#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_NormalRefReads_WU	i_NormalVAF_WU	i_NormalVarReads_WU	i_ORegAnno_bin	i_RNARefReads_WU	i_RNAVAF_WU	i_RNAVarReads_WU	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_Start_position_hg18	i_TumorRefReads_WU	i_TumorVAF_WU	i_TumorVarReads_WU	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_deletion_substructures	i_domain	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_name	i_gene_type	i_havana_transcript	i_reference	i_refseq_mrna_id	i_secondary_variant_classification	i_stop	i_strand	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_type	i_ucsc_cons	i_variant
SYTL5	94122	genome.wustl.edu	37	X	37935911	37935911	+	Missense_Mutation	SNP	G	G	A	rs370179164		TCGA-AB-2929-03A-01W-0732-08	TCGA-AB-2929-11A-01W-0732-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3ca5c769-b07c-4a68-818d-ab2bb8141170	0aa884ea-58b7-4079-a204-be6fe7e90a24	g.chrX:37935911G>A	ENST00000357972.5	+	6	1192	c.646G>A	c.(646-648)Ggt>Agt	p.G216S	TM4SF2_ENST00000465127.1_Intron|SYTL5_ENST00000297875.2_Missense_Mutation_p.G216S|SYTL5_ENST00000456733.2_Missense_Mutation_p.G216S			Q8TDW5	SYTL5_HUMAN	synaptotagmin-like 5	216					exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)	membrane (GO:0016020)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(23)|prostate(1)|skin(2)|urinary_tract(1)	44						GGACTTAGACGGTCAACATTT	0.418																																						dbGAP											0			X						G	SER/GLY,SER/GLY,SER/GLY	0,3833		0,0,1631,571	136.0	97.0	110.0		646,646,646	-2.2	0.0	X		110	1,6727		0,1,2427,1872	no	missense,missense,missense	SYTL5	NM_138780.2,NM_001163335.1,NM_001163334.1	56,56,56	0,1,4058,2443	AA,AG,GG,G		0.0149,0.0,0.0095	benign,benign,benign	216/731,216/731,216/753	37935911	1,10560	2202	4300	6502	37820855	SO:0001583	missense	0				CCDS14244.1, CCDS55399.1	Xp21.1	2008-02-05			ENSG00000147041	ENSG00000147041			15589	protein-coding gene	gene with protein product	"""exophilin 9"""						Standard	NM_138780		Approved		uc004ddx.3	Q8TDW5	OTTHUMG00000033176	ENST00000357972.5:c.646G>A	X.37:g.37935911G>A	ENSP00000350657:p.Gly216Ser	Somatic	84	4.55	4		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	37820855	131	36.84	77	A2RRF2	Missense_Mutation	SNP	HMMPfam_C2,HMMSmart_C2,HMMPfam_RPH3A_effector,superfamily_C2_CaLB,superfamily_FYVE_PHD_ZnF	p.G216S	ENST00000357972.5	37	c.646	CCDS14244.1	X	.	.	.	.	.	.	.	.	.	.	G	0.662	-0.805483	0.02819	0.0	1.49E-4	ENSG00000147041	ENST00000297875;ENST00000357972;ENST00000456733	T;T;T	0.18960	2.18;2.18;2.5	4.55	-2.23	0.06930	.	1.606140	0.02799	N	0.123007	T	0.05502	0.0145	N	0.00972	-1.085	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.04013	0.0;0.001	T	0.35798	-0.9774	10	0.02654	T	1	-6.4804	4.8368	0.13469	0.4589:0.0:0.3913:0.1498	.	216;216	A2RRF2;Q8TDW5	.;SYTL5_HUMAN	S	216	ENSP00000297875:G216S;ENSP00000350657:G216S;ENSP00000395220:G216S	ENSP00000297875:G216S	G	+	1	0	SYTL5	37820855	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	0.089000	0.15002	-0.139000	0.11414	-0.322000	0.08575	GGT	-	HMMPfam_RPH3A_effector		0.418	SYTL5-201	KNOWN	basic|CCDS	protein_coding	SYTL5	protein_coding	OTTHUMT00000080883.1	G	NM_138780		37820855	+1	no_errors	NM_138780.1	genbank	human	provisional	54_36p	missense	SNP	0.109	A
Unknown	0	genome.wustl.edu	37	X	105570794	105570794	+	IGR	SNP	G	G	A			TCGA-AB-2929-03A-01W-0732-08	TCGA-AB-2929-11A-01W-0732-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3ca5c769-b07c-4a68-818d-ab2bb8141170	0aa884ea-58b7-4079-a204-be6fe7e90a24	g.chrX:105570794G>A								MUM1L1 (117845 upstream) : Y_RNA (99003 downstream)																							TTGGGGTGGAGAAGATGTTCA	0.433																																						dbGAP											0			X																																								105457450	SO:0001628	intergenic_variant	0																															X.37:g.105570794G>A		Somatic	73	2.63	2		9	0.00	0	WXS	Illumina HiSeq	Phase_IV	105457450	35	64.42	67		Missense_Mutation	SNP	HMMPfam_CHGN,superfamily_Nucleotide-diphospho-sugar transferases	p.E9K		37	c.25		X																																																																																			-	HMMPfam_CHGN,superfamily_Nucleotide-diphospho-sugar transferases	0	0.433					LOC644504			G			105457450	+1	no_errors	XM_001128075.1	genbank	human	model	54_36p	missense	SNP	1.000	A
BRCC3	79184	genome.wustl.edu	37	X	154305490	154305490	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AB-2929-03A-01W-0732-08	TCGA-AB-2929-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3ca5c769-b07c-4a68-818d-ab2bb8141170	0aa884ea-58b7-4079-a204-be6fe7e90a24	g.chrX:154305490C>T	ENST00000369462.1	+	4	266	c.241C>T	c.(241-243)Cga>Tga	p.R81*	BRCC3_ENST00000399042.1_Nonsense_Mutation_p.R81*|BRCC3_ENST00000369459.2_Nonsense_Mutation_p.R81*|BRCC3_ENST00000340647.4_Nonsense_Mutation_p.R82*|BRCC3_ENST00000330045.7_Nonsense_Mutation_p.R81*|MTCP1_ENST00000362018.2_Intron	NM_024332.3	NP_077308.1	P46736	BRCC3_HUMAN	BRCA1/BRCA2-containing complex, subunit 3	81	MPN.				double-strand break repair (GO:0006302)|G2 DNA damage checkpoint (GO:0031572)|histone H2A K63-linked deubiquitination (GO:0070537)|positive regulation of DNA repair (GO:0045739)|protein K63-linked deubiquitination (GO:0070536)|regulation of catalytic activity (GO:0050790)|response to ionizing radiation (GO:0010212)|response to X-ray (GO:0010165)	BRCA1-A complex (GO:0070531)|BRISC complex (GO:0070552)|nuclear ubiquitin ligase complex (GO:0000152)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	enzyme regulator activity (GO:0030234)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|polyubiquitin binding (GO:0031593)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.R81*(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|pancreas(1)|skin(1)	22	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					CATCATCTTACGACGTTCTGA	0.428																																						dbGAP											1	Substitution - Nonsense(1)	haematopoietic_and_lymphoid_tissue(1)	X											115.0	97.0	103.0					X																	154305490		1874	4100	5974	153958684	SO:0001587	stop_gained	0			X64643	CCDS56610.1, CCDS56611.1, CCDS56612.1	Xq28	2013-05-29	2005-11-21	2005-11-21	ENSG00000185515	ENSG00000185515			24185	protein-coding gene	gene with protein product	"""Lys-63-specific deubiquitinase"""	300617	"""chromosome X open reading frame 53"""	CXorf53		1303175, 14636569	Standard	NM_024332		Approved	C6.1A, BRCC36	uc004fna.3	P46736	OTTHUMG00000022658	ENST00000369462.1:c.241C>T	X.37:g.154305490C>T	ENSP00000358474:p.Arg81*	Somatic	96	4.90	5		1	91.67	11	WXS	Illumina HiSeq	Phase_IV	153958684	48	54.95	61	A6QRF8|A6QRF9|A8MUX5|A8MWH0|A9Z1Y0|A9Z1Y5|B1B062|B4DQN7|Q16107|Q53YX5|Q9BTZ6	Nonsense_Mutation	SNP	HMMPfam_Mov34,HMMSmart_SM00232,superfamily_JAB1/MPN domain	p.R81*	ENST00000369462.1	37	c.241	CCDS56611.1	X	.	.	.	.	.	.	.	.	.	.	C	32	5.108171	0.94292	.	.	ENSG00000185515	ENST00000340647;ENST00000330045;ENST00000369459;ENST00000369462;ENST00000411985;ENST00000399042;ENST00000457026;ENST00000399026	.	.	.	5.15	3.27	0.37495	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06891	T	0.86	-8.9678	11.8326	0.52305	0.3103:0.6897:0.0:0.0	.	.	.	.	X	82;81;81;81;57;81;81;23	.	ENSP00000328641:R81X	R	+	1	2	BRCC3	153958684	1.000000	0.71417	0.998000	0.56505	0.954000	0.61252	4.280000	0.58959	1.072000	0.40860	-0.317000	0.08691	CGA	-	HMMPfam_Mov34,HMMSmart_SM00232,superfamily_JAB1/MPN domain		0.428	BRCC3-001	KNOWN	basic|CCDS	protein_coding	BRCC3	protein_coding	OTTHUMT00000058788.4	C	NM_024332		153958684	+1	no_errors	NM_024332.1	genbank	human	reviewed	54_36p	nonsense	SNP	1.000	T
SYPL2	284612	genome.wustl.edu	37	1	110019500	110019500	+	Silent	SNP	G	G	A			TCGA-AB-2929-03A-01W-0732-08	TCGA-AB-2929-11A-01W-0732-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3ca5c769-b07c-4a68-818d-ab2bb8141170	0aa884ea-58b7-4079-a204-be6fe7e90a24	g.chr1:110019500G>A	ENST00000369872.3	+	4	573	c.357G>A	c.(355-357)gtG>gtA	p.V119V	SYPL2_ENST00000401021.3_Silent_p.V119V	NM_001040709.1	NP_001035799.1	Q5VXT5	SYPL2_HUMAN	synaptophysin-like 2	119	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				cellular calcium ion homeostasis (GO:0006874)|substantia nigra development (GO:0021762)	integral component of synaptic vesicle membrane (GO:0030285)	transporter activity (GO:0005215)			breast(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	16		all_epithelial(167;2.83e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Colorectal(144;0.0129)|Lung(183;0.0436)|READ - Rectum adenocarcinoma(129;0.0698)|Epithelial(280;0.0808)|all cancers(265;0.0869)|LUSC - Lung squamous cell carcinoma(189;0.231)		AGTTCTTCGTGACCCTTGGCA	0.542																																						dbGAP											0			1											105.0	107.0	106.0					1																	110019500		1996	4170	6166	109821023	SO:0001819	synonymous_variant	0			AK131459	CCDS41365.1	1p13.3	2008-02-05			ENSG00000143028	ENSG00000143028			27638	protein-coding gene	gene with protein product	"""mitsugumin-29"""					12975309	Standard	NM_001040709		Approved	Mg29	uc001dxp.3	Q5VXT5	OTTHUMG00000010969	ENST00000369872.3:c.357G>A	1.37:g.110019500G>A		Somatic	82	5.75	5		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	109821023	145	35.53	81	A8K0E8|A8KAL7|I0IT67|Q6ZMX1	Silent	SNP	HMMPfam_MARVEL	p.V119	ENST00000369872.3	37	c.357	CCDS41365.1	1																																																																																			-	HMMPfam_MARVEL		0.542	SYPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SYPL2	protein_coding	OTTHUMT00000030191.1	G	NM_001006603		109821023	+1	no_errors	NM_001040709.1	genbank	human	validated	54_36p	silent	SNP	1.000	A
NTSR2	23620	genome.wustl.edu	37	2	11800178	11800178	+	Missense_Mutation	SNP	G	G	A	rs377014236		TCGA-AB-2929-03A-01W-0732-08	TCGA-AB-2929-11A-01W-0732-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3ca5c769-b07c-4a68-818d-ab2bb8141170	0aa884ea-58b7-4079-a204-be6fe7e90a24	g.chr2:11800178G>A	ENST00000306928.5	-	3	1014	c.980C>T	c.(979-981)gCg>gTg	p.A327V		NM_012344.3	NP_036476	O95665	NTR2_HUMAN	neurotensin receptor 2	327					cell surface receptor signaling pathway (GO:0007166)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|regulation of membrane potential (GO:0042391)|sensory perception (GO:0007600)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled neurotensin receptor activity (GO:0016492)|G-protein coupled receptor activity (GO:0004930)	p.A327V(1)		breast(1)|large_intestine(7)|lung(7)|prostate(1)|urinary_tract(1)	17	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.129)|OV - Ovarian serous cystadenocarcinoma(76;0.24)	Levocabastine(DB01106)	CTCAGTCCACGCGTCATCAGG	0.597													G|||	1	0.000199681	0.0	0.0	5008	,	,		21195	0.0		0.0	False		,,,				2504	0.001					dbGAP											1	Substitution - Missense(1)	large_intestine(1)	2						G	VAL/ALA	0,4406		0,0,2203	103.0	87.0	93.0		980	-6.0	0.0	2		93	1,8599	1.2+/-3.3	0,1,4299	no	missense	NTSR2	NM_012344.3	64	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	327/411	11800178	1,13005	2203	4300	6503	11717629	SO:0001583	missense	0			Y10148	CCDS1681.1	2p25.1	2012-08-08			ENSG00000169006	ENSG00000169006		"""GPCR / Class A : Neurotensin receptors"""	8040	protein-coding gene	gene with protein product		605538				8647296, 9851594	Standard	NM_012344		Approved	NTR2	uc002rbq.4	O95665	OTTHUMG00000119083	ENST00000306928.5:c.980C>T	2.37:g.11800178G>A	ENSP00000303686:p.Ala327Val	Somatic	47	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	11717629	71	26.26	26	Q53QQ5|Q57Z87|Q8IY58|Q8TBH6	Missense_Mutation	SNP	HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_Family A G protein-coupled receptor-like	p.A327V	ENST00000306928.5	37	c.980	CCDS1681.1	2	.	