#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
TTN	7273	genome.wustl.edu	37	2	179476545	179476545	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2993-03A-01D-0739-09	TCGA-AB-2993-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	4e956c79-d82b-4d89-9d05-7133e0caf740	c537a524-b89a-4738-8bbe-b00f335d4a75	g.chr2:179476545C>T	ENST00000591111.1	-	218	45792	c.45568G>A	c.(45568-45570)Gaa>Aaa	p.E15190K	TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.E16831K|TTN_ENST00000342992.6_Missense_Mutation_p.E14263K|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.E7766K|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.E7891K|TTN_ENST00000342175.6_Missense_Mutation_p.E7958K|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000590807.1_RNA			Q8WZ42	TITIN_HUMAN	titin	15190	Fibronectin type-III 10. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.E7766K(3)|p.E14263K(3)|p.E7958K(3)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ACTCCAGCTTCATTTTCAGCC	0.443																																						dbGAP											9	Substitution - Missense(9)	haematopoietic_and_lymphoid_tissue(9)	2											139.0	133.0	134.0					2																	179476545		1931	4141	6072	179184790	SO:0001583	missense	0			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.45568G>A	2.37:g.179476545C>T	ENSP00000465570:p.Glu15190Lys	10721	15.75	2174		49	51.49	52	179184790	8955	43.5733333333333	7039	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	HMMSmart_SM00219,HMMSmart_SM00220,PatternScan_IG_MHC,HMMSmart_SM00406,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_fn3,HMMSmart_SM00060,HMMPfam_PPAK,PatternScan_PROTEIN_KINASE_TYR,superfamily_Fibronectin type III,superfamily_Concanavalin A-like lectins/glucanases,superfamily_Protein kinase-like (PK-like),superfamily_WD40 repeat-like,HMMPfam_I-set,HMMPfam_ig,HMMPfam_Titin_Z,HMMPfam_Pkinase,PatternScan_FGGY_KINASES_1,PatternScan_PEROXIDASE_1,superfamily_Immunoglobulin,superfamily_vWA-like,superfamily_Positive stranded ssRNA viruses	p.E12813K	ENST00000591111.1	37	c.38437		2	.	.	.	.	.	.	.	.	.	.	C	16.55	3.155610	0.57259	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.56776	0.44;0.44;0.44;0.44	5.97	5.97	0.96955	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.65407	0.2688	L	0.29908	0.895	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.83275	0.996;0.996;0.996;0.996	T	0.66760	-0.5842	9	0.87932	D	0	.	20.4097	0.99016	0.0:1.0:0.0:0.0	.	7766;7891;7958;15190	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	K	14263;7766;7958;7891;7766	ENSP00000343764:E14263K;ENSP00000434586:E7766K;ENSP00000340554:E7958K;ENSP00000352154:E7891K	ENSP00000340554:E7958K	E	-	1	0	TTN	179184790	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.770000	0.85390	2.828000	0.97474	0.650000	0.86243	GAA	-	HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III,superfamily_Concanavalin A-like lectins/glucanases,superfamily_WD40 repeat-like,superfamily_vWA-like,superfamily_Positive stranded ssRNA viruses		0.443	TTN-019	PUTATIVE	basic	protein_coding	TTN	protein_coding	OTTHUMT00000460310.1	C	NM_133378		179184790	-1	no_errors	ENST00000375038	ensembl	human	known	54_36p	missense	SNP	1.000	T
UBA6-AS1	550112	genome.wustl.edu	37	4	68904788	68904788	+	RNA	SNP	G	G	A			TCGA-AB-2993-03A-01D-0739-09	TCGA-AB-2993-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	4e956c79-d82b-4d89-9d05-7133e0caf740	c537a524-b89a-4738-8bbe-b00f335d4a75	g.chr4:68904788G>A	ENST00000500538.2	+	0	1905									UBA6 antisense RNA 1 (head to head)																		CCGCAGCATCGTGTTTCAAGT	0.483																																						dbGAP											0			4																																								68587383			0					4q13.2	2014-01-15			ENSG00000248049	ENSG00000248049		"""Long non-coding RNAs"""	49083	non-coding RNA	RNA, long non-coding							Standard	NR_015439		Approved	LOC550112			OTTHUMG00000160769		4.37:g.68904788G>A		11376	13.1466666666667	1773		0	100.00	1	68587383	9969	46.5666666666667	9083		RNA	SNP	-	NULL	ENST00000500538.2	37	NULL		4																																																																																			-	-		0.483	UBA6-AS1-002	KNOWN	basic	antisense	LOC339970	antisense	OTTHUMT00000362199.2	G			68587383	+1	pseudogene	XR_038239.1	genbank	human	model	54_36p	rna	SNP	0.001	A
CDHR2	54825	genome.wustl.edu	37	5	176016333	176016333	+	Missense_Mutation	SNP	C	C	T	rs371676123		TCGA-AB-2993-03A-01D-0739-09	TCGA-AB-2993-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	4e956c79-d82b-4d89-9d05-7133e0caf740	c537a524-b89a-4738-8bbe-b00f335d4a75	g.chr5:176016333C>T	ENST00000510636.1	+	23	3285	c.3011C>T	c.(3010-3012)cCg>cTg	p.P1004L	CDHR2_ENST00000506348.1_Missense_Mutation_p.P1004L|CDHR2_ENST00000261944.5_Missense_Mutation_p.P1004L	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	1004	Cadherin 9. {ECO:0000255|PROSITE- ProRule:PRU00043}.		P -> L (in an acute myeloid leukemia sample; somatic mutation). {ECO:0000269|PubMed:18987736}.		cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P1004L(3)		breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|liver(1)|lung(23)|ovary(3)|prostate(5)|skin(4)|urinary_tract(1)	56						TTCCGCAGGCCGGTGACCAGC	0.612																																						dbGAP											3	Substitution - Missense(3)	haematopoietic_and_lymphoid_tissue(3)	5							LEU/PRO,LEU/PRO	1,4405	2.1+/-5.4	0,1,2202	96.0	101.0	99.0		3011,3011	3.7	0.1	5		99	0,8600		0,0,4300	no	missense,missense	CDHR2	NM_001171976.1,NM_017675.4	98,98	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign,benign	1004/1311,1004/1311	176016333	1,13005	2203	4300	6503	175948939	SO:0001583	missense	0			AB047004	CCDS34297.1	5q35.2	2011-07-01	2010-01-25	2010-01-25		ENSG00000074276		"""Cadherins / Cadherin-related"""	18231	protein-coding gene	gene with protein product	"""protocadherin LKC"""		"""protocadherin 24"""	PCDH24		11082270, 12117771	Standard	NM_001171976		Approved	PC-LKC, FLJ20124, FLJ20383, PCLKC	uc003mem.2	Q9BYE9		ENST00000510636.1:c.3011C>T	5.37:g.176016333C>T	ENSP00000424565:p.Pro1004Leu	8521	8.65666666666667	794		NA	NA	NA	175948939	5120	47.8133333333333	5094	A1L3U4|A6NC80|Q9NXP8	Missense_Mutation	SNP	HMMPfam_Cadherin,HMMSmart_CA,PatternScan_CADHERIN_1,superfamily_Cadherin	p.P1004L	ENST00000510636.1	37	c.3011	CCDS34297.1	5	.	.	.	.	.	.	.	.	.	.	c	1.021	-0.684722	0.03328	2.27E-4	0.0	ENSG00000074276	ENST00000510636;ENST00000261944;ENST00000506348	T;T;T	0.44881	0.91;0.91;0.91	4.8	3.65	0.41850	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.08179	0.0204	N	0.00025	-2.675	0.31570	N	0.656484	B	0.10296	0.003	B	0.04013	0.001	T	0.13953	-1.0490	9	0.17832	T	0.49	-9.988	9.6679	0.39996	0.0:0.0846:0.0:0.9154	.	1004	Q9BYE9	CDHR2_HUMAN	L	1004	ENSP00000424565:P1004L;ENSP00000261944:P1004L;ENSP00000421078:P1004L	ENSP00000261944:P1004L	P	+	2	0	CDHR2	175948939	1.000000	0.71417	0.130000	0.21974	0.033000	0.12548	3.586000	0.53950	0.711000	0.32018	-0.400000	0.06385	CCG	-	HMMPfam_Cadherin,HMMSmart_CA,superfamily_Cadherin		0.612	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PCDH24	protein_coding	OTTHUMT00000372201.1	C	NM_017675		175948939	+1	no_errors	NM_017675.3	genbank	human	reviewed	54_36p	missense	SNP	0.982	T
CALHM3	119395	genome.wustl.edu	37	10	105238745	105238745	+	Silent	SNP	C	C	T	rs376646721		TCGA-AB-2993-03A-01D-0739-09	TCGA-AB-2993-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	4e956c79-d82b-4d89-9d05-7133e0caf740	c537a524-b89a-4738-8bbe-b00f335d4a75	g.chr10:105238745C>T	ENST00000369783.4	-	1	252	c.45G>A	c.(43-45)tcG>tcA	p.S15S	RP11-225H22.5_ENST00000453753.1_RNA	NM_001129742.1	NP_001123214.1	Q86XJ0	CAHM3_HUMAN	calcium homeostasis modulator 3	15					ion transport (GO:0006811)	integral component of membrane (GO:0016021)		p.S15S(3)		kidney(1)|large_intestine(1)	2						TCACCGACTCCGAGCTTGACT	0.592													C|||	1	0.000199681	0.0	0.0	5008	,	,		19289	0.0		0.0	False		,,,				2504	0.001					dbGAP											3	Substitution - coding silent(3)	haematopoietic_and_lymphoid_tissue(3)	10						C		0,1384		0,0,692	95.0	100.0	98.0		45	-11.1	0.2	10		98	2,3180		0,2,1589	no	coding-synonymous	CALHM3	NM_001129742.1		0,2,2281	TT,TC,CC		0.0629,0.0,0.0438		15/345	105238745	2,4564	692	1591	2283	105228735	SO:0001819	synonymous_variant	0			BC043367	CCDS44476.1	10q24.33	2008-07-02	2008-07-02	2008-07-02	ENSG00000183128	ENSG00000183128			23458	protein-coding gene	gene with protein product			"""family with sequence similarity 26, member A"""	FAM26A		18585350	Standard	NM_001129742		Approved	bA225H22.7	uc001kxg.4	Q86XJ0	OTTHUMG00000018989	ENST00000369783.4:c.45G>A	10.37:g.105238745C>T		11285	20.5166666666667	3078		NA	NA	NA	105228735	9204	44.19	7466	Q5W090|Q8IXR2	Silent	SNP	NULL	p.S15	ENST00000369783.4	37	c.45	CCDS44476.1	10																																																																																			-	NULL		0.592	CALHM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CALHM3	protein_coding	OTTHUMT00000050157.1	C	NM_182494		105228735	-1	no_errors	ENST00000369783	ensembl	human	known	54_36p	silent	SNP	0.104	T
SMC3	9126	genome.wustl.edu	37	10	112356176	112356176	+	Missense_Mutation	SNP	G	G	T			TCGA-AB-2993-03A-01D-0739-09	TCGA-AB-2993-11A-01D-0739-09	G	G	G	T	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	4e956c79-d82b-4d89-9d05-7133e0caf740	c537a524-b89a-4738-8bbe-b00f335d4a75	g.chr10:112356176G>T	ENST00000361804.4	+	19	2110	c.1984G>T	c.(1984-1986)Ggt>Tgt	p.G662C		NM_005445.3	NP_005436.1	Q9UQE7	SMC3_HUMAN	structural maintenance of chromosomes 3	662	Flexible hinge.				DNA repair (GO:0006281)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid cohesion (GO:0007064)|mitotic spindle organization (GO:0007052)|negative regulation of DNA endoreduplication (GO:0032876)|regulation of DNA replication (GO:0006275)|signal transduction (GO:0007165)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	basement membrane (GO:0005604)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cohesin core heterodimer (GO:0008280)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear matrix (GO:0016363)|nuclear meiotic cohesin complex (GO:0034991)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|dynein binding (GO:0045502)|microtubule motor activity (GO:0003777)|protein heterodimerization activity (GO:0046982)	p.G662C(3)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(5)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.00206)|all cancers(201;0.0227)|BRCA - Breast invasive