#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_NormalRefReads_WU	i_NormalVAF_WU	i_NormalVarReads_WU	i_ORegAnno_bin	i_RNARefReads_WU	i_RNAVAF_WU	i_RNAVarReads_WU	i_Start_position_hg18	i_TumorRefReads_WU	i_TumorVAF_WU	i_TumorVarReads_WU	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_deletion_substructures	i_domain	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_name	i_gene_type	i_havana_transcript	i_reference	i_refseq_mrna_id	i_secondary_variant_classification	i_stop	i_strand	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_type	i_ucsc_cons	i_variant
GYG2	8908	genome.wustl.edu	37	X	2793884	2793884	+	Missense_Mutation	SNP	G	G	A	rs201655808		TCGA-AB-2830-03B-01W-0728-08	TCGA-AB-2830-11B-01W-0728-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	f72fb885-99dd-486a-8f06-cf886c085f60	303971a6-646d-43e9-aa4c-18a133db1161	g.chrX:2793884G>A	ENST00000381163.3	+	10	1447	c.1165G>A	c.(1165-1167)Gtg>Atg	p.V389M	GYG2_ENST00000381161.1_Intron|GYG2_ENST00000398806.3_Missense_Mutation_p.V358M|GYG2_ENST00000338623.5_Missense_Mutation_p.V389M|GYG2_ENST00000542787.1_Intron	NM_001079855.1|NM_001184702.1|NM_003918.2	NP_001073324.1|NP_001171631.1|NP_003909.2	O15488	GLYG2_HUMAN	glycogenin 2	389					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	glycogenin glucosyltransferase activity (GO:0008466)			endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)	13		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				GACTCCTGCCGTGATAACGTG	0.438													G|||	1	0.000264901	0.0	0.0014	3775	,	,		13009	0.0		0.0	False		,,,				2504	0.0					dbGAP											0			X											118.0	86.0	97.0					X																	2793884		2203	4299	6502	2803884	SO:0001583	missense	0			U94361	CCDS14121.1, CCDS48074.1	Xp22.3	2013-02-22			ENSG00000056998	ENSG00000056998	2.4.1.186	"""Glycosyltransferase family 8 domain containing"""	4700	protein-coding gene	gene with protein product	"""glycogenin glucosyltransferase"""	300198				9857012	Standard	NM_001079855		Approved	GN-2	uc004cqs.1	O15488	OTTHUMG00000021079	ENST00000381163.3:c.1165G>A	X.37:g.2793884G>A	ENSP00000370555:p.Val389Met	58	3.33	2		NA	NA	NA	2803884	69	33.01	34	B7WNN6|O15485|O15486|O15487|O15489|O15490	Missense_Mutation	SNP	HMMPfam_Glyco_transf_8,superfamily_Nucleotide-diphospho-sugar transferases	p.V389M	ENST00000381163.3	37	c.1165	CCDS14121.1	X	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	7.529|7.529	0.658320|0.658320	0.14645|0.14645	.|.	.|.	ENSG00000056998|ENSG00000056998	ENST00000381157|ENST00000398806;ENST00000381163;ENST00000338623	.|T;T;T	.|0.43688	.|0.94;1.26;1.18	2.22|2.22	2.22|2.22	0.28083|0.28083	.|.	.|2.079510	.|0.03023	.|N	.|0.151083	T|T	0.28732|0.28732	0.0712|0.0712	N|N	0.14661|0.14661	0.345|0.345	0.21627|0.21627	N|N	0.999614|0.999614	.|D;D;D;D;D	.|0.56521	.|0.976;0.958;0.958;0.976;0.958	.|B;B;B;B;B	.|0.41571	.|0.272;0.36;0.14;0.272;0.14	T|T	0.29971|0.29971	-0.9994|-0.9994	5|10	.|0.42905	.|T	.|0.14	.|.	7.5401|7.5401	0.27733|0.27733	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|389;349;358;358;389	.|O15488-6;O15488-3;A8K8Y1;O15488-2;O15488	.|.;.;.;.;GLYG2_HUMAN	H|M	207|358;389;389	.|ENSP00000381786:V358M;ENSP00000370555:V389M;ENSP00000341273:V389M	.|ENSP00000341273:V389M	R|V	+|+	2|1	0|0	GYG2|GYG2	2803884|2803884	0.001000|0.001000	0.12720|0.12720	0.002000|0.002000	0.10522|0.10522	0.002000|0.002000	0.02628|0.02628	0.945000|0.945000	0.29056|0.29056	1.160000|1.160000	0.42584|0.42584	0.508000|0.508000	0.49915|0.49915	CGT|GTG	-	NULL		0.438	GYG2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	GYG2	protein_coding	OTTHUMT00000055645.1	G	NM_003918		2803884	+1	no_errors	NM_003918.1	genbank	human	validated	54_36p	missense	SNP	0.001	A
SCML2	10389	genome.wustl.edu	37	X	18343050	18343050	+	Missense_Mutation	SNP	C	C	A			TCGA-AB-2830-03B-01W-0728-08	TCGA-AB-2830-11B-01W-0728-08	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	f72fb885-99dd-486a-8f06-cf886c085f60	303971a6-646d-43e9-aa4c-18a133db1161	g.chrX:18343050C>A	ENST00000251900.4	-	4	298	c.139G>T	c.(139-141)Gct>Tct	p.A47S		NM_006089.2	NP_006080.1	Q9UQR0	SCML2_HUMAN	sex comb on midleg-like 2 (Drosophila)	47					anatomical structure morphogenesis (GO:0009653)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|PcG protein complex (GO:0031519)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	36	Hepatocellular(33;0.183)					TCTGAAGGAGCACTTATAGAC	0.378																																					Esophageal Squamous(100;1252 1965 19021 35517)	dbGAP											0			X											127.0	114.0	119.0					X																	18343050		2203	4300	6503	18252971	SO:0001583	missense	0			Y18004	CCDS14185.1	Xp22	2013-01-10	2001-11-28		ENSG00000102098	ENSG00000102098		"""Sterile alpha motif (SAM) domain containing"""	10581	protein-coding gene	gene with protein product		300208	"""sex comb on midleg (Drosophila)-like 2"""			10331946	Standard	NM_006089		Approved		uc004cyl.2	Q9UQR0	OTTHUMG00000021212	ENST00000251900.4:c.139G>T	X.37:g.18343050C>A	ENSP00000251900:p.Ala47Ser	33	8.11	3		22	0.00	0	18252971	51	40.00	34	Q5JXE6|Q86U98|Q8IWD0|Q8NDP2|Q9UGC5	Missense_Mutation	SNP	HMMPfam_SAM_1,HMMSmart_SM00454,HMMPfam_MBT,HMMSmart_SM00561,superfamily_SAM/Pointed domain,superfamily_Tudor/PWWP/MBT	p.A47S	ENST00000251900.4	37	c.139	CCDS14185.1	X	.	.	.	.	.	.	.	.	.	.	C	27.6	4.848953	0.91277	.	.	ENSG00000102098	ENST00000251900	T	0.33654	1.4	4.62	4.62	0.57501	.	0.000000	0.85682	D	0.000000	T	0.66858	0.2832	M	0.88181	2.935	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.75642	-0.3247	10	0.72032	D	0.01	.	17.0152	0.86416	0.0:1.0:0.0:0.0	.	47	Q9UQR0	SCML2_HUMAN	S	47	ENSP00000251900:A47S	ENSP00000251900:A47S	A	-	1	0	SCML2	18252971	1.000000	0.71417	0.999000	0.59377	0.984000	0.73092	7.354000	0.79424	2.023000	0.59567	0.513000	0.50165	GCT	-	HMMSmart_SM00561,superfamily_Tudor/PWWP/MBT		0.378	SCML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SCML2	protein_coding	OTTHUMT00000055941.1	C	NM_006089		18252971	-1	no_errors	NM_006089.2	genbank	human	validated	54_36p	missense	SNP	1.000	A