.	.	.	.	.	.	.	.	.	G	7.480	0.648529	0.14516	0.0	1.16E-4	ENSG00000169006	ENST00000306928	T	0.74315	-0.83	3.33	-6.04	0.02178	GPCR, rhodopsin-like superfamily (1);	3.522020	0.00649	N	0.000556	T	0.50497	0.1619	N	0.14661	0.345	0.09310	N	1	B	0.31290	0.318	B	0.24269	0.052	T	0.44787	-0.9305	10	0.15952	T	0.53	0.7382	6.8186	0.23845	0.0:0.1572:0.3673:0.4755	.	327	O95665	NTR2_HUMAN	V	327	ENSP00000303686:A327V	ENSP00000303686:A327V	A	-	2	0	NTSR2	11717629	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	0.071000	0.14594	-1.535000	0.01740	-1.313000	0.01306	GCG	-	HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like		0.597	NTSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NTSR2	protein_coding	OTTHUMT00000239297.1	G			11717629	-1	no_errors	NM_012344.3	genbank	human	reviewed	54_36p	missense	SNP	0.001	A
SF3B1	23451	genome.wustl.edu	37	2	198266834	198266834	+	Missense_Mutation	SNP	T	T	C	rs559063155		TCGA-AB-2929-03A-01W-0732-08	TCGA-AB-2929-11A-01W-0732-08	T	T	T	C	T	T	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3ca5c769-b07c-4a68-818d-ab2bb8141170	0aa884ea-58b7-4079-a204-be6fe7e90a24	g.chr2:198266834T>C	ENST00000335508.6	-	15	2189	c.2098A>G	c.(2098-2100)Aaa>Gaa	p.K700E	SNORA4_ENST00000365564.1_RNA|SF3B1_ENST00000462613.1_5'UTR	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	700					anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)	p.K700E(179)|p.Q699_K700del(2)		NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			GTCCGAACTTTCTGCTGCTCA	0.408			Mis		myelodysplastic syndrome								T|||	1	0.000199681	0.0	0.0	5008	,	,		17946	0.0		0.0	False		,,,				2504	0.001					dbGAP		Dom	yes		2	2q33.1	23451	"""splicing factor 3b, subunit 1, 155kDa"""		L	181	Substitution - Missense(179)|Deletion - In frame(2)	haematopoietic_and_lymphoid_tissue(153)|NS(20)|breast(5)|pancreas(2)|central_nervous_system(1)	2																																								197975079	SO:0001583	missense	0			AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"""splicing factor 3b, subunit 1, 155kD"""			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.2098A>G	2.37:g.198266834T>C	ENSP00000335321:p.Lys700Glu	Somatic	44	0.00	0		291	46.99	258	WXS	Illumina HiSeq	Phase_IV	197975079	57	49.57	57	E9PCH3	Missense_Mutation	SNP	HMMPfam_HEAT,HMMPfam_SF3b1,superfamily_ARM repeat	p.K700E	ENST00000335508.6	37	c.2098	CCDS33356.1	2	.	.	.	.	.	.	.	.	.	.	T	33	5.243295	0.95272	.	.	ENSG00000115524	ENST00000335508	T	0.63580	-0.05	6.02	6.02	0.97574	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.85609	0.5736	H	0.95504	3.68	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.89820	0.3988	10	0.87932	D	0	.	16.542	0.84395	0.0:0.0:0.0:1.0	.	700	O75533	SF3B1_HUMAN	E	700	ENSP00000335321:K700E	ENSP00000335321:K700E	K	-	1	0	SF3B1	197975079	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.555000	0.82223	2.304000	0.77564	0.528000	0.53228	AAA	-	HMMPfam_HEAT,superfamily_ARM repeat		0.408	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SF3B1	protein_coding	OTTHUMT00000335245.2	T			197975079	-1	no_errors	NM_012433.1	genbank	human	reviewed	54_36p	missense	SNP	1.000	C
LINC00969	440993	genome.wustl.edu	37	3	195390553	195390553	+	lincRNA	SNP	A	A	G	rs201494538		TCGA-AB-2929-03A-01W-0732-08	TCGA-AB-2929-11A-01W-0732-08	A	A	A	G	A	A	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3ca5c769-b07c-4a68-818d-ab2bb8141170	0aa884ea-58b7-4079-a204-be6fe7e90a24	g.chr3:195390553A>G	ENST00000445430.1	+	0	397									long intergenic non-protein coding RNA 969																		TGGCATTTCTATGACACCGTG	0.592																																						dbGAP											0			3																																								196875734			0			AK128346		3q29	2013-06-07			ENSG00000242086	ENSG00000242086		"""Long non-coding RNAs"""	48729	non-coding RNA	RNA, long non-coding							Standard	XR_427455		Approved				OTTHUMG00000155834		3.37:g.195390553A>G		Somatic	8	0.00	0		4	0.00	0	WXS	Illumina HiSeq	Phase_IV	196875734	15	31.82	7		Missense_Mutation	SNP	HMMPfam_FAD_binding_2,HMMPfam_Succ_DH_flav_C,superfamily_Succ_DH_flav_C,superfamily_SSF51905,superfamily_SSF56425	p.Y65C	ENST00000445430.1	37	c.194		3																																																																																			-	HMMPfam_FAD_binding_2,superfamily_SSF51905		0.592	LINC00969-038	KNOWN	basic	lincRNA	ENSG00000214135	lincRNA	OTTHUMT00000341951.1	A			196875734	+1	no_start_codon:no_stop_codon	ENST00000397590	ensembl	human	known	54_36p	missense	SNP	1.000	G
CD74	972	genome.wustl.edu	37	5	149784252	149784252	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2929-03A-01W-0732-08	TCGA-AB-2929-11A-01W-0732-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3ca5c769-b07c-4a68-818d-ab2bb8141170	0aa884ea-58b7-4079-a204-be6fe7e90a24	g.chr5:149784252G>A	ENST00000009530.7	-	6	617	c.616C>T	c.