#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
ATG4C	84938	genome.wustl.edu	37	1	63300494	63300494	+	Missense_Mutation	SNP	G	G	T			TCGA-AB-2870-03A-01W-0732-08	TCGA-AB-2870-11A-01W-0732-08	G	G	G	T	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	9ad67fd3-5750-42ab-b4e2-55133613a3e4	ab21f718-4b02-4b59-9590-a0de74285788	g.chr1:63300494G>T	ENST00000317868.4	+	9	1267	c.1060G>T	c.(1060-1062)Gat>Tat	p.D354Y	ATG4C_ENST00000371120.3_Missense_Mutation_p.D354Y	NM_032852.3	NP_116241.2	Q96DT6	ATG4C_HUMAN	autophagy related 4C, cysteine peptidase	354					autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|protein targeting to membrane (GO:0006612)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)	cysteine-type endopeptidase activity (GO:0004197)|peptidase activity (GO:0008233)		ATG4C/FBXO38(2)	NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(3)|ovary(1)|prostate(2)	19						ATCTTTTGTAGATGTCAGCAT	0.333																																						dbGAP											0			1											170.0	146.0	154.0					1																	63300494		2203	4300	6503	63073082	SO:0001583	missense	0			AK027773	CCDS623.1	1p31.3	2014-02-12	2012-06-06	2005-09-11	ENSG00000125703	ENSG00000125703			16040	protein-coding gene	gene with protein product		611339	"""AUT (S. cerevisiae)-like 1, cysteine endopeptidase; AUT-like 1, cysteine endopeptidase (S. cerevisiae)"", ""APG4 autophagy 4 homolog C (S. cerevisiae)"", ""ATG4 autophagy related 4 homolog C (S. cerevisiae)"""	AUTL1, APG4C		12446702	Standard	NM_032852		Approved	FLJ14867, AUTL3	uc001dau.3	Q96DT6	OTTHUMG00000009142	ENST00000317868.4:c.1060G>T	1.37:g.63300494G>T	ENSP00000322159:p.Asp354Tyr	86	7.53	7		21	30.00	9	63073082	308	28.67	125	A6NLR8|D3DQ58|Q96K04	Missense_Mutation	SNP	HMMPfam_Peptidase_C54	p.D354Y	ENST00000317868.4	37	c.1060	CCDS623.1	1	.	.	.	.	.	.	.	.	.	.	G	19.65	3.866644	0.72065	.	.	ENSG00000125703	ENST00000317868;ENST00000371120;ENST00000540025;ENST00000414558	T;T	0.46063	0.88;0.88	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	T	0.68403	0.2997	M	0.90082	3.085	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.75593	-0.3264	10	0.87932	D	0	-20.1388	19.1737	0.93594	0.0:0.0:1.0:0.0	.	354	Q96DT6	ATG4C_HUMAN	Y	354;354;354;98	ENSP00000322159:D354Y;ENSP00000360161:D354Y	ENSP00000322159:D354Y	D	+	1	0	ATG4C	63073082	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.577000	0.82486	2.622000	0.88805	0.585000	0.79938	GAT	-	HMMPfam_Peptidase_C54		0.333	ATG4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ATG4C	protein_coding	OTTHUMT00000025332.2	G	NM_032852		63073082	+1	no_errors	NM_032852.2	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
NRAS	4893	genome.wustl.edu	37	1	115256530	115256530	+	Missense_Mutation	SNP	G	G	T	rs121913254		TCGA-AB-2870-03A-01W-0732-08	TCGA-AB-2870-11A-01W-0732-08	G	G	G	T	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	9ad67fd3-5750-42ab-b4e2-55133613a3e4	ab21f718-4b02-4b59-9590-a0de74285788	g.chr1:115256530G>T	ENST00000369535.4	-	3	434	c.181C>A	c.(181-183)Caa>Aaa	p.Q61K		NM_002524.4	NP_002515.1	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	61			Q -> K (in CMNS and NCMS; somatic mutation). {ECO:0000269|PubMed:23392294}.|Q -> R (in CMNS, NCMS and KNEN; also found in lung carcinoma cell and melanoma; dbSNP:rs11554290). {ECO:0000269|PubMed:18633438, ECO:0000269|PubMed:22499344, ECO:0000269|PubMed:23392294, ECO:0000269|PubMed:3276402}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of skeletal muscle tissue development (GO:0048642)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|small GTPase mediated signal transduction (GO:0007264)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.Q61K(595)|p.Q61E(9)|p.Q61L(3)|p.Q61R(2)|p.G60>?