TBC1D8B	54885	genome.wustl.edu	37	X	106069437	106069437	+	Missense_Mutation	SNP	T	T	A			TCGA-AB-2830-03B-01W-0728-08	TCGA-AB-2830-11B-01W-0728-08	T	T	T	A	T	T	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	f72fb885-99dd-486a-8f06-cf886c085f60	303971a6-646d-43e9-aa4c-18a133db1161	g.chrX:106069437T>A	ENST00000357242.5	+	6	1179	c.1005T>A	c.(1003-1005)aaT>aaA	p.N335K	TBC1D8B_ENST00000481617.2_Missense_Mutation_p.N335K|TBC1D8B_ENST00000310452.2_Missense_Mutation_p.N335K|TBC1D8B_ENST00000276175.3_Missense_Mutation_p.N335K	NM_017752.2	NP_060222.2	Q0IIM8	TBC8B_HUMAN	TBC1 domain family, member 8B (with GRAM domain)	335	GRAM 2.						calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)	p.N335_Q336insN(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(6)|liver(4)|lung(15)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						AAGATGGCAATCAGTGTAGTG	0.348																																						dbGAP											1	Insertion - In frame(1)	breast(1)	X											96.0	90.0	92.0					X																	106069437		2203	4300	6503	105956093	SO:0001583	missense	0			AK123957	CCDS14522.1, CCDS14523.1	Xq22.3	2013-01-10			ENSG00000133138	ENSG00000133138		"""EF-hand domain containing"""	24715	protein-coding gene	gene with protein product						8889548	Standard	NM_017752		Approved	FLJ20298, RP11-321G1.1	uc004emo.3	Q0IIM8	OTTHUMG00000022152	ENST00000357242.5:c.1005T>A	X.37:g.106069437T>A	ENSP00000349781:p.Asn335Lys	19	0.00	0		4	0.00	0	105956093	125	19.87	31	B9A6K5|B9A6K6|Q5JRB7|Q6ZVX5|Q9NXE3	Missense_Mutation	SNP	HMMPfam_TBC,HMMSmart_SM00164,superfamily_Ypt/Rab-GAP domain of gyp1p,HMMPfam_GRAM,HMMSmart_SM00568,PatternScan_EF_HAND_1,superfamily_EF-hand	p.N335K	ENST00000357242.5	37	c.1005	CCDS14522.1	X	.	.	.	.	.	.	.	.	.	.	T	7.119	0.577609	0.13686	.	.	ENSG00000133138	ENST00000357242;ENST00000310452;ENST00000481617;ENST00000276175	D;D;D;D	0.86562	-2.14;-2.14;-2.14;-2.14	5.65	3.28	0.37604	GRAM (2);	0.344632	0.32624	N	0.005852	T	0.79575	0.4469	L	0.53249	1.67	0.32155	N	0.583713	B;B;B	0.30146	0.015;0.066;0.27	B;B;B	0.31946	0.075;0.063;0.138	T	0.70346	-0.4897	10	0.05959	T	0.93	-9.4821	6.9748	0.24669	0.0:0.2564:0.0:0.7436	.	335;335;335	Q0IIM8;B9A6K6;D6RFZ2	TBC8B_HUMAN;.;.	K	335	ENSP00000349781:N335K;ENSP00000310675:N335K;ENSP00000421375:N335K;ENSP00000276175:N335K	ENSP00000276175:N335K	N	+	3	2	TBC1D8B	105956093	0.946000	0.32159	0.384000	0.26145	0.358000	0.29455	0.605000	0.24179	0.765000	0.33221	0.417000	0.27973	AAT	-	HMMPfam_GRAM,HMMSmart_SM00568		0.348	TBC1D8B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	TBC1D8B	protein_coding	OTTHUMT00000057807.2	T	NM_017752		105956093	+1	no_errors	NM_017752.2	genbank	human	validated	54_36p	missense	SNP	0.976	A
AIFM1	9131	genome.wustl.edu	37	X	129283541	129283541	+	Silent	SNP	G	G	A			TCGA-AB-2830-03B-01W-0728-08	TCGA-AB-2830-11B-01W-0728-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	f72fb885-99dd-486a-8f06-cf886c085f60	303971a6-646d-43e9-aa4c-18a133db1161	g.chrX:129283541G>A	ENST00000287295.3	-	3	482	c.252C>T	c.(250-252)gcC>gcT	p.A84A	AIFM1_ENST00000319908.3_Silent_p.A80A|AIFM1_ENST00000535724.1_5'UTR|AIFM1_ENST00000346424.2_Intron	NM_001130847.3|NM_004208.3	NP_001124319.1|NP_004199.1	O95831	AIFM1_HUMAN	apoptosis-inducing factor, mitochondrion-associated, 1	84					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|cell redox homeostasis (GO:0045454)|chromosome condensation (GO:0030261)|DNA catabolic process (GO:0006308)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|mitochondrial respiratory chain complex I assembly (GO:0032981)|neuron apoptotic process (GO:0051402)|neuron differentiation (GO:0030182)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic DNA fragmentation (GO:1902510)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|electron carrier activity (GO:0009055)|FAD binding (GO:0071949)|NAD(P)H oxidase activity (GO:0016174)|oxidoreductase activity, acting on NAD(P)H (GO:0016651)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|liver(2)|lung(8)|ovary(4)|prostate(2)|urinary_tract(1)	30					Flavin adenine dinucleotide(DB03147)	TAGTCTTGTAGGCCTGCGGAT	0.378																																						dbGAP											0			X											168.0	149.0	156.0					X																	129283541		2202	4300	6502	129111222	SO:0001819	synonymous_variant	0			AF100928	CCDS14618.1, CCDS14619.1, CCDS48167.1	Xq26.1	2014-01-30	2006-11-16	2006-11-16	ENSG00000156709	ENSG00000156709			8768	protein-coding gene	gene with protein product		300169	"""programmed cell death 8 (apoptosis-inducing factor)"", ""neuropathy, axonal, motor-sensory with deafness and mental retardation (Cowchock syndrome)"""	PDCD8, NAMSD		9989411, 23217327	Standard	NM_004208		Approved	AIF, CMTX4	uc004evg.3	O95831	OTTHUMG00000022392	ENST00000287295.3:c.252C>T	X.37:g.129283541G>A		141	2.08	3		33	0.00	0	129111222	53	31.17	24	A4QPB4|B1ALN1|B2RB08|D3DTE9|Q1L6K4|Q1L6K6|Q2QKE4|Q5JUZ7|Q6I9X6|Q9Y3I3|Q9Y3I4	Silent	SNP	HMMPfam_Pyr_redox_2,superfamily_FAD/NAD-linked reductases dimerisation (C-terminal) domain,superfamily_FAD/NAD(P)-binding domain	p.A84	ENST00000287295.3	37	c.252	CCDS14618.1	X																																																																																			-	NULL		0.378	AIFM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	AIFM1	protein_coding	OTTHUMT00000058247.2	G			129111222	-1	no_errors	NM_004208.1	genbank	human	reviewed	54_36p	silent	SNP	1.000	A