(616-618)Cca>Tca	p.P206S	CD74_ENST00000353334.6_Missense_Mutation_p.P206S|CD74_ENST00000524315.1_Intron|CD74_ENST00000377795.3_Intron			P04233	HG2A_HUMAN	CD74 molecule, major histocompatibility complex, class II invariant chain	206					activation of MAPK activity (GO:0000187)|antigen processing and presentation of endogenous antigen (GO:0019883)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell proliferation (GO:0008283)|chaperone mediated protein folding requiring cofactor (GO:0051085)|defense response (GO:0006952)|immunoglobulin mediated immune response (GO:0016064)|intracellular protein transport (GO:0006886)|macrophage migration inhibitory factor signaling pathway (GO:0035691)|negative regulation of apoptotic process (GO:0043066)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of mature B cell apoptotic process (GO:0002906)|negative regulation of peptide secretion (GO:0002792)|negative regulation of T cell differentiation (GO:0045581)|negative thymic T cell selection (GO:0045060)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000343)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of type 2 immune response (GO:0002830)|positive thymic T cell selection (GO:0045059)|prostaglandin biosynthetic process (GO:0001516)|protein complex assembly (GO:0006461)|regulation of macrophage activation (GO:0043030)|signal transduction (GO:0007165)|T cell selection (GO:0045058)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|lysosomal lumen (GO:0043202)|lysosomal membrane (GO:0005765)|macrophage migration inhibitory factor receptor complex (GO:0035692)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|multivesicular body (GO:0005771)|NOS2-CD74 complex (GO:0035693)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)|vacuole (GO:0005773)	beta-amyloid binding (GO:0001540)|cytokine binding (GO:0019955)|cytokine receptor activity (GO:0004896)|identical protein binding (GO:0042802)|macrophage migration inhibitory factor binding (GO:0035718)|MHC class II protein binding (GO:0042289)|MHC class II protein binding, via antigen binding groove (GO:0042658)|MHC class II protein complex binding (GO:0023026)|protein binding involved in protein folding (GO:0044183)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)	5		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CCTTTCGGTGGAGCGTCAGTG	0.592			T	ROS1	NSCLC																																	dbGAP		Dom	yes		5	5q32	972	"""CD74 molecule, major histocompatibility complex, class II invariant chain"""		E	0			5											41.0	41.0	41.0					5																	149784252		1943	4129	6072	149764445	SO:0001583	missense	0				CCDS34276.1, CCDS47308.1, CCDS47309.1	5q32	2012-09-20	2006-03-28		ENSG00000019582	ENSG00000019582		"""CD molecules"""	1697	protein-coding gene	gene with protein product	"""HLA-DR-gamma"", ""Ia-associated invariant chain"", ""gamma chain of class II antigens"", ""MHC HLA-DR gamma chain"""	142790	"""CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated)"""	DHLAG		6324166, 3001652	Standard	NM_004355		Approved		uc003lsc.3	P04233	OTTHUMG00000163559	ENST00000009530.7:c.616C>T	5.37:g.149784252G>A	ENSP00000009530:p.Pro206Ser	Somatic	53	3.57	2		1915	51.11	2008	WXS	Illumina HiSeq	Phase_IV	149764445	68	41.53	49	A8K7R1|B4DNE8|D3DQG3|D3DQG4|Q14597|Q29832|Q5U0J8|Q8SNA0|Q8WLP6	Missense_Mutation	SNP	HMMPfam_Thyroglobulin_1,HMMSmart_SM00211,PatternScan_THYROGLOBULIN_1_1,superfamily_Thyroglobulin type-1 domain,HMMPfam_MHCassoc_trimer,superfamily_Class II MHC-associated invariant chain ectoplasmic trimerization domain,HMMPfam_MHC2-interact	p.P206S	ENST00000009530.7	37	c.616	CCDS47309.1	5	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.17|18.17	3.563440|3.563440	0.65651|0.65651	.|.	.|.	ENSG00000019582|ENSG00000019582	ENST00000353334;ENST00000009530|ENST00000518797	T|.	0.63255|.	-0.03|.	5.56|5.56	1.5|1.5	0.22942|0.22942	MHC class II-associated invariant chain, trimerisation (3);Thyroglobulin type-1 (1);|.	0.427242|.	0.27155|.	N|.	0.020663|.	T|T	0.44953|0.44953	0.1318|0.1318	M|M	0.70595|0.70595	2.14|2.14	0.09310|0.09310	N|N	1|1	P;B;P;B|.	0.36909|.	0.573;0.275;0.568;0.43|.	P;B;B;B|.	0.47827|.	0.558;0.116;0.229;0.211|.	T|T	0.36625|0.36625	-0.9740|-0.9740	10|5	0.37606|.	T|.	0.19|.	-1.4533|-1.4533	4.8471|4.8471	0.13519|0.13519	0.1703:0.0:0.5313:0.2984|0.1703:0.0:0.5313:0.2984	.|.	206;206;206;118|.	A9YLN4;P04233-2;P04233;B4DUJ2|.	.;.;HG2A_HUMAN;.|.	S|F	206|200	ENSP00000009530:P206S|.	ENSP00000009530:P206S|.	P|S	-|-	1|2	0|0	CD74|CD74	149764445|149764445	0.738000|0.738000	0.28186|0.28186	0.011000|0.011000	0.14972|0.14972	0.916000|0.916000	0.54674|0.54674	1.622000|1.622000	0.36997|0.36997	0.681000|0.681000	0.31386|0.31386	0.491000|0.491000	0.48974|0.48974	CCA|TCC	-	superfamily_Thyroglobulin type-1 domain,HMMPfam_MHCassoc_trimer,superfamily_Class II MHC-associated invariant chain ectoplasmic trimerization domain		0.592	CD74-003	KNOWN	basic|appris_principal|CCDS	protein_coding	CD74	protein_coding	OTTHUMT00000374178.1	G	NM_004355		149764445	-1	no_errors	NM_001025159.1	genbank	human	validated	54_36p	missense	SNP	0.002	A
HIVEP1	3096	genome.wustl.edu	37	6	12125884	12125884	+	Silent	SNP	G	G	A	rs200675112		TCGA-AB-2929-03A-01W-0732-08	TCGA-AB-2929-11A-01W-0732-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3ca5c769-b07c-4a68-818d-ab2bb8141170	0aa884ea-58b7-4079-a204-be6fe7e90a24	g.chr6:12125884G>A	ENST00000379388.2	+	4	6188	c.5856G>A	c.(5854-5856)tcG>tcA	p.S1952S	HIVEP1_ENST00000541134.1_5'Flank	NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	1952					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				GGCAGAAGTCGTTGCATTTGC	0.448													G|||	1	0.000199681	0.0	0.0014	5008	,	,		19281	0.0		0.0	False		,,,				2504	0.0					dbGAP											0			6						G		2,3780		0,2,1889	102.0	97.0	99.0		5856	-3.2	0.1	6		99	0,8222		0,0,4111	no	coding-synonymous	HIVEP1	NM_002114.2		0,2,6000	AA,AG,GG		0.0,0.0529,0.0167		1952/2719	12125884	2,12002	1891	4111	6002	12233870	SO:0001819	synonymous_variant	0			J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"""Zinc fingers, C2H2-type"""	4920	protein-coding gene	gene with protein product		194540	"""human immunodeficiency virus type I enhancer-binding protein 1"", ""zinc finger protein 40"""	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.5856G>A	6.37:g.12125884G>A		Somatic	41	2.38	1		10	37.50	6	WXS	Illumina HiSeq	Phase_IV	12233870	50	37.50	30	B2RTU3|Q14122|Q5MPB1|Q5VW60	Silent	SNP	HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers	p.S1952	ENST00000379388.2	37	c.5856	CCDS43426.1	6																																																																																			-	NULL		0.448	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HIVEP1	protein_coding	OTTHUMT00000039870.2	G	NM_002114		12233870	+1	no_errors	NM_002114.2	genbank	human	validated	54_36p	silent	SNP	0.006	A
