#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_NormalRefReads_WU	i_NormalVAF_WU	i_NormalVarReads_WU	i_ORegAnno_bin	i_RNARefReads_WU	i_RNAVAF_WU	i_RNAVarReads_WU	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_Start_position_hg18	i_TumorRefReads_WU	i_TumorVAF_WU	i_TumorVarReads_WU	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_deletion_substructures	i_domain	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_name	i_gene_type	i_havana_transcript	i_reference	i_refseq_mrna_id	i_secondary_variant_classification	i_stop	i_strand	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_type	i_ucsc_cons	i_variant
MTMR8	55613	genome.wustl.edu	37	X	63488602	63488602	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2971-03A-01D-0739-09	TCGA-AB-2971-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	62d20b8b-a793-432a-895c-d496cd3fae2c	3b98ab49-9ae4-461a-8e29-be6e97425d04	g.chrX:63488602C>T	ENST00000374852.3	-	14	1997	c.1930G>A	c.(1930-1932)Gag>Aag	p.E644K	MTMR8_ENST00000453546.1_Intron	NM_017677.3	NP_060147.2	Q96EF0	MTMR8_HUMAN	myotubularin related protein 8	644						nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)	p.0?(2)|p.E644K(1)		breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|skin(3)	37						CCCGTAGCCTCAAAGGTGCAC	0.532																																						dbGAP											3	Whole gene deletion(2)|Substitution - Missense(1)	ovary(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)	X											83.0	71.0	75.0					X																	63488602		2203	4300	6503	63405327	SO:0001583	missense	0			AK000133	CCDS14379.1	Xq11.2-q12	2013-01-11			ENSG00000102043	ENSG00000102043		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	16825	protein-coding gene	gene with protein product						11275328	Standard	NM_017677		Approved	FLJ20126	uc004dvs.3	Q96EF0	OTTHUMG00000021707	ENST00000374852.3:c.1930G>A	X.37:g.63488602C>T	ENSP00000363985:p.Glu644Lys	Somatic	882	6.95	66		0	100.00	1	WXS	Illumina HiSeq	Phase_IV	63405327	737	46.13	632	Q5JT99|Q9NXP6	Missense_Mutation	SNP	HMMSmart_SM00404,HMMPfam_Myotub-related,PatternScan_TYR_PHOSPHATASE_1,superfamily_PH domain-like,superfamily_(Phosphotyrosine protein) phosphatases II	p.E644K	ENST00000374852.3	37	c.1930	CCDS14379.1	X	.	.	.	.	.	.	.	.	.	.	C	8.027	0.760945	0.15914	.	.	ENSG00000102043	ENST00000374852;ENST00000247400	D	0.94330	-3.4	2.5	-2.38	0.06622	.	.	.	.	.	T	0.80974	0.4727	N	0.08118	0	0.09310	N	0.999999	B	0.09022	0.002	B	0.01281	0.0	T	0.67581	-0.5634	9	0.40728	T	0.16	.	2.3702	0.04329	0.2365:0.2738:0.0:0.4897	.	644	Q96EF0	MTMR8_HUMAN	K	644;530	ENSP00000363985:E644K	ENSP00000247400:E530K	E	-	1	0	MTMR8	63405327	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	-0.054000	0.11826	-0.395000	0.07715	0.513000	0.50165	GAG	-	NULL		0.532	MTMR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MTMR8	protein_coding	OTTHUMT00000056949.2	C	NM_017677		63405327	-1	no_errors	NM_017677.2	genbank	human	provisional	54_36p	missense	SNP	0.003	T
SAP130	79595	genome.wustl.edu	37	2	128770686	128770686	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2971-03A-01D-0739-09	TCGA-AB-2971-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	62d20b8b-a793-432a-895c-d496cd3fae2c	3b98ab49-9ae4-461a-8e29-be6e97425d04	g.chr2:128770686G>A	ENST00000259235.3	-	6	869	c.740C>T	c.(739-741)aCa>aTa	p.T247I	SAP130_ENST00000357702.5_Missense_Mutation_p.T247I|SAP130_ENST00000259234.6_Missense_Mutation_p.T221I	NM_024545.3	NP_078821.2	Q9H0E3	SP130_HUMAN	Sin3A-associated protein, 130kDa	247					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|STAGA complex (GO:0030914)	transcription coactivator activity (GO:0003713)	p.T247I(1)		NS(4)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(2)	45	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0771)		CCTCAGGACTGTGGTTACTTT	0.463																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	2											73.0	67.0	69.0					2																	128770686		2203	4300	6503	128487156	SO:0001583	missense	0			BC017453	CCDS2153.1, CCDS54397.1	2q14.3	2008-02-05	2006-02-02		ENSG00000136715	ENSG00000136715			29813	protein-coding gene	gene with protein product		609697	"""sin3A-associated protein, 130kDa"""			11230166, 12724404	Standard	NM_001145928		Approved	FLJ12761	uc010fmd.2	Q9H0E3	OTTHUMG00000131571	ENST00000259235.3:c.740C>T	2.37:g.128770686G>A	ENSP00000259235:p.Thr247Ile	Somatic	364	5.70	22		16	40.74	11	WXS	Illumina HiSeq	Phase_IV	128487156	269	47.46	243	B7ZLM3|C9K0X9|Q4ZFV4|Q53T46|Q8WVW4|Q9H9G8	Missense_Mutation	SNP	NULL	p.T247I	ENST00000259235.3	37	c.740	CCDS2153.1	2	.	