#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
PTPRZ1	5803	genome.wustl.edu	37	7	121652082	121652082	+	Silent	SNP	G	G	C			TCGA-ZB-A96G-01A-11D-A428-09	TCGA-ZB-A96G-10A-01D-A42B-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ee2308ce-4b4b-4d83-9865-5485b968686e	1cbd7dff-ae2c-49e7-9762-1c026803f159	g.chr7:121652082G>C	ENST00000393386.2	+	12	3393	c.2982G>C	c.(2980-2982)ggG>ggC	p.G994G	PTPRZ1_ENST00000449182.1_Intron|PTPRZ1_ENST00000483028.1_Intron	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	994					axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.G994G(2)		NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						CTGGTGATGGGGAATGGTCTG	0.448																																							0											2	Substitution - coding silent(2)	central_nervous_system(2)											135.0	134.0	134.0					7																	121652082		2203	4300	6503	SO:0001819	synonymous_variant	0			M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.2982G>C	7.37:g.121652082G>C			A4D0W5|C9JFM0|O76043|Q9UDR6	Silent	SNP	pfam_Tyr_Pase_rcpt/non-rcpt,pfam_Carbonic_anhydrase_a,pfam_Fibronectin_type3,superfamily_Carbonic_anhydrase_a,superfamily_Fibronectin_type3,smart_Fibronectin_type3,smart_Tyr_Pase_rcpt/non-rcpt,smart_Tyr_Pase_cat,pfscan_Fibronectin_type3,pfscan_Tyr/Dual-sp_Pase,pfscan_Tyr_Pase_rcpt/non-rcpt,pfscan_Carbonic_anhydrase_a,prints_Tyr_Pase_rcpt/non-rcpt	p.G994	ENST00000393386.2	37	c.2982	CCDS34740.1	7																																																																																			0	NULL		0.448	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PTPRZ1	protein_coding	OTTHUMT00000347288.1	81	237	0	0.00	0	0	G	NM_002851	0	0		121652082	1	no_errors	ENST00000393386	ensembl	human	known	74_37	silent	55	194	8.33	4.43	5	9	SNP	0.983	C
TAF1L	138474	genome.wustl.edu	37	9	32633957	32633957	+	Missense_Mutation	SNP	A	A	T			TCGA-ZB-A96G-01A-11D-A428-09	TCGA-ZB-A96G-10A-01D-A42B-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ee2308ce-4b4b-4d83-9865-5485b968686e	1cbd7dff-ae2c-49e7-9762-1c026803f159	g.chr9:32633957A>T	ENST00000242310.4	-	1	1710	c.1621T>A	c.(1621-1623)Tct>Act	p.S541T	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	541					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)			breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		GGGGAGTTAGAGGTGGCCTCT	0.493																																							0											0													151.0	151.0	151.0					9																	32633957		2203	4300	6503	SO:0001583	missense	0			AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"""TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"""			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.1621T>A	9.37:g.32633957A>T	ENSP00000418379:p.Ser541Thr		Q0VG57	Missense_Mutation	SNP	pirsf_TAF1_animal,pfam_TFIID_sub1_DUF3591,pfam_Bromodomain,pfam_TAF_II_230-bd,superfamily_Bromodomain,superfamily_TAF_II_230-bd,smart_Bromodomain,prints_Bromodomain,pfscan_Bromodomain	p.S541T	ENST00000242310.4	37	c.1621	CCDS35003.1	9	.	.	.	.	.	.	.	.	.	.	A	14.44	2.536434	0.45176	.	.	ENSG00000122728	ENST00000242310	T	0.07444	3.19	1.16	1.16	0.20824	.	0.065614	0.64402	D	0.000005	T	0.03871	0.0109	N	0.16368	0.405	0.37334	D	0.910086	B	0.13145	0.007	B	0.14578	0.011	T	0.41215	-0.9521	10	0.09338	T	0.73	.	6.3765	0.21511	1.0:0.0:0.0:0.0	.	541	Q8IZX4	TAF1L_HUMAN	T	541	ENSP00000418379:S541T	ENSP00000418379:S541T	S	-	1	0	TAF1L	32623957	1.000000	0.71417	0.987000	0.45799	0.753000	0.42808	4.407000	0.59754	0.426000	0.26116	0.164000	0.16699	TCT	0	pirsf_TAF1_animal		0.493	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TAF1L	protein_coding	OTTHUMT00000052012.2	115	69	0	0.00	0	0	A		0	0		32633957	-1	no_errors	ENST00000242310	ensembl	human	known	74_37	missense	76	52	9.52	7.14	8	4	SNP	1	T