ATP11C	286410	genome.wustl.edu	37	X	138813876	138813876	+	Silent	SNP	G	G	A			TCGA-AB-2830-03B-01W-0728-08	TCGA-AB-2830-11B-01W-0728-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	f72fb885-99dd-486a-8f06-cf886c085f60	303971a6-646d-43e9-aa4c-18a133db1161	g.chrX:138813876G>A	ENST00000327569.3	-	29	3434	c.3336C>T	c.(3334-3336)tcC>tcT	p.S1112S	ATP11C_ENST00000460773.1_5'UTR|ATP11C_ENST00000370557.1_Intron|ATP11C_ENST00000361648.2_Intron	NM_173694.4	NP_775965	Q8NB49	AT11C_HUMAN	ATPase, class VI, type 11C	1112					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|positive regulation of B cell differentiation (GO:0045579)|pre-B cell differentiation (GO:0002329)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(2)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(31)|ovary(5)|prostate(1)|skin(3)	75	Acute lymphoblastic leukemia(192;0.000127)					AAGGTCTGGCGGATAATGAGT	0.388																																						dbGAP											0			X											110.0	96.0	101.0					X																	138813876		2203	4299	6502	138641542	SO:0001819	synonymous_variant	0			AJ580094	CCDS14668.1, CCDS35410.1	Xq27.1	2011-06-09	2007-09-19		ENSG00000101974	ENSG00000101974		"""ATPases / P-type"""	13554	protein-coding gene	gene with protein product		300516	"""ATPase, Class VI, type 11C"""			11015572	Standard	NM_173694		Approved	ATPIG, ATPIQ	uc004faz.3	Q8NB49	OTTHUMG00000022538	ENST00000327569.3:c.3336C>T	X.37:g.138813876G>A		62	0.00	0		4	0.00	0	138641542	96	13.51	15	Q5JT69|Q5JT70|Q5JT71|Q5JT72|Q5JT73|Q6ZND5|Q6ZU50|Q6ZUP7|Q70IJ9|Q70IK0|Q8WX24	Silent	SNP	HMMPfam_E1-E2_ATPase,PatternScan_ATPASE_E1_E2,superfamily_HAD-like,superfamily_Calcium ATPase transduction domain A,superfamily_Metal cation-transporting ATPase ATP-binding domain N	p.S1112	ENST00000327569.3	37	c.3336	CCDS14668.1	X	.	.	.	.	.	.	.	.	.	.	G	4.612	0.113812	0.08831	.	.	ENSG00000101974	ENST00000433868	.	.	.	5.44	3.57	0.40892	.	.	.	.	.	T	0.45915	0.1366	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43294	-0.9400	4	.	.	.	.	3.0576	0.06189	0.1005:0.2677:0.4802:0.1516	.	.	.	.	C	145	.	.	R	-	1	0	ATP11C	138641542	0.989000	0.36119	0.985000	0.45067	0.999000	0.98932	2.343000	0.44001	2.433000	0.82419	0.600000	0.82982	CGC	-	NULL		0.388	ATP11C-008	KNOWN	basic|CCDS	protein_coding	ATP11C	protein_coding	OTTHUMT00000354945.1	G	NM_173694		138641542	-1	no_errors	NM_173694.1	genbank	human	validated	54_36p	silent	SNP	0.956	A
MECR	51102	genome.wustl.edu	37	1	29543130	29543130	+	Missense_Mutation	SNP	T	T	C	rs201700021		TCGA-AB-2830-03B-01W-0728-08	TCGA-AB-2830-11B-01W-0728-08	T	T	T	C	T	T	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	f72fb885-99dd-486a-8f06-cf886c085f60	303971a6-646d-43e9-aa4c-18a133db1161	g.chr1:29543130T>C	ENST00000263702.6	-	2	269	c.244A>G	c.(244-246)Atc>Gtc	p.I82V	MECR_ENST00000373791.3_Missense_Mutation_p.I6V|MECR_ENST00000489248.1_5'UTR			Q9BV79	MECR_HUMAN	mitochondrial trans-2-enoyl-CoA reductase	82					fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	trans-2-enoyl-CoA reductase (NADPH) activity (GO:0019166)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(2)|prostate(1)	11		Colorectal(325;0.000389)|Breast(348;0.00765)|Lung NSC(340;0.0081)|all_lung(284;0.00914)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.39e-07)|COAD - Colon adenocarcinoma(152;2.04e-05)|STAD - Stomach adenocarcinoma(196;0.0195)|BRCA - Breast invasive adenocarcinoma(304;0.053)|READ - Rectum adenocarcinoma(331;0.0649)|KIRC - Kidney renal clear cell carcinoma(1967;0.137)		GATGGATTGATAGGGGCCGCC	0.458													T|||	1	0.000199681	0.0008	0.0	5008	,	,		19429	0.0		0.0	False		,,,				2504	0.0					dbGAP											0			1											226.0	228.0	227.0					1																	29543130		2203	4300	6503	29415717	SO:0001583	missense	0				CCDS30659.1, CCDS30660.1	1p35.3	2012-09-20			ENSG00000116353	ENSG00000116353	1.3.1.38		19691	protein-coding gene	gene with protein product	"""nuclear receptor binding factor 1"", ""mitochondrial 2-enoyl thioester reductase"""	608205				9795230, 12654921	Standard	XM_005245885		Approved	CGI-63, NRBF1, FASN2B	uc001brq.1	Q9BV79	OTTHUMG00000059082	ENST00000263702.6:c.244A>G	1.37:g.29543130T>C	ENSP00000263702:p.Ile82Val	290	1.36	4		15	46.43	13	29415717	59	23.38	18	B3KT72|Q5SYU0|Q5SYU1|Q5SYU2|Q6IBU9|Q9Y373	Missense_Mutation	SNP	superfamily_GroES-like,HMMPfam_ADH_zinc_N,HMMPfam_ADH_N,superfamily_NAD(P)-binding Rossmann-fold domains	p.I82V	ENST00000263702.6	37	c.244	CCDS30659.1	1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	T	11.39	1.624739	0.28889	.	.	ENSG00000116353	ENST00000373791;ENST00000263702	T;T	0.48201	0.82;0.82	5.87	0.892	0.19230	GroES-like (1);Alcohol dehydrogenase GroES-like (1);	0.138837	0.64402	N	0.000004	T	0.28532	0.0706	N	0.16233	0.39	0.58432	D	0.999995	B	0.13145	0.007	B	0.30572	0.117	T	0.03673	-1.1014	10	0.20519	T	0.43	.	7.2893	0.26356	0.0:0.4375:0.0:0.5625	.	82	Q9BV79	MECR_HUMAN	V	6;82	ENSP00000362896:I6V;ENSP00000263702:I82V	ENSP00000263702:I82V	I	-	1	0	MECR	29415717	0.998000	0.40836	0.997000	0.53966	0.999000	0.98932	0.568000	0.23623	0.152000	0.19188	0.529000	0.55759	ATC	-	superfamily_GroES-like,HMMPfam_ADH_N		0.458	MECR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MECR	protein_coding	OTTHUMT00000130740.1	T	NM_016011		29415717	-1	no_errors	NM_016011.1	genbank	human	validated	54_36p	missense	SNP	0.997	C