.	.	.	.	.	.	.	.	.	G	17.08	3.298473	0.60195	.	.	ENSG00000136715	ENST00000357702;ENST00000259235;ENST00000259234;ENST00000424298	.	.	.	5.56	5.56	0.83823	.	0.043458	0.85682	D	0.000000	T	0.65678	0.2714	L	0.27053	0.805	0.80722	D	1	D;D;D	0.76494	0.985;0.998;0.999	P;D;D	0.66351	0.714;0.943;0.93	T	0.66618	-0.5878	9	0.49607	T	0.09	-14.0266	19.5058	0.95114	0.0:0.0:1.0:0.0	.	247;221;247	B7ZLM3;Q96DP1;Q9H0E3	.;.;SP130_HUMAN	I	247;247;221;221	.	ENSP00000259234:T221I	T	-	2	0	SAP130	128487156	1.000000	0.71417	0.986000	0.45419	0.992000	0.81027	6.876000	0.75556	2.611000	0.88343	0.561000	0.74099	ACA	-	NULL		0.463	SAP130-001	KNOWN	basic|CCDS	protein_coding	SAP130	protein_coding	OTTHUMT00000254436.3	G	NM_024545		128487156	-1	no_errors	NM_024545.1	genbank	human	validated	54_36p	missense	SNP	0.999	A
RBM44	375316	genome.wustl.edu	37	2	238742984	238742984	+	Silent	SNP	A	A	G			TCGA-AB-2971-03A-01D-0739-09	TCGA-AB-2971-11A-01D-0739-09	A	A	A	G	A	A	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	62d20b8b-a793-432a-895c-d496cd3fae2c	3b98ab49-9ae4-461a-8e29-be6e97425d04	g.chr2:238742984A>G	ENST00000409864.1	+	15	3353	c.3099A>G	c.(3097-3099)ttA>ttG	p.L1033L	RBM44_ENST00000316997.4_Silent_p.L1033L			Q6ZP01	RBM44_HUMAN	RNA binding motif protein 44	1032						cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)	nucleotide binding (GO:0000166)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)	p.L1033L(1)		breast(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(7)|ovary(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	33		Breast(86;0.0042)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;3.74e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.3e-11)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000118)|Lung(119;0.0112)|LUSC - Lung squamous cell carcinoma(224;0.0266)		TGAATGGCTTATCTATTACTA	0.308																																						dbGAP											1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	2											36.0	35.0	35.0					2																	238742984		1803	4043	5846	238407723	SO:0001819	synonymous_variant	0			AK097730	CCDS46554.1	2q37.3	2013-02-12			ENSG00000177483	ENSG00000177483		"""RNA binding motif (RRM) containing"""	24756	protein-coding gene	gene with protein product							Standard	NM_001080504		Approved	FLJ40411	uc002vxi.4	Q6ZP01	OTTHUMG00000152937	ENST00000409864.1:c.3099A>G	2.37:g.238742984A>G		Somatic	344	7.77	29		2	0.00	0	WXS	Illumina HiSeq	Phase_IV	238407723	285	40.29	193	A0AUW3	Silent	SNP	HMMPfam_RRM_1,HMMSmart_RRM,superfamily_SSF54928	p.L1032	ENST00000409864.1	37	c.3096	CCDS46554.1	2																																																																																			-	NULL		0.308	RBM44-004	KNOWN	basic|appris_principal|CCDS	protein_coding	RBM44	protein_coding	OTTHUMT00000328733.2	A	NM_001080504		238407723	+1	no_errors	NM_001080504.2	genbank	human	validated	54_36p	silent	SNP	0.992	G
TET2	54790	genome.wustl.edu	37	4	106197255	106197255	+	Missense_Mutation	SNP	C	C	A			TCGA-AB-2971-03A-01D-0739-09	TCGA-AB-2971-11A-01D-0739-09	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	62d20b8b-a793-432a-895c-d496cd3fae2c	3b98ab49-9ae4-461a-8e29-be6e97425d04	g.chr4:106197255C>A	ENST00000540549.1	+	11	6448	c.5588C>A	c.(5587-5589)gCc>gAc	p.A1863D	TET2_ENST00000513237.1_Missense_Mutation_p.A1884D|TET2_ENST00000380013.4_Missense_Mutation_p.A1863D|TET2_ENST00000545826.1_3'UTR			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	1863					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.A1863D(1)		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)		GGGGGAGTGGCCGTGGCTCCA	0.542			"""Mis N, F"""		MDS																																	dbGAP		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	4											54.0	50.0	51.0					4																	106197255		692	1591	2283	106416704	SO:0001583	missense	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.5588C>A	4.37:g.106197255C>A	ENSP00000442788:p.Ala1863Asp	Somatic	424	9.36	44		30	53.85	35	WXS	Illumina HiSeq	Phase_IV	106416704	672	44.84	547	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Missense_Mutation	SNP	NULL	p.A665D	ENST00000540549.1	37	c.1994	CCDS47120.1	4	.	