#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_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	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_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	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_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	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_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	i_ccds_id	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_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_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
DHX16	8449	broad.mit.edu	37	6	30633377	30633377	+	Missense_Mutation	SNP	C	C	T	rs139415113		TCGA-S7-A7WU-01A-11D-A35I-08	TCGA-S7-A7WU-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02290cdf-4c2d-4eb4-b0ff-2b9989c6a2fb	7e54767e-763c-4d5f-a1d0-3eed338704c3	g.chr6:30633377C>T	ENST00000376442.3	-	5	995	c.800G>A	c.(799-801)cGg>cAg	p.R267Q		NM_001164239.1|NM_003587.4	NP_001157711.1|NP_003578.2	O60231	DHX16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 16	267					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			kidney(2)|ovary(2)	4						GAGCTCCTGCCGCTCGTGCCG	0.627																																						ENST00000376442.3																			0				kidney(2)|ovary(2)	4						c.(799-801)cGg>cAg		DEAH (Asp-Glu-Ala-His) box polypeptide 16		C	GLN/ARG,GLN/ARG	0,3020		0,0,1510	69.0	70.0	69.0		620,800	3.3	0.9	6	dbSNP_134	69	1,5415		0,1,2707	yes	missense,missense	DHX16	NM_001164239.1,NM_003587.4	43,43	0,1,4217	TT,TC,CC		0.0185,0.0,0.0119	benign,benign	207/982,267/1042	30633377	1,8435	1510	2708	4218	SO:0001583	missense	8449				mRNA processing|RNA splicing	nucleus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|RNA helicase activity	g.chr6:30633377C>T	AB001601	CCDS4685.1	6p21.3	2010-02-17	2003-06-13	2003-06-20	ENSG00000204560	ENSG00000204560		"""DEAH-boxes"""	2739	protein-coding gene	gene with protein product		603405	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 16"""	DDX16		9547260	Standard	NM_003587		Approved	DBP2, Prp2, PRPF2	uc003nqz.3	O60231	OTTHUMG00000031060	ENST00000376442.3:c.800G>A	6.37:g.30633377C>T	ENSP00000365625:p.Arg267Gln						p.R267Q	NM_001164239.1|NM_003587.4	NP_001157711.1|NP_003578.2	O60231	DHX16_HUMAN			5	995	-			267					O60322|Q5JP45|Q969X7|Q96QC1	Missense_Mutation	SNP	ENST00000376442.3	37	c.800G>A	CCDS4685.1	.	.	.	.	.	.	.	.	.	.	c	14.92	2.678259	0.47886	0.0	1.85E-4	ENSG00000204560	ENST00000376442;ENST00000415603	T;T	0.46063	0.88;0.88	5.12	3.31	0.37934	.	0.427120	0.24039	N	0.042112	T	0.09158	0.0226	N	0.16656	0.425	0.58432	D	0.999995	B;B	0.23650	0.089;0.024	B;B	0.14578	0.011;0.006	T	0.09271	-1.0682	10	0.33141	T	0.24	.	3.6175	0.08083	0.1795:0.566:0.0:0.2545	.	207;267	B4DZ28;O60231	.;DHX16_HUMAN	Q	267;207	ENSP00000365625:R267Q;ENSP00000399101:R207Q	ENSP00000365625:R267Q	R	-	2	0	DHX16	30741356	0.000000	0.05858	0.942000	0.38095	0.883000	0.51084	-0.421000	0.07053	0.699000	0.31761	0.586000	0.80456	CGG		0.627	DHX16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076076.2	NM_003587		3	43	0	0	0	1	0	3	43				
MAP3K4	4216	broad.mit.edu	37	6	161519378	161519378	+	Missense_Mutation	SNP	C	C	T			TCGA-S7-A7WU-01A-11D-A35I-08	TCGA-S7-A7WU-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02290cdf-4c2d-4eb4-b0ff-2b9989c6a2fb	7e54767e-763c-4d5f-a1d0-3eed338704c3	g.chr6:161519378C>T	ENST00000392142.4	+	17	3741	c.3593C>T	c.