RC3H2	54542	genome.wustl.edu	37	9	125621159	125621159	+	Missense_Mutation	SNP	T	T	C			TCGA-ZB-A96G-01A-11D-A428-09	TCGA-ZB-A96G-10A-01D-A42B-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ee2308ce-4b4b-4d83-9865-5485b968686e	1cbd7dff-ae2c-49e7-9762-1c026803f159	g.chr9:125621159T>C	ENST00000373670.1	-	11	2672	c.2072A>G	c.(2071-2073)tAt>tGt	p.Y691C	RC3H2_ENST00000357244.2_Missense_Mutation_p.Y691C|RC3H2_ENST00000423239.2_Missense_Mutation_p.Y691C			Q9HBD1	RC3H2_HUMAN	ring finger and CCCH-type domains 2	691	Pro-rich.				B cell homeostasis (GO:0001782)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymph node development (GO:0048535)|multicellular organism growth (GO:0035264)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|post-embryonic development (GO:0009791)|posttranscriptional regulation of gene expression (GO:0010608)|protein polyubiquitination (GO:0000209)|spleen development (GO:0048536)|T cell homeostasis (GO:0043029)|T cell proliferation (GO:0042098)|T follicular helper cell differentiation (GO:0061470)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(6)|large_intestine(4)|liver(1)|lung(11)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	33						CACAGGAGCATACATTCCAGA	0.493																																							0											0													140.0	143.0	142.0					9																	125621159		1986	4162	6148	SO:0001583	missense	0			AK000308	CCDS43874.1, CCDS48014.1	9q34	2013-01-18	2010-09-15	2007-02-06	ENSG00000056586	ENSG00000056586		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, CCCH-type domain containing"""	21461	protein-coding gene	gene with protein product		615231	"""membrane associated DNA binding protein"", ""ring finger and CCCH-type zinc finger domains 2"""	MNAB		10938276	Standard	NM_001100588		Approved	FLJ20301, FLJ20713, RNF164	uc010mwc.1	Q9HBD1	OTTHUMG00000020632	ENST00000373670.1:c.2072A>G	9.37:g.125621159T>C	ENSP00000362774:p.Tyr691Cys		Q4VXB1|Q5JPD7|Q86ST6|Q8N3D6|Q96F27|Q9H5J2|Q9HBD2|Q9NWN9|Q9NXE1	Missense_Mutation	SNP	pfam_Znf_CCCH,smart_Znf_RING,smart_Znf_CCCH,pfscan_Znf_RING	p.Y691C	ENST00000373670.1	37	c.2072	CCDS43874.1	9	.	.	.	.	.	.	.	.	.	.	T	18.89	3.719963	0.68844	.	.	ENSG00000056586	ENST00000373670;ENST00000357244;ENST00000373663;ENST00000423239	T;T;T	0.58210	0.35;0.35;0.4	5.57	5.57	0.84162	.	0.127353	0.56097	D	0.000030	T	0.61937	0.2387	L	0.34521	1.04	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.79784	0.984;0.993	T	0.65001	-0.6274	10	0.66056	D	0.02	-18.5553	13.4654	0.61251	0.0:0.0:0.0:1.0	.	691;691	Q9HBD1;Q9HBD1-4	RC3H2_HUMAN;.	C	691;691;562;691	ENSP00000362774:Y691C;ENSP00000349783:Y691C;ENSP00000411767:Y691C	ENSP00000349783:Y691C	Y	-	2	0	RC3H2	124660980	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.700000	0.74619	2.109000	0.64355	0.533000	0.62120	TAT	0	NULL		0.493	RC3H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RC3H2	protein_coding	OTTHUMT00000053966.1	83	139	0	0.00	0	0	T	NM_018835	0	0		125621159	-1	no_errors	ENST00000357244	ensembl	human	known	74_37	missense	67	106	8.22	7.02	6	8	SNP	1	C
SYNE2	23224	genome.wustl.edu	37	14	64453318	64453318	+	Missense_Mutation	SNP	A	A	G	rs556342048		TCGA-ZB-A96G-01A-11D-A428-09	TCGA-ZB-A96G-10A-01D-A42B-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ee2308ce-4b4b-4d83-9865-5485b968686e	1cbd7dff-ae2c-49e7-9762-1c026803f159	g.chr14:64453318A>G	ENST00000344113.4	+	19	2508	c.2296A>G	c.