adenocarcinoma(275;0.127)		CAGCCATCGGGGTGCTCTAAC	0.348																																						dbGAP											3	Substitution - Missense(3)	haematopoietic_and_lymphoid_tissue(3)	10											108.0	109.0	108.0					10																	112356176		2203	4300	6503	112346166	SO:0001583	missense	0			AF020043	CCDS31285.1	10q25	2014-09-17	2006-07-06	2006-07-06	ENSG00000108055	ENSG00000108055		"""Structural maintenance of chromosomes proteins"", ""Proteoglycans / Extracellular Matrix : Other"""	2468	protein-coding gene	gene with protein product	"""bamacan proteoglycan"""	606062	"""chondroitin sulfate proteoglycan 6 (bamacan)"""	CSPG6		9506951, 10358101	Standard	NM_005445		Approved	HCAP, BAM, SMC3L1, bamacan	uc001kze.3	Q9UQE7	OTTHUMG00000019042	ENST00000361804.4:c.1984G>T	10.37:g.112356176G>T	ENSP00000354720:p.Gly662Cys	8761	21.7966666666667	2734		38	53.66	44	112346166	9082	50.2833333333333	7834	A8K156|O60464|Q5T482	Missense_Mutation	SNP	HMMPfam_SMC_N,HMMPfam_SMC_hinge,superfamily_Smc hinge domain,PatternScan_ABC_TRANSPORTER_1,superfamily_P-loop containing nucleoside triphosphate hydrolases,superfamily_BAG domain	p.G662C	ENST00000361804.4	37	c.1984	CCDS31285.1	10	.	.	.	.	.	.	.	.	.	.	G	16.83	3.230613	0.58777	.	.	ENSG00000108055	ENST00000361804	D	0.96073	-3.9	5.33	5.33	0.75918	SMCs flexible hinge (1);RecF/RecN/SMC (1);	0.000000	0.85682	D	0.000000	D	0.98413	0.9472	M	0.93375	3.41	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99486	1.0949	10	0.87932	D	0	.	19.0314	0.92959	0.0:0.0:1.0:0.0	.	662	Q9UQE7	SMC3_HUMAN	C	662	ENSP00000354720:G662C	ENSP00000354720:G662C	G	+	1	0	SMC3	112346166	1.000000	0.71417	0.998000	0.56505	0.060000	0.15804	9.372000	0.97165	2.489000	0.83994	0.313000	0.20887	GGT	-	HMMPfam_SMC_N,superfamily_Smc hinge domain,superfamily_P-loop containing nucleoside triphosphate hydrolases		0.348	SMC3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	SMC3	protein_coding	OTTHUMT00000050337.1	G	NM_005445		112346166	+1	no_errors	NM_005445.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
GPR123	84435	genome.wustl.edu	37	10	134884545	134884545	+	Missense_Mutation	SNP	C	C	T	rs181856403		TCGA-AB-2993-03A-01D-0739-09	TCGA-AB-2993-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	4e956c79-d82b-4d89-9d05-7133e0caf740	c537a524-b89a-4738-8bbe-b00f335d4a75	g.chr10:134884545C>T	ENST00000607359.1	+	1	113	c.113C>T	c.(112-114)aCa>aTa	p.T38I				Q86SQ6	GP123_HUMAN	G protein-coupled receptor 123	453					G-protein coupled receptor signaling pathway (GO:0007186)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.T38I(3)		endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(3)	14		all_cancers(35;1.8e-10)|all_epithelial(44;8.95e-09)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0585)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;9.16e-06)|Epithelial(32;1.21e-05)|all cancers(32;1.63e-05)		GGGGGCCGGACACCACAGTCA	0.662													C|||	1	0.000199681	0.0	0.0	5008	,	,		14528	0.001		0.0	False		,,,				2504	0.0					dbGAP											3	Substitution - Missense(3)	haematopoietic_and_lymphoid_tissue(3)	10											24.0	27.0	26.0					10																	134884545		1562	3569	5131	134734535	SO:0001583	missense	0			AB058731	CCDS41580.1	10q26	2014-08-08			ENSG00000197177	ENSG00000197177		"""-"", ""GPCR / Class B : Orphans"""	13838	protein-coding gene	gene with protein product		612302				12565841	Standard	XM_005252695		Approved	KIAA1828	uc001llw.3	Q86SQ6	OTTHUMG00000019304	ENST00000607359.1:c.113C>T	10.37:g.134884545C>T	ENSP00000475778:p.Thr38Ile	8148	20.1333333333333	2276		NA	NA	NA	134734535	6337	49.96	7481	A5HL16|A6NG50|Q5T234|Q86SN7|Q96JJ9	Missense_Mutation	SNP	HMMPfam_7tm_2,PatternScan_G_PROTEIN_RECEP_F2_2	p.T38I	ENST00000607359.1	37	c.113		10	2	9.157509157509158E-4	0	0.0	0	0.0	1	0.0017482517482517483	1	0.0013192612137203166	C	3.568	-0.088283	0.07097	.	.	ENSG00000197177	ENST00000368577;ENST00000392609	.	.	.	1.69	0.659	0.17861	.	.	.	.	.	T	0.35740	0.0942	.	.	.	.	.	.	B	0.21821	0.061	B	0.12837	0.008	T	0.27502	-1.0072	6	0.87932	D	0	.	7.6303	0.28236	0.0:0.8167:0.0:0.1833	.	38	Q86SQ6-1	.	I	38	.	ENSP00000357566:T38I	T	+	2	0	GPR123	134734535	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.021000	0.12504	-0.483000	0.06772	-1.786000	0.00637	ACA	-	NULL		0.662	GPR123-004	PUTATIVE	basic|appris_candidate_longest	protein_coding	GPR123	protein_coding	OTTHUMT00000316904.2	C			134734535	+1	no_errors	ENST00000368577	ensembl	human	known	54_36p	missense	SNP	0.000	T
RPLP0P2	113157	genome.wustl.edu	37	11	61396344	61396344	+	RNA	SNP	C	C	T			TCGA-AB-2993-03A-01D-0739-09	TCGA-AB-2993-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	4e956c79-d82b-4d89-9d05-7133e0caf740	c537a524-b89a-4738-8bbe-b00f335d4a75	g.chr11:61396344C>T	ENST00000496593.1	+	0	267					NR_002775.2				ribosomal protein, large, P0 pseudogene 2																		TTCCCATCTCCTTCCTGGAAG	0.527											OREG0021007	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										dbGAP											0			11																																								61152920			0			BC010523		11q12.2	2014-08-07			ENSG00000243742	ENSG00000243742		"""L ribosomal proteins"""	17960	pseudogene	pseudogene						19123937, 25089627	Standard	NR_002775		Approved		uc001nrz.1		OTTHUMG00000158396		11.37:g.61396344C>T		15911	11.01	1847	1053	NA	NA	NA	61152920	10880	39.0366666666667	7475		RNA	SNP	-	NULL	ENST00000496593.1	37	NULL		11																																																																																			-	-		0.527	RPLP0P2-002	KNOWN	basic	processed_transcript	RPLP0P2	pseudogene	OTTHUMT00000350911.1	C	NR_002775		61152920	+1	pseudogene	NR_002775.2	genbank	human	inferred	54_36p	rna	SNP	0.000	T