(3592-3594)gCt>gTt	p.A1198V	MAP3K4_ENST00000366919.2_Intron|MAP3K4_ENST00000366920.2_Missense_Mutation_p.A1194V|MAP3K4_ENST00000348824.7_Intron	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	1198	Poly-Ala.				activation of MAPKK activity (GO:0000186)|chorionic trophoblast cell differentiation (GO:0060718)|intracellular signal transduction (GO:0035556)|male germ-line sex determination (GO:0019100)|MAPK cascade (GO:0000165)|placenta development (GO:0001890)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of p38MAPK cascade (GO:1900745)|regulation of gene expression (GO:0010468)|response to UV-C (GO:0010225)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)			breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|lung(28)|ovary(3)|skin(2)|stomach(1)	77		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		gctgctgctgctgctgttgct	0.597																																						ENST00000392142.4																			0				breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|lung(28)|ovary(3)|skin(2)|stomach(1)	77						c.(3592-3594)gCt>gTt		mitogen-activated protein kinase kinase kinase 4							93.0	92.0	92.0					6																	161519378		2203	4299	6502	SO:0001583	missense	4216				activation of MAPKK activity|JNK cascade|positive regulation of JUN kinase activity	perinuclear region of cytoplasm	ATP binding|MAP kinase kinase kinase activity|metal ion binding|protein binding	g.chr6:161519378C>T	AF002715	CCDS34565.1, CCDS34566.1, CCDS75544.1	6q26	2012-10-02			ENSG00000085511	ENSG00000085511		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6856	protein-coding gene	gene with protein product		602425		MEKK4		9305639	Standard	XM_005266988		Approved	MTK1, MAPKKK4, KIAA0213	uc003qtn.3	Q9Y6R4	OTTHUMG00000015968	ENST00000392142.4:c.3593C>T	6.37:g.161519378C>T	ENSP00000375986:p.Ala1198Val					MAP3K4_ENST00000366919.2_Intron|MAP3K4_ENST00000366920.2_Missense_Mutation_p.A1194V|MAP3K4_ENST00000348824.7_Intron	p.A1198V	NM_005922.2	NP_005913.2	Q9Y6R4	M3K4_HUMAN		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)	17	3741	+		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)	1198			Poly-Ala.		A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Missense_Mutation	SNP	ENST00000392142.4	37	c.3593C>T	CCDS34565.1	.	.	.	.	.	.	.	.	.	.	C	0.027	-1.360800	0.01245	.	.	ENSG00000085511	ENST00000392142;ENST00000366920	T;T	0.71103	-0.54;-0.53	2.29	2.29	0.28610	.	0.754387	0.11657	N	0.542271	T	0.51227	0.1662	N	0.19112	0.55	0.26345	N	0.977309	B;D	0.57571	0.073;0.98	B;D	0.65443	0.037;0.935	T	0.39354	-0.9618	10	0.10377	T	0.69	-7.006	8.5531	0.33465	0.0:1.0:0.0:0.0	.	1194;1198	F5H538;Q9Y6R4	.;M3K4_HUMAN	V	1198;1194	ENSP00000375986:A1198V;ENSP00000355887:A1194V	ENSP00000355887:A1194V	A	+	2	0	MAP3K4	161439368	0.010000	0.17322	0.105000	0.21289	0.511000	0.34104	0.116000	0.15561	1.726000	0.51525	0.366000	0.22137	GCT		0.597	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3			6	129	0	0	0	1	0	6	129				
USH2A	7399	broad.mit.edu	37	1	215823955	215823955	+	Silent	SNP	G	G	A	rs147037435	byFrequency	TCGA-S7-A7WU-01A-11D-A35I-08	TCGA-S7-A7WU-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02290cdf-4c2d-4eb4-b0ff-2b9989c6a2fb	7e54767e-763c-4d5f-a1d0-3eed338704c3	g.chr1:215823955G>A	ENST00000307340.3	-	65	14708	c.14322C>T	c.(14320-14322)agC>agT	p.S4774S	USH2A_ENST00000366943.2_Silent_p.S4774S	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	4774	Fibronectin type-III 33. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		CCCCATGGGCGCTGCTGGAGA	0.483										HNSCC(13;0.011)			G|||	3	0.000599042	0.0023	0.0	5008	,	,		15781	0.0		0.0	False		,,,				2504	0.0					ENST00000366943.2																			0				NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527						c.