DNMT3A	1788	genome.wustl.edu	37	2	25457242	25457242	+	Missense_Mutation	SNP	C	C	G	rs147001633	byFrequency	TCGA-AB-2830-03B-01W-0728-08	TCGA-AB-2830-11B-01W-0728-08	C	C	C	G	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	f72fb885-99dd-486a-8f06-cf886c085f60	303971a6-646d-43e9-aa4c-18a133db1161	g.chr2:25457242C>G	ENST00000264709.3	-	23	2982	c.2645G>C	c.(2644-2646)cGc>cCc	p.R882P	DNMT3A_ENST00000402667.1_Missense_Mutation_p.R659P|DNMT3A_ENST00000321117.5_Missense_Mutation_p.R882P|DNMT3A_ENST00000380746.4_Missense_Mutation_p.R693P|DNMT3A_ENST00000474887.1_5'Flank	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	882	SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.		R -> C (in a patient with chronic myelomonocytic leukemia; somatic mutation). {ECO:0000269|PubMed:21828135}.|R -> H (in a patient with chronic myelomonocytic leukemia; somatic mutation). {ECO:0000269|PubMed:21828135}.|R -> P (in a patient with chronic myelomonocytic leukemia; somatic mutation). {ECO:0000269|PubMed:21828135}.		C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)	p.R882H(209)|p.R882P(5)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCTCGCCAAGCGGCTCATGTT	0.592			"""Mis, F, N, S"""		AML																																	dbGAP		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	214	Substitution - Missense(214)	haematopoietic_and_lymphoid_tissue(214)	2											56.0	51.0	53.0					2																	25457242		2203	4300	6503	25310746	SO:0001583	missense	0				CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.2645G>C	2.37:g.25457242C>G	ENSP00000264709:p.Arg882Pro	155	7.14	12		37	37.70	23	25310746	48	21.31	13	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Missense_Mutation	SNP	HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT	p.R882P	ENST00000264709.3	37	c.2645	CCDS33157.1	2	.	.	.	.	.	.	.	.	.	.	C	20.8	4.055280	0.75960	.	.	ENSG00000119772	ENST00000380746;ENST00000321117;ENST00000264709;ENST00000402667	D;D;D;D	0.97186	-4.28;-4.28;-4.28;-4.28	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	D	0.97402	0.9150	M	0.64170	1.965	0.80722	D	1	P;D	0.76494	0.855;0.999	B;P	0.53954	0.18;0.738	D	0.97884	1.0293	10	0.87932	D	0	-8.768	18.4404	0.90665	0.0:1.0:0.0:0.0	.	882;693	Q9Y6K1;E9PEB8	DNM3A_HUMAN;.	P	693;882;882;659	ENSP00000370122:R693P;ENSP00000324375:R882P;ENSP00000264709:R882P;ENSP00000384237:R659P	ENSP00000264709:R882P	R	-	2	0	DNMT3A	25310746	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.814000	0.86154	2.698000	0.92095	0.561000	0.74099	CGC	-	superfamily_S-adenosyl-L-methionine-dependent methyltransferases		0.592	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	DNMT3A	protein_coding	OTTHUMT00000211587.1	C	NM_022552		25310746	-1	no_errors	NM_022552.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	G
SH3BP4	23677	genome.wustl.edu	37	2	235950773	235950773	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2830-03B-01W-0728-08	TCGA-AB-2830-11B-01W-0728-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	f72fb885-99dd-486a-8f06-cf886c085f60	303971a6-646d-43e9-aa4c-18a133db1161	g.chr2:235950773G>A	ENST00000409212.1	+	4	1867	c.1360G>A	c.(1360-1362)Gtg>Atg	p.V454M	SH3BP4_ENST00000344528.4_Missense_Mutation_p.V454M|SH3BP4_ENST00000392011.2_Missense_Mutation_p.V454M			Q9P0V3	SH3B4_HUMAN	SH3-domain binding protein 4	454					cellular response to amino acid stimulus (GO:0071230)|endocytosis (GO:0006897)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of GTPase activity (GO:0034260)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|protein localization to lysosome (GO:0061462)|regulation of catalytic activity (GO:0050790)	coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	GDP-dissociation inhibitor activity (GO:0005092)|identical protein binding (GO:0042802)|Ras GTPase binding (GO:0017016)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(6)|stomach(3)|urinary_tract(2)	44		Breast(86;0.000332)|Renal(207;0.00339)|all_lung(227;0.00458)|all_hematologic(139;0.0296)|Lung NSC(271;0.0419)		Epithelial(121;7.66e-20)|BRCA - Breast invasive adenocarcinoma(100;0.000402)|Lung(119;0.00299)|LUSC - Lung squamous cell carcinoma(224;0.00645)|GBM - Glioblastoma multiforme(43;0.237)		CGTGGCTGTCGTGGCCCATGG	0.572																																						dbGAP											0			2											54.0	51.0	52.0					2																	235950773		2203	4300	6503	235615512	SO:0001583	missense	0			AF147747	CCDS2513.1	2q37.1-q37.2	2008-05-15			ENSG00000130147	ENSG00000130147			10826	protein-coding gene	gene with protein product		605611				10644451	Standard	NM_014521		Approved		uc002vvp.3	Q9P0V3	OTTHUMG00000133292	ENST00000409212.1:c.1360G>A	2.37:g.235950773G>A	ENSP00000386862:p.Val454Met	22	0.00	0		NA	NA	NA	235615512	50	16.67	10	O95082|Q309A3|Q53QD0|Q53TD1	Missense_Mutation	SNP	HMMPfam_SH3_1,HMMSmart_SM00326,superfamily_SH3-domain,HMMPfam_SH3_2	p.V454M	ENST00000409212.1	37	c.1360	CCDS2513.1	2	.	.	.	.	.	.	.	.	.	.	G	15.93	2.977341	0.53720	.	.	ENSG00000130147	ENST00000392011;ENST00000420127;ENST00000409212;ENST00000344528	T;T;T	0.16897	2.31;2.31;2.31	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.43055	0.1230	M	0.66939	2.045	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.22871	-1.0204	10	0.72032	D	0.01	-8.1114	18.2252	0.89915	0.0:0.0:1.0:0.0	.	454;454	A8K594;Q9P0V3	.;SH3B4_HUMAN	M	454	ENSP00000375867:V454M;ENSP00000386862:V454M;ENSP00000340237:V454M	ENSP00000340237:V454M	V	+	1	0	SH3BP4	235615512	1.000000	0.71417	0.067000	0.19924	0.289000	0.27227	5.493000	0.66899	2.633000	0.89246	0.655000	0.94253	GTG	-	NULL		0.572	SH3BP4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	SH3BP4	protein_coding	OTTHUMT00000329763.1	G			235615512	+1	no_errors	NM_014521.2	genbank	human	reviewed	54_36p	missense	SNP	0.948	A