(2296-2298)Atg>Gtg	p.M766V	SYNE2_ENST00000358025.3_Missense_Mutation_p.M766V|SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000554584.1_Missense_Mutation_p.M766V	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	766					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		GGACACCTCAATGGAAGAATC	0.343													A|||	1	0.000199681	0.0	0.0	5008	,	,		18670	0.001		0.0	False		,,,				2504	0.0						0.9998,0.0001997											0													126.0	119.0	121.0					14																	64453318		1863	4102	5965	SO:0001583	missense	0			AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"""nuclear envelope spectrin repeat-2"", ""nucleus and actin connecting element"""	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.2296A>G	14.37:g.64453318A>G	ENSP00000341781:p.Met766Val		Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	pfam_CH-domain,pfam_KASH,pfam_Spectrin_repeat,pfam_CAMSAP_CH,superfamily_CH-domain,smart_CH-domain,smart_Spectrin/alpha-actinin,pfscan_CH-domain,pfscan_KASH	p.M766V	ENST00000344113.4	37	c.2296	CCDS41963.1	14	.	.	.	.	.	.	.	.	.	.	A	0.086	-1.174940	0.01646	.	.	ENSG00000054654	ENST00000358025;ENST00000344113;ENST00000554584;ENST00000261678	T;T;T	0.56103	0.85;0.85;0.48	5.67	-11.3	0.00108	.	1.636630	0.03437	N	0.208638	T	0.21962	0.0529	N	0.01705	-0.755	0.09310	N	0.999996	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.24870	-1.0148	10	0.20046	T	0.44	.	12.394	0.55374	0.2103:0.0:0.6355:0.1542	.	766;766	Q8WXH0;Q8WXH0-2	SYNE2_HUMAN;.	V	766	ENSP00000350719:M766V;ENSP00000341781:M766V;ENSP00000452570:M766V	ENSP00000261678:M766V	M	+	1	0	SYNE2	63523071	0.000000	0.05858	0.000000	0.03702	0.032000	0.12392	-2.925000	0.00691	-2.953000	0.00292	-2.133000	0.00342	ATG	0	NULL		0.343	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SYNE2	protein_coding	OTTHUMT00000276994.2	185	223	0	0.00	0	0	A	NM_182914	rs556342048	A->G		64453318	1	no_errors	ENST00000358025	ensembl	human	known	74_37	missense	100	169	7.41	8.65	8	16	SNP	0	G
TSPEAR	54084	genome.wustl.edu	37	21	45945637	45945637	+	Missense_Mutation	SNP	T	T	C			TCGA-ZB-A96G-01A-11D-A428-09	TCGA-ZB-A96G-10A-01D-A42B-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ee2308ce-4b4b-4d83-9865-5485b968686e	1cbd7dff-ae2c-49e7-9762-1c026803f159	g.chr21:45945637T>C	ENST00000323084.4	-	8	1300	c.1235A>G	c.(1234-1236)aAg>aGg	p.K412R	C21orf90_ENST00000465978.1_Intron|TSPEAR_ENST00000397916.1_Missense_Mutation_p.K344R	NM_001272037.1|NM_144991.2	NP_001258966.1|NP_659428.2	Q8WU66	TSEAR_HUMAN	thrombospondin-type laminin G domain and EAR repeats	412					sensory perception of sound (GO:0007605)	cell surface (GO:0009986)|ciliary membrane (GO:0060170)|extracellular region (GO:0005576)|stereocilium (GO:0032420)				breast(1)|central_nervous_system(6)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)	37						TGGGGTAAACTTCAGCTTTCT	0.522																																							0											0													199.0	196.0	197.0					21																	45945637		2203	4300	6503	SO:0001583	missense	0			AJ487962	CCDS13712.1, CCDS74801.1	21q22.3	2012-10-30	2011-01-25	2011-01-25	ENSG00000175894	ENSG00000175894			1268	protein-coding gene	gene with protein product		612920	"""chromosome 21 open reading frame 29"", ""deafness, autosomal recessive 98"""	C21orf29, DFNB98		12095917, 22678063	Standard	NM_144991		Approved	MGC11251, TSP-EAR	uc002zfe.1	Q8WU66	OTTHUMG00000041215	ENST00000323084.4:c.1235A>G	21.37:g.45945637T>C	ENSP00000321987:p.Lys412Arg			Missense_Mutation	SNP	pfam_EPTP,superfamily_ConA-like_lec_gl_sf,smart_Laminin_G,pfscan_EAR	p.K412R	ENST00000323084.4	37	c.1235	CCDS13712.1	21	.	.	.	.	.	.	.	.	.	.	T	9.318	1.057346	0.19907	.	.	ENSG00000175894	ENST00000323084;ENST00000397918;ENST00000397916;ENST00000341581	T;T	0.81163	-1.46;-1.46	4.32	3.23	0.37069	.	0.163459	0.52532	N	0.000075	T	0.67011	0.2848	L	0.37750	1.13	0.80722	D	1	B	0.09022	0.002	B	0.13407	0.009	T	0.54529	-0.8280	10	0.15499	T	0.54	-6.8571	7.0656	0.25149	0.0:0.1191:0.0:0.8809	.	412	Q8WU66	TSEAR_HUMAN	R	412;265;344;413	ENSP00000321987:K412R;ENSP00000381012:K344R	ENSP00000321987:K412R	K	-	2	0	TSPEAR	44770065	0.991000	0.36638	0.981000	0.43875	0.840000	0.47671	1.697000	0.37784	0.731000	0.32448	0.402000	0.26972	AAG	0	pfam_EPTP,pfscan_EAR		0.522	TSPEAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TSPEAR	protein_coding	OTTHUMT00000098761.1	51	173	0	0.00	0	0	T	NM_144991	0	0		45945637	-1	no_errors	ENST00000323084	ensembl	human	known	74_37	missense	59	129	9.23	7.19	6	10	SNP	0.993	C