(14320-14322)agC>agT		Usher syndrome 2A (autosomal recessive, mild)		G		9,4397	15.5+/-35.6	0,9,2194	74.0	74.0	74.0		14322	0.2	0.0	1	dbSNP_134	74	0,8600		0,0,4300	no	coding-synonymous	USH2A	NM_206933.2		0,9,6494	AA,AG,GG		0.0,0.2043,0.0692		4774/5203	215823955	9,12997	2203	4300	6503	SO:0001819	synonymous_variant	7399				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding	g.chr1:215823955G>A	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.14322C>T	1.37:g.215823955G>A		HNSCC(13;0.011)				USH2A_ENST00000307340.3_Silent_p.S4774S	p.S4774S			O75445	USH2A_HUMAN		OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)	65	14708	-			4774			Fibronectin type-III 33.		Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	37	c.14322C>T	CCDS31025.1																																																																																				0.483	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		16	23	0	0	0	1	0	16	23				
SPATA16	83893	broad.mit.edu	37	3	172642091	172642091	+	Silent	SNP	G	G	A	rs536087951	byFrequency	TCGA-S7-A7WU-01A-11D-A35I-08	TCGA-S7-A7WU-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02290cdf-4c2d-4eb4-b0ff-2b9989c6a2fb	7e54767e-763c-4d5f-a1d0-3eed338704c3	g.chr3:172642091G>A	ENST00000351008.3	-	8	1428	c.1245C>T	c.(1243-1245)ttC>ttT	p.F415F		NM_031955.5	NP_114161.3	Q9BXB7	SPT16_HUMAN	spermatogenesis associated 16	415					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)				breast(2)|cervix(1)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	43	Ovarian(172;0.00319)|Breast(254;0.197)		LUSC - Lung squamous cell carcinoma(14;1.48e-14)|Lung(28;6.63e-14)			TGGTCAGACCGAAAGGTGTTT	0.338													G|||	4	0.000798722	0.0	0.0	5008	,	,		17650	0.004		0.0	False		,,,				2504	0.0					ENST00000351008.3																			0				breast(2)|cervix(1)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	43						c.(1243-1245)ttC>ttT		spermatogenesis associated 16							102.0	98.0	99.0					3																	172642091		2203	4300	6503	SO:0001819	synonymous_variant	83893				cell differentiation|multicellular organismal development|spermatogenesis	Golgi apparatus	binding	g.chr3:172642091G>A	AF345909	CCDS3221.1	3q26.31	2009-01-05			ENSG00000144962	ENSG00000144962			29935	protein-coding gene	gene with protein product		609856				12529416, 17847006	Standard	NM_031955		Approved	NYD-SP12	uc003fin.4	Q9BXB7	OTTHUMG00000156865	ENST00000351008.3:c.1245C>T	3.37:g.172642091G>A							p.F415F	NM_031955.5	NP_114161.3	Q9BXB7	SPT16_HUMAN	LUSC - Lung squamous cell carcinoma(14;1.48e-14)|Lung(28;6.63e-14)		8	1428	-	Ovarian(172;0.00319)|Breast(254;0.197)		415					Q0R0N4|Q0R0S0|Q0R0W2|Q0R129|Q0R131|Q0R140|Q0R1B8|Q0R1G5|Q0R1I2|Q0R1J6|Q0R1S4|Q0R202|Q0R280|Q0R2F8|Q0R2N6|Q0R2N7|Q0R2R0|Q0R2R1|Q0R2S3|Q0R2S4|Q0R2S5|Q0R2T4|Q0R2T7|Q0R2U2|Q0R2U8|Q0R2U9|Q0R2V5|Q0R2V7|Q8NE67	Silent	SNP	ENST00000351008.3	37	c.1245C>T	CCDS3221.1																																																																																				0.338	SPATA16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346322.1	NM_031955		7	55	0	0	0	1	0	7	55				
KIF3C	3797	broad.mit.edu	37	2	26203255	26203255	+	Missense_Mutation	SNP	G	G	A	rs377274965		TCGA-S7-A7WU-01A-11D-A35I-08	TCGA-S7-A7WU-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02290cdf-4c2d-4eb4-b0ff-2b9989c6a2fb	7e54767e-763c-4d5f-a1d0-3eed338704c3	g.chr2:26203255G>A	ENST00000264712.3	-	1	2111	c.1532C>T	c.(1531-1533)gCg>gTg	p.A511V	KIF3C_ENST00000405914.1_Missense_Mutation_p.A511V	NM_002254.6	NP_002245	O14782	KIF3C_HUMAN	kinesin family member 3C	511					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|organelle transport along microtubule (GO:0072384)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(8)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GTACTTGGCCGCAAGCAGCTC	0.627													G|||	1	0.000199681	0.0	0.0	5008	,	,		14501	0.0		0.0	False		,,,				2504	0.001					ENST00000264712.3																			0				breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(8)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						c.