(1)		NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		TACTCTTCTTGTCCAGCTGTA	0.458	Q61K(CHP212_AUTONOMIC_GANGLIA)|Q61K(HCC15_LUNG)|Q61K(HS936T_SKIN)|Q61K(HS944T_SKIN)|Q61K(HT1080_SOFT_TISSUE)|Q61K(HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61K(M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61K(NCIH1299_LUNG)|Q61K(NCIH2087_LUNG)|Q61K(OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61K(SKNAS_AUTONOMIC_GANGLIA)|Q61K(SKNSH_AUTONOMIC_GANGLIA)|Q61K(TYKNU_OVARY)	50	Mis		"""melanoma, MM, AML, thyroid"""				Noonan syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)																												dbGAP		Dom	yes		1	1p13.2	4893	neuroblastoma RAS viral (v-ras) oncogene homolog		"""L, E"""	610	Substitution - Missense(609)|Complex(1)	skin(372)|haematopoietic_and_lymphoid_tissue(73)|thyroid(55)|NS(29)|large_intestine(28)|soft_tissue(16)|lung(12)|autonomic_ganglia(6)|liver(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|cervix(2)|endometrium(2)|pancreas(2)|meninges(1)|kidney(1)|biliary_tract(1)|stomach(1)|ovary(1)|bone(1)	1											180.0	156.0	164.0					1																	115256530		2203	4300	6503	115058053	SO:0001583	missense	0	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	BC005219	CCDS877.1	1p13.2	2014-09-17			ENSG00000213281	ENSG00000213281			7989	protein-coding gene	gene with protein product		164790					Standard	NM_002524		Approved	N-ras	uc009wgu.3	P01111	OTTHUMG00000012059	ENST00000369535.4:c.181C>A	1.37:g.115256530G>T	ENSP00000358548:p.Gln61Lys	73	3.95	3		96	14.29	16	115058053	245	18.21	55	Q14971|Q15104|Q15282	Missense_Mutation	SNP	HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases	p.Q61K	ENST00000369535.4	37	c.181	CCDS877.1	1	.	.	.	.	.	.	.	.	.	.	G	33	5.255564	0.95336	.	.	ENSG00000213281	ENST00000369535	D	0.83506	-1.73	5.08	5.08	0.68730	Small GTP-binding protein domain (1);	0.000000	0.53938	U	0.000043	D	0.91845	0.7419	H	0.95850	3.73	0.80722	D	1	P	0.51791	0.948	P	0.54759	0.76	D	0.93711	0.7024	10	0.62326	D	0.03	.	18.6626	0.91477	0.0:0.0:1.0:0.0	.	61	P01111	RASN_HUMAN	K	61	ENSP00000358548:Q61K	ENSP00000358548:Q61K	Q	-	1	0	NRAS	115058053	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.520000	0.98027	2.624000	0.88883	0.655000	0.94253	CAA	-	HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases		0.458	NRAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NRAS	protein_coding	OTTHUMT00000033395.2	G	NM_002524		115058053	-1	no_errors	NM_002524.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
SEMA4A	64218	genome.wustl.edu	37	1	156146280	156146280	+	Missense_Mutation	SNP	A	A	G	rs376576562		TCGA-AB-2870-03A-01W-0732-08	TCGA-AB-2870-11A-01W-0732-08	A	A	A	G	A	A	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	9ad67fd3-5750-42ab-b4e2-55133613a3e4	ab21f718-4b02-4b59-9590-a0de74285788	g.chr1:156146280A>G	ENST00000368285.3	+	15	2045	c.1778A>G	c.(1777-1779)cAt>cGt	p.H593R	SEMA4A_ENST00000368282.1_Missense_Mutation_p.H593R|SEMA4A_ENST00000368284.1_Missense_Mutation_p.H461R|SEMA4A_ENST00000355014.2_Missense_Mutation_p.H593R|SEMA4A_ENST00000368286.2_Missense_Mutation_p.H461R	NM_001193300.1|NM_022367.3	NP_001180229.1|NP_071762.2	Q9H3S1	SEM4A_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A	593	Ig-like C2-type.