TNC	3371	genome.wustl.edu	37	9	117803360	117803360	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2929-03A-01W-0732-08	TCGA-AB-2929-11A-01W-0732-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3ca5c769-b07c-4a68-818d-ab2bb8141170	0aa884ea-58b7-4079-a204-be6fe7e90a24	g.chr9:117803360G>A	ENST00000350763.4	-	19	5663	c.5252C>T	c.(5251-5253)aCa>aTa	p.T1751I	TNC_ENST00000535648.1_Missense_Mutation_p.T1296I|TNC_ENST00000542877.1_Missense_Mutation_p.T1388I|TNC_ENST00000423613.2_Missense_Mutation_p.T1478I|TNC_ENST00000340094.3_Missense_Mutation_p.T1387I|TNC_ENST00000537320.1_Missense_Mutation_p.T1114I|TNC_ENST00000345230.3_Missense_Mutation_p.T1114I|TNC_ENST00000341037.4_Missense_Mutation_p.T1569I|TNC_ENST00000346706.3_Missense_Mutation_p.T1205I	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	1751	Fibronectin type-III 13. {ECO:0000255|PROSITE-ProRule:PRU00316}.				bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)			NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						CATGGAGGGTGTACCTGGAAC	0.468																																						dbGAP											0			9											148.0	115.0	126.0					9																	117803360		2203	4300	6503	116843181	SO:0001583	missense	0				CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	5318	protein-coding gene	gene with protein product	"""hexabrachion (tenascin)"""	187380	"""hexabrachion (tenascin C, cytotactin)"", ""deafness, autosomal dominant 56"""	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.5252C>T	9.37:g.117803360G>A	ENSP00000265131:p.Thr1751Ile	Somatic	97	2.02	2		16	38.46	10	WXS	Illumina HiSeq	Phase_IV	116843181	173	40.00	116	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Missense_Mutation	SNP	HMMPfam_Fibrinogen_C,HMMSmart_FBG,superfamily_Fibrinogen_a/b/g_C,HMMPfam_fn3,HMMSmart_FN3,HMMPfam_EGF,HMMSmart_EGF,superfamily_FN_III-like,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_2	p.T1751I	ENST00000350763.4	37	c.5252	CCDS6811.1	9	.	.	.	.	.	.	.	.	.	.	G	10.88	1.474208	0.26423	.	.	ENSG00000041982	ENST00000340094;ENST00000535648;ENST00000346706;ENST00000345230;ENST00000350763;ENST00000341037;ENST00000423613;ENST00000537320;ENST00000542877	T;T;T;T;T;T;T;T;T	0.57752	0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38	6.08	1.03	0.20045	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.429588	0.28736	N	0.014310	T	0.38506	0.1043	L	0.41415	1.275	0.09310	N	1	B;B	0.14805	0.011;0.001	B;B	0.22152	0.038;0.009	T	0.24083	-1.0170	10	0.39692	T	0.17	.	6.3655	0.21453	0.1816:0.0:0.5946:0.2238	.	1478;1751	E9PC84;P24821	.;TENA_HUMAN	I	1387;1296;1205;1114;1751;1569;1478;1114;1388	ENSP00000344400:T1387I;ENSP00000438152:T1296I;ENSP00000344555:T1205I;ENSP00000345861:T1114I;ENSP00000265131:T1751I;ENSP00000339553:T1569I;ENSP00000411406:T1478I;ENSP00000443478:T1114I;ENSP00000442242:T1388I	ENSP00000344400:T1387I	T	-	2	0	TNC	116843181	0.055000	0.20627	0.001000	0.08648	0.002000	0.02628	1.915000	0.39976	0.144000	0.18951	-0.825000	0.03093	ACA	-	HMMPfam_fn3,HMMSmart_FN3,superfamily_FN_III-like		0.468	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TNC	protein_coding	OTTHUMT00000055418.2	G	NM_002160		116843181	-1	no_errors	NM_002160.2	genbank	human	validated	54_36p	missense	SNP	0.001	A
ITIH2	3698	genome.wustl.edu	37	10	7791219	7791219	+	Silent	SNP	C	C	T			TCGA-AB-2929-03A-01W-0732-08	TCGA-AB-2929-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3ca5c769-b07c-4a68-818d-ab2bb8141170	0aa884ea-58b7-4079-a204-be6fe7e90a24	g.chr10:7791219C>T	ENST00000358415.4	+	21	2929	c.2763C>T	c.(2761-2763)aaC>aaT	p.N921N	ITIH2_ENST00000379587.4_Silent_p.N910N	NM_002216.2	NP_002207.2	P19823	ITIH2_HUMAN	inter-alpha-trypsin inhibitor heavy chain 2	921					hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(2)|breast(1)|endometrium(8)|kidney(1)|large_intestine(17)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64						TTGTGCACAACAGTGGAAAAG	0.463																																						dbGAP											0			10											223.0	198.0	206.0					10																	7791219		2203	4300	6503	7831225	SO:0001819	synonymous_variant	0			X07173	CCDS31141.1	10p14	2011-10-26	2011-10-26		ENSG00000151655	ENSG00000151655			6167	protein-coding gene	gene with protein product		146640	"""inter-alpha (globulin) inhibitor, H2 polypeptide"""			1385302, 10100603	Standard	NM_002216		Approved	H2P	uc001ijs.3	P19823	OTTHUMG00000017633	ENST00000358415.4:c.2763C>T	10.37:g.7791219C>T		Somatic	59	6.35	4		10	52.38	11	WXS	Illumina HiSeq	Phase_IV	7831225	78	43.57	61	Q14659|Q15484|Q5T986	Silent	SNP	HMMPfam_VWA,HMMSmart_VWA,HMMSmart_VIT,HMMPfam_ITI_HC_C,HMMPfam_VIT,superfamily_SSF53300	p.N921	ENST00000358415.4	37	c.2763	CCDS31141.1	10																																																																																			-	HMMPfam_ITI_HC_C		0.463	ITIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ITIH2	protein_coding	OTTHUMT00000046678.2	C	NM_002216		7831225	+1	no_errors	NM_002216.2	genbank	human	validated	54_36p	silent	SNP	1.000	T
