#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_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_ORegAnno_bin	i_Start_position_hg18	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
C11orf42	160298	genome.wustl.edu	37	11	6232211	6232211	+	Missense_Mutation	SNP	G	G	A			TCGA-09-1664-01A-01W-0639-09	TCGA-09-1664-11A-01W-0639-09	G	G					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	8364585f-d532-4c26-9e0e-22cbfaeaf683	396c481e-d6ec-456f-a9dc-5740e9bfb22c	g.chr11:6232211G>A	ENST00000316375.2	+	3	991	c.941G>A	c.(940-942)gGg>gAg	p.G314E	FAM160A2_ENST00000529360.1_5'Flank	NM_173525.2	NP_775796.2	Q8N5U0	CK042_HUMAN	chromosome 11 open reading frame 42	314										endometrium(3)|kidney(3)|large_intestine(1)|lung(4)|ovary(2)|skin(1)|soft_tissue(1)	15		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.95e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GACCCCGACGGGCACTCCATG	0.632																																																0			11											23.0	27.0	25.0					11																	6232211		2198	4293	6491	6188787	SO:0001583	missense	160298			BC031612	CCDS7759.1	11p15.4	2012-08-09			ENSG00000180878	ENSG00000180878			28541	protein-coding gene	gene with protein product						12477932	Standard	NM_173525		Approved	MGC34805	uc001mcj.3	Q8N5U0	OTTHUMG00000133377	ENST00000316375.2:c.941G>A	11.37:g.6232211G>A	ENSP00000321021:p.Gly314Glu		6188787		Missense_Mutation	SNP	NULL	p.G314E	ENST00000316375.2	37	c.941	CCDS7759.1	11	.	.	.	.	.	.	.	.	.	.	G	8.819	0.937061	0.18206	.	.	ENSG00000180878	ENST00000316375	T	0.41758	0.99	4.84	4.84	0.62591	.	0.140513	0.33161	N	0.005205	T	0.23532	0.0569	N	0.08118	0	0.29694	N	0.840693	B	0.22414	0.069	B	0.19391	0.025	T	0.09707	-1.0662	10	0.26408	T	0.33	-8.087	13.2978	0.60307	0.0:0.0:1.0:0.0	.	314	Q8N5U0	CK042_HUMAN	E	314	ENSP00000321021:G314E	ENSP00000321021:G314E	G	+	2	0	C11orf42	6188787	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.633000	0.61318	2.497000	0.84241	0.484000	0.47621	GGG	-	NULL		0.632	C11orf42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	C11orf42	protein_coding	OTTHUMT00000257227.2	G	NM_173525		6188787	+1	no_errors	NM_173525	genbank	human	predicted	54_36p	missense	SNP	1.000	A
TAS2R1	50834	genome.wustl.edu	37	5	9629690	9629690	+	Missense_Mutation	SNP	A	A	G			TCGA-09-1664-01A-01W-0639-09	TCGA-09-1664-11A-01W-0639-09	A	A					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	8364585f-d532-4c26-9e0e-22cbfaeaf683	396c481e-d6ec-456f-a9dc-5740e9bfb22c	g.chr5:9629690A>G	ENST00000382492.2	-	1	773	c.455T>C	c.(454-456)gTc>gCc	p.V152A	CTD-2001E22.1_ENST00000504182.2_RNA	NM_019599.2	NP_062545.1	Q9NYW7	TA2R1_HUMAN	taste receptor, type 2, member 1	152					chemosensory behavior (GO:0007635)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(19)|ovary(3)|prostate(1)|skin(1)|stomach(1)	39						GAAGTATGGGACCATAAACCC	0.393																																																0			5											71.0	78.0	76.0					5																	9629690		2203	4300	6503	9682690	SO:0001583	missense	50834			AF227129	CCDS3876.1	5p15	2012-08-22			ENSG00000169777	ENSG00000169777		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14909	protein-coding gene	gene with protein product		604796				10761934, 10766242	Standard	NM_019599		Approved	T2R1, TRB7	uc003jem.1	Q9NYW7	OTTHUMG00000090500	ENST00000382492.2:c.455T>C	5.37:g.9629690A>G	ENSP00000371932:p.Val152Ala		9682690	Q646G8	Missense_Mutation	SNP	HMMPfam_TAS2R,superfamily_SSF81321	p.V152A	ENST00000382492.2	37	c.455	CCDS3876.1	5	.	