.	.	.	.	.	.	.	.	.	C	28.3	4.904971	0.92035	.	.	ENSG00000168769	ENST00000540549;ENST00000513237;ENST00000380013	T;T;T	0.14640	2.49;2.49;2.49	5.33	5.33	0.75918	Methylcytosine dioxygenase TET, double-stranded beta helix fold domain (1);	.	.	.	.	T	0.42988	0.1227	M	0.81802	2.56	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.43065	-0.9414	9	0.87932	D	0	-12.2809	19.031	0.92957	0.0:1.0:0.0:0.0	.	1884;1863	E7EQS8;Q6N021	.;TET2_HUMAN	D	1863;1884;1863	ENSP00000442788:A1863D;ENSP00000425443:A1884D;ENSP00000369351:A1863D	ENSP00000369351:A1863D	A	+	2	0	TET2	106416704	1.000000	0.71417	0.970000	0.41538	0.994000	0.84299	7.277000	0.78572	2.477000	0.83638	0.591000	0.81541	GCC	-	NULL		0.542	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	TET2	protein_coding	OTTHUMT00000253952.2	C	NM_017628		106416704	+1	no_start_codon	ENST00000265149	ensembl	human	known	54_36p	missense	SNP	0.997	A
BMP5	653	genome.wustl.edu	37	6	55638913	55638913	+	Nonsense_Mutation	SNP	G	G	A	rs550837639		TCGA-AB-2971-03A-01D-0739-09	TCGA-AB-2971-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	62d20b8b-a793-432a-895c-d496cd3fae2c	3b98ab49-9ae4-461a-8e29-be6e97425d04	g.chr6:55638913G>A	ENST00000370830.3	-	4	1659	c.961C>T	c.(961-963)Cga>Tga	p.R321*	BMP5_ENST00000446683.2_Nonsense_Mutation_p.R321*	NM_021073.2	NP_066551.1	P22003	BMP5_HUMAN	bone morphogenetic protein 5	321					cartilage development (GO:0051216)|growth (GO:0040007)|male genitalia development (GO:0030539)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of steroid biosynthetic process (GO:0010894)|ossification (GO:0001503)|pattern specification process (GO:0007389)|positive regulation of dendrite development (GO:1900006)|positive regulation of DNA-dependent DNA replication (GO:2000105)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal system development (GO:0001501)|type B pancreatic cell development (GO:0003323)	extracellular space (GO:0005615)|membrane-bounded vesicle (GO:0031988)	BMP receptor binding (GO:0070700)	p.R321*(1)		cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)	45	Lung NSC(77;0.0462)		LUSC - Lung squamous cell carcinoma(124;0.181)			TGATTTTTTCGTTTGTTGGCT	0.473													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18020	0.0		0.0	False		,,,				2504	0.0					dbGAP											1	Substitution - Nonsense(1)	haematopoietic_and_lymphoid_tissue(1)	6											202.0	173.0	183.0					6																	55638913		2203	4300	6503	55746872	SO:0001587	stop_gained	0				CCDS4958.1	6p12.1	2014-01-30			ENSG00000112175	ENSG00000112175		"""Bone morphogenetic proteins"", ""Endogenous ligands"""	1072	protein-coding gene	gene with protein product		112265				1427904, 11580864	Standard	NM_021073		Approved		uc003pcq.3	P22003	OTTHUMG00000014903	ENST00000370830.3:c.961C>T	6.37:g.55638913G>A	ENSP00000359866:p.Arg321*	Somatic	515	8.85	50		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	55746872	545	45.28	451	B4E0Y4|Q9H547|Q9NTM5	Nonsense_Mutation	SNP	HMMPfam_TGFb_propeptide,HMMPfam_TGF_beta,HMMSmart_TGFB,PatternScan_TGF_BETA_1,superfamily_SSF57501	p.R321*	ENST00000370830.3	37	c.961	CCDS4958.1	6	.	.	.	.	.	.	.	.	.	.	G	43	10.295298	0.99378	.	.	ENSG00000112175	ENST00000370830;ENST00000446683	.	.	.	5.74	-0.0584	0.13797	.	0.052929	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	17.0604	0.86546	0.0:0.0:0.1964:0.8036	.	.	.	.	X	321	.	ENSP00000359866:R321X	R	-	1	2	BMP5	55746872	1.000000	0.71417	0.967000	0.41034	0.992000	0.81027	1.558000	0.36309	0.033000	0.15463	0.655000	0.94253	CGA	-	NULL		0.473	BMP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	BMP5	protein_coding	OTTHUMT00000041000.1	G			55746872	-1	no_errors	NM_021073.2	genbank	human	reviewed	54_36p	nonsense	SNP	1.000	A