(1531-1533)gCg>gTg		kinesin family member 3C		G	VAL/ALA	0,4406		0,0,2203	47.0	46.0	46.0		1532	5.6	0.7	2		46	1,8599	1.2+/-3.3	0,1,4299	no	missense	KIF3C	NM_002254.6	64	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	511/794	26203255	1,13005	2203	4300	6503	SO:0001583	missense	3797				blood coagulation|microtubule-based movement	cytosol|kinesin complex|microtubule	ATP binding|microtubule motor activity	g.chr2:26203255G>A		CCDS1719.1	2p23	2008-02-05			ENSG00000084731	ENSG00000084731		"""Kinesins"""	6321	protein-coding gene	gene with protein product		602845				9480755	Standard	NM_002254		Approved		uc002rgu.2	O14782	OTTHUMG00000094797	ENST00000264712.3:c.1532C>T	2.37:g.26203255G>A	ENSP00000264712:p.Ala511Val					KIF3C_ENST00000405914.1_Missense_Mutation_p.A511V	p.A511V	NM_002254.6	NP_002245.4	O14782	KIF3C_HUMAN			1	2111	-	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)		511					O43544|Q4ZG18|Q53SX5|Q562F7	Missense_Mutation	SNP	ENST00000264712.3	37	c.1532C>T	CCDS1719.1	.	.	.	.	.	.	.	.	.	.	G	11.38	1.621697	0.28889	0.0	1.16E-4	ENSG00000084731	ENST00000264712;ENST00000542511;ENST00000405914	T;T	0.73575	-0.76;-0.76	5.62	5.62	0.85841	.	0.211050	0.49916	D	0.000138	T	0.63058	0.2479	L	0.31371	0.925	0.49915	D	0.99983	B;D	0.56035	0.449;0.974	B;B	0.38225	0.061;0.268	T	0.64626	-0.6363	10	0.31617	T	0.26	.	18.223	0.89907	0.0:0.0:1.0:0.0	.	511;511	B7ZM25;O14782	.;KIF3C_HUMAN	V	511;317;511	ENSP00000264712:A511V;ENSP00000385030:A511V	ENSP00000264712:A511V	A	-	2	0	KIF3C	26056759	0.972000	0.33761	0.677000	0.29947	0.998000	0.95712	2.566000	0.45948	2.653000	0.90120	0.655000	0.94253	GCG		0.627	KIF3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211611.1			3	21	0	0	0	1	0	3	21				
TRBV5-4	28611	broad.mit.edu	37	7	142168862	142168862	+	RNA	SNP	A	A	G			TCGA-S7-A7WU-01A-11D-A35I-08	TCGA-S7-A7WU-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02290cdf-4c2d-4eb4-b0ff-2b9989c6a2fb	7e54767e-763c-4d5f-a1d0-3eed338704c3	g.chr7:142168862A>G	ENST00000454561.2	-	0	183									T cell receptor beta variable 5-4																		TGGGCCAGGCAGCACTGCACC	0.597																																						ENST00000454561.2																			0																				28.0	28.0	28.0					7																	142168862		1933	4131	6064			28611							g.chr7:142168862A>G	L36092		7q34	2012-02-07			ENSG00000230099	ENSG00000230099		"""T cell receptors / TRB locus"""	12221	other	T cell receptor gene						8650574	Standard	NG_001333		Approved	TRBV54, TCRBV5S4, TCRBV5S6A3N2T			OTTHUMG00000158524		7.37:g.142168862A>G														0	183	-									RNA	SNP	ENST00000454561.2	37																																																																																						0.597	TRBV5-4-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	TR_V_gene	TR_V_gene	OTTHUMT00000351230.2	NG_001333		3	28	0	0	0	1	0	3	28				
LOC101927209	101927209	broad.mit.edu	37	1	142713773	142713774	+	lincRNA	DNP	CA	CA	GG	rs201023195|rs199933143		TCGA-S7-A7WU-01A-11D-A35I-08	TCGA-S7-A7WU-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02290cdf-4c2d-4eb4-b0ff-2b9989c6a2fb	7e54767e-763c-4d5f-a1d0-3eed338704c3	g.chr1:142713773_142713774CA>GG	ENST00000610091.1	-	0	1884_1885																											TCTTTTTCCACATTGTCATTTT	0.282																																						ENST00000369381.2																			0																																																			101927209							g.chr1:142713773C>G|g.chr1:142713774A>G																												Exception_encountered	1.37:g.142713773_142713774delinsGG														0	832|831	-									RNA	SNP	ENST00000610091.1	37																																																																																						0.282	RP11-417J8.6-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000037265.2			4	77	0	0	0	1	0	4	77				