.	.	.	.	.	.	.	.	.	A	6.248	0.413889	0.11870	.	.	ENSG00000169777	ENST00000382492	T	0.00776	5.71	5.43	-7.01	0.01594	.	3.276450	0.01706	U	0.027478	T	0.00695	0.0023	L	0.39020	1.185	0.09310	N	1	B	0.22909	0.077	B	0.17098	0.017	T	0.46345	-0.9198	9	.	.	.	.	2.0224	0.03512	0.3906:0.0929:0.3285:0.188	.	152	Q9NYW7	TA2R1_HUMAN	A	152	ENSP00000371932:V152A	.	V	-	2	0	TAS2R1	9682690	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.314000	0.08092	-1.748000	0.01332	-0.242000	0.12053	GTC	-	HMMPfam_TAS2R,superfamily_SSF81321		0.393	TAS2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TAS2R1	protein_coding	OTTHUMT00000206988.2	A			9682690	-1	no_errors	NM_019599	genbank	human	reviewed	54_36p	missense	SNP	0.000	G
NBEAP3	100418905	genome.wustl.edu	37	22	16123724	16123724	+	IGR	SNP	C	C	T			TCGA-09-1664-01A-01W-0639-09	TCGA-09-1664-11A-01W-0639-09	C	C					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	8364585f-d532-4c26-9e0e-22cbfaeaf683	396c481e-d6ec-456f-a9dc-5740e9bfb22c	g.chr22:16123724C>T								LA16c-4G1.3 (60488 upstream) : AP000525.9 (24254 downstream)																							CCTGAATCACCGCAAGAACAA	0.627																																																0			22																																								14503724	SO:0001628	intergenic_variant	729057																															22.37:g.16123724C>T			14503724		RNA	SNP	-	NULL		37	NULL		22																																																																																			-	-	0	0.627					LOC729057			C			14503724	+1	no_errors	XR_042044	genbank	human	model	54_36p	rna	SNP	1.000	T
KRAS	3845	genome.wustl.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	A	rs121913529		TCGA-09-1664-01A-01W-0639-09	TCGA-09-1664-11A-01W-0639-09	C	C					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	8364585f-d532-4c26-9e0e-22cbfaeaf683	396c481e-d6ec-456f-a9dc-5740e9bfb22c	g.chr12:25398284C>A	ENST00000256078.4	-	2	98	c.35G>T	c.(34-36)gGt>gTt	p.G12V	KRAS_ENST00000556131.1_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V|KRAS_ENST00000311936.3_Missense_Mutation_p.G12V	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)		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	3845	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>T	12.37:g.25398284C>A	ENSP00000256078:p.Gly12Val		25289551	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	HMMSmart_SM00173,superfamily_P-loop containing nucleoside triphosphate hydrolases,HMMSmart_SM00175,HMMPfam_Ras,HMMSmart_SM00174,HMMSmart_SM00176	p.G12V	ENST00000256078.4	37	c.35	CCDS8703.1	12	.	.	.	.	.	.	.	.	.	.	C	27.2	4.808637	0.90707	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90373	0.6987	M	0.90650	3.135	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.72625	0.969;0.978	D	0.91773	0.5429	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	V	12	ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V	ENSP00000256078:G12V	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_SM00173,superfamily_P-loop containing nucleoside triphosphate hydrolases,HMMSmart_SM00175,HMMPfam_Ras,HMMSmart_SM00174,HMMSmart_SM00176		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	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