PTPRN2	5799	genome.wustl.edu	37	7	157396754	157396754	+	Silent	SNP	C	C	T			TCGA-AB-2971-03A-01D-0739-09	TCGA-AB-2971-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	62d20b8b-a793-432a-895c-d496cd3fae2c	3b98ab49-9ae4-461a-8e29-be6e97425d04	g.chr7:157396754C>T	ENST00000389418.4	-	16	2367	c.2358G>A	c.(2356-2358)cgG>cgA	p.R786R	PTPRN2_ENST00000409483.1_Silent_p.R748R|PTPRN2_ENST00000389416.4_Silent_p.R769R|PTPRN2_ENST00000389413.3_Silent_p.R757R|PTPRN2_ENST00000404321.2_Silent_p.R809R	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	786	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.R786R(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		TCAGCAGGACCCGGGAGTGGT	0.632																																						dbGAP											1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	7											103.0	80.0	88.0					7																	157396754		2203	4300	6503	157089515	SO:0001819	synonymous_variant	0			AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9677	protein-coding gene	gene with protein product	"""IAR PTPRP"""	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.2358G>A	7.37:g.157396754C>T		Somatic	169	3.98	7		1	50.00	1	WXS	Illumina HiSeq	Phase_IV	157089515	90	43.04	68	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Silent	SNP	HMMPfam_Y_phosphatase,HMMSmart_SM00194,HMMSmart_SM00404,PatternScan_TYR_PHOSPHATASE_1,superfamily_(Phosphotyrosine protein) phosphatases II	p.R786	ENST00000389418.4	37	c.2358	CCDS5947.1	7																																																																																			-	HMMPfam_Y_phosphatase,HMMSmart_SM00194,superfamily_(Phosphotyrosine protein) phosphatases II		0.632	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PTPRN2	protein_coding	OTTHUMT00000353214.1	C			157089515	-1	no_errors	NM_002847.3	genbank	human	reviewed	54_36p	silent	SNP	1.000	T
LINC00963	100506190	genome.wustl.edu	37	9	132253242	132253242	+	RNA	SNP	T	T	G			TCGA-AB-2971-03A-01D-0739-09	TCGA-AB-2971-11A-01D-0739-09	T	T	T	G	T	T	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	62d20b8b-a793-432a-895c-d496cd3fae2c	3b98ab49-9ae4-461a-8e29-be6e97425d04	g.chr9:132253242T>G	ENST00000419300.3	+	0	200									long intergenic non-protein coding RNA 963																		taagctcacatctgtctggag	0.532																																						dbGAP											0			9																																								131293063			0					9q34.11	2014-04-03			ENSG00000204054	ENSG00000204054		"""Long non-coding RNAs"""	48716	non-coding RNA	RNA, long non-coding						24691949	Standard	NR_038955		Approved				OTTHUMG00000020783		9.37:g.132253242T>G		Somatic	207	9.57	22		1	80.00	4	WXS	Illumina HiSeq	Phase_IV	131293063	87	46.63	76		Missense_Mutation	SNP	NULL	p.H161Q	ENST00000419300.3	37	c.483		9																																																																																			-	NULL		0.532	LINC00963-007	KNOWN	basic	lincRNA	LOC100128077	processed_transcript	OTTHUMT00000106519.3	T			131293063	+1	no_errors	XM_001726459.1	genbank	human	model	54_36p	missense	SNP	0.001	G
WEE1	7465	genome.wustl.edu	37	11	9610036	9610036	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2971-03A-01D-0739-09	TCGA-AB-2971-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	62d20b8b-a793-432a-895c-d496cd3fae2c	3b98ab49-9ae4-461a-8e29-be6e97425d04	g.chr11:9610036G>A	ENST00000450114.2	+	11	2081	c.1828G>A	c.(1828-1830)Gaa>Aaa	p.E610K	WEE1_ENST00000299613.6_Missense_Mutation_p.E396K	NM_003390.3	NP_003381.1	P30291	WEE1_HUMAN	WEE1 G2 checkpoint kinase	610					blood coagulation (GO:0007596)|establishment of cell polarity (GO:0030010)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|neuron projection morphogenesis (GO:0048812)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.E610K(1)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	23				all cancers(16;4.59e-09)|Epithelial(150;3.15e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0484)		TGCAGCTGAGGAAAGAGCACT	0.428																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	11											125.0	120.0	122.0					11																	9610036		2201	4294	6495	9566612	SO:0001583	missense	0			X62048	