UNC13C	440279	broad.mit.edu	37	15	54556464	54556464	+	Frame_Shift_Del	DEL	C	C	-			TCGA-S7-A7WU-01A-11D-A35I-08	TCGA-S7-A7WU-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02290cdf-4c2d-4eb4-b0ff-2b9989c6a2fb	7e54767e-763c-4d5f-a1d0-3eed338704c3	g.chr15:54556464delC	ENST00000260323.11	+	8	3547	c.3547delC	c.(3547-3549)ccafs	p.P1183fs	UNC13C_ENST00000537900.1_Frame_Shift_Del_p.P1181fs|UNC13C_ENST00000545554.1_Frame_Shift_Del_p.P1183fs	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	1183					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		GAAAAACCGGCCAGAAGTATT	0.408																																						ENST00000545554.1																			0				breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121						c.(3547-3549)cafs		unc-13 homolog C (C. elegans)							53.0	50.0	51.0					15																	54556464		1819	4068	5887	SO:0001589	frameshift_variant	440279				exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding	g.chr15:54556464delC	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.3547delC	15.37:g.54556464delC	ENSP00000260323:p.Pro1183fs					UNC13C_ENST00000537900.1_Frame_Shift_Del_p.P1181fs|UNC13C_ENST00000260323.11_Frame_Shift_Del_p.P1183fs	p.P1183fs			Q8NB66	UN13C_HUMAN		GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)	8	3547	+			1183					Q0P613|Q8ND48|Q96NP3	Frame_Shift_Del	DEL	ENST00000260323.11	37	c.3547delC	CCDS45264.1																																																																																				0.408	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		2	4						2	4	---	---	---	---
CTB-134H23.3	0	broad.mit.edu	37	16	29113498	29113498	+	RNA	DEL	T	T	-	rs11366120	byFrequency	TCGA-S7-A7WU-01A-11D-A35I-08	TCGA-S7-A7WU-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02290cdf-4c2d-4eb4-b0ff-2b9989c6a2fb	7e54767e-763c-4d5f-a1d0-3eed338704c3	g.chr16:29113498delT	ENST00000562618.1	-	0	1840				RRN3P2_ENST00000564580.1_RNA																							AGGAGGTGGAttttttttttc	0.542													|||unknown(NO_COVERAGE)	2145	0.428315	0.5507	0.4856	5008	,	,		13214	0.248		0.4334	False		,,,				2504	0.4029					ENST00000564580.1																			0																																																			653390							g.chr16:29113498delT																													16.37:g.29113498delT														0	1360	+									RNA	DEL	ENST00000562618.1	37																																																																																						0.542	CTB-134H23.3-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000433241.1			3	5						3	5	---	---	---	---
KIZ-AS1	101929591	broad.mit.edu	37	20	21142441	21142442	+	RNA	INS	-	-	A	rs377451007|rs113752643|rs570165711	byFrequency	TCGA-S7-A7WU-01A-11D-A35I-08	TCGA-S7-A7WU-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02290cdf-4c2d-4eb4-b0ff-2b9989c6a2fb	7e54767e-763c-4d5f-a1d0-3eed338704c3	g.chr20:21142441_21142442insA	ENST00000591761.1	-	0	5142				RP5-872K7.7_ENST00000425746.2_RNA|PLK1S1_ENST00000457464.1_RNA																							TTCATTTCTGGAAAAAAAAAAA	0.366																																						ENST00000591761.1																			0																																																			101929591							g.chr20:21142441_21142442insA																													20.37:g.21142452_21142452dupA						PLK1S1_ENST00000457464.1_RNA|RP5-872K7.7_ENST00000425746.2_RNA								0	5142	-									RNA	INS	ENST00000591761.1	37																																																																																						0.366	RP4-777D9.2-002	KNOWN	basic	antisense	antisense	OTTHUMT00000078258.2			3	3						3	3	---	---	---	---