THRB	7068	genome.wustl.edu	37	3	24169122	24169122	+	Missense_Mutation	SNP	G	G	A	rs387906515|rs121918689|rs121918697		TCGA-AB-2830-03B-01W-0728-08	TCGA-AB-2830-11B-01W-0728-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	f72fb885-99dd-486a-8f06-cf886c085f60	303971a6-646d-43e9-aa4c-18a133db1161	g.chr3:24169122G>A	ENST00000356447.4	-	9	1296	c.1012C>T	c.(1012-1014)Cgg>Tgg	p.R338W	THRB_ENST00000396671.2_Missense_Mutation_p.R338W|THRB_ENST00000416420.1_Missense_Mutation_p.R338W|THRB_ENST00000280696.5_Missense_Mutation_p.R353W	NM_000461.4|NM_001128177.1	NP_000452.2|NP_001121649.1	P10828	THB_HUMAN	thyroid hormone receptor, beta	338	Interaction with NR2F6.|Ligand-binding.		R -> W (in GTHR). {ECO:0000269|PubMed:16804041, ECO:0000269|PubMed:8514853, ECO:0000269|PubMed:8889584}.		female courtship behavior (GO:0008050)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of female receptivity (GO:0007621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of heart contraction (GO:0008016)|sensory perception of sound (GO:0007605)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|Type I pneumocyte differentiation (GO:0060509)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|thyroid hormone binding (GO:0070324)|thyroid hormone receptor activity (GO:0004887)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(6)|pancreas(2)|prostate(1)|skin(3)	19					Dextrothyroxine(DB00509)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)	AGCTGGCCCCGTGTCACTGCC	0.532																																					Melanoma(21;896 1043 15021 37958)	dbGAP											0			3	GRCh37	CD910557|CM930706	THRB	D|M	rs121918697						137.0	129.0	132.0					3																	24169122		2203	4300	6503	24144126	SO:0001583	missense	0				CCDS2641.1	3p24.2	2013-01-16	2011-05-19		ENSG00000151090	ENSG00000151090		"""Nuclear hormone receptors"""	11799	protein-coding gene	gene with protein product	"""avian erythroblastic leukemia viral (v-erb-a) oncogene homolog 2"", ""oncogene ERBA2"", ""generalized resistance to thyroid hormone"", ""thyroid hormone receptor beta 1"""	190160	"""thyroid hormone receptor, beta (avian erythroblastic leukemia viral (v-erb-a) oncogene homolog 2)"", ""pituitary resistance to thyroid hormone"", ""thyroid hormone receptor, beta (erythroblastic leukemia viral (v-erb-a) oncogene homolog 2, avian)"""	ERBA2, PRTH		1973914, 8040303	Standard	NM_000461		Approved	THRB1, THRB2, NR1A2, THR1, ERBA-BETA, GRTH	uc003ccy.4	P10828	OTTHUMG00000130478	ENST00000356447.4:c.1012C>T	3.37:g.24169122G>A	ENSP00000348827:p.Arg338Trp	117	8.59	11		NA	NA	NA	24144126	86	18.10	19	B3KU79|P37243|Q13986|Q3KP35|Q6WGL2|Q9UD41	Missense_Mutation	SNP	HMMPfam_Hormone_recep,HMMSmart_SM00430,HMMPfam_zf-C4,HMMSmart_SM00399,PatternScan_NUCLEAR_REC_DBD_1,superfamily_Nuclear receptor ligand-binding domain,superfamily_Glucocorticoid receptor-like (DNA-binding domain)	p.R338W	ENST00000356447.4	37	c.1012	CCDS2641.1	3	.	.	.	.	.	.	.	.	.	.	G	23.4	4.406244	0.83230	.	.	ENSG00000151090	ENST00000396671;ENST00000356447;ENST00000416420;ENST00000280696	D;D;D;D	0.97041	-4.22;-4.22;-4.22;-4.22	5.97	5.03	0.67393	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.000000	0.64402	D	0.000003	D	0.97967	0.9331	M	0.71920	2.185	0.80722	A	1	D	0.89917	1.0	D	0.79108	0.992	D	0.98737	1.0715	9	0.87932	D	0	.	13.8891	0.63726	0.0:0.0:0.7421:0.2579	.	338	P10828	THB_HUMAN	W	338;338;338;353	ENSP00000379904:R338W;ENSP00000348827:R338W;ENSP00000414444:R338W;ENSP00000280696:R353W	ENSP00000280696:R353W	R	-	1	2	THRB	24144126	1.000000	0.71417	0.985000	0.45067	0.997000	0.91878	4.183000	0.58317	2.836000	0.97738	0.655000	0.94253	CGG	-	HMMPfam_Hormone_recep,HMMSmart_SM00430,superfamily_Nuclear receptor ligand-binding domain		0.532	THRB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	THRB	protein_coding	OTTHUMT00000252877.3	G	NM_000461		24144126	-1	no_errors	NM_000461.4	genbank	human	reviewed	54_36p	missense	SNP	0.991	A
HIVEP2	3097	genome.wustl.edu	37	6	143093951	143093951	+	Missense_Mutation	SNP	C	C	T	rs201987264		TCGA-AB-2830-03B-01W-0728-08	TCGA-AB-2830-11B-01W-0728-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	f72fb885-99dd-486a-8f06-cf886c085f60	303971a6-646d-43e9-aa4c-18a133db1161	g.chr6:143093951C>T	ENST00000367604.1	-	4	2564	c.1925G>A	c.(1924-1926)cGg>cAg	p.R642Q	HIVEP2_ENST00000012134.2_Missense_Mutation_p.R642Q|HIVEP2_ENST00000367603.2_Missense_Mutation_p.R642Q			P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer binding protein 2	642					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(19)|lung(35)|ovary(4)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	100				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		ATAGGGTTTCCGACAGACATC	0.453																																					Esophageal Squamous(107;843 1510 13293 16805 42198)	dbGAP											0			6						C	GLN/ARG	0,3882		0,0,1941	160.0	152.0	155.0		1925	3.7	1.0	6		155	2,8270		0,2,4134	yes	missense	HIVEP2	NM_006734.3	43	0,2,6075	TT,TC,CC		0.0242,0.0,0.0165	possibly-damaging	642/2447	143093951	2,12152	1941	4136	6077	143135644	SO:0001583	missense	0			M60119	CCDS43510.1	6q23-q24	2013-01-08	2001-11-28		ENSG00000010818	ENSG00000010818		"""Zinc fingers, C2H2-type"""	4921	protein-coding gene	gene with protein product	"""c-myc intron binding protein 1"""	143054	"""human immunodeficiency virus type I enhancer-binding protein 2"""			1733857, 2022670	Standard	NM_006734		Approved	MBP-2, HIV-EP2, MIBP1, ZAS2, Schnurri-2, ZNF40B	uc003qjd.3	P31629	OTTHUMG00000015713	ENST00000367604.1:c.1925G>A	6.37:g.143093951C>T	ENSP00000356576:p.Arg642Gln	46	7.84	4		18	14.29	3	143135644	62	34.74	33	Q02646|Q5THT5|Q9NS05	Missense_Mutation	SNP	HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667	p.R642Q	ENST00000367604.1	37	c.1925	CCDS43510.1	6	.	.	.	.	.	.	.	.	.	.	C	17.01	3.279426	0.59758	0.0	2.42E-4	ENSG00000010818	ENST00000367604;ENST00000367603;ENST00000012134	T;T;T	0.11169	2.8;2.8;2.8	5.48	3.7	0.42460	.	0.203292	0.35179	N	0.003390	T	0.04092	0.0114	L	0.60455	1.87	0.26948	N	0.966109	B	0.13145	0.007	B	0.04013	0.001	T	0.32455	-0.9906	10	0.56958	D	0.05	-12.4442	7.2987	0.26408	0.0:0.7142:0.1389:0.147	.	642	P31629	ZEP2_HUMAN	Q	642	ENSP00000356576:R642Q;ENSP00000356575:R642Q;ENSP00000012134:R642Q	ENSP00000012134:R642Q	R	-	2	0	HIVEP2	143135644	1.000000	0.71417	0.979000	0.43373	0.965000	0.64279	1.721000	0.38032	0.686000	0.31488	0.655000	0.94253	CGG	-	NULL		0.453	HIVEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HIVEP2	protein_coding	OTTHUMT00000042495.1	C			143135644	-1	no_errors	NM_006734.3	genbank	human	provisional	54_36p	missense	SNP	0.983	T