CCDS7800.1, CCDS44536.1	11p15.4	2013-10-21	2013-10-21		ENSG00000166483	ENSG00000166483			12761	protein-coding gene	gene with protein product		193525	"""wee1+ (S. pombe) homolog"", ""WEE1 homolog (S. pombe)"""			1840647	Standard	NM_003390		Approved		uc001mhs.3	P30291	OTTHUMG00000165863	ENST00000450114.2:c.1828G>A	11.37:g.9610036G>A	ENSP00000402084:p.Glu610Lys	Somatic	509	2.67	14		19	40.62	13	WXS	Illumina HiSeq	Phase_IV	9566612	231	38.73	146	B3KVE1|D3DQV0	Missense_Mutation	SNP	PatternScan_PROTEIN_KINASE_ST,superfamily_Kinase_like,PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase	p.E610K	ENST00000450114.2	37	c.1828	CCDS7800.1	11	.	.	.	.	.	.	.	.	.	.	G	26.3	4.723931	0.89298	.	.	ENSG00000166483	ENST00000450114;ENST00000299613;ENST00000527848	T;T;T	0.54071	0.68;0.59;0.74	5.31	5.31	0.75309	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.50990	0.1648	L	0.46157	1.445	0.80722	D	1	D	0.53151	0.958	P	0.45138	0.471	T	0.44236	-0.9341	10	0.18276	T	0.48	-16.3277	18.9901	0.92788	0.0:0.0:1.0:0.0	.	610	P30291	WEE1_HUMAN	K	610;396;62	ENSP00000402084:E610K;ENSP00000299613:E396K;ENSP00000432284:E62K	ENSP00000299613:E396K	E	+	1	0	WEE1	9566612	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.060000	0.93907	2.489000	0.83994	0.563000	0.77884	GAA	-	NULL		0.428	WEE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	WEE1	protein_coding	OTTHUMT00000386757.1	G	NM_003390		9566612	+1	no_errors	NM_003390.1	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
E2F8	79733	genome.wustl.edu	37	11	19251105	19251105	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AB-2971-03A-01D-0739-09	TCGA-AB-2971-11A-01D-0739-09	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	62d20b8b-a793-432a-895c-d496cd3fae2c	3b98ab49-9ae4-461a-8e29-be6e97425d04	g.chr11:19251105C>A	ENST00000527884.1	-	10	2021	c.1789G>T	c.(1789-1791)Gag>Tag	p.E597*	E2F8_ENST00000250024.4_Nonsense_Mutation_p.E597*|RP11-428C19.4_ENST00000527978.1_RNA	NM_001256371.1|NM_001256372.1	NP_001243300.1|NP_001243301.1	A0AVK6	E2F8_HUMAN	E2F transcription factor 8	597					cell cycle comprising mitosis without cytokinesis (GO:0033301)|chorionic trophoblast cell differentiation (GO:0060718)|hepatocyte differentiation (GO:0070365)|negative regulation of cytokinesis (GO:0032466)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|placenta development (GO:0001890)|positive regulation of DNA endoreduplication (GO:0032877)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sprouting angiogenesis (GO:0002040)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.E597*(1)		breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						CCAGCTGGCTCCCTGGTTCGG	0.522																																						dbGAP											1	Substitution - Nonsense(1)	haematopoietic_and_lymphoid_tissue(1)	11											133.0	122.0	126.0					11																	19251105		2199	4293	6492	19207681	SO:0001587	stop_gained	0				CCDS7849.1	11p15	2008-02-05			ENSG00000129173	ENSG00000129173			24727	protein-coding gene	gene with protein product		612047				15722552	Standard	NM_024680		Approved	FLJ23311	uc001mpo.2	A0AVK6	OTTHUMG00000166102	ENST00000527884.1:c.1789G>T	11.37:g.19251105C>A	ENSP00000434199:p.Glu597*	Somatic	650	5.66	39		2	33.33	1	WXS	Illumina HiSeq	Phase_IV	19207681	350	48.98	336	A8K9H3|Q2VPJ3|Q3C1U6|Q5BKY4|Q8N340|Q9H5M0	Nonsense_Mutation	SNP	"HMMPfam_E2F_TDP,superfamily_""Winged helix"" DNA-binding domain"	p.E597*	ENST00000527884.1	37	c.1789	CCDS7849.1	11	.	.	.	.	.	.	.	.	.	.	C	38	6.885646	0.97908	.	.	ENSG00000129173	ENST00000527884;ENST00000396159;ENST00000250024	.	.	.	5.35	5.35	0.76521	.	0.395690	0.27941	N	0.017240	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-20.7618	11.353	0.49598	0.0:0.916:0.0:0.084	.	.	.	.	X	597	.	ENSP00000250024:E597X	E	-	1	0	E2F8	19207681	0.933000	0.31639	0.322000	0.25334	0.707000	0.40811	2.972000	0.49256	2.503000	0.84419	0.655000	0.94253	GAG	-	NULL		0.522	E2F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	E2F8	protein_coding	OTTHUMT00000387830.1	C	NM_024680		19207681	-1	no_errors	NM_024680.2	genbank	human	validated	54_36p	nonsense	SNP	0.065	A