TPH1	7166	genome.wustl.edu	37	11	18044466	18044466	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AB-2929-03A-01W-0732-08	TCGA-AB-2929-11A-01W-0732-08	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3ca5c769-b07c-4a68-818d-ab2bb8141170	0aa884ea-58b7-4079-a204-be6fe7e90a24	g.chr11:18044466C>A	ENST00000250018.2	-	9	1601	c.1039G>T	c.(1039-1041)Gga>Tga	p.G347*	TPH1_ENST00000525406.1_5'UTR|RP1-59M18.2_ENST00000525523.1_RNA|TPH1_ENST00000341556.2_Nonsense_Mutation_p.G347*	NM_004179.2	NP_004170.1	P17752	TPH1_HUMAN	tryptophan hydroxylase 1	347					aromatic amino acid family metabolic process (GO:0009072)|bone remodeling (GO:0046849)|cellular nitrogen compound metabolic process (GO:0034641)|circadian rhythm (GO:0007623)|indolalkylamine biosynthetic process (GO:0046219)|mammary gland alveolus development (GO:0060749)|negative regulation of ossification (GO:0030279)|response to immobilization stress (GO:0035902)|serotonin biosynthetic process (GO:0042427)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|neuron projection (GO:0043005)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|tryptophan 5-monooxygenase activity (GO:0004510)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(14)|prostate(1)|stomach(1)	25					L-Tryptophan(DB00150)|Tetrahydrobiopterin(DB00360)	TTGGCATGTCCAGAAAGTGCA	0.353																																						dbGAP											0			11											92.0	86.0	88.0					11																	18044466		2200	4293	6493	18001042	SO:0001587	stop_gained	0			X52836	CCDS7829.1	11p15.3-p14	2012-10-02	2008-07-31	2003-04-04	ENSG00000129167	ENSG00000129167	1.14.16.4		12008	protein-coding gene	gene with protein product	"""tryptophan 5-monooxygenase"""	191060	"""tryptophan hydroxylase (tryptophan 5-monooxygenase)"""	TPRH, TPH		1463016	Standard	NM_004179		Approved		uc001mnp.2	P17752	OTTHUMG00000166421	ENST00000250018.2:c.1039G>T	11.37:g.18044466C>A	ENSP00000250018:p.Gly347*	Somatic	83	3.49	3		1	50.00	1	WXS	Illumina HiSeq	Phase_IV	18001042	94	38.96	60	D3DQX6|O95188|O95189|Q16736|Q3KPG8	Nonsense_Mutation	SNP	HMMPfam_ACT,PatternScan_BIOPTERIN_HYDROXYL,HMMPfam_Biopterin_H,superfamily_Aromatic aminoacid monoxygenases catalytic and oligomerization domains,superfamily_ACT-like	p.G347*	ENST00000250018.2	37	c.1039	CCDS7829.1	11	.	.	.	.	.	.	.	.	.	.	C	45	11.783009	0.99602	.	.	ENSG00000129167	ENST00000250018;ENST00000341556	.	.	.	5.78	5.78	0.91487	.	0.048717	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-10.2209	20.017	0.97481	0.0:1.0:0.0:0.0	.	.	.	.	X	347	.	ENSP00000250018:G347X	G	-	1	0	TPH1	18001042	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.818000	0.86416	2.732000	0.93576	0.555000	0.69702	GGA	-	HMMPfam_Biopterin_H,superfamily_Aromatic aminoacid monoxygenases catalytic and oligomerization domains		0.353	TPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TPH1	protein_coding	OTTHUMT00000389696.1	C	NM_004179		18001042	-1	no_errors	NM_004179.1	genbank	human	provisional	54_36p	nonsense	SNP	1.000	A
E2F8	79733	genome.wustl.edu	37	11	19252361	19252361	+	Missense_Mutation	SNP	A	A	G			TCGA-AB-2929-03A-01W-0732-08	TCGA-AB-2929-11A-01W-0732-08	A	A	A	G	A	A	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3ca5c769-b07c-4a68-818d-ab2bb8141170	0aa884ea-58b7-4079-a204-be6fe7e90a24	g.chr11:19252361A>G	ENST00000527884.1	-	8	1319	c.1087T>C	c.(1087-1089)Ttt>Ctt	p.F363L	RP11-428C19.4_ENST00000527978.1_RNA|E2F8_ENST00000250024.4_Missense_Mutation_p.F363L	NM_001256371.1|NM_001256372.1	NP_001243300.1|NP_001243301.1	A0AVK6	E2F8_HUMAN	E2F transcription factor 8	363					cell cycle comprising mitosis without cytokinesis (GO:0033301)|chorionic trophoblast cell differentiation (GO:0060718)|hepatocyte differentiation (GO:0070365)|negative regulation of cytokinesis (GO:0032466)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|placenta development (GO:0001890)|positive regulation of DNA endoreduplication (GO:0032877)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sprouting angiogenesis (GO:0002040)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						GAGGGAGTAAAATGAATGACT	0.423																																						dbGAP											0			11											54.0	53.0	53.0					11																	19252361		2199	4293	6492	19208937	SO:0001583	missense	0				CCDS7849.1	11p15	2008-02-05			ENSG00000129173	ENSG00000129173			24727	protein-coding gene	gene with protein product		612047				15722552	Standard	NM_024680		Approved	FLJ23311	uc001mpo.2	A0AVK6	OTTHUMG00000166102	ENST00000527884.1:c.1087T>C	11.37:g.19252361A>G	ENSP00000434199:p.Phe363Leu	Somatic	89	5.21	5		4	33.33	2	WXS	Illumina HiSeq	Phase_IV	19208937	101	42.31	77	A8K9H3|Q2VPJ3|Q3C1U6|Q5BKY4|Q8N340|Q9H5M0	Missense_Mutation	SNP	"HMMPfam_E2F_TDP,superfamily_""Winged helix"" DNA-binding domain"	p.F363L	ENST00000527884.1	37	c.1087	CCDS7849.1	11	.	.	.	.	.	.	.	.	.	.	A	2.618	-0.289170	0.05605	.	.	ENSG00000129173	ENST00000527884;ENST00000396159;ENST00000250024	T;T	0.15603	2.41;2.41	5.76	-0.629	0.11533	.	0.798109	0.12099	N	0.499694	T	0.04137	0.0115	N	0.02802	-0.49	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38845	-0.9642	10	0.02654	T	1	-0.1226	1.4763	0.02427	0.2851:0.2782:0.3019:0.1348	.	363	A0AVK6	E2F8_HUMAN	L	363	ENSP00000434199:F363L;ENSP00000250024:F363L	ENSP00000250024:F363L	F	-	1	0	E2F8	19208937	0.004000	0.15560	0.000000	0.03702	0.004000	0.04260	0.427000	0.21379	-0.122000	0.11766	0.533000	0.62120	TTT	-	NULL		0.423	E2F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	E2F8	protein_coding	OTTHUMT00000387830.1	A	NM_024680		19208937	-1	no_errors	NM_024680.2	genbank	human	validated	54_36p	missense	SNP	0.000	G