SLC15A1	6564	genome.wustl.edu	37	13	99378392	99378392	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AB-2993-03A-01D-0739-09	TCGA-AB-2993-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	4e956c79-d82b-4d89-9d05-7133e0caf740	c537a524-b89a-4738-8bbe-b00f335d4a75	g.chr13:99378392C>T	ENST00000376503.5	-	4	285	c.230G>A	c.(229-231)tGg>tAg	p.W77*		NM_005073.3	NP_005064.1	P46059	S15A1_HUMAN	solute carrier family 15 (oligopeptide transporter), member 1	77					digestion (GO:0007586)|ion transport (GO:0006811)|protein transport (GO:0015031)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	peptide:proton symporter activity (GO:0015333)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)	p.W77*(3)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	30	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Aminolevulinic acid(DB00855)|Amoxicillin(DB01060)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benazepril(DB00542)|Benzylpenicillin(DB01053)|Captopril(DB01197)|Cefaclor(DB00833)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefmetazole(DB00274)|Cefotaxime(DB00493)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftibuten(DB01415)|Ceftizoxime(DB01332)|Ceftriaxone(DB01212)|Cefuroxime(DB01112)|Cephalexin(DB00567)|Chlorpropamide(DB00672)|Cilazapril(DB01340)|Cloxacillin(DB01147)|Cyclacillin(DB01000)|Dicloxacillin(DB00485)|Enalapril(DB00584)|Fluvastatin(DB01095)|Fosinopril(DB00492)|Glyburide(DB01016)|L-DOPA(DB01235)|Lisinopril(DB00722)|Methyldopa(DB00968)|Midodrine(DB00211)|Moexipril(DB00691)|Nateglinide(DB00731)|Oseltamivir(DB00198)|Oxacillin(DB00713)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Spirapril(DB01348)|Tolbutamide(DB01124)|Trandolapril(DB00519)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	CTTTCCCAGCCACGAGTCGGC	0.473																																						dbGAP											3	Substitution - Nonsense(3)	haematopoietic_and_lymphoid_tissue(3)	13											51.0	47.0	49.0					13																	99378392		2203	4300	6503	98176393	SO:0001587	stop_gained	0			U13173	CCDS9489.1	13q32.3	2013-05-22			ENSG00000088386	ENSG00000088386		"""Solute carriers"""	10920	protein-coding gene	gene with protein product	"""peptide transporter HPEPT1"", ""bA551M18.1.1 (solute carrier family 15 (oligopeptide transporter) member 1)"", ""solute carrier family 15 oligopeptide transporter member 1"""	600544				7896779	Standard	NM_005073		Approved	PEPT1, HPECT1, HPEPT1	uc001vno.3	P46059	OTTHUMG00000017255	ENST00000376503.5:c.230G>A	13.37:g.99378392C>T	ENSP00000365686:p.Trp77*	9390	15.6766666666667	1998		NA	NA	NA	98176393	8439	51.5	9910	Q5VW82	Nonsense_Mutation	SNP	HMMPfam_PTR2,superfamily_MFS general substrate transporter,PatternScan_PTR2_1,PatternScan_PTR2_2	p.W77*	ENST00000376503.5	37	c.230	CCDS9489.1	13	.	.	.	.	.	.	.	.	.	.	C	37	6.178180	0.97352	.	.	ENSG00000088386	ENST00000376503;ENST00000376494;ENST00000313260	.	.	.	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-40.6234	20.8794	0.99867	0.0:1.0:0.0:0.0	.	.	.	.	X	77;45;87	.	ENSP00000318937:W87X	W	-	2	0	SLC15A1	98176393	1.000000	0.71417	1.000000	0.80357	0.211000	0.24417	7.794000	0.85869	2.941000	0.99782	0.655000	0.94253	TGG	-	superfamily_MFS general substrate transporter,PatternScan_PTR2_1		0.473	SLC15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC15A1	protein_coding	OTTHUMT00000045560.3	C	NM_005073		98176393	-1	no_errors	NM_005073.3	genbank	human	validated	54_36p	nonsense	SNP	1.000	T
GPR183	1880	genome.wustl.edu	37	13	99947387	99947387	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2993-03A-01D-0739-09	TCGA-AB-2993-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	4e956c79-d82b-4d89-9d05-7133e0caf740	c537a524-b89a-4738-8bbe-b00f335d4a75	g.chr13:99947387G>A	ENST00000376414.4	-	2	1096	c.1013C>T	c.(1012-1014)gCc>gTc	p.A338V	UBAC2_ENST00000376440.2_Intron|UBAC2_ENST00000403766.3_Intron	NM_004951.4	NP_004942.1	P32249	GP183_HUMAN	G protein-coupled receptor 183	338			A -> V (in an acute myeloid leukemia sample; somatic mutation). {ECO:0000269|PubMed:18987736}.		G-protein coupled receptor signaling pathway (GO:0007186)|humoral immune response (GO:0006959)|immune response (GO:0006955)|mature B cell differentiation involved in immune response (GO:0002313)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|oxysterol binding (GO:0008142)	p.A338V(3)		cervix(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(10)|prostate(1)|skin(1)	23						TTCTTCAGGGGCTGACTTCAC	0.378																																						dbGAP											3	Substitution - Missense(3)	haematopoietic_and_lymphoid_tissue(3)	13											123.0	119.0	120.0					13																	99947387		2203	4300	6503	98745388	SO:0001583	missense	0			L08177	CCDS9492.1	13q32.3	2012-08-21	2008-07-21	2008-07-21	ENSG00000169508	ENSG00000169508		"""GPCR / Class A : Orphans"""	3128	protein-coding gene	gene with protein product	"""EBV-induced G-protein coupled receptor 2"""	605741	"""Epstein-Barr virus induced gene 2 (lymphocyte-specific G protein-coupled receptor)"""	EBI2		8383238	Standard	NM_004951		Approved		uc001vog.3	P32249	OTTHUMG00000017263	ENST00000376414.4:c.1013C>T	13.37:g.99947387G>A	ENSP00000365596:p.Ala338Val	7168	20.4166666666667	1857		27	62.50	45	98745388	4671	47.1566666666667	3872	B2R8N5|Q53F99|Q5JUH7	Missense_Mutation	SNP	HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321	p.A338V	ENST00000376414.4	37	c.1013	CCDS9492.1	13	.	