DNM1P46	196968	genome.wustl.edu	37	15	100331825	100331825	+	RNA	SNP	C	C	T			TCGA-AB-2971-03A-01D-0739-09	TCGA-AB-2971-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	62d20b8b-a793-432a-895c-d496cd3fae2c	3b98ab49-9ae4-461a-8e29-be6e97425d04	g.chr15:100331825C>T	ENST00000341853.1	-	0	2366				AC090825.1_ENST00000408584.1_RNA|RN7SL484P_ENST00000462651.2_RNA	NR_003260.1		Q6ZS02	DMP46_HUMAN	DNM1 pseudogene 46							microtubule (GO:0005874)	GTPase activity (GO:0003924)	p.D26D(1)									ACCCAGAGGACCTGGAGAGCT	0.607																																						dbGAP											1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	15											73.0	73.0	73.0					15																	100331825		876	1991	2867	98149348			0			AJ576275		15q26.3	2013-04-25			ENSG00000182397	ENSG00000182397			35199	pseudogene	pseudogene			"""chromosome 15 open reading frame 51"""	DNM1DN14@, C15orf51			Standard	NR_003260		Approved	DNM1DN14.2, FLJ45937, DKFZp434I1020	uc021sxl.1	Q6ZS02	OTTHUMG00000149852		15.37:g.100331825C>T		Somatic	313	5.95	20		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	98149348	203	51.20	213	Q3ZCN3	Silent	SNP	NULL	p.D33	ENST00000341853.1	37	c.99		15																																																																																			-	NULL		0.607	DNM1P46-002	KNOWN	basic	processed_transcript	LOC644800	pseudogene	OTTHUMT00000313543.1	C	NR_003260		98149348	+1	no_errors	XM_001715415.1	genbank	human	model	54_36p	silent	SNP	0.992	T
CNTNAP4	85445	genome.wustl.edu	37	16	76461380	76461380	+	Missense_Mutation	SNP	T	T	A			TCGA-AB-2971-03A-01D-0739-09	TCGA-AB-2971-11A-01D-0739-09	T	T	T	A	T	T	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	62d20b8b-a793-432a-895c-d496cd3fae2c	3b98ab49-9ae4-461a-8e29-be6e97425d04	g.chr16:76461380T>A	ENST00000476707.1	+	3	570	c.431T>A	c.(430-432)gTt>gAt	p.V144D	CNTNAP4_ENST00000377504.4_Missense_Mutation_p.V140D|CNTNAP4_ENST00000478060.1_Missense_Mutation_p.V116D|CNTNAP4_ENST00000469589.1_3'UTR|CNTNAP4_ENST00000307431.8_Missense_Mutation_p.V140D			Q9C0A0	CNTP4_HUMAN	contactin associated protein-like 4	141	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.				cell adhesion (GO:0007155)|regulation of grooming behavior (GO:2000821)|regulation of synaptic transmission, dopaminergic (GO:0032225)|regulation of synaptic transmission, GABAergic (GO:0032228)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|presynaptic membrane (GO:0042734)		p.V116D(2)		breast(4)|central_nervous_system(1)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(33)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	64						GCAGACAGTGTTGTGTACTAT	0.423																																						dbGAP											2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(2)	16											198.0	196.0	197.0					16																	76461380		2198	4300	6498	75018881	SO:0001583	missense	0			AB051550	CCDS10924.1, CCDS10924.2, CCDS73915.1	16q23.1	2008-02-05			ENSG00000152910	ENSG00000152910			18747	protein-coding gene	gene with protein product		610518				12093160	Standard	NM_033401		Approved	CASPR4, KIAA1763	uc010chb.1	Q9C0A0	OTTHUMG00000137617	ENST00000476707.1:c.431T>A	16.37:g.76461380T>A	ENSP00000417628:p.Val144Asp	Somatic	1284	7.02	97		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	75018881	1084	43.93	851	E9PFZ6|Q86YZ7	Missense_Mutation	SNP	HMMPfam_F5_F8_type_C,HMMSmart_SM00231,PatternScan_FA58C_1,PatternScan_FA58C_2,HMMSmart_SM00282,superfamily_Fibrinogen C-terminal domain-like,HMMPfam_EGF,HMMSmart_SM00181,superfamily_Galactose-binding domain-like,superfamily_Concanavalin A-like lectins/glucanases,HMMPfam_Laminin_G_2	p.V116D	ENST00000476707.1	37	c.347		16	.	.	.	.	.	.	.	.	.	.	T	25.7	4.669518	0.88348	.	.	ENSG00000152910	ENST00000307431;ENST00000377504;ENST00000478060;ENST00000476707	D;D;D;D	0.98264	-4.83;-4.83;-4.83;-4.83	4.98	4.98	0.66077	Coagulation factor 5/8 C-terminal type domain (3);Galactose-binding domain-like (1);	0.000000	0.34652	N	0.003798	D	0.98871	0.9618	.	.	.	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.998;0.999	D;D;D;D	0.87578	0.998;0.997;0.995;0.996	D	0.99774	1.1025	9	0.87932	D	0	.	14.8097	0.69985	0.0:0.0:0.0:1.0	.	116;144;116;141	E9PFZ6;E9PDN6;Q96M80;Q9C0A0	.;.;.;CNTP4_HUMAN	D	140;140;116;144	ENSP00000306893:V140D;ENSP00000439733:V140D;ENSP00000418741:V116D;ENSP00000417628:V144D	ENSP00000306893:V140D	V	+	2	0	CNTNAP4	75018881	1.000000	0.71417	0.992000	0.48379	0.994000	0.84299	5.975000	0.70475	2.232000	0.73038	0.533000	0.62120	GTT	-	HMMPfam_F5_F8_type_C,HMMSmart_SM00231,superfamily_Galactose-binding domain-like		0.423	CNTNAP4-005	PUTATIVE	basic	protein_coding	CNTNAP4	protein_coding	OTTHUMT00000348216.1	T	NM_033401		75018881	+1	no_errors	NM_138994.3	genbank	human	validated	54_36p	missense	SNP	0.998	A