OR8B12	219858	genome.wustl.edu	37	11	124412936	124412936	+	Silent	SNP	G	G	A			TCGA-AB-2929-03A-01W-0732-08	TCGA-AB-2929-11A-01W-0732-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3ca5c769-b07c-4a68-818d-ab2bb8141170	0aa884ea-58b7-4079-a204-be6fe7e90a24	g.chr11:124412936G>A	ENST00000306842.2	-	1	639	c.615C>T	c.(613-615)gaC>gaT	p.D205D		NM_001005195.1	NP_001005195.1	Q8NGG6	OR8BC_HUMAN	olfactory receptor, family 8, subfamily B, member 12	205						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0213)		GCATTCCAACGTCAACAGCCA	0.448																																						dbGAP											0			11											98.0	76.0	83.0					11																	124412936		2201	4299	6500	123918146	SO:0001819	synonymous_variant	0				CCDS31711.1	11q24.2	2013-09-24			ENSG00000170953	ENSG00000170953		"""GPCR / Class A : Olfactory receptors"""	15307	protein-coding gene	gene with protein product							Standard	NM_001005195		Approved		uc010sam.2	Q8NGG6	OTTHUMG00000165922	ENST00000306842.2:c.615C>T	11.37:g.124412936G>A		Somatic	68	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	123918146	133	22.09	38	B2RNF6|Q6IEW8|Q96RC7	Silent	SNP	HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_Family A G protein-coupled receptor-like	p.D205	ENST00000306842.2	37	c.615	CCDS31711.1	11																																																																																			-	HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like		0.448	OR8B12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR8B12	protein_coding	OTTHUMT00000387061.1	G			123918146	-1	no_errors	NM_001005195.1	genbank	human	provisional	54_36p	silent	SNP	0.006	A
KRAS	3845	genome.wustl.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	rs121913529		TCGA-AB-2929-03A-01W-0732-08	TCGA-AB-2929-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3ca5c769-b07c-4a68-818d-ab2bb8141170	0aa884ea-58b7-4079-a204-be6fe7e90a24	g.chr12:25398284C>T	ENST00000256078.4	-	2	98	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000311936.3_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000556131.1_Missense_Mutation_p.G12D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|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)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|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)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"""pancreatic, colorectal, lung, thyroid, AML, others"""				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)	dbGAP		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"""L, E, M, O"""	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	12											91.0	81.0	85.0					12																	25398284		2203	4300	6503	25289551	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;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"""v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog"", ""v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"""	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>A	12.37:g.25398284C>T	ENSP00000256078:p.Gly12Asp	Somatic	22	8.00	2		0	100.00	18	WXS	Illumina HiSeq	Phase_IV	25289551	16	69.81	37	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	HMMSmart_SM00176,HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases	p.G12D	ENST00000256078.4	37	c.35	CCDS8703.1	12	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT	-	HMMSmart_SM00176,HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	KRAS	protein_coding	OTTHUMT00000412232.1	C	NM_033360		25289551	-1	no_errors	NM_033360.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
ALDH1A3	220	genome.wustl.edu	37	15	101427864	101427864	+	Missense_Mutation	SNP	C	C	T	rs199537142		TCGA-AB-2929-03A-01W-0732-08	TCGA-AB-2929-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3ca5c769-b07c-4a68-818d-ab2bb8141170	0aa884ea-58b7-4079-a204-be6fe7e90a24	g.chr15:101427864C>T	ENST00000329841.5	+	3	824	c.292C>T	c.(292-294)Cgg>Tgg	p.R98W	RP11-66B24.8_ENST00000558568.1_lincRNA|ALDH1A3_ENST00000346623.6_Missense_Mutation_p.R98W|ALDH1A3_ENST00000560555.1_3'UTR	NM_000693.2	NP_000684.2	P47895	AL1A3_HUMAN	aldehyde dehydrogenase 1 family, member A3	98					embryonic eye morphogenesis (GO:0048048)|face development (GO:0060324)|inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|nucleus accumbens development (GO:0021768)|olfactory pit development (GO:0060166)|optic cup morphogenesis involved in camera-type eye development (GO:0002072)|positive regulation of apoptotic process (GO:0043065)|retinal metabolic process (GO:0042574)|retinoic acid biosynthetic process (GO:0002138)|retinoic acid metabolic process (GO:0042573)|retinol metabolic process (GO:0042572)|righting reflex (GO:0060013)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)|NAD+ binding (GO:0070403)|protein homodimerization activity (GO:0042803)|thyroid hormone binding (GO:0070324)			NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(7)|lung(9)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	27	Lung NSC(78;0.00144)|all_lung(78;0.0018)|Melanoma(26;0.00852)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.0766)|Lung(145;0.103)		Vitamin A(DB00162)	GAGTCGTGGGCGGCTGCTGCA	0.682																																						dbGAP											0			15						C	TRP/ARG	0,4406		0,0,2203	50.0	54.0	53.0		292	1.2	0.9	15		53	1,8597	1.2+/-3.3	0,1,4298	yes	missense	ALDH1A3	NM_000693.2	101	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	benign	98/513	101427864	1,13003	2203	4299	6502	99245387	SO:0001583	missense	0			U07919	CCDS10389.1	15q26	2010-05-07			ENSG00000184254	ENSG00000184254	1.2.1.5	"""Aldehyde dehydrogenases"""	409	protein-coding gene	gene with protein product	"""retinaldehyde dehydrogenase 3"""	600463		ALDH6		7698756	Standard	XR_111558		Approved	RALDH3	uc002bwn.4	P47895	OTTHUMG00000149870	ENST00000329841.5:c.292C>T	15.37:g.101427864C>T	ENSP00000332256:p.Arg98Trp	Somatic	14	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	99245387	24	41.86	18	Q6NT64	Missense_Mutation	SNP	HMMPfam_Aldedh,PatternScan_ALDEHYDE_DEHYDR_CYS,PatternScan_ALDEHYDE_DEHYDR_GLU,superfamily_Aldehyde_DH/Histidinol_DH	p.R98W	ENST00000329841.5	37	c.292	CCDS10389.1	15	.	