MLLT4	4301	genome.wustl.edu	37	6	168366692	168366694	+	In_Frame_Del	DEL	GAG	GAG	-			TCGA-ZB-A96G-01A-11D-A428-09	TCGA-ZB-A96G-10A-01D-A42B-09	GAG	GAG	GAG	-	GAG	GAG	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ee2308ce-4b4b-4d83-9865-5485b968686e	1cbd7dff-ae2c-49e7-9762-1c026803f159	g.chr6:168366692_168366694delGAG	ENST00000447894.2	+	31	5203_5205	c.5203_5205delGAG	c.(5203-5205)gagdel	p.E1740del	MLLT4_ENST00000400822.3_In_Frame_Del_p.E1750del|MLLT4_ENST00000366806.2_In_Frame_Del_p.E1740del|MLLT4_ENST00000392112.1_Intron|MLLT4_ENST00000351017.4_In_Frame_Del_p.E1747del			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	1740					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(13)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)		TGCATACAATgaggaggaggagg	0.581			T	MLL	AL																																		0		Dom	yes		6	6q27	4301	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AF6)"""		L	0										35,2895		2,31,1432						1.1	0.0			7	53,5815		5,43,2886	no	intron	MLLT4	NM_001207008.1		7,74,4318	A1A1,A1R,RR		0.9032,1.1945,1.0002				88,8710				SO:0001651	inframe_deletion	0			AB011399	CCDS47517.1, CCDS75553.1	6q27	2008-02-05	2001-11-28		ENSG00000130396	ENSG00000130396			7137	protein-coding gene	gene with protein product		159559	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 4"""			8242616	Standard	NM_001040000		Approved	AF-6, AF6	uc021zij.1	P55196	OTTHUMG00000016031	ENST00000447894.2:c.5203_5205delGAG	6.37:g.168366701_168366703delGAG	ENSP00000404595:p.Glu1740del		O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	In_Frame_Del	DEL	pfam_Ras-assoc,pfam_Dil_domain,pfam_PDZ,pfam_FHA_dom,superfamily_PDZ,superfamily_SMAD_FHA_domain,smart_Ras-assoc,smart_FHA_dom,smart_PDZ,pfscan_Dilute,pfscan_PDZ,pfscan_Ras-assoc	p.E1738in_frame_del	ENST00000447894.2	37	c.5203_5205		6																																																																																			0	NULL		0.581	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	MLLT4	protein_coding	OTTHUMT00000372077.1	38	150	0	1.32	0	2	GAG	NM_005936	0	0		168366694	1	no_errors	ENST00000366806	ensembl	human	known	74_37	in_frame_del	35	113	10.26	5.04	4	6	DEL	1.000:1.000:1.000	0
FAM230A	653203	genome.wustl.edu	37	22	20710651	20710651	+	Missense_Mutation	SNP	C	C	T			TCGA-ZB-A96G-01A-11D-A428-09	TCGA-ZB-A96G-10A-01D-A42B-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	ee2308ce-4b4b-4d83-9865-5485b968686e	1cbd7dff-ae2c-49e7-9762-1c026803f159	g.chr22:20710651C>T	ENST00000434783.3	+	8	2567	c.2383C>T	c.(2383-2385)Ccc>Tcc	p.P795S	USP41_ENST00000486536.2_Intron|USP41_ENST00000454608.2_Intron					family with sequence similarity 230, member A																		GAGGTCGCTGCCCAGGGCATC	0.667																																							0											0																																										SO:0001583	missense	0			JX456222		22q11.21	2014-08-13			ENSG00000188280	ENSG00000188280			45045	other	unknown							Standard	XM_006724099		Approved	DGCR15			OTTHUMG00000150686	ENST00000434783.3:c.2383C>T	22.37:g.20710651C>T	ENSP00000463576:p.Pro795Ser			Missense_Mutation	SNP	pfam_Ret-finger_pr-like_3_antisense,superfamily_Kinase-like_dom	p.P795S	ENST00000434783.3	37	c.2383		22																																																																																			0	NULL		0.667	FAM230A-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	FAM230A	protein_coding	OTTHUMT00000319609.4	114	5	0	0.00	0	0	C		0	0		20710651	1	no_errors	ENST00000434783	ensembl	human	known	74_37	missense	116	6	7.2	0.00	9	0	SNP	0	T