TMEM222	84065	genome.wustl.edu	37	1	27661930	27661930	+	Silent	SNP	C	C	T	rs200116563	byFrequency	TCGA-09-1664-01A-01W-0639-09	TCGA-09-1664-11A-01W-0639-09	C	C					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	8364585f-d532-4c26-9e0e-22cbfaeaf683	396c481e-d6ec-456f-a9dc-5740e9bfb22c	g.chr1:27661930C>T	ENST00000374076.4	+	6	638	c.600C>T	c.(598-600)acC>acT	p.T200T	TMEM222_ENST00000608611.1_Silent_p.T167T	NM_032125.2	NP_115501.2	Q9H0R3	TM222_HUMAN	transmembrane protein 222	200						integral component of membrane (GO:0016021)				biliary_tract(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)	7						TCATCCTCACCGTCAGCCTGG	0.597													C|||	2	0.000399361	0.0008	0.0	5008	,	,		18565	0.001		0.0	False		,,,				2504	0.0															0			1											180.0	131.0	148.0					1																	27661930		2203	4300	6503	27534517	SO:0001819	synonymous_variant	84065			AL136683	CCDS297.2	1p36.11	2008-07-07	2008-07-07	2008-07-07	ENSG00000186501	ENSG00000186501			25363	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 160"""	C1orf160		11230166	Standard	NM_032125		Approved	DKFZP564D0478	uc001bnr.4	Q9H0R3	OTTHUMG00000004410	ENST00000374076.4:c.600C>T	1.37:g.27661930C>T			27534517	D3DPL6|Q53HD8|Q5FVE9	Silent	SNP	HMMPfam_DUF778	p.T200	ENST00000374076.4	37	c.600	CCDS297.2	1																																																																																			-	NULL		0.597	TMEM222-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	TMEM222	protein_coding	OTTHUMT00000012809.2	C	NM_032125		27534517	+1	no_errors	NM_032125	genbank	human	validated	54_36p	silent	SNP	0.267	T
NCR3	259197	genome.wustl.edu	37	6	31557656	31557656	+	Missense_Mutation	SNP	G	G	C			TCGA-09-1664-01A-01W-0639-09	TCGA-09-1664-11A-01W-0639-09	G	G					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	8364585f-d532-4c26-9e0e-22cbfaeaf683	396c481e-d6ec-456f-a9dc-5740e9bfb22c	g.chr6:31557656G>C	ENST00000340027.5	-	2	554	c.291C>G	c.(289-291)gaC>gaG	p.D97E	NCR3_ENST00000376071.4_Missense_Mutation_p.D72E|NCR3_ENST00000491161.1_5'UTR|NCR3_ENST00000376073.4_Missense_Mutation_p.D97E|NCR3_ENST00000376072.3_Missense_Mutation_p.D97E	NM_147130.2	NP_667341.1	O14931	NCTR3_HUMAN	natural cytotoxicity triggering receptor 3	97	Ig-like.				cell recognition (GO:0008037)|immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)	integral component of plasma membrane (GO:0005887)				cervix(1)|large_intestine(2)|liver(1)|lung(2)|ovary(1)|skin(2)	9						GGCCTCGCACGTCCCGGATGT	0.627																																																0			6											138.0	130.0	133.0					6																	31557656		1511	2709	4220	31665635	SO:0001583	missense	259197			AB055881	CCDS34397.1, CCDS47401.1, CCDS47402.1	6p21.3	2013-01-11	2002-11-13	2002-11-15	ENSG00000204475	ENSG00000204475		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	19077	protein-coding gene	gene with protein product		611550	"""lymphocyte antigen 117"""	LY117		8824804, 11782277	Standard	NM_001145466		Approved	1C7, NKp30, CD337	uc003nuv.2	O14931	OTTHUMG00000031123	ENST00000340027.5:c.291C>G	6.37:g.31557656G>C	ENSP00000342156:p.Asp97Glu		31665635	B0S8F2|B0S8F4|B0S8F5|O14930|O14932|O95667|O95668|O95669|Q5ST89|Q5ST90|Q5ST91|Q5ST92|Q5STA3	Missense_Mutation	SNP	superfamily_Immunoglobulin,HMMPfam_V-set,HMMSmart_SM00409	p.D97E	ENST00000340027.5	37	c.291	CCDS34397.1	6	.	