.	.	.	.	.	.	.	.	.	G	16.60	3.169651	0.57584	.	.	ENSG00000169508	ENST00000376414	T	0.38077	1.16	5.9	5.05	0.67936	.	0.253544	0.40385	N	0.001118	T	0.24122	0.0584	L	0.27053	0.805	0.43364	D	0.995441	B	0.14012	0.009	B	0.09377	0.004	T	0.06570	-1.0819	9	.	.	.	.	10.5696	0.45192	0.07:0.0:0.7895:0.1405	.	338	P32249	GP183_HUMAN	V	338	ENSP00000365596:A338V	.	A	-	2	0	GPR183	98745388	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.178000	0.58284	1.499000	0.48617	0.650000	0.86243	GCC	-	superfamily_SSF81321		0.378	GPR183-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GPR183	protein_coding	OTTHUMT00000045582.2	G	NM_004951		98745388	-1	no_errors	NM_004951.4	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
CDH24	64403	genome.wustl.edu	37	14	23518426	23518426	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AB-2993-03A-01D-0739-09	TCGA-AB-2993-11A-01D-0739-09	G	G	G	T	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	4e956c79-d82b-4d89-9d05-7133e0caf740	c537a524-b89a-4738-8bbe-b00f335d4a75	g.chr14:23518426G>T	ENST00000267383.5	-	11	1862	c.1770C>A	c.(1768-1770)taC>taA	p.Y590*	CDH24_ENST00000487137.2_Nonsense_Mutation_p.Y552*|CDH24_ENST00000554034.1_Nonsense_Mutation_p.Y552*|CDH24_ENST00000397359.3_Nonsense_Mutation_p.Y590*|CDH24_ENST00000485922.1_5'UTR			Q86UP0	CAD24_HUMAN	cadherin 24, type 2	590	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|delta-catenin binding (GO:0070097)	p.Y552*(3)		breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	26	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.00654)		TGGGAACCAAGTAGGGGGCAT	0.647																																						dbGAP											3	Substitution - Nonsense(3)	haematopoietic_and_lymphoid_tissue(3)	14											12.0	16.0	14.0					14																	23518426		2191	4275	6466	22588266	SO:0001587	stop_gained	0			AL137477	CCDS9585.1, CCDS9586.1	14q11.2	2010-08-20	2009-11-20		ENSG00000139880	ENSG00000139880		"""Cadherins / Major cadherins"""	14265	protein-coding gene	gene with protein product			"""cadherin-like 24"""			12734196	Standard	NM_022478		Approved	CDH11L	uc001wil.3	Q86UP0	OTTHUMG00000028715	ENST00000267383.5:c.1770C>A	14.37:g.23518426G>T	ENSP00000267383:p.Tyr590*	4577	15.62	1166		3	40.00	2	22588266	4405	46.8733333333333	5022	D3DS44|Q86UP1|Q9NT84	Nonsense_Mutation	SNP	HMMPfam_Cadherin_C,HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,superfamily_Cadherin-like	p.Y590*	ENST00000267383.5	37	c.1770	CCDS9585.1	14	.	.	.	.	.	.	.	.	.	.	G	38	6.908988	0.97928	.	.	ENSG00000139880	ENST00000397359;ENST00000487137;ENST00000554034;ENST00000267383	.	.	.	5.06	3.18	0.36537	.	0.374952	0.24557	N	0.037514	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	4.954	0.14029	0.1956:0.1714:0.633:0.0	.	.	.	.	X	590;552;552;590	.	ENSP00000267383:Y590X	Y	-	3	2	CDH24	22588266	1.000000	0.71417	0.993000	0.49108	0.978000	0.69477	2.954000	0.49113	0.678000	0.31325	-0.150000	0.13652	TAC	-	HMMPfam_Cadherin,superfamily_Cadherin-like		0.647	CDH24-006	KNOWN	basic|CCDS	protein_coding	CDH24	protein_coding	OTTHUMT00000257241.2	G	NM_022478		22588266	-1	no_errors	NM_022478.3	genbank	human	validated	54_36p	nonsense	SNP	0.998	T
PDXDC1	23042	genome.wustl.edu	37	16	15122791	15122791	+	Missense_Mutation	SNP	G	G	A	rs376863120		TCGA-AB-2993-03A-01D-0739-09	TCGA-AB-2993-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	4e956c79-d82b-4d89-9d05-7133e0caf740	c537a524-b89a-4738-8bbe-b00f335d4a75	g.chr16:15122791G>A	ENST00000396410.4	+	15	1358	c.1261G>A	c.(1261-1263)Gag>Aag	p.E421K	PDXDC1_ENST00000455313.2_Missense_Mutation_p.E398K|PDXDC1_ENST00000535621.2_Missense_Mutation_p.E421K|PDXDC1_ENST00000450288.2_Missense_Mutation_p.E393K|PDXDC1_ENST00000563679.1_Missense_Mutation_p.E439K|PDXDC1_ENST00000325823.7_Missense_Mutation_p.E406K|PDXDC1_ENST00000447912.2_Missense_Mutation_p.E330K|PDXDC1_ENST00000569715.1_Missense_Mutation_p.E394K	NM_015027.2	NP_055842.2	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain containing 1	421					carboxylic acid metabolic process (GO:0019752)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)	carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)	p.E421K(3)		central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(10)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						AGTCGGCCGGGAGAGGCACTC	0.587																																						dbGAP											3	Substitution - Missense(3)	haematopoietic_and_lymphoid_tissue(3)	16						G	LYS/GLU	0,4394		0,0,2197	93.0	80.0	84.0		1261	4.2	1.0	16		84	1,8599		0,1,4299	no	missense	PDXDC1	NM_015027.2	56	0,1,6496	AA,AG,GG		0.0116,0.0,0.0077	benign	421/789	15122791	1,12993	2197	4300	6497	15030292	SO:0001583	missense	0			AK025504, BX647809	CCDS32393.1, CCDS66954.1, CCDS66957.1, CCDS73830.1, CCDS73831.1	16p13.11	2008-02-05							28995	protein-coding gene	gene with protein product		614244					Standard	XM_005255173		Approved	KIAA0251	uc002dda.4	Q6P996	OTTHUMG00000166304	ENST00000396410.4:c.1261G>A	16.37:g.15122791G>A	ENSP00000379691:p.Glu421Lys	8684	8.48	778		44	26.23	16	15030292	12623	28.0866666666667	4597	B4DR55|B4DSL3|E7EMH5|E7EPL4|H3BNZ1|O00236|Q4F6X7|Q6PID7|Q86YF1|Q8N4Q9|Q8TBS5	Missense_Mutation	SNP	HMMPfam_Pyridoxal_deC,superfamily_PLP-dependent transferases	p.E421K	ENST00000396410.4	37	c.1261	CCDS32393.1	16	.	