FAM208B	54906	genome.wustl.edu	37	10	5772585	5772585	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2830-03B-01W-0728-08	TCGA-AB-2830-11B-01W-0728-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	f72fb885-99dd-486a-8f06-cf886c085f60	303971a6-646d-43e9-aa4c-18a133db1161	g.chr10:5772585G>A	ENST00000328090.5	+	11	1248	c.623G>A	c.(622-624)cGt>cAt	p.R208H	RP11-336A10.2_ENST00000411512.2_RNA	NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	208																	TTAGTAAAGCGTCATTTCCAA	0.413																																						dbGAP											0			10											128.0	119.0	122.0					10																	5772585		1872	4114	5986	5812591	SO:0001583	missense	0			BX649177	CCDS41485.1	10p15.1	2011-09-14	2011-09-14	2011-09-14	ENSG00000108021	ENSG00000108021			23484	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 18"""	C10orf18		12477932	Standard	NM_017782		Approved	FLJ20360, bA318E3.2, KIAA2006	uc001iij.3	Q5VWN6	OTTHUMG00000017605	ENST00000328090.5:c.623G>A	10.37:g.5772585G>A	ENSP00000328426:p.Arg208His	77	0.00	0		19	48.65	18	5812591	72	22.58	21	Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	Missense_Mutation	SNP	NULL	p.R208H	ENST00000328090.5	37	c.623	CCDS41485.1	10	.	.	.	.	.	.	.	.	.	.	G	0.012	-1.678381	0.00751	.	.	ENSG00000108021	ENST00000328090;ENST00000442808	T	0.03801	3.8	5.98	-8.14	0.01069	.	1.277740	0.04936	N	0.457827	T	0.01558	0.0050	N	0.00521	-1.4	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.49978	-0.8881	10	0.02654	T	1	.	19.832	0.96639	0.3188:0.0:0.6812:0.0	.	208	Q5VWN6	F208B_HUMAN	H	208	ENSP00000328426:R208H	ENSP00000328426:R208H	R	+	2	0	C10orf18	5812591	0.001000	0.12720	0.000000	0.03702	0.093000	0.18481	-0.260000	0.08708	-2.031000	0.00928	-1.412000	0.01120	CGT	-	NULL		0.413	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	C10orf18	protein_coding	OTTHUMT00000046571.2	G	NM_017782		5812591	+1	no_errors	NM_017782.3	genbank	human	validated	54_36p	missense	SNP	0.005	A
PHC1P1	653441	genome.wustl.edu	37	12	55806130	55806130	+	IGR	SNP	G	G	A			TCGA-AB-2830-03B-01W-0728-08	TCGA-AB-2830-11B-01W-0728-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	f72fb885-99dd-486a-8f06-cf886c085f60	303971a6-646d-43e9-aa4c-18a133db1161	g.chr12:55806130G>A								OR6C65 (10841 upstream) : OR6C76 (13907 downstream)																							CGCACTTCAGGAGATTCGCCT	0.542																																						dbGAP											0			12																																								54092397	SO:0001628	intergenic_variant	0																															12.37:g.55806130G>A		16	5.88	1		41	0.00	0	54092397	25	30.56	11		Silent	SNP	HMMPfam_SAM_1,HMMSmart_SM00454,HMMPfam_zf-FCS,superfamily_SAM/Pointed domain	p.L797		37	c.2391		12																																																																																			-	HMMPfam_zf-FCS	0	0.542					PHC1B			G			54092397	-1	no_errors	ENST00000326184	ensembl	human	known	54_36p	silent	SNP	0.250	A
MAPKBP1	23005	genome.wustl.edu	37	15	42104229	42104229	+	Silent	SNP	G	G	A	rs202026599		TCGA-AB-2830-03B-01W-0728-08	TCGA-AB-2830-11B-01W-0728-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	f72fb885-99dd-486a-8f06-cf886c085f60	303971a6-646d-43e9-aa4c-18a133db1161	g.chr15:42104229G>A	ENST00000456763.2	+	6	598	c.402G>A	c.(400-402)aaG>aaA	p.K134K	MAPKBP1_ENST00000457542.2_Silent_p.K134K|MAPKBP1_ENST00000221214.6_Silent_p.K134K|MAPKBP1_ENST00000260357.7_Silent_p.K22K|MAPKBP1_ENST00000514566.1_Silent_p.K134K	NM_001128608.1	NP_001122080.1	O60336	MABP1_HUMAN	mitogen-activated protein kinase binding protein 1	134										breast(6)|central_nervous_system(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225)		AGGAGCACAAGTATGGTGTGG	0.592											OREG0023077	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	g|||	1	0.000199681	0.0008	0.0	5008	,	,		19792	0.0		0.0	False		,,,				2504	0.0					dbGAP											0			15											157.0	127.0	137.0					15																	42104229		2203	4300	6503	39891521	SO:0001819	synonymous_variant	0			AB011168	CCDS32201.1, CCDS45239.1, CCDS58359.1	15q15.1	2013-01-10	2008-01-30		ENSG00000137802	ENSG00000137802		"""WD repeat domain containing"""	29536	protein-coding gene	gene with protein product			"""mitogen activated protein kinase binding protein 1"""			9628581, 10471813	Standard	NM_014994		Approved	KIAA0596	uc001zok.4	O60336	OTTHUMG00000160227	ENST00000456763.2:c.402G>A	15.37:g.42104229G>A		260	4.06	11	906	24	57.14	32	39891521	65	33.67	33	A6NM93|A8K8P9|Q14CB5|Q14CD8|Q49AJ8|Q5W9G9	Silent	SNP	HMMSmart_SM00320,PatternScan_PTS_HPR_SER,superfamily_WD40 repeat-like,HMMPfam_WD40	p.K134	ENST00000456763.2	37	c.402	CCDS45239.1	15																																																																																			-	HMMSmart_SM00320,superfamily_WD40 repeat-like,HMMPfam_WD40		0.592	MAPKBP1-002	KNOWN	basic|CCDS	protein_coding	MAPKBP1	protein_coding	OTTHUMT00000359745.1	G	NM_014994		39891521	+1	no_errors	NM_014994.1	genbank	human	validated	54_36p	silent	SNP	0.999	A