.	.	.	.	.	.	.	.	.	C	14.35	2.508901	0.44660	0.0	1.16E-4	ENSG00000184254	ENST00000329841;ENST00000415812;ENST00000346623	T;T	0.78246	-1.16;2.29	5.66	1.16	0.20824	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.334108	0.31312	N	0.007878	T	0.80144	0.4569	H	0.94582	3.555	0.20307	N	0.999914	B;B;B	0.25312	0.019;0.123;0.123	B;B;B	0.08055	0.001;0.003;0.002	T	0.74612	-0.3607	10	0.59425	D	0.04	.	9.6022	0.39612	0.4172:0.5103:0.0:0.0725	.	109;98;98	Q7Z3A2;B2R5T2;P47895	.;.;AL1A3_HUMAN	W	98;98;109	ENSP00000332256:R98W;ENSP00000343294:R109W	ENSP00000332256:R98W	R	+	1	2	ALDH1A3	99245387	0.000000	0.05858	0.883000	0.34634	0.826000	0.46750	-0.048000	0.11944	0.712000	0.32039	0.655000	0.94253	CGG	-	HMMPfam_Aldedh,superfamily_Aldehyde_DH/Histidinol_DH		0.682	ALDH1A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ALDH1A3	protein_coding	OTTHUMT00000313620.2	C			99245387	+1	no_errors	NM_000693.2	genbank	human	reviewed	54_36p	missense	SNP	0.960	T
CD70	970	genome.wustl.edu	37	19	6586144	6586144	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2929-03A-01W-0732-08	TCGA-AB-2929-11A-01W-0732-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3ca5c769-b07c-4a68-818d-ab2bb8141170	0aa884ea-58b7-4079-a204-be6fe7e90a24	g.chr19:6586144G>A	ENST00000245903.3	-	3	618	c.469C>T	c.(469-471)Cgc>Tgc	p.R157C	CD70_ENST00000423145.3_Intron	NM_001252.3	NP_001243.1	P32970	CD70_HUMAN	CD70 molecule	157					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|extrinsic apoptotic signaling pathway (GO:0097191)|immune response (GO:0006955)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	protease binding (GO:0002020)|receptor binding (GO:0005102)			endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|skin(1)	11						GGCGTCAGGCGCTGGGAGGCA	0.617																																					Pancreas(183;2617 2876 10173 34193)	dbGAP											0			19											94.0	78.0	83.0					19																	6586144		2203	4300	6503	6537144	SO:0001583	missense	0			L08096	CCDS12170.1	19p13	2013-05-22	2006-10-27	2006-10-27		ENSG00000125726		"""Tumor necrosis factor (ligand) superfamily"", ""CD molecules"""	11937	protein-coding gene	gene with protein product		602840	"""tumor necrosis factor (ligand) superfamily, member 7"""	CD27LG, TNFSF7		8387892, 8120384	Standard	NM_001252		Approved	CD27L	uc002mfi.3	P32970		ENST00000245903.3:c.469C>T	19.37:g.6586144G>A	ENSP00000245903:p.Arg157Cys	Somatic	83	8.70	8		11	45.00	9	WXS	Illumina HiSeq	Phase_IV	6537144	151	32.89	74	B4DPR8|Q53XX4|Q96J57	Missense_Mutation	SNP	HMMPfam_TNF,HMMSmart_SM00207,PatternScan_TNF_1,superfamily_TNF-like	p.R157C	ENST00000245903.3	37	c.469	CCDS12170.1	19	.	.	.	.	.	.	.	.	.	.	G	13.98	2.399436	0.42512	.	.	ENSG00000125726	ENST00000245903	T	0.64260	-0.09	4.42	3.29	0.37713	Tumour necrosis factor (3);Tumour necrosis factor-like (2);	0.138969	0.33712	N	0.004629	T	0.66056	0.2751	L	0.32530	0.975	0.39797	D	0.972516	D	0.89917	1.0	D	0.72075	0.976	T	0.69079	-0.5240	10	0.66056	D	0.02	.	9.7663	0.40563	0.0:0.2111:0.7889:0.0	.	157	P32970	CD70_HUMAN	C	157	ENSP00000245903:R157C	ENSP00000245903:R157C	R	-	1	0	CD70	6537144	1.000000	0.71417	1.000000	0.80357	0.111000	0.19643	2.494000	0.45329	2.184000	0.69523	0.556000	0.70494	CGC	-	HMMPfam_TNF,HMMSmart_SM00207,superfamily_TNF-like		0.617	CD70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CD70	protein_coding	OTTHUMT00000457860.1	G			6537144	-1	no_errors	NM_001252.3	genbank	human	reviewed	54_36p	missense	SNP	0.958	A
PCDHGA10	56106	genome.wustl.edu	37	5	140793765	140793767	+	In_Frame_Del	DEL	AGA	AGA	-			TCGA-AB-2929-03A-01W-0732-08	TCGA-AB-2929-11A-01W-0732-08	AGA	AGA	AGA	-	AGA	AGA	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3ca5c769-b07c-4a68-818d-ab2bb8141170	0aa884ea-58b7-4079-a204-be6fe7e90a24	g.chr5:140793765_140793767delAGA	ENST00000398610.2	+	1	1023_1025	c.1023_1025delAGA	c.(1021-1026)gtagaa>gta	p.E342del	PCDHGA7_ENST00000518325.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron	NM_018913.2|NM_032090.1	NP_061736.1|NP_114479.1	Q9Y5H3	PCDGA_HUMAN	protocadherin gamma subfamily A, 10	342	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGATTACAGTAGAAGATGTAAAT	0.394																																						dbGAP											0			5																																								140773951	SO:0001651	inframe_deletion	0				CCDS47292.1, CCDS75343.1	5q31	2010-01-26			ENSG00000253846	ENSG00000253846		"""Cadherins / Protocadherins : Clustered"""	8697	other	protocadherin		606297				10380929	Standard	NM_018913		Approved	PCDH-GAMMA-A10		Q9Y5H3	OTTHUMG00000163688	ENST00000398610.2:c.1023_1025delAGA	5.37:g.140793768_140793770delAGA	ENSP00000381611:p.Glu342del	Somatic	0	0.00	0		0	0.00	0	WXS	Illumina HiSeq	Phase_IV	140773949	0	27.91	12	Q9Y5E0	In_Frame_Del	DEL	HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,HMMPfam_Cadherin_2,superfamily_Cadherin-like	p.E342in_frame_del	ENST00000398610.2	37	c.1023_1025	CCDS47292.1	5																																																																																			-	HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,superfamily_Cadherin-like		0.394	PCDHGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PCDHGA10	protein_coding	OTTHUMT00000374747.1	AGA	NM_018913		140773951	+1	no_errors	NM_018913.2	genbank	human	reviewed	54_36p	in_frame_del	DEL	0.002:0.003:0.175	-
