117501		"""maestro heat-like repeat containing"""	26287	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 129"""	C1orf129			Standard	NM_025063		Approved	FLJ23550, ARMC11	uc010plz.2	Q5TGP6	OTTHUMG00000041456	ENST00000367759.4:c.1901T>C	1.37:g.170985470T>C	ENSP00000356733:p.Met634Thr		A0PJM0|A0PJM2|F5GWX6|Q9H5D7	Missense_Mutation	SNP	superfamily_ARM-type_fold	p.M634T	ENST00000367759.4	37	c.1901	CCDS53429.1	1	.	.	.	.	.	.	.	.	.	.	T	13.21	2.170374	0.38315	.	.	ENSG00000117501	ENST00000367759	T	0.66815	-0.23	5.4	5.4	0.78164	.	.	.	.	.	T	0.59418	0.2192	L	0.27053	0.805	0.27476	N	0.952727	D	0.67145	0.996	D	0.63793	0.918	T	0.59241	-0.7491	9	0.66056	D	0.02	.	12.106	0.53813	0.0:0.0:0.0:1.0	.	634	F5GWX6	.	T	634	ENSP00000356733:M634T	ENSP00000356733:M634T	M	+	2	0	C1orf129	169252094	1.000000	0.71417	1.000000	0.80357	0.016000	0.09150	3.545000	0.53648	2.167000	0.68274	0.528000	0.53228	ATG	0	superfamily_ARM-type_fold		0.433	MROH9-201	KNOWN	basic|appris_principal|CCDS	protein_coding	MROH9	protein_coding		43	217	0	0.00	0	0	T	NM_025063	0	0		170985470	1	no_errors	ENST00000367759	ensembl	human	known	74_37	missense	45	188	11.76	6.47	6	13	SNP	1	C
TPR	7175	genome.wustl.edu	37	1	186313052	186313052	+	Silent	SNP	A	A	T			TCGA-ZT-A8OM-01A-11D-A428-09	TCGA-ZT-A8OM-10A-01D-A42B-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	0679e9b5-d798-4515-b290-39f2800eb027	0fe4d4c7-74a4-4caa-81c4-434984fd134a	g.chr1:186313052A>T	ENST00000367478.4	-	26	3884	c.3588T>A	c.(3586-3588)atT>atA	p.I1196I		NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	1196					carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)			autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		GAATTTCCAAAATTTGTTCTT	0.338			T	NTRK1	papillary thyroid																																		0		Dom	yes		1	1q25	7175	translocated promoter region		E	0													73.0	65.0	67.0					1																	186313052		1834	4085	5919	SO:0001819	synonymous_variant	0			U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"""translocated promoter region (to activated MET oncogene)"""			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.3588T>A	1.37:g.186313052A>T			Q15655|Q5SWY0|Q99968	Silent	SNP	pfam_TPR_MLP1_2,superfamily_Prefoldin,superfamily_tRNA-bd_arm	p.I1196	ENST00000367478.4	37	c.3588	CCDS41446.1	1																																																																																			0	NULL		0.338	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TPR	protein_coding	OTTHUMT00000086353.2	67	232	0	0.00	0	0	A	NM_003292	0	0		186313052	-1	no_errors	ENST00000367478	ensembl	human	known	74_37	silent	78	267	11.24	6.97	10	20	SNP	0.507	T
NR1D2	9975	genome.wustl.edu	37	3	24018736	24018736	+	Silent	SNP	C	C	A			TCGA-ZT-A8OM-01A-11D-A428-09	TCGA-ZT-A8OM-10A-01D-A42B-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	0679e9b5-d798-4515-b290-39f2800eb027	0fe4d4c7-74a4-4caa-81c4-434984fd134a	g.chr3:24018736C>A	ENST00000312521.4	+	8	1885	c.1566C>A	c.(1564-1566)gtC>gtA	p.V522V	NR1D2_ENST00000492552.1_3'UTR	NM_001145425.1|NM_005126.4	NP_001138897.1|NP_005117	Q14995	NR1D2_HUMAN	nuclear receptor subfamily 1, group D, member 2	522	Interaction with ZNHIT1.|Ligand-binding.				gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|lipid homeostasis (GO:0055088)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of circadian rhythm (GO:0042752)|regulation of energy homeostasis (GO:2000505)|regulation of inflammatory response (GO:0050727)|regulation of lipid metabolic process (GO:0019216)|regulation of skeletal muscle cell differentiation (GO:2001014)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			NS(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	22						TAGAAAACGTCAACTCTGTGG	0.338																																							0											0													62.0	65.0	64.0					3																	24018736		2203	4300	6503	SO:0001819	synonymous_variant	0			BC045613	CCDS33718.1	3p24.1	2013-01-16			ENSG00000174738	ENSG00000174738		"""Nuclear hormone receptors"""	7963	protein-coding gene	gene with protein product		602304				7997240, 10198169	Standard	NM_005126		Approved	BD73, RVR, EAR-1r, HZF2, Hs.37288	uc003ccs.2	Q14995	OTTHUMG00000155659	ENST00000312521.4:c.1566C>A	3.37:g.24018736C>A			B2R8Q3|O00402|Q86XD4	Silent	SNP	pfam_Znf_hrmn_rcpt,pfam_Nucl_hrmn_rcpt_lig-bd_core,superfamily_Nucl_hormone_rcpt_ligand-bd,smart_Znf_hrmn_rcpt,smart_Nucl_hrmn_rcpt_lig-bd_core,pfscan_Znf_hrmn_rcpt,prints_Str_hrmn_rcpt,prints_Znf_hrmn_rcpt	p.V522	ENST00000312521.4	37	c.1566	CCDS33718.1	3																																																																																			0	pfam_Nucl_hrmn_rcpt_lig-bd_core,superfamily_Nucl_hormone_rcpt_ligand-bd,smart_Nucl_hrmn_rcpt_lig-bd_core		0.338	NR1D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NR1D2	protein_coding	OTTHUMT00000341017.3	72	227	0	0.44	0	1	C		0	0		24018736	1	no_errors	ENST00000312521	ensembl	human	known	74_37	silent	114	221	8.8	7.53	11	18	SNP	1	A
BFSP2	8419	genome.wustl.edu	37	3	133191216	133191216	+	Missense_Mutation	SNP	G	G	A			TCGA-ZT-A8OM-01A-11D-A428-09	TCGA-ZT-A8OM-10A-01D-A42B-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	0679e9b5-d798-4515-b290-39f2800eb027	0fe4d4c7-74a4-4caa-81c4-434984fd134a	g.chr3:133191216G>A	ENST00000302334.2	+	6	1140	c.1051G>A	c.(1051-1053)Gat>Aat	p.D351N	BFSP2_ENST00000511434.1_3'UTR	NM_003571.2	NP_003562.1	Q13515	BFSP2_HUMAN	beaded filament structural protein 2, phakinin	351	Rod.				cell maturation (GO:0048469)|intermediate filament cytoskeleton organization (GO:0045104)|lens fiber cell development (GO:0070307)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of eye lens (GO:0005212)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|urinary_tract(1)	13						CACCTTGCACGATGCCAAGCA	0.627																																							0											0													30.0	32.0	32.0					3																	133191216		2203	4300	6503	SO:0001583	missense	0			U48224	CCDS33859.1	3q22.1	2013-01-16			ENSG00000170819	ENSG00000170819		"""Intermediate filaments type VI, eye lens intermediate filaments"""	1041	protein-coding gene	gene with protein product		603212					Standard	NM_003571		Approved	CP47, CP49, LIFL-L, phakinin	uc003epn.1	Q13515	OTTHUMG00000159719	ENST00000302334.2:c.1051G>A	3.37:g.133191216G>A	ENSP00000304987:p.Asp351Asn		Q14D32|Q9HBW5	Missense_Mutation	SNP	pfam_IF,prints_Keratin_I	p.D351N	ENST00000302334.2	37	c.1051	CCDS33859.1	3	.	.	.	.	.	.	.	.	.	.	g	35	5.474835	0.96291	.	.	ENSG00000170819	ENST00000302334	D	0.90261	-2.64	5.13	5.13	0.70059	Filament (1);	0.000000	0.56097	D	0.000022	D	0.94853	0.8337	M	0.65498	2.005	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95334	0.8432	10	0.87932	D	0	-30.7727	18.605	0.91263	0.0:0.0:1.0:0.0	.	351	Q13515	BFSP2_HUMAN	N	351	ENSP00000304987:D351N	ENSP00000304987:D351N	D	+	1	0	BFSP2	134673906	1.000000	0.71417	0.983000	0.44433	0.989000	0.77384	7.417000	0.80156	2.390000	0.81377	0.556000	0.70494	GAT	0	pfam_IF		0.627	BFSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	BFSP2	protein_coding	OTTHUMT00000357031.1	47	89	0	0.00	0	0	G		0	0		133191216	1	no_errors	ENST00000302334	ensembl	human	known	74_37	missense	61	76	7.58	11.49	5	10	SNP	1	A