.	.	.	.	.	.	.	.	.	G	12.29	1.894137	0.33442	0.0	1.16E-4	ENSG00000179889	ENST00000325823;ENST00000447912;ENST00000535621;ENST00000396410;ENST00000450288;ENST00000537781;ENST00000455313	T;T;T;T;T;T	0.26810	1.72;2.24;2.23;1.71;1.72;1.79	5.23	4.25	0.50352	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.145401	0.64402	D	0.000011	T	0.24624	0.0597	M	0.65975	2.015	0.50467	D	0.999874	B;B;B;B;B;B	0.26672	0.039;0.156;0.034;0.022;0.039;0.061	B;B;B;B;B;B	0.24848	0.015;0.024;0.035;0.015;0.015;0.056	T	0.04191	-1.0970	10	0.20519	T	0.43	-18.0485	8.8256	0.35052	0.0821:0.1515:0.7664:0.0	.	393;330;421;393;421;398	E7EPL4;E7EMH5;Q86XE2;B4DR55;Q6P996;Q6P996-2	.;.;.;.;PDXD1_HUMAN;.	K	406;330;421;421;393;127;398	ENSP00000322807:E406K;ENSP00000400310:E330K;ENSP00000437835:E421K;ENSP00000379691:E421K;ENSP00000391147:E393K;ENSP00000406703:E398K	ENSP00000322807:E406K	E	+	1	0	PDXDC1	15030292	1.000000	0.71417	1.000000	0.80357	0.034000	0.12701	3.044000	0.49830	1.294000	0.44707	0.655000	0.94253	GAG	-	superfamily_PLP-dependent transferases		0.587	PDXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PDXDC1	protein_coding	OTTHUMT00000389065.2	G	NM_015027		15030292	+1	no_errors	NM_015027.2	genbank	human	validated	54_36p	missense	SNP	0.936	A
RP11-580I16.2	0	genome.wustl.edu	37	17	45713886	45713886	+	RNA	SNP	G	G	T			TCGA-AB-2993-03A-01D-0739-09	TCGA-AB-2993-11A-01D-0739-09	G	G	G	T	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	4e956c79-d82b-4d89-9d05-7133e0caf740	c537a524-b89a-4738-8bbe-b00f335d4a75	g.chr17:45713886G>T	ENST00000580045.1	-	0	102				RP11-580I16.2_ENST00000582066.1_RNA|RP11-580I16.2_ENST00000582389.1_RNA|RP11-580I16.2_ENST00000584391.1_RNA																							acctatactggaatatcctgt	0.458																																						dbGAP											0			17																																								43068885			0																															17.37:g.45713886G>T		10094	15.19	1803		2	0.00	0	43068885	9861	45.1966666666667	7311		Missense_Mutation	SNP	NULL	p.F46L	ENST00000580045.1	37	c.138		17																																																																																			-	NULL		0.458	RP11-580I16.2-002	KNOWN	basic	antisense	LOC728896	antisense	OTTHUMT00000441346.1	G			43068885	-1	no_errors	XM_001719193.1	genbank	human	model	54_36p	missense	SNP	0.078	T
PTPRT	11122	genome.wustl.edu	37	20	40730840	40730840	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2993-03A-01D-0739-09	TCGA-AB-2993-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	4e956c79-d82b-4d89-9d05-7133e0caf740	c537a524-b89a-4738-8bbe-b00f335d4a75	g.chr20:40730840G>A	ENST00000373187.1	-	26	3637	c.3638C>T	c.(3637-3639)cCt>cTt	p.P1213L	PTPRT_ENST00000356100.2_Missense_Mutation_p.P1222L|PTPRT_ENST00000373201.1_Missense_Mutation_p.P1203L|PTPRT_ENST00000373193.3_Missense_Mutation_p.P1216L|PTPRT_ENST00000373184.1_Missense_Mutation_p.P1223L|PTPRT_ENST00000373198.4_Missense_Mutation_p.P1232L|PTPRT_ENST00000373190.1_Missense_Mutation_p.P1212L			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	1213	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.		P -> L (in an acute myeloid leukemia sample; somatic mutation). {ECO:0000269|PubMed:18987736}.		cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)	p.P1235L(3)		NS(2)|breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(12)|large_intestine(26)|liver(1)|lung(63)|ovary(8)|pancreas(2)|prostate(5)|skin(35)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	176		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				GCGGTCCAGAGGCAGCACGTC	0.577																																						dbGAP											3	Substitution - Missense(3)	haematopoietic_and_lymphoid_tissue(3)	20											80.0	84.0	83.0					20																	40730840		2149	4273	6422	40164254	SO:0001583	missense	0			AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.3638C>T	20.37:g.40730840G>A	ENSP00000362283:p.Pro1213Leu	7222	20.2533333333333	1981		NA	NA	NA	40164254	6478	45.2433333333333	5396	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Missense_Mutation	SNP	HMMPfam_Y_phosphatase,HMMSmart_SM00194,HMMPfam_MAM,HMMSmart_SM00137,PatternScan_MAM_1,HMMSmart_SM00404,HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III,PatternScan_TYR_PHOSPHATASE_1,superfamily_Immunoglobulin,superfamily_(Phosphotyrosine protein) phosphatases II	p.P1232L	ENST00000373187.1	37	c.3695	CCDS42874.1	20	.	.	.	.	.	.	.	.	.	.	G	24.8	4.567279	0.86439	.	.	ENSG00000196090	ENST00000373190;ENST00000373187;ENST00000373193;ENST00000356100;ENST00000373198;ENST00000373184;ENST00000373201	T;T;T;T;T;T;T	0.17854	2.25;2.25;2.25;2.25;2.25;2.25;2.25	5.48	5.48	0.80851	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.060296	0.64402	D	0.000003	T	0.52869	0.1761	H	0.94847	3.59	0.80722	D	1	P;P	0.51933	0.949;0.929	P;P	0.59825	0.786;0.864	T	0.66850	-0.5819	10	0.87932	D	0	.	19.354	0.94404	0.0:0.0:1.0:0.0	.	1235;1213	O14522-1;O14522	.;PTPRT_HUMAN	L	1212;1213;1216;1222;1235;1223;1203	ENSP00000362286:P1212L;ENSP00000362283:P1213L;ENSP00000362289:P1216L;ENSP00000348408:P1222L;ENSP00000362294:P1235L;ENSP00000362280:P1223L;ENSP00000362297:P1203L	ENSP00000348408:P1222L	P	-	2	0	PTPRT	40164254	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.869000	0.99810	2.588000	0.87417	0.650000	0.86243	CCT	-	HMMPfam_Y_phosphatase,HMMSmart_SM00194,superfamily_(Phosphotyrosine protein) phosphatases II		0.577	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	PTPRT	protein_coding	OTTHUMT00000080315.1	G			40164254	-1	no_errors	NM_133170.5	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
DSCAM	1826	genome.wustl.edu	37	21	41414445	41414445	+	Silent	SNP	A	A	G			TCGA-AB-2993-03A-01D-0739-09	TCGA-AB-2993-11A-01D-0739-09	A	A	A	G	A	A	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	4e956c79-d82b-4d89-9d05-7133e0caf740	c537a524-b89a-4738-8bbe-b00f335d4a75	g.chr21:41414445A>G	ENST00000400454.1	-	32	6016	c.5539T>C	c.(5539-5541)Ttg>Ctg	p.L1847L		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	1847					cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.L1847L(3)		NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				CCTGCCGTCAACTGCTCCGAT	0.562																																					Melanoma(134;970 1778 1785 21664 32388)	dbGAP											3	Substitution - coding silent(3)	haematopoietic_and_lymphoid_tissue(3)	21											203.0	195.0	197.0					21																	41414445		2134	4238	6372	40336315	SO:0001819	synonymous_variant	0			AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.5539T>C	21.37:g.41414445A>G		8549	14.9733333333333	1538		NA	NA	NA	40336315	7622	50.64	7923	O60468	Silent	SNP	HMMSmart_SM00406,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III,HMMPfam_I-set,HMMPfam_ig,superfamily_Immunoglobulin	p.L1847	ENST00000400454.1	37	c.5539	CCDS42929.1	21																																																																																			-	NULL		0.562	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DSCAM	protein_coding	OTTHUMT00000195029.1	A	NM_001389		40336315	-1	no_errors	NM_001389.3	genbank	human	validated	54_36p	silent	SNP	1.000	G
DNMT3A	1788	genome.wustl.edu	37	2	25463514	25463514	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AB-2993-03A-01D-0739-09	TCGA-AB-2993-11A-01D-0739-09	A	A	A	-	A	A	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	4e956c79-d82b-4d89-9d05-7133e0caf740	c537a524-b89a-4738-8bbe-b00f335d4a75	g.chr2:25463514delA	ENST00000264709.3	-	18	2505	c.2168delT	c.(2167-2169)ctcfs	p.L723fs	DNMT3A_ENST00000402667.1_Frame_Shift_Del_p.L500fs|DNMT3A_ENST00000380746.4_Frame_Shift_Del_p.L534fs|DNMT3A_ENST00000321117.5_Frame_Shift_Del_p.L723fs|DNMT3A_ENST00000474887.1_5'UTR	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	723	SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				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.L723fs*56(4)		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)					CCTACCGTAGAGGCCCTTGCG	0.577			"""Mis, F, N, S"""		AML																																	dbGAP		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	4	Deletion - Frameshift(4)	haematopoietic_and_lymphoid_tissue(4)	2											140.0	117.0	125.0					2																	25463514		2203	4300	6503	25317018	SO:0001589	frameshift_variant	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.2168delT	2.37:g.25463514delA	ENSP00000264709:p.Leu723fs	1146	13.80	187		25	0.00	0	25317018	400	45.28	360	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Frame_Shift_Del	DEL	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.L723fs	ENST00000264709.3	37	c.2168	CCDS33157.1	2																																																																																			-	HMMPfam_DNA_methylase,superfamily_S-adenosyl-L-methionine-dependent methyltransferases		0.577	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	DNMT3A	protein_coding	OTTHUMT00000211587.1	A	NM_022552		25317018	-1	no_errors	NM_022552.3	genbank	human	reviewed	54_36p	frame_shift_del	DEL	0.999	-
NPM1	4869	genome.wustl.edu	37	5	170837547	170837548	+	Frame_Shift_Ins	INS	-	-	CATG			TCGA-AB-2993-03A-01D-0739-09	TCGA-AB-2993-11A-01D-0739-09	-	-	-	CATG	-	-	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	4e956c79-d82b-4d89-9d05-7133e0caf740	c537a524-b89a-4738-8bbe-b00f335d4a75	g.chr5:170837547_170837548insCATG	ENST00000296930.5	+	11	1164_1165	c.863_864insCATG	c.(862-867)tggcagfs	p.WQ288fs	NPM1_ENST00000517671.1_Frame_Shift_Ins_p.WQ288fs|NPM1_ENST00000351986.6_Frame_Shift_Ins_p.WQ259fs	NM_002520.6	NP_002511.1	P06748	NPM_HUMAN	nucleophosmin (nucleolar phosphoprotein B23, numatrin)	288	Required for nucleolar localization.			WQWRKSL -> CLAVEEVSLRK (in Ref. 6; AAW67752/AAW67755). {ECO:0000305}.|WQWRKSL -> CMAVEEVSLRK (in Ref. 6; AAW67753 and 7; ABC40399). {ECO:0000305}.|WQWRKSL -> CVAVEEVSLRK (in Ref. 6; AAW67754). {ECO:0000305}.	cell aging (GO:0007569)|CENP-A containing nucleosome assembly (GO:0034080)|centrosome cycle (GO:0007098)|DNA repair (GO:0006281)|intracellular protein transport (GO:0006886)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of centrosome duplication (GO:0010826)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|nucleocytoplasmic transport (GO:0006913)|nucleosome assembly (GO:0006334)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of translation (GO:0045727)|protein localization (GO:0008104)|protein oligomerization (GO:0051259)|regulation of centriole replication (GO:0046599)|regulation of eIF2 alpha phosphorylation by dsRNA (GO:0060735)|regulation of endodeoxyribonuclease activity (GO:0032071)|regulation of endoribonuclease activity (GO:0060699)|response to stress (GO:0006950)|ribosome assembly (GO:0042255)|signal transduction (GO:0007165)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle pole centrosome (GO:0031616)	histone binding (GO:0042393)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)|ribosomal large subunit binding (GO:0043023)|ribosomal small subunit binding (GO:0043024)|RNA binding (GO:0003723)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|unfolded protein binding (GO:0051082)	p.W288fs*12(2114)|p.W288fs*10(9)|p.Q289fs*11(3)|p.W288*(1)	NPM1/ALK(632)	central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(4261)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	4269	Renal(175;0.000159)|Lung NSC(126;0.00576)|all_lung(126;0.00963)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CAAGATCTCTGGCAGTGGAGGA	0.312			"""T, F """	"""ALK, RARA, MLF1"""	"""NHL, APL, AML"""																																	dbGAP		Dom	yes		5	5q35	4869	"""nucleophosmin (nucleolar phosphoprotein B23, numatrin)"""		L	2127	Insertion - Frameshift(2118)|Complex - frameshift(8)|Substitution - Nonsense(1)	haematopoietic_and_lymphoid_tissue(2127)	5																																								170770153	SO:0001589	frameshift_variant	0			M26697	CCDS4376.1, CCDS4377.1, CCDS43399.1	5q35.1	2014-09-17			ENSG00000181163	ENSG00000181163			7910	protein-coding gene	gene with protein product	"""nucleolar phosphoprotein B23"", ""numatrin"", ""nucleophosmin/nucleoplasmin family, member 1"""	164040				8471164, 8122112	Standard	NM_002520		Approved	B23, NPM	uc003mbi.3	P06748	OTTHUMG00000130465	Exception_encountered	5.37:g.170837547_170837548insCATG	ENSP00000296930:p.Trp288fs	NA	NA	NA		NA	NA	NA	170770152	NA	NA	NA	A8K3N7|B5BU00|D3DQL6|P08693|Q12826|Q13440|Q13441|Q14115|Q5EU94|Q5EU95|Q5EU96|Q5EU97|Q5EU98|Q5EU99|Q6V962|Q8WTW5|Q96AT6|Q96DC4|Q96EA5|Q9BYG9|Q9UDJ7	Frame_Shift_Ins	INS	HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain	p.W288fs	ENST00000296930.5	37	c.863_864	CCDS4376.1	5																																																																																			-	NULL		0.312	NPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NPM1	protein_coding	OTTHUMT00000252858.2	-	NM_002520		170770153	+1	no_errors	NM_002520.1	genbank	human	validated	54_36p	frame_shift_ins	INS	1.000:1.000	CATG
FLT3	2322	genome.wustl.edu	37	13	28608273	28608274	+	In_Frame_Ins	INS	-	-	GAAATCAACGTAGAAGTACTCATTATCTGA			TCGA-AB-2993-03A-01D-0739-09	TCGA-AB-2993-11A-01D-0739-09	-	-	-	GAAATCAACGTAGAAGTACTCATTATCTGA	-	-	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	4e956c79-d82b-4d89-9d05-7133e0caf740	c537a524-b89a-4738-8bbe-b00f335d4a75	g.chr13:28608273_28608274insGAAATCAACGTAGAAGTACTCATTATCTGA	ENST00000241453.7	-	14	1863_1864	c.1782_1783insTCAGATAATGAGTACTTCTACGTTGATTTC	c.(1780-1785)ttcaga>ttcTCAGATAATGAGTACTTCTACGTTGATTTCaga	p.593_594insFSDNEYFYVD	FLT3_ENST00000537084.1_In_Frame_Ins_p.593_594insFSDNEYFYVD|FLT3_ENST00000380982.4_In_Frame_Ins_p.593_594insFSDNEYFYVD	NM_004119.2	NP_004110.2	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	593	Important for normal regulation of the kinase activity and for maintaining the kinase in an inactive state in the absence of bound ligand.				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.F594_R595insSDNEYFYVDF(2)|p.F594_R595ins12(2)|p.F590_F594>L(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)	TCATATTCTCTGAAATCAACGT	0.381			"""Mis, O"""		"""AML, ALL"""																																	dbGAP		Dom	yes		13	13q12	2322	fms-related tyrosine kinase 3		L	5	Insertion - In frame(4)|Complex - deletion inframe(1)	haematopoietic_and_lymphoid_tissue(5)	13																																								27506274	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.1753_1782dupTCAGATAATGAGTACTTCTACGTTGATTTC	13.37:g.28608273_28608274insGAAATCAACGTAGAAGTACTCATTATCTGA	ENSP00000241453:p.Asp593_Phe594insPheSerAspAsnGluTyrPheTyrValAsp	NA	NA	NA		NA	NA	NA	27506273	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.594in_frame_insSDNEYFYVDF	ENST00000241453.7	37	c.1783_1782	CCDS31953.1	13																																																																																			-	superfamily_Kinase_like		0.381	FLT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	FLT3	protein_coding	OTTHUMT00000044319.2	-			27506274	-1	no_errors	NM_004119.2	genbank	human	reviewed	54_36p	in_frame_ins	INS	1.000:1.000	GAAATCAACGTAGAAGTACTCATTATCTGA