ABCC11	85320	genome.wustl.edu	37	16	48244997	48244997	+	Silent	SNP	G	G	A	rs139456533		TCGA-AB-2830-03B-01W-0728-08	TCGA-AB-2830-11B-01W-0728-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	f72fb885-99dd-486a-8f06-cf886c085f60	303971a6-646d-43e9-aa4c-18a133db1161	g.chr16:48244997G>A	ENST00000394747.1	-	10	1819	c.1470C>T	c.(1468-1470)atC>atT	p.I490I	ABCC11_ENST00000537808.1_Silent_p.I490I|ABCC11_ENST00000394748.1_Silent_p.I490I|ABCC11_ENST00000356608.2_Silent_p.I490I|ABCC11_ENST00000353782.5_Silent_p.I490I	NM_033151.3	NP_149163.2	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 11	490					organic anion transport (GO:0015711)|purine nucleotide transport (GO:0015865)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)|purine nucleotide transmembrane transporter activity (GO:0015216)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(3)|prostate(2)|skin(5)|urinary_tract(2)	83		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)			Conjugated Estrogens(DB00286)|Folic Acid(DB00158)|Indomethacin(DB00328)|Methotrexate(DB00563)|Probenecid(DB01032)	CCCCATTGACGATCCCGGGAC	0.577																																						dbGAP											0			16						G	,,	0,4402		0,0,2201	108.0	99.0	102.0		1470,1470,1470	-9.3	0.0	16	dbSNP_134	102	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	ABCC11	NM_032583.3,NM_033151.3,NM_145186.2	,,	0,2,6499	AA,AG,GG		0.0233,0.0,0.0154	,,	490/1383,490/1383,490/1345	48244997	2,13000	2201	4300	6501	46802498	SO:0001819	synonymous_variant	0			AF367202	CCDS10732.1, CCDS10733.1	16q12	2012-03-14			ENSG00000121270	ENSG00000121270		"""ATP binding cassette transporters / subfamily C"""	14639	protein-coding gene	gene with protein product		607040				11483364, 11435397	Standard	NM_033151		Approved	MRP8	uc002efg.1	Q96J66	OTTHUMG00000133146	ENST00000394747.1:c.1470C>T	16.37:g.48244997G>A		184	8.42	17		NA	NA	NA	46802498	117	34.27	61	Q8TDJ0|Q96JA6|Q9BX80	Silent	SNP	HMMPfam_ABC_membrane,HMMPfam_ABC_tran,HMMSmart_SM00382,superfamily_Multidrug resistance ABC transporter MsbA N-terminal domain,PatternScan_ABC_TRANSPORTER_1,superfamily_P-loop containing nucleoside triphosphate hydrolases	p.I490	ENST00000394747.1	37	c.1470	CCDS10732.1	16																																																																																			-	superfamily_Multidrug resistance ABC transporter MsbA N-terminal domain		0.577	ABCC11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	ABCC11	protein_coding	OTTHUMT00000429984.1	G	NM_032583		46802498	-1	no_errors	NM_032583.3	genbank	human	reviewed	54_36p	silent	SNP	0.000	A
TUBGCP6	85378	genome.wustl.edu	37	22	50671779	50671779	+	Missense_Mutation	SNP	A	A	G			TCGA-AB-2830-03B-01W-0728-08	TCGA-AB-2830-11B-01W-0728-08	A	A	A	G	A	A	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	f72fb885-99dd-486a-8f06-cf886c085f60	303971a6-646d-43e9-aa4c-18a133db1161	g.chr22:50671779A>G	ENST00000248846.5	-	3	1186	c.1082T>C	c.(1081-1083)aTt>aCt	p.I361T	TUBGCP6_ENST00000439308.2_Missense_Mutation_p.I361T			Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	361					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)			breast(4)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(13)|ovary(3)|prostate(2)|skin(2)	45		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)		CACGACCCCAATCAAGACGTT	0.647																																						dbGAP											0			22											109.0	59.0	76.0					22																	50671779		2203	4300	6503	49013906	SO:0001583	missense	0			AB051456	CCDS14087.1	22q13.31-q13.33	2008-07-01			ENSG00000128159	ENSG00000128159			18127	protein-coding gene	gene with protein product	"""gamma-tubulin complex component 6"""	610053				11694571, 11258795	Standard	XR_244458		Approved	GCP6, KIAA1669, DJ402G11.6	uc003bkb.1	Q96RT7	OTTHUMG00000030150	ENST00000248846.5:c.1082T>C	22.37:g.50671779A>G	ENSP00000248846:p.Ile361Thr	38	2.56	1		68	42.37	50	49013906	30	28.57	12	Q5JZ80|Q6PJ40|Q86YE9|Q9BY91|Q9UGX3|Q9UGX4	Missense_Mutation	SNP	HMMPfam_Spc97_Spc98	p.I361T	ENST00000248846.5	37	c.1082	CCDS14087.1	22	.	.	.	.	.	.	.	.	.	.	A	21.4	4.141159	0.77775	.	.	ENSG00000128159	ENST00000248846;ENST00000439308	T;T	0.07567	3.18;3.18	5.69	5.69	0.88448	.	0.771111	0.12746	N	0.442600	T	0.22322	0.0538	L	0.47190	1.495	0.49687	D	0.999811	D;D	0.69078	0.994;0.997	P;D	0.65140	0.902;0.932	T	0.00426	-1.1746	10	0.35671	T	0.21	.	15.6139	0.76750	1.0:0.0:0.0:0.0	.	361;361	B2RWN4;Q96RT7	.;GCP6_HUMAN	T	361	ENSP00000248846:I361T;ENSP00000397387:I361T	ENSP00000248846:I361T	I	-	2	0	TUBGCP6	49013906	1.000000	0.71417	0.088000	0.20740	0.719000	0.41307	9.210000	0.95106	2.171000	0.68590	0.459000	0.35465	ATT	-	HMMPfam_Spc97_Spc98		0.647	TUBGCP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TUBGCP6	protein_coding	OTTHUMT00000075004.3	A	NM_020461		49013906	-1	no_errors	NM_020461.3	genbank	human	reviewed	54_36p	missense	SNP	0.999	G
TET2	54790	genome.wustl.edu	37	4	106190863	106190864	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AB-2830-03B-01W-0728-08	TCGA-AB-2830-11B-01W-0728-08	-	-	-	G	-	-	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	f72fb885-99dd-486a-8f06-cf886c085f60	303971a6-646d-43e9-aa4c-18a133db1161	g.chr4:106190863_106190864insG	ENST00000540549.1	+	9	5001_5002	c.4141_4142insG	c.(4141-4143)gccfs	p.A1381fs	TET2_ENST00000380013.4_Frame_Shift_Ins_p.A1381fs|TET2_ENST00000513237.1_Frame_Shift_Ins_p.A1402fs|TET2_ENST00000545826.1_3'UTR			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	1381					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)			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)		CTGTGCTCATGCCCACAGAGAC	0.5			"""Mis N, F"""		MDS																																	dbGAP		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	0			4																																								106410313	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.4141dupG	4.37:g.106190863_106190863dupG	ENSP00000442788:p.Ala1381fs	30	0.00	0		12	0.00	0	106410312	98	0.00	0	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Frame_Shift_Ins	INS	NULL	p.A183fs	ENST00000540549.1	37	c.547_548	CCDS47120.1	4																																																																																			-	NULL		0.500	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	TET2	protein_coding	OTTHUMT00000253952.2	-	NM_017628		106410313	+1	no_start_codon	ENST00000265149	ensembl	human	known	54_36p	frame_shift_ins	INS	1.000:1.000	G