GGTLC1	92086	genome.wustl.edu	37	20	23971112	23971112	+	5'Flank	SNP	C	C	T			TCGA-AB-2971-03A-01D-0739-09	TCGA-AB-2971-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	62d20b8b-a793-432a-895c-d496cd3fae2c	3b98ab49-9ae4-461a-8e29-be6e97425d04	g.chr20:23971112C>T	ENST00000335694.4	-	0	0					NM_178311.2	NP_842563.1	Q9BX51	GGTL1_HUMAN	gamma-glutamyltransferase light chain 1						glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)	gamma-glutamyltransferase activity (GO:0003840)	p.Y222Y(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	15						CCAGCTCCTACAGCTCTACGG	0.627																																						dbGAP											1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	20																																								23919112	SO:0001631	upstream_gene_variant	0			AL133466	CCDS13163.1	20p11.21	2010-07-14	2008-03-10	2008-03-10	ENSG00000149435	ENSG00000149435		"""Gamma-glutamyltransferases"""	16437	protein-coding gene	gene with protein product		612338	"""gamma-glutamyltransferase-like activity 4"", ""gamma-glutamyltransferase-like activity 3"""	GGTLA4, GGTLA3		10843999, 18357469	Standard	NM_178311		Approved	dJ831C21.2, dJ831C21.1	uc002wtu.3	Q9BX51	OTTHUMG00000032095		20.37:g.23971112C>T	Exception_encountered	Somatic	119	7.75	10		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	23919112	89	43.40	69	D3DW43|Q08246	Silent	SNP	NULL	p.Y222	ENST00000335694.4	37	c.666	CCDS13163.1	20																																																																																			-	NULL		0.627	GGTLC1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	ENSG00000167390	protein_coding	OTTHUMT00000078366.2	C	NM_178311.2		23919112	+1	no_stop_codon	ENST00000319850	ensembl	human	known	54_36p	silent	SNP	0.044	T
MAPK1	5594	genome.wustl.edu	37	22	22153395	22153395	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2971-03A-01D-0739-09	TCGA-AB-2971-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	62d20b8b-a793-432a-895c-d496cd3fae2c	3b98ab49-9ae4-461a-8e29-be6e97425d04	g.chr22:22153395C>T	ENST00000215832.6	-	4	703	c.515G>A	c.(514-516)cGt>cAt	p.R172H	MAPK1_ENST00000398822.3_Missense_Mutation_p.R172H|MAPK1_ENST00000544786.1_Missense_Mutation_p.R172H	NM_002745.4	NP_002736.3	P28482	MK01_HUMAN	mitogen-activated protein kinase 1	172	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|caveolin-mediated endocytosis (GO:0072584)|cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|chemotaxis (GO:0006935)|cytosine metabolic process (GO:0019858)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|labyrinthine layer blood vessel development (GO:0060716)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|mammary gland epithelial cell proliferation (GO:0033598)|MAPK cascade (GO:0000165)|MAPK import into nucleus (GO:0000189)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cell differentiation (GO:0045596)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|Ras protein signal transduction (GO:0007265)|regulation of cytoskeleton organization (GO:0051493)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of Golgi inheritance (GO:0090170)|regulation of protein stability (GO:0031647)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of stress-activated MAPK cascade (GO:0032872)|response to epidermal growth factor (GO:0070849)|response to estrogen (GO:0043627)|response to exogenous dsRNA (GO:0043330)|response to stress (GO:0006950)|response to toxic substance (GO:0009636)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|mitotic spindle (GO:0072686)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perikaryon (GO:0043204)|protein complex (GO:0043234)|pseudopodium (GO:0031143)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MAP kinase activity (GO:0004707)|phosphatase binding (GO:0019902)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)	p.R172H(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Colorectal(54;0.105)	all_lung(157;3.89e-05)		READ - Rectum adenocarcinoma(21;0.0689)	Arsenic trioxide(DB01169)|Isoprenaline(DB01064)	ATCTGCAACACGGGCCAGGCC	0.408																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	22											73.0	65.0	67.0					22																	22153395		2203	4300	6503	20483395	SO:0001583	missense	0			M84489	CCDS13795.1	22q11.2	2014-09-17			ENSG00000100030	ENSG00000100030	2.7.11.1	"""Mitogen-activated protein kinase cascade / Kinases"""	6871	protein-coding gene	gene with protein product		176948		PRKM2, PRKM1			Standard	NM_138957		Approved	ERK, ERK2, p41mapk, MAPK2	uc002zvn.3	P28482	OTTHUMG00000030508	ENST00000215832.6:c.515G>A	22.37:g.22153395C>T	ENSP00000215832:p.Arg172His	Somatic	557	7.28	44		41	51.76	44	WXS	Illumina HiSeq	Phase_IV	20483395	675	44.64	546	A8CZ64	Missense_Mutation	SNP	HMMSmart_SM00219,HMMSmart_SM00220,PatternScan_MAPK,PatternScan_PROTEIN_KINASE_ST,superfamily_Protein kinase-like (PK-like),PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase	p.R172H	ENST00000215832.6	37	c.515	CCDS13795.1	22	.	.	.	.	.	.	.	.	.	.	C	35	5.533706	0.96460	.	.	ENSG00000100030	ENST00000215832;ENST00000415911;ENST00000398822;ENST00000544786	T;T;T	0.67523	-0.27;-0.27;-0.27	5.14	5.14	0.70334	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.85492	0.5709	M	0.90019	3.08	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.76575	0.988;0.985	D	0.88309	0.2955	10	0.87932	D	0	-0.4286	18.7977	0.92001	0.0:1.0:0.0:0.0	.	172;172	A8CZ64;P28482	.;MK01_HUMAN	H	172;160;172;172	ENSP00000215832:R172H;ENSP00000381803:R172H;ENSP00000440842:R172H	ENSP00000215832:R172H	R	-	2	0	MAPK1	20483395	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.651000	0.83577	2.666000	0.90696	0.561000	0.74099	CGT	-	HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase		0.408	MAPK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	MAPK1	protein_coding	OTTHUMT00000075396.2	C			20483395	-1	no_errors	NM_002745.4	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
TET2	54790	genome.wustl.edu	37	4	106158309	106158309	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AB-2971-03A-01D-0739-09	TCGA-AB-2971-11A-01D-0739-09	T	T	T	-	T	T	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	62d20b8b-a793-432a-895c-d496cd3fae2c	3b98ab49-9ae4-461a-8e29-be6e97425d04	g.chr4:106158309delT	ENST00000540549.1	+	3	4070	c.3210delT	c.(3208-3210)actfs	p.T1070fs	TET2_ENST00000513237.1_Frame_Shift_Del_p.T1091fs|TET2_ENST00000394764.1_Frame_Shift_Del_p.T1070fs|TET2_ENST00000380013.4_Frame_Shift_Del_p.T1070fs|TET2_ENST00000413648.2_Frame_Shift_Del_p.T1070fs|TET2_ENST00000545826.1_Frame_Shift_Del_p.T1070fs|TET2_ENST00000305737.2_Frame_Shift_Del_p.T1070fs			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	1070					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.A1071fs*11(1)		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)		GACAAACCACTGCTGCAGAAC	0.418			"""Mis N, F"""		MDS																																	dbGAP		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	1	Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(1)	4											81.0	79.0	79.0					4																	106158309		2203	4300	6503	106377758	SO:0001589	frameshift_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.3210delT	4.37:g.106158309delT	ENSP00000442788:p.Thr1070fs	Somatic	467	5.44	27		95	43.35	75	WXS	Illumina HiSeq	Phase_IV	106377758	475	45.10	414	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Frame_Shift_Del	DEL	NULL	p.A1071fs	ENST00000540549.1	37	c.3210	CCDS47120.1	4																																																																																			-	NULL		0.418	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	TET2	protein_coding	OTTHUMT00000253952.2	T	NM_017628		106377758	+1	no_errors	NM_017628.1	genbank	human	validated	54_36p	frame_shift_del	DEL	0.932	-