MME	4311	genome.wustl.edu	37	3	154832820	154832820	+	Silent	SNP	G	G	A	rs201425951		TCGA-ZT-A8OM-01A-11D-A428-09	TCGA-ZT-A8OM-10A-01D-A42B-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	0679e9b5-d798-4515-b290-39f2800eb027	0fe4d4c7-74a4-4caa-81c4-434984fd134a	g.chr3:154832820G>A	ENST00000460393.1	+	4	354	c.234G>A	c.(232-234)gaG>gaA	p.E78E	MME_ENST00000492661.1_Silent_p.E78E|MME_ENST00000493237.1_Silent_p.E78E|MME_ENST00000477669.1_3'UTR|MME_ENST00000360490.2_Silent_p.E78E|MME_ENST00000462745.1_Silent_p.E78E	NM_000902.3|NM_007287.2	NP_000893.2|NP_009218.2	P08473	NEP_HUMAN	membrane metallo-endopeptidase	78					angiotensin maturation (GO:0002003)|beta-amyloid metabolic process (GO:0050435)|cellular protein metabolic process (GO:0044267)|cellular response to cytokine stimulus (GO:0071345)|cellular response to UV-A (GO:0071492)|cellular response to UV-B (GO:0071493)|creatinine metabolic process (GO:0046449)|kidney development (GO:0001822)|peptide metabolic process (GO:0006518)|proteolysis (GO:0006508)|replicative senescence (GO:0090399)|sensory perception of pain (GO:0019233)	axon (GO:0030424)|brush border (GO:0005903)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuron projection terminus (GO:0044306)|plasma membrane (GO:0005886)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)	endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(31)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)|Liraglutide(DB06655)	CCACCACTGAGCCTTGTACAG	0.433																																							0											0													120.0	115.0	117.0					3																	154832820		2203	4300	6503	SO:0001819	synonymous_variant	0				CCDS3172.1	3q25.2	2012-01-31	2007-02-21		ENSG00000196549	ENSG00000196549	3.4.24.11	"""CD molecules"""	7154	protein-coding gene	gene with protein product	"""neutral endopeptidase"", ""enkephalinase"", ""neprilysin"""	120520					Standard	NM_007287		Approved	CALLA, CD10, NEP	uc003fad.1	P08473	OTTHUMG00000158455	ENST00000460393.1:c.234G>A	3.37:g.154832820G>A			A8K6U6|D3DNJ9|Q3MIX4	Silent	SNP	pfam_Peptidase_M13_N,pfam_Peptidase_M13_C,prints_Peptidase_M13_C	p.E78	ENST00000460393.1	37	c.234	CCDS3172.1	3																																																																																			0	NULL		0.433	MME-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MME	protein_coding	OTTHUMT00000351076.1	48	175	0	0.00	0	0	G	NM_000902	rs201425951	G->A,C		154832820	1	no_errors	ENST00000360490	ensembl	human	known	74_37	silent	75	133	12.79	6.34	11	9	SNP	0.911	A
LPAL2	80350	genome.wustl.edu	37	6	160888623	160888623	+	RNA	SNP	C	C	G			TCGA-ZT-A8OM-01A-11D-A428-09	TCGA-ZT-A8OM-10A-01D-A42B-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	0679e9b5-d798-4515-b290-39f2800eb027	0fe4d4c7-74a4-4caa-81c4-434984fd134a	g.chr6:160888623C>G	ENST00000335388.5	-	0	1633					NR_028092.1		Q16609	LPAL2_HUMAN	lipoprotein, Lp(a)-like 2, pseudogene							extracellular region (GO:0005576)				large_intestine(1)|lung(4)	5		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.214)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)		GTCGGAGGAGCGACCACAGTC	0.527																																							0											0																																												0			U19517		6q26-q27	2010-10-27	2010-10-27	2004-02-18	ENSG00000213071	ENSG00000213071			21210	pseudogene	pseudogene		611682	"""apolipoprotein A-like"", ""lipoprotein, Lp(a)-like 2"""	APOAL		7749817, 7679504	Standard	NR_028092		Approved	APOARGC	uc011efy.2	Q16609	OTTHUMG00000015952		6.37:g.160888623C>G			E1P5B4	RNA	SNP	0	NULL	ENST00000335388.5	37	NULL		6																																																																																			0	0		0.527	LPAL2-003	KNOWN	basic	processed_transcript	LPAL2	pseudogene	OTTHUMT00000042950.1	34	27	0	0.00	0	0	C	NM_024492	0	0		160888623	-1	no_errors	ENST00000335388	ensembl	human	known	74_37	rna	69	26	11.54	12.90	9	4	SNP	0	G
STAT6	6778	genome.wustl.edu	37	12	57499106	57499106	+	Missense_Mutation	SNP	T	T	G			TCGA-ZT-A8OM-01A-11D-A428-09	TCGA-ZT-A8OM-10A-01D-A42B-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	0679e9b5-d798-4515-b290-39f2800eb027	0fe4d4c7-74a4-4caa-81c4-434984fd134a	g.chr12:57499106T>G	ENST00000300134.3	-	9	1154	c.829A>C	c.(829-831)Aag>Cag	p.K277Q	STAT6_ENST00000454075.3_Missense_Mutation_p.K277Q|STAT6_ENST00000556155.1_Missense_Mutation_p.K277Q|STAT6_ENST00000538913.2_Missense_Mutation_p.K167Q|STAT6_ENST00000537215.2_Missense_Mutation_p.K167Q|STAT6_ENST00000543873.2_Missense_Mutation_p.K277Q	NM_001178078.1|NM_003153.4	NP_001171549.1|NP_003144.3	P42226	STAT6_HUMAN	signal transducer and activator of transcription 6, interleukin-4 induced	277					cellular response to hydrogen peroxide (GO:0070301)|cellular response to reactive nitrogen species (GO:1902170)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|mammary gland epithelial cell proliferation (GO:0033598)|mammary gland morphogenesis (GO:0060443)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of isotype switching to IgE isotypes (GO:0048295)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|T-helper 1 cell lineage commitment (GO:0002296)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane raft (GO:0045121)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|protein phosphatase binding (GO:0019903)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(2)|lung(8)|ovary(4)|skin(1)	28						GGGGGCTGCTTCTCCACCAGG	0.612																																							0											0													33.0	37.0	36.0					12																	57499106		2203	4300	6503	SO:0001583	missense	0			BC005823, BQ028928	CCDS8931.1, CCDS53804.1	12q13	2013-02-14				ENSG00000166888		"""SH2 domain containing"""	11368	protein-coding gene	gene with protein product		601512				9605853, 8085155	Standard	NM_003153		Approved	D12S1644, IL-4-STAT	uc001sna.3	P42226		ENST00000300134.3:c.829A>C	12.37:g.57499106T>G	ENSP00000300134:p.Lys277Gln		A8K316|B7ZA27|F5GXI9|Q5FBW5|Q71UP4	Missense_Mutation	SNP	pfam_STAT_TF_DNA-bd,pfam_STAT_TF_alpha,pfam_STAT_TF_prot_interaction,pfam_SH2,superfamily_p53-like_TF_DNA-bd,superfamily_STAT_TF_coiled-coil,superfamily_STAT_TF_prot_interaction,smart_STAT_TF_prot_interaction,smart_SH2,pfscan_SH2	p.K277Q	ENST00000300134.3	37	c.829	CCDS8931.1	12	.	.	.	.	.	.	.	.	.	.	T	22.7	4.324981	0.81580	.	.	ENSG00000166888	ENST00000300134;ENST00000535201;ENST00000538913;ENST00000543873;ENST00000556155;ENST00000537215;ENST00000454075;ENST00000542721;ENST00000542516	D;D;D;D;D;D	0.89270	-2.49;-2.49;-2.49;-2.49;-2.49;-2.49	4.64	4.64	0.57946	STAT transcription factor, DNA-binding, subdomain (1);STAT transcription factor, DNA-binding (1);p53-like transcription factor, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.93429	0.7904	M	0.73962	2.25	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.93959	0.7239	10	0.87932	D	0	-22.8734	12.063	0.53572	0.0:0.0:0.0:1.0	.	277;277	A8K4S9;P42226	.;STAT6_HUMAN	Q	277;167;167;277;277;167;277;167;277	ENSP00000300134:K277Q;ENSP00000445409:K167Q;ENSP00000438451:K277Q;ENSP00000451742:K277Q;ENSP00000444530:K167Q;ENSP00000401486:K277Q	ENSP00000300134:K277Q	K	-	1	0	STAT6	55785373	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.704000	0.84595	1.947000	0.56498	0.459000	0.35465	AAG	0	pfam_STAT_TF_DNA-bd,superfamily_p53-like_TF_DNA-bd		0.612	STAT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	STAT6	protein_coding	OTTHUMT00000412248.3	44	86	0	0.00	0	0	T	NM_003153	0	0		57499106	-1	no_errors	ENST00000300134	ensembl	human	known	74_37	missense	65	70	13.33	9.09	10	7	SNP	1	G
RPL23A	6147	genome.wustl.edu	37	17	27049790	27049790	+	Missense_Mutation	SNP	A	A	G			TCGA-ZT-A8OM-01A-11D-A428-09	TCGA-ZT-A8OM-10A-01D-A42B-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	0679e9b5-d798-4515-b290-39f2800eb027	0fe4d4c7-74a4-4caa-81c4-434984fd134a	g.chr17:27049790A>G	ENST00000422514.2	+	3	872	c.259A>G	c.(259-261)Atg>Gtg	p.M87V	SNORD42A_ENST00000459584.1_RNA|RPL23A_ENST00000472628.1_Start_Codon_SNP_p.M1V|SNORD42B_ENST00000458893.1_RNA|RPL23A_ENST00000394938.4_Missense_Mutation_p.M125V|SNORD4B_ENST00000459083.1_RNA|SNORD4A_ENST00000459174.1_RNA|AC010761.8_ENST00000582718.1_RNA|RPL23A_ENST00000496182.1_Start_Codon_SNP_p.M1V	NM_000984.5	NP_000975.2	P62750	RL23A_HUMAN	ribosomal protein L23a	87					cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			endometrium(1)|lung(3)|ovary(1)	5	Lung NSC(42;0.00431)					TGAGTCTGCCATGAAGAAGAT	0.473																																							0											0													55.0	55.0	55.0					17																	27049790		2203	4297	6500	SO:0001583	missense	0			U43701	CCDS11241.1	17q11.2	2011-04-06			ENSG00000198242	ENSG00000198242		"""L ribosomal proteins"""	10317	protein-coding gene	gene with protein product		602326				9417910	Standard	NM_000984		Approved	L23A	uc002hci.3	P62750	OTTHUMG00000132684	ENST00000422514.2:c.259A>G	17.37:g.27049790A>G	ENSP00000389103:p.Met87Val		B2R5B2|P29316|P39024|Q92774	Missense_Mutation	SNP	pfam_Ribosomal_L23/L25_N,pfam_Ribosomal_L25/23,superfamily_Ribosomal_L23/L15e_core_dom,tigrfam_Ribosomal_L23	p.M87V	ENST00000422514.2	37	c.259	CCDS11241.1	17	.	.	.	.	.	.	.	.	.	.	A	18.80	3.701227	0.68501	.	.	ENSG00000198242	ENST00000422514;ENST00000394938;ENST00000394935	T;T	0.42131	0.98;0.98	5.27	5.27	0.74061	Ribosomal protein L23/L15e (1);Nucleotide-binding, alpha-beta plait (1);	0.000000	0.42964	U	0.000625	T	0.48295	0.1492	M	0.77486	2.375	0.80722	D	1	B	0.33583	0.418	B	0.35550	0.205	T	0.54193	-0.8330	10	0.59425	D	0.04	0.0047	14.7149	0.69259	1.0:0.0:0.0:0.0	.	87	P62750	RL23A_HUMAN	V	87;125;89	ENSP00000389103:M87V;ENSP00000378396:M125V	ENSP00000378393:M89V	M	+	1	0	RPL23A	24073917	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.066000	0.71185	2.127000	0.65507	0.524000	0.50904	ATG	0	pfam_Ribosomal_L25/23,superfamily_Ribosomal_L23/L15e_core_dom,tigrfam_Ribosomal_L23		0.473	RPL23A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RPL23A	protein_coding	OTTHUMT00000255975.1	46	0	0	0.00	0	0	A	NM_000984	0	0		27049790	1	no_errors	ENST00000422514	ensembl	human	known	74_37	missense	50	0	7.41	0.00	4	0	SNP	1	G
NF1	4763	genome.wustl.edu	37	17	29683580	29683580	+	Missense_Mutation	SNP	C	C	G			TCGA-ZT-A8OM-01A-11D-A428-09	TCGA-ZT-A8OM-10A-01D-A42B-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	0679e9b5-d798-4515-b290-39f2800eb027	0fe4d4c7-74a4-4caa-81c4-434984fd134a	g.chr17:29683580C>G	ENST00000358273.4	+	52	8101	c.7718C>G	c.(7717-7719)gCa>gGa	p.A2573G	NF1_ENST00000417592.2_3'UTR|NF1_ENST00000444181.2_Missense_Mutation_p.A366G|NF1_ENST00000356175.3_Missense_Mutation_p.A2552G	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	2573					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(3)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		AGGAGAGTAGCAGAAACTGAT	0.378			"""D, Mis, N, F, S, O"""		"""neurofibroma, glioma"""	"""neurofibroma, glioma"""			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																													0	yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	11	Whole gene deletion(8)|Unknown(3)	soft_tissue(7)|autonomic_ganglia(2)|lung(1)|central_nervous_system(1)											89.0	76.0	80.0					17																	29683580		2203	4300	6503	SO:0001583	missense	0	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"""neurofibromatosis"", ""von Recklinghausen disease"", ""Watson disease"""	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.7718C>G	17.37:g.29683580C>G	ENSP00000351015:p.Ala2573Gly		O00662|Q14284|Q14930|Q14931|Q9UMK3	Missense_Mutation	SNP	pfam_RasGAP,superfamily_Rho_GTPase_activation_prot,superfamily_ARM-type_fold,superfamily_CRAL-TRIO_dom,smart_RasGAP,smart_CRAL-TRIO_dom,pfscan_CRAL-TRIO_dom,pfscan_RasGAP	p.A2573G	ENST00000358273.4	37	c.7718	CCDS42292.1	17	.	.	.	.	.	.	.	.	.	.	C	18.40	3.614864	0.66672	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735;ENST00000444181	T;T;T;T	0.48836	3.13;3.29;2.97;0.8	5.66	5.66	0.87406	Armadillo-type fold (1);	0.049987	0.85682	D	0.000000	T	0.45397	0.1340	L	0.40543	1.245	0.80722	D	1	B;B;B	0.33612	0.419;0.229;0.0	B;B;B	0.35278	0.143;0.199;0.002	T	0.29941	-0.9995	10	0.38643	T	0.18	.	20.1253	0.97977	0.0:1.0:0.0:0.0	.	366;2552;2573	B4DXH1;P21359-2;P21359	.;.;NF1_HUMAN	G	2573;2552;2218;366	ENSP00000351015:A2573G;ENSP00000348498:A2552G;ENSP00000389907:A2218G;ENSP00000396481:A366G	ENSP00000348498:A2552G	A	+	2	0	NF1	26707706	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.115000	0.77110	2.832000	0.97577	0.655000	0.94253	GCA	0	superfamily_ARM-type_fold		0.378	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NF1	protein_coding	OTTHUMT00000256351.2	59	268	0	0.37	0	1	C	NM_000267	0	0		29683580	1	no_errors	ENST00000358273	ensembl	human	known	74_37	missense	79	241	7.06	9.74	6	26	SNP	1	G
SPATA5	166378	genome.wustl.edu	37	4	123928724	123928749	+	Intron	DEL	TGTGTGTGTGTGTGTGTGTGTGTGTG	TGTGTGTGTGTGTGTGTGTGTGTGTG	-	rs112099221|rs200478794|rs368779194|rs112656406|rs148702654		TCGA-ZT-A8OM-01A-11D-A428-09	TCGA-ZT-A8OM-10A-01D-A42B-09	TGTGTGTGTGTGTGTGTGTGTGTGTG	TGTGTGTGTGTGTGTGTGTGTGTGTG					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	0679e9b5-d798-4515-b290-39f2800eb027	0fe4d4c7-74a4-4caa-81c4-434984fd134a	g.chr4:123928724_123928749delTGTGTGTGTGTGTGTGTGTGTGTGTG	ENST00000274008.4	+	11	1938				AC109357.1_ENST00000401335.1_RNA|SPATA5_ENST00000422835.2_Intron	NM_145207.2	NP_660208.2	Q8NB90	SPAT5_HUMAN	spermatogenesis associated 5						cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)			endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24						tgtgtgtatatgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg	0.358																																							0											0																																										SO:0001627	intron_variant	0			AF361489	CCDS3730.1	4q28.1	2010-04-21			ENSG00000145375	ENSG00000145375		"""ATPases / AAA-type"""	18119	protein-coding gene	gene with protein product	"""ATPase family gene 2 homolog (S. cerevisiae)"""	613940				16465403	Standard	NM_145207		Approved	SPAF, AFG2	uc003iez.4	Q8NB90	OTTHUMG00000133074	ENST00000274008.4:c.1870-20592TGTGTGTGTGTGTGTGTGTGTGTGTG>-	4.37:g.123928724_123928749delTGTGTGTGTGTGTGTGTGTGTGTGTG			C9JT97|Q86XW1|Q8NI20|Q8TDL7	RNA	DEL	0	NULL	ENST00000274008.4	37	NULL	CCDS3730.1	4																																																																																			0	0		0.358	SPATA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ENSG00000216154	protein_coding	OTTHUMT00000256714.2	18	0	5.26	0.00	1	0	TGTGTGTGTGTGTGTGTGTGTGTGTG	NM_145207	rs148702654	ATGTGTGTGTGTGTGTGTGTGTGTGTG->A		123928749	-1	no_errors	ENST00000401335	ensembl	human	novel	74_37	rna	29	0	14.71	0.00	5	0	DEL	0.008:0.004:0.004:0.003:0.003:0.003:0.005:0.006:0.007:0.007:0.007:0.006:0.005:0.003:0.004:0.003:0.005:0.006:0.012:0.017:0.021:0.026:0.029:0.032:0.035:0.037	0
MAML2	84441	genome.wustl.edu	37	11	95825372	95825374	+	In_Frame_Del	DEL	TGT	TGT	-	rs60727839|rs543548810|rs112603485|rs141671766	byFrequency	TCGA-ZT-A8OM-01A-11D-A428-09	TCGA-ZT-A8OM-10A-01D-A42B-09	TGT	TGT					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	0679e9b5-d798-4515-b290-39f2800eb027	0fe4d4c7-74a4-4caa-81c4-434984fd134a	g.chr11:95825372_95825374delTGT	ENST00000524717.1	-	2	3105_3107	c.1821_1823delACA	c.(1819-1824)caacag>cag	p.607_608QQ>Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	607					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)	p.Q607Q(1)	CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				ctgctgctgctgttgctgctgct	0.532			T	"""MECT1, CRTC3"""	salivary gland mucoepidermoid																																		0		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	1	Substitution - coding silent(1)	endometrium(1)																																								SO:0001651	inframe_deletion	0			AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"""mastermind (Drosophila)-like 2"""			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.1821_1823delACA	11.37:g.95825372_95825374delTGT	ENSP00000434552:p.Gln621del		A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	In_Frame_Del	DEL	pfam_Neuroggenic_mastermind-like_N	p.Q611in_frame_del	ENST00000524717.1	37	c.1823_1821	CCDS44714.1	11																																																																																			0	NULL		0.532	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MAML2	protein_coding	OTTHUMT00000395540.1	35	2	2.78	0.00	1	0	TGT		0	0		95825374	-1	no_errors	ENST00000524717	ensembl	human	known	74_37	in_frame_del	27	8	15.62	0.00	5	0	DEL	0.003:0.003:0.003	0