TET2	54790	genome.wustl.edu	37	4	106193855	106193855	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AB-2830-03B-01W-0728-08	TCGA-AB-2830-11B-01W-0728-08	A	A	A	-	A	A	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	f72fb885-99dd-486a-8f06-cf886c085f60	303971a6-646d-43e9-aa4c-18a133db1161	g.chr4:106193855delA	ENST00000540549.1	+	10	5177	c.4317delA	c.(4315-4317)aaafs	p.K1439fs	TET2_ENST00000380013.4_Frame_Shift_Del_p.K1439fs|TET2_ENST00000513237.1_Frame_Shift_Del_p.K1460fs|TET2_ENST00000545826.1_3'UTR			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	1439					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.R1440fs*37(1)|p.K1439fs*9(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)		AGGAGAAAAAACGGAGTGGTG	0.478			"""Mis N, F"""		MDS																																	dbGAP		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	2	Deletion - Frameshift(2)	haematopoietic_and_lymphoid_tissue(2)	4											162.0	153.0	156.0					4																	106193855		692	1591	2283	106413304	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.4317delA	4.37:g.106193855delA	ENSP00000442788:p.Lys1439fs	36	0.00	0		35	0.00	0	106413304	123	0.00	0	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Frame_Shift_Del	DEL	NULL	p.K241fs	ENST00000540549.1	37	c.723	CCDS47120.1	4																																																																																			-	NULL		0.478	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	TET2	protein_coding	OTTHUMT00000253952.2	A	NM_017628		106413304	+1	no_start_codon	ENST00000265149	ensembl	human	known	54_36p	frame_shift_del	DEL	0.000	-
FLT3	2322	genome.wustl.edu	37	13	28608242	28608243	+	In_Frame_Ins	INS	-	-	ACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTACCCCCTCGGGGGG			TCGA-AB-2830-03B-01W-0728-08	TCGA-AB-2830-11B-01W-0728-08	-	-	-	ACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTACCCCCTCGGGGGG	-	-	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	f72fb885-99dd-486a-8f06-cf886c085f60	303971a6-646d-43e9-aa4c-18a133db1161	g.chr13:28608242_28608243insACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTACCCCCTCGGGGGG	ENST00000241453.7	-	14	1894_1895	c.1813_1814insCCCCCCGAGGGGGTAATGAGTACTTCTACGTTGATTTCAGAGAATATGAATATGATCTCAAATGGGAGT	c.(1813-1815)ttt>tCCCCCCGAGGGGGTAATGAGTACTTCTACGTTGATTTCAGAGAATATGAATATGATCTCAAATGGGAGTtt	p.604_605insSPRGGNEYFYVDFREYEYDLKWE	FLT3_ENST00000380982.4_In_Frame_Ins_p.604_605insSPRGGNEYFYVDFREYEYDLKWE|FLT3_ENST00000537084.1_In_Frame_Ins_p.604_605insSPRGGNEYFYVDFREYEYDLKWE	NM_004119.2	NP_004110.2	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	604					B cell differentiation (GO:0030183)|cellular response to cytokine stimulus (GO:0071345)|common myeloid progenitor cell proliferation (GO:0035726)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell differentiation (GO:0097028)|hemopoiesis (GO:0030097)|leukocyte homeostasis (GO:0001776)|lymphocyte proliferation (GO:0046651)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|pro-B cell differentiation (GO:0002328)|pro-T cell differentiation (GO:0002572)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor signaling pathway (GO:0038084)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|cytokine receptor activity (GO:0004896)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.E604_F605insREYEYDLKWE(1)|p.E604_F605ins15(1)|p.605_606>GSSDNEYFYVDFREYEYDLKWEF(1)|p.E604_F605ins22(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(12329)|kidney(2)|large_intestine(8)|lung(30)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12390	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Ponatinib(DB08901)|Sorafenib(DB00398)|Sunitinib(DB01268)	TTCTCTTGGAAACTCCCATTTG	0.381			"""Mis, O"""		"""AML, ALL"""																																	dbGAP		Dom	yes		13	13q12	2322	fms-related tyrosine kinase 3		L	4	Insertion - In frame(3)|Complex - insertion inframe(1)	haematopoietic_and_lymphoid_tissue(4)	13																																								27506243	SO:0001652	inframe_insertion	0			U02687	CCDS31953.1	13q12	2014-09-17			ENSG00000122025	ENSG00000122025	2.7.10.1	"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3765	protein-coding gene	gene with protein product		136351				8394751	Standard	NM_004119		Approved	STK1, FLK2, CD135	uc001urw.3	P36888	OTTHUMG00000016646	ENST00000241453.7:c.1813_1814insCCCCCCGAGGGGGTAATGAGTACTTCTACGTTGATTTCAGAGAATATGAATATGATCTCAAATGGGAGT	13.37:g.28608242_28608243insACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTACCCCCTCGGGGGG	ENSP00000241453:p.Glu604_Phe605insSerProArgGlyGlyAsnGluTyrPheTyrValAspPheArgGluTyrGluTyrAspLeuLysTrpGlu	NA	NA	NA		NA	NA	NA	27506242	NA	NA	NA	A0AVG9|B7ZLT7|B7ZLT8|F5H0A0|Q13414	In_Frame_Ins	INS	HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726	p.605in_frame_insSPRGGNEYFYVDFREYEYDLKWE	ENST00000241453.7	37	c.1814_1813	CCDS31953.1	13																																																																																			-	superfamily_Kinase_like		0.381	FLT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	FLT3	protein_coding	OTTHUMT00000044319.2	-			27506243	-1	no_errors	NM_004119.2	genbank	human	reviewed	54_36p	in_frame_ins	INS	1.000:1.000	ACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTACCCCCTCGGGGGG