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|regulation of cell shape (GO:0008360)|regulation of endothelial cell migration (GO:0010594)|semaphorin-plexin signaling pathway (GO:0071526)|T-helper 1 cell differentiation (GO:0045063)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|ovary(2)|skin(2)	5	Hepatocellular(266;0.158)					TATTGGAGTCATGGCCCAGCA	0.552																																						dbGAP											0			1						A	ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS	1,4405	2.1+/-5.4	0,1,2202	96.0	93.0	94.0		1778,1778,1382,1778	3.9	0.8	1		94	0,8600		0,0,4300	no	missense,missense,missense,missense	SEMA4A	NM_001193300.1,NM_001193301.1,NM_001193302.1,NM_022367.3	29,29,29,29	0,1,6502	GG,GA,AA		0.0,0.0227,0.0077	benign,benign,benign,benign	593/762,593/762,461/630,593/762	156146280	1,13005	2203	4300	6503	154412904	SO:0001583	missense	0			AK022416	CCDS1132.1, CCDS53378.1	1q22	2014-01-28			ENSG00000196189	ENSG00000196189		"""Semaphorins"""	10729	protein-coding gene	gene with protein product		607292		SEMAB		7748561	Standard	NM_022367		Approved	SemB, FLJ12287, CORD10	uc009wrq.3	Q9H3S1	OTTHUMG00000014042	ENST00000368285.3:c.1778A>G	1.37:g.156146280A>G	ENSP00000357268:p.His593Arg	229	11.92	31		58	42.16	43	154412904	348	47.08	314	B2RDH8|B3KR76|Q5TCI5|Q5TCJ6|Q8WUA9	Missense_Mutation	SNP	HMMPfam_Sema,HMMSmart_Sema,superfamily_Sema,HMMPfam_PSI,HMMSmart_PSI,superfamily_Plexin-like_fold	p.H593R	ENST00000368285.3	37	c.1778	CCDS1132.1	1	.	.	.	.	.	.	.	.	.	.	A	7.226	0.598282	0.13939	2.27E-4	0.0	ENSG00000196189	ENST00000355014;ENST00000368285;ENST00000368284;ENST00000368283;ENST00000544376;ENST00000368286;ENST00000368282	T;T;T;T;T	0.16597	2.33;2.33;2.53;2.53;2.33	5.01	3.87	0.44632	.	0.355532	0.32488	N	0.006030	T	0.04497	0.0123	L	0.42245	1.32	0.30038	N	0.812859	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.38607	-0.9653	10	0.21014	T	0.42	.	7.5733	0.27920	0.9012:0.0:0.0988:0.0	.	461;593	Q5TCJ6;Q9H3S1	.;SEM4A_HUMAN	R	593;593;461;555;555;461;593	ENSP00000347117:H593R;ENSP00000357268:H593R;ENSP00000357267:H461R;ENSP00000357269:H461R;ENSP00000357265:H593R	ENSP00000347117:H593R	H	+	2	0	SEMA4A	154412904	0.005000	0.15991	0.752000	0.31206	0.547000	0.35210	0.163000	0.16520	0.758000	0.33059	0.260000	0.18958	CAT	-	NULL		0.552	SEMA4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SEMA4A	protein_coding	OTTHUMT00000039484.2	A	NM_022367		154412904	+1	no_errors	NM_022367.2	genbank	human	provisional	54_36p	missense	SNP	0.437	G
SPEG	10290	genome.wustl.edu	37	2	220343888	220343888	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AB-2870-03A-01W-0732-08	TCGA-AB-2870-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	9ad67fd3-5750-42ab-b4e2-55133613a3e4	ab21f718-4b02-4b59-9590-a0de74285788	g.chr2:220343888C>T	ENST00000312358.7	+	23	5182	c.5050C>T	c.(5050-5052)Cga>Tga	p.R1684*	AC053503.11_ENST00000429882.1_RNA|SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	1684	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		GCTGCTGGAGCGAATCGCCAG	0.637																																						dbGAP											0			2											62.0	72.0	68.0					2																	220343888		2091	4220	6311	220052132	SO:0001587	stop_gained	0			BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"""Immunoglobulin superfamily / I-set domain containing"""	16901	protein-coding gene	gene with protein product		615950	"""aortic preferentially expressed gene 1"""	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.5050C>T	2.37:g.220343888C>T	ENSP00000311684:p.Arg1684*	79	12.22	11		NA	NA	NA	220052132	88	42.31	66	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Nonsense_Mutation	SNP	HMMSmart_SM00219,HMMSmart_SM00220,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_fn3,HMMSmart_SM00060,PatternScan_PROTEIN_KINASE_ST,superfamily_Fibronectin type III,superfamily_Protein kinase-like (PK-like),HMMPfam_I-set,PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase,superfamily_Immunoglobulin	p.R1684*	ENST00000312358.7	37	c.5050	CCDS42824.1	2	.	.	.	.	.	.	.	.	.	.	C	45	11.450810	0.99562	.	.	ENSG00000072195	ENST00000312358;ENST00000265327	.	.	.	4.42	-1.39	0.08997	.	0.000000	0.33959	N	0.004382	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.6932	0.77473	0.7705:0.2295:0.0:0.0	.	.	.	.	X	1684	.	ENSP00000265327:R1684X	R	+	1	2	SPEG	220052132	0.990000	0.36364	0.985000	0.45067	0.976000	0.68499	1.819000	0.39022	-0.144000	0.11314	-0.314000	0.08810	CGA	-	HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase		0.637	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	SPEG	protein_coding	OTTHUMT00000130252.2	C	NM_005876		220052132	+1	no_errors	NM_005876.4	genbank	human	validated	54_36p	nonsense	SNP	0.643	T
COL12A1	1303	genome.wustl.edu	37	6	75902048	75902048	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2870-03A-01W-0732-08	TCGA-AB-2870-11A-01W-0732-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	9ad67fd3-5750-42ab-b4e2-55133613a3e4	ab21f718-4b02-4b59-9590-a0de74285788	g.chr6:75902048G>A	ENST00000322507.8	-	4	523	c.214C>T	c.(214-216)Ctt>Ttt	p.L72F	COL12A1_ENST00000416123.2_Missense_Mutation_p.L72F|COL12A1_ENST00000345356.6_Intron|COL12A1_ENST00000483888.2_Missense_Mutation_p.L72F	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	72	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						CTAGCTGAAAGGGTAAATTCT	0.328																																						dbGAP											0			6											95.0	82.0	86.0					6																	75902048		1804	4073	5877	75958768	SO:0001583	missense	0			U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"", ""Fibronectin type III domain containing"""	2188	protein-coding gene	gene with protein product	"""collagen type XII proteoglycan"""	120320	"""collagen, type XII, alpha 1-like"""	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.214C>T	6.37:g.75902048G>A	ENSP00000325146:p.Leu72Phe	29	6.45	2		NA	NA	NA	75958768	153	40.00	104	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	HMMPfam_VWA,HMMSmart_SM00327,HMMSmart_SM00210,HMMPfam_fn3,HMMSmart_SM00060,HMMPfam_Collagen,superfamily_Fibronectin type III,superfamily_Concanavalin A-like lectins/glucanases,superfamily_vWA-like	p.L72F	ENST00000322507.8	37	c.214	CCDS43482.1	6	.	.	.	.	.	.	.	.	.	.	G	28.6	4.932830	0.92458	.	.	ENSG00000111799	ENST00000322507;ENST00000432784;ENST00000416123;ENST00000483888	T;T;T	0.59502	0.26;0.26;0.26	5.91	5.91	0.95273	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000005	T	0.75228	0.3821	M	0.78456	2.415	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	T	0.76296	-0.3011	10	0.72032	D	0.01	.	20.3011	0.98612	0.0:0.0:1.0:0.0	.	72	Q99715	COCA1_HUMAN	F	72	ENSP00000325146:L72F;ENSP00000412864:L72F;ENSP00000421216:L72F	ENSP00000325146:L72F	L	-	1	0	COL12A1	75958768	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.967000	0.70403	2.804000	0.96469	0.650000	0.86243	CTT	-	HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III		0.328	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	COL12A1	protein_coding	OTTHUMT00000041249.3	G	NM_004370		75958768	-1	no_errors	NM_004370.5	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
OR10W1	81341	genome.wustl.edu	37	11	58035232	58035232	+	Silent	SNP	G	G	A			TCGA-AB-2870-03A-01W-0732-08	TCGA-AB-2870-11A-01W-0732-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	9ad67fd3-5750-42ab-b4e2-55133613a3e4	ab21f718-4b02-4b59-9590-a0de74285788	g.chr11:58035232G>A	ENST00000395079.2	-	1	500	c.99C>T	c.(97-99)aaC>aaT	p.N33N		NM_207374.3	NP_997257.2	Q8NGF6	O10W1_HUMAN	olfactory receptor, family 10, subfamily W, member 1	33						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(2)|large_intestine(2)|lung(19)|ovary(2)|skin(1)	26		Breast(21;0.0589)				CAATGAGAATGTTCCCAGTGA	0.468																																						dbGAP											0			11											95.0	79.0	85.0					11																	58035232		2201	4295	6496	57791808	SO:0001819	synonymous_variant	0			AB065850	CCDS7968.1	11q12.1	2012-08-09	2004-03-04	2004-03-05		ENSG00000172772		"""GPCR / Class A : Olfactory receptors"""	15139	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily W, member 1 pseudogene"""	OR10W1P			Standard	NM_207374		Approved		uc001nmq.1	Q8NGF6		ENST00000395079.2:c.99C>T	11.37:g.58035232G>A		90	12.62	13		NA	NA	NA	57791808	262	44.97	219	A2RUD2|A8MTE1|Q6UXQ2	Silent	SNP	HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321	p.N33	ENST00000395079.2	37	c.99	CCDS7968.1	11																																																																																			-	HMMPfam_7tm_1,superfamily_SSF81321		0.468	OR10W1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR10W1	protein_coding	OTTHUMT00000394704.1	G	NM_207374		57791808	-1	no_errors	NM_207374.2	genbank	human	provisional	54_36p	silent	SNP	0.032	A
POLR3B	55703	genome.wustl.edu	37	12	106770184	106770184	+	Missense_Mutation	SNP	C	C	T	rs145075371		TCGA-AB-2870-03A-01W-0732-08	TCGA-AB-2870-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	9ad67fd3-5750-42ab-b4e2-55133613a3e4	ab21f718-4b02-4b59-9590-a0de74285788	g.chr12:106770184C>T	ENST00000228347.4	+	7	674	c.452C>T	c.(451-453)aCg>aTg	p.T151M	POLR3B_ENST00000539066.1_Missense_Mutation_p.T93M	NM_018082.5	NP_060552.4	Q9NW08	RPC2_HUMAN	polymerase (RNA) III (DNA directed) polypeptide B	151					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|ribonucleoside binding (GO:0032549)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(22)|ovary(1)|prostate(3)|skin(3)|urinary_tract(2)	57						ACAGGAAAAACGCCAGCAGAA	0.368																																						dbGAP											0			12						C	MET/THR,MET/THR	0,4406		0,0,2203	145.0	128.0	134.0		278,452	5.5	1.0	12	dbSNP_134	134	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	POLR3B	NM_001160708.1,NM_018082.5	81,81	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	93/1076,151/1134	106770184	1,13005	2203	4300	6503	105294314	SO:0001583	missense	0			AY092084	CCDS9105.1, CCDS53824.1	12q23.3	2014-08-12			ENSG00000013503	ENSG00000013503		"""RNA polymerase subunits"""	30348	protein-coding gene	gene with protein product		614366				12391170	Standard	NM_018082		Approved	RPC2, FLJ10388	uc001tlp.3	Q9NW08	OTTHUMG00000170077	ENST00000228347.4:c.452C>T	12.37:g.106770184C>T	ENSP00000228347:p.Thr151Met	96	5.88	6		3	70.00	7	105294314	188	40.31	131	A8K6H0|B3KV73|F5H1E6|Q9NW59	Missense_Mutation	SNP	HMMPfam_RNA_pol_Rpb2_6,PatternScan_RNA_POL_BETA,HMMPfam_RNA_pol_Rpb2_7,HMMPfam_RNA_pol_Rpb2_2,HMMPfam_RNA_pol_Rpb2_1,HMMPfam_RNA_pol_Rpb2_3,HMMPfam_RNA_pol_Rpb2_4,HMMPfam_RNA_pol_Rpb2_5,superfamily_beta and beta-prime subunits of DNA dependent RNA-polymerase	p.T151M	ENST00000228347.4	37	c.452	CCDS9105.1	12	.	.	.	.	.	.	.	.	.	.	C	19.47	3.833132	0.71258	0.0	1.16E-4	ENSG00000013503	ENST00000228347;ENST00000551370;ENST00000539066	T;T	0.77877	-1.13;-1.13	5.47	5.47	0.80525	RNA polymerase, beta subunit, protrusion (1);	0.000000	0.85682	D	0.000000	T	0.78929	0.4361	M	0.69523	2.12	0.80722	D	1	P	0.39480	0.675	B	0.37239	0.244	T	0.82090	-0.0629	10	0.87932	D	0	-9.5472	19.6948	0.96021	0.0:1.0:0.0:0.0	.	151	Q9NW08	RPC2_HUMAN	M	151;151;93	ENSP00000228347:T151M;ENSP00000445721:T93M	ENSP00000228347:T151M	T	+	2	0	POLR3B	105294314	1.000000	0.71417	0.971000	0.41717	0.965000	0.64279	7.341000	0.79300	2.723000	0.93209	0.655000	0.94253	ACG	-	HMMPfam_RNA_pol_Rpb2_1,superfamily_beta and beta-prime subunits of DNA dependent RNA-polymerase		0.368	POLR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	POLR3B	protein_coding	OTTHUMT00000407166.1	C	NM_018082		105294314	+1	no_errors	NM_018082.4	genbank	human	provisional	54_36p	missense	SNP	0.998	T
FLT3	2322	genome.wustl.edu	37	13	28608258	28608275	+	In_Frame_Del	DEL	CATATTCATATTCTCTGA	CATATTCATATTCTCTGA	GGGGTGGGGGGG			TCGA-AB-2870-03A-01W-0732-08	TCGA-AB-2870-11A-01W-0732-08	CATATTCATATTCTCTGA	CATATTCATATTCTCTGA	CATATTCATATTCTCTGA	GGGGTGGGGGGG	CATATTCATATTCTCTGA	CATATTCATATTCTCTGA	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	9ad67fd3-5750-42ab-b4e2-55133613a3e4	ab21f718-4b02-4b59-9590-a0de74285788	g.chr13:28608258_28608275delCATATTCATATTCTCTGA	ENST00000241453.7	-	14	1862_1879	c.1781_1798delTCAGAGAATATGAATATG	c.(1780-1800)ttcagagaatatgaatatgat>tat	p.594_600FREYEYD>Y	FLT3_ENST00000380982.4_In_Frame_Del_p.594_600FREYEYD>Y|FLT3_ENST00000537084.1_In_Frame_Del_p.594_600FREYEYD>Y	NM_004119.2	NP_004110.2	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	594	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.E596_Y597ins12(3)|p.F594_R595ins12(2)|p.Y599_D600insPAPQIMSTSTLISENMNIA(2)|p.Y599_D600ins15(2)|p.Y599F(2)|p.F594_R595insSDNEYFYVDF(2)|p.Y597_E598ins26(2)|p.R595_E596insDFYVDFR(1)|p.E598_Y599ins22(1)|p.E598_Y599ins25(1)|p.595_596>DNEYFYVDFR(1)|p.E598_Y599insFYVDFREYE(1)|p.593_594>WGYFYVD(1)|p.E598>DMISPEDMK(1)|p.D600_L601insVDFREYEY(1)|p.F590_F594>L(1)|p.Y599_D600>NEYFYVDFREYEY(1)|p.Y599_D600insFDFREYE(1)|p.Y597_E598ins18(1)|p.597_598>DYVDFREY(1)|p.R595_E596ins13(1)|p.E598_Y599insWDFREYE(1)|p.E598_Y599ins14(1)|p.Y597_E598insEYDLKWEFG(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)	CATTTGAGATCATATTCATATTCTCTGAAATCAACGTA	0.367			"""Mis, O"""		"""AML, ALL"""																																	dbGAP		Dom	yes		13	13q12	2322	fms-related tyrosine kinase 3		L	32	Insertion - In frame(25)|Complex - insertion inframe(4)|Substitution - Missense(2)|Complex - deletion inframe(1)	haematopoietic_and_lymphoid_tissue(32)	13																																								27506275	SO:0001651	inframe_deletion	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.1781_1798delTCAGAGAATATGAATATG	13.37:g.28608258_28608275delCATATTCATATTCTCTGA	ENSP00000241453:p.Phe594_Asp600delinsTyr	NA	NA	NA		NA	NA	NA	27506258	NA	NA	NA	A0AVG9|B7ZLT7|B7ZLT8|F5H0A0|Q13414	In_Frame_Ins	DEL	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.595in_frame_insPPTP	ENST00000241453.7	37	c.1798_1781	CCDS31953.1	13																																																																																			-	superfamily_Kinase_like		0.367	FLT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	FLT3	protein_coding	OTTHUMT00000044319.2	CATATTCATATTCTCTGA			27506275	-1	no_errors	NM_004119.2	genbank	human	reviewed	54_36p	in_frame_ins	INS	1.000:1.000:1.000:0.999:0.789:0.821:0.816:0.676:0.765:0.789:0.794:0.991:0.997:0.996:0.999:1.000:1.000:1.000	GGGGTGGGGGGG
HCN4	10021	genome.wustl.edu	37	15	73624519	73624519	+	Silent	SNP	G	G	A			TCGA-AB-2870-03A-01W-0732-08	TCGA-AB-2870-11A-01W-0732-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	9ad67fd3-5750-42ab-b4e2-55133613a3e4	ab21f718-4b02-4b59-9590-a0de74285788	g.chr15:73624519G>A	ENST00000261917.3	-	3	2317	c.1324C>T	c.(1324-1326)Cta>Tta	p.L442L		NM_005477.2	NP_005468.1	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 4	442					blood circulation (GO:0008015)|cation transport (GO:0006812)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)	cAMP binding (GO:0030552)|cation channel activity (GO:0005261)|identical protein binding (GO:0042802)|intracellular cAMP activated cation channel activity (GO:0005222)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(13)|liver(1)|lung(18)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				COAD - Colon adenocarcinoma(1;0.142)		AAGTCCTGTAGCATGGGTACC	0.632																																						dbGAP											0			15											105.0	85.0	92.0					15																	73624519		2198	4297	6495	71411572	SO:0001819	synonymous_variant	0			AJ132429	CCDS10248.1	15q24.1	2011-07-05			ENSG00000138622	ENSG00000138622		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	16882	protein-coding gene	gene with protein product		605206				10228147, 10430953, 16382102	Standard	NM_005477		Approved		uc002avp.3	Q9Y3Q4	OTTHUMG00000137563	ENST00000261917.3:c.1324C>T	15.37:g.73624519G>A		28	3.45	1		NA	NA	NA	71411572	77	45.07	64	Q9UMQ7	Silent	SNP	HMMPfam_cNMP_binding,HMMSmart_cNMP,HMMPfam_Ion_trans,HMMPfam_Ion_trans_N,PatternScan_CNMP_BINDING_1,PatternScan_CNMP_BINDING_2,superfamily_cNMP_binding,superfamily_SSF81324	p.L442	ENST00000261917.3	37	c.1324	CCDS10248.1	15																																																																																			-	HMMPfam_Ion_trans,superfamily_SSF81324		0.632	HCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HCN4	protein_coding	OTTHUMT00000268900.2	G	NM_005477		71411572	-1	no_errors	NM_005477.2	genbank	human	reviewed	54_36p	silent	SNP	1.000	A
NAGPA	51172	genome.wustl.edu	37	16	5078916	5078916	+	Silent	SNP	G	G	C			TCGA-AB-2870-03A-01W-0732-08	TCGA-AB-2870-11A-01W-0732-08	G	G	G	C	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	9ad67fd3-5750-42ab-b4e2-55133613a3e4	ab21f718-4b02-4b59-9590-a0de74285788	g.chr16:5078916G>C	ENST00000312251.3	-	5	904	c.885C>G	c.(883-885)ctC>ctG	p.L295L	NAGPA_ENST00000381955.3_Silent_p.L295L|RP11-165E7.1_ENST00000588778.1_RNA|NAGPA_ENST00000564922.1_5'Flank	NM_016256.3	NP_057340.2	Q9UK23	NAGPA_HUMAN	N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase	295					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|lysosome organization (GO:0007040)|protein glycosylation (GO:0006486)|protein targeting to lysosome (GO:0006622)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase activity (GO:0003944)			endometrium(4)|large_intestine(4)|lung(3)|urinary_tract(1)	12					N-Acetyl-D-glucosamine(DB00141)	AGGTCCCGTTGAGCACAAAGG	0.592																																						dbGAP											0			16											151.0	139.0	143.0					16																	5078916		2197	4300	6497	5018917	SO:0001819	synonymous_variant	0			AF187072	CCDS10527.1	16p13.3	2008-02-05			ENSG00000103174	ENSG00000103174	3.1.4.45		17378	protein-coding gene	gene with protein product		607985				10551838, 12058031	Standard	NM_016256		Approved	APAA, UCE	uc002cyg.3	Q9UK23	OTTHUMG00000090515	ENST00000312251.3:c.885C>G	16.37:g.5078916G>C		59	9.09	6		21	56.25	27	5018917	75	51.25	82	B2RAS1|Q96EJ8	Silent	SNP	HMMSmart_EGF,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_2	p.L295	ENST00000312251.3	37	c.885	CCDS10527.1	16																																																																																			-	NULL		0.592	NAGPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NAGPA	protein_coding	OTTHUMT00000207003.1	G	NM_016256		5018917	-1	no_errors	NM_016256.2	genbank	human	reviewed	54_36p	silent	SNP	0.994	C
COL5A3	50509	genome.wustl.edu	37	19	10112274	10112274	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2870-03A-01W-0732-08	TCGA-AB-2870-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	9ad67fd3-5750-42ab-b4e2-55133613a3e4	ab21f718-4b02-4b59-9590-a0de74285788	g.chr19:10112274C>T	ENST00000264828.3	-	8	1121	c.1036G>A	c.(1036-1038)Gga>Aga	p.G346R		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	346	Nonhelical region.				axon guidance (GO:0007411)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(11)|kidney(23)|large_intestine(12)|liver(2)|lung(35)|ovary(8)|prostate(5)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	116			Epithelial(33;7.11e-05)			GAATCATCTCCTTCTTCATCC	0.542											OREG0025228	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										dbGAP											0			19											106.0	101.0	103.0					19																	10112274		2203	4300	6503	9973274	SO:0001583	missense	0			AF177941	CCDS12222.1	19p13.2	2013-01-16			ENSG00000080573	ENSG00000080573		"""Collagens"""	14864	protein-coding gene	gene with protein product		120216				10722718	Standard	NM_015719		Approved		uc002mmq.1	P25940	OTTHUMG00000150019	ENST00000264828.3:c.1036G>A	19.37:g.10112274C>T	ENSP00000264828:p.Gly346Arg	117	5.65	7	662	NA	NA	NA	9973274	205	40.00	138	Q9NZQ6	Missense_Mutation	SNP	HMMPfam_COLFI,HMMSmart_SM00038,HMMSmart_SM00210,HMMPfam_Collagen,superfamily_Concanavalin A-like lectins/glucanases,HMMPfam_Laminin_G_2	p.G346R	ENST00000264828.3	37	c.1036	CCDS12222.1	19	.	.	.	.	.	.	.	.	.	.	C	8.463	0.855791	0.17106	.	.	ENSG00000080573	ENST00000264828	D	0.89123	-2.47	4.55	-0.545	0.11843	.	2.438730	0.01925	U	0.040796	T	0.76765	0.4033	N	0.08118	0	0.09310	N	0.999995	B	0.02656	0.0	B	0.04013	0.001	T	0.65307	-0.6200	10	0.44086	T	0.13	.	3.4471	0.07484	0.3627:0.431:0.0:0.2064	.	346	P25940	CO5A3_HUMAN	R	346	ENSP00000264828:G346R	ENSP00000264828:G346R	G	-	1	0	COL5A3	9973274	0.001000	0.12720	0.360000	0.25837	0.497000	0.33675	-0.368000	0.07543	0.164000	0.19529	0.462000	0.41574	GGA	-	NULL		0.542	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	COL5A3	protein_coding	OTTHUMT00000315788.1	C	NM_015719		9973274	-1	no_errors	NM_015719.3	genbank	human	reviewed	54_36p	missense	SNP	0.014	T
Unknown	0	genome.wustl.edu	37	Unknown	0	0	+	IGR	DEL	A	A	-			TCGA-AB-2870-03A-01W-0732-08	TCGA-AB-2870-11A-01W-0732-08	A	A	A	-	A	A	Verified	Invalid:failed_liftOver	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	9ad67fd3-5750-42ab-b4e2-55133613a3e4	ab21f718-4b02-4b59-9590-a0de74285788	g.chrUnknown:0delA								None (None upstream) : None (None downstream)																								0.0																																						dbGAP											0			7																																								40084184	SO:0001628	intergenic_variant	0																															Unknown.37:g.0delA		1	0.00	0		0	0.00	0	40084184	5	0.00	0		Frame_Shift_Del	DEL	HMMSmart_SM00219,HMMSmart_SM00220,PatternScan_PROTEIN_KINASE_ST,superfamily_Protein kinase-like (PK-like),PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase	p.Y946fs		37	c.2836		7																																																																																			-	HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase	0	0					CDC2L5			A			40084184	+1	no_errors	NM_003718.3	genbank	human	reviewed	54_36p	frame_shift_del	DEL	0.975	-