.	.	.	.	.	.	.	.	.	G	3.499	-0.102190	0.06967	.	.	ENSG00000204475	ENST00000340027;ENST00000376073;ENST00000376072;ENST00000376071	T;T;T;T	0.28255	1.62;1.62;1.62;4.18	4.01	1.18	0.20946	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.683649	0.13384	N	0.391928	T	0.13713	0.0332	M	0.70595	2.14	0.09310	N	1	B;B;B	0.27229	0.03;0.172;0.1	B;B;B	0.29524	0.031;0.103;0.089	T	0.26121	-1.0112	10	0.42905	T	0.14	-4.8696	6.1659	0.20390	0.338:0.0:0.662:0.0	.	97;97;97	O14931-2;Q05D23;O14931	.;.;NCTR3_HUMAN	E	97;97;97;72	ENSP00000342156:D97E;ENSP00000365241:D97E;ENSP00000365240:D97E;ENSP00000365239:D72E	ENSP00000342156:D97E	D	-	3	2	NCR3	31665635	0.000000	0.05858	0.000000	0.03702	0.157000	0.22087	0.430000	0.21428	0.106000	0.17784	0.585000	0.79938	GAC	-	superfamily_Immunoglobulin,HMMPfam_V-set,HMMSmart_SM00409		0.627	NCR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NCR3	protein_coding	OTTHUMT00000076210.2	G			31665635	-1	no_errors	NM_147130	genbank	human	validated	54_36p	missense	SNP	0.037	C
DMD	1756	genome.wustl.edu	37	X	31893420	31893420	+	Missense_Mutation	SNP	T	T	A			TCGA-09-1664-01A-01W-0639-09	TCGA-09-1664-11A-01W-0639-09	T	T					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	8364585f-d532-4c26-9e0e-22cbfaeaf683	396c481e-d6ec-456f-a9dc-5740e9bfb22c	g.chrX:31893420T>A	ENST00000357033.4	-	48	7189	c.6983A>T	c.(6982-6984)aAa>aTa	p.K2328I	DMD_ENST00000474231.1_5'UTR|DMD_ENST00000541735.1_5'UTR|DMD_ENST00000359836.1_5'UTR|DMD_ENST00000378707.3_5'UTR|DMD_ENST00000378677.2_Missense_Mutation_p.K2324I|DMD_ENST00000343523.2_5'UTR	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	2328			Missing (in DMD).		cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				TTCAAGCTTTTTTTCAAGCTG	0.363																																																0			X											73.0	59.0	63.0					X																	31893420		2201	4300	6501	31803341	SO:0001583	missense	1756			AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"""muscular dystrophy, Duchenne and Becker types"""	300377	"""dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272"", ""mental retardation, X-linked 85"""	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.6983A>T	X.37:g.31893420T>A	ENSP00000354923:p.Lys2328Ile		31803341	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	superfamily_Calponin-homology domain CH-domain,HMMPfam_CH,PatternScan_ACTININ_1,HMMSmart_SM00033,PatternScan_ACTININ_2,HMMPfam_Spectrin,superfamily_Spectrin repeat,HMMSmart_SM00150,superfamily_t-snare proteins,superfamily_WW domain,HMMSmart_SM00456,HMMPfam_WW,PatternScan_WW_DOMAIN_1,superfamily_EF-hand,HMMPfam_efhand_1,HMMPfam_efhand_2,HMMPfam_ZZ,HMMSmart_SM00291,PatternScan_ZF_ZZ_1,superfamily_Prefoldin	p.K2328I	ENST00000357033.4	37	c.6983	CCDS14233.1	X	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	7.277|7.277	0.608276|0.608276	0.14002|0.14002	.|.	.|.	ENSG00000198947|ENSG00000198947	ENST00000534884;ENST00000378682;ENST00000378684;ENST00000358062;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280|ENST00000465285	T;T;T|.	0.36157|.	3.93;1.27;1.27|.	0.694|0.694	0.694|0.694	0.18062|0.18062	.|.	.|.	.|.	.|.	.|.	T|T	0.31888|0.31888	0.0811|0.0811	N|N	0.08118|0.08118	0|0	0.58432|0.58432	D|D	0.999999|0.999999	B;B;P;P;B|.	0.51240|.	0.018;0.0;0.943;0.943;0.011|.	B;B;P;P;B|.	0.52598|.	0.006;0.0;0.703;0.703;0.0|.	T|T	0.04551|0.04551	-1.0943|-1.0943	8|4	0.37606|.	T|.	0.19|.	.|.	.|.	.|.	.|.	.|.	2320;2328;2324;987;984|.	P11532-4;P11532;E9PDN5;E7EQS7;E7EQS6|.	.;DMD_HUMAN;.;.;.|.	I|N	2320;987;984;24;2324;2328;2328;2205|56	ENSP00000350765:K24I;ENSP00000367948:K2324I;ENSP00000354923:K2328I|.	ENSP00000354923:K2328I|.	K|K	-|-	2|3	0|2	DMD|DMD	31803341|31803341	0.995000|0.995000	0.38212|0.38212	0.867000|0.867000	0.34043|0.34043	0.789000|0.789000	0.44602|0.44602	0.449000|0.449000	0.21744|0.21744	0.496000|0.496000	0.27904|0.27904	0.486000|0.486000	0.48141|0.48141	AAA|AAA	-	superfamily_Spectrin repeat		0.363	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DMD	protein_coding	OTTHUMT00000056182.2	T	NM_004006		31803341	-1	no_errors	NM_004006	genbank	human	reviewed	54_36p	missense	SNP	0.956	A
DLGAP3	58512	genome.wustl.edu	37	1	35370751	35370751	+	Silent	SNP	C	C	T			TCGA-09-1664-01A-01W-0639-09	TCGA-09-1664-11A-01W-0639-09	C	C					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	8364585f-d532-4c26-9e0e-22cbfaeaf683	396c481e-d6ec-456f-a9dc-5740e9bfb22c	g.chr1:35370751C>T	ENST00000373347.1	-	3	502	c.234G>A	c.(232-234)gcG>gcA	p.A78A	DLGAP3_ENST00000235180.4_Silent_p.A78A|DLGAP3_ENST00000495979.1_5'Flank			O95886	DLGP3_HUMAN	discs, large (Drosophila) homolog-associated protein 3	78					cell-cell signaling (GO:0007267)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)	beta-amyloid binding (GO:0001540)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(23)|ovary(4)|prostate(3)|skin(3)|urinary_tract(1)	46		Myeloproliferative disorder(586;0.0393)				CCCCGGCCCCCGCTGGCCCTC	0.692																																																0			1											5.0	6.0	5.0					1																	35370751		2121	4150	6271	35143338	SO:0001819	synonymous_variant	58512			AF131778	CCDS30670.1	1p35.3-p34.1	2008-02-05			ENSG00000116544	ENSG00000116544			30368	protein-coding gene	gene with protein product		611413				8619474, 9110174	Standard	NM_001080418		Approved	SAPAP3, DAP3	uc001byc.3	O95886	OTTHUMG00000004049	ENST00000373347.1:c.234G>A	1.37:g.35370751C>T			35143338	Q5TDD5|Q9H3X7	Silent	SNP	HMMPfam_GKAP	p.A78	ENST00000373347.1	37	c.234	CCDS30670.1	1																																																																																			-	NULL		0.692	DLGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DLGAP3	protein_coding	OTTHUMT00000011554.1	C	NM_021234		35143338	-1	no_errors	NM_001080418	genbank	human	provisional	54_36p	silent	SNP	0.414	T
ZFP82	284406	genome.wustl.edu	37	19	36885079	36885079	+	Intron	SNP	T	T	C			TCGA-09-1664-01A-01W-0639-09	TCGA-09-1664-11A-01W-0639-09	T	T					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	8364585f-d532-4c26-9e0e-22cbfaeaf683	396c481e-d6ec-456f-a9dc-5740e9bfb22c	g.chr19:36885079T>C	ENST00000392161.3	-	5	472				ZFP82_ENST00000392171.1_Missense_Mutation_p.T55A	NM_133466.2	NP_597723.1	Q8N141	ZFP82_HUMAN	ZFP82 zinc finger protein						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						ATTTCTAATGTAGAAATAAAA	0.284																																																0			19																																								41576919	SO:0001627	intron_variant	284406			AL834267	CCDS12493.1	19q13.13	2013-01-08	2012-11-27	2008-07-01		ENSG00000181007		"""Zinc fingers, C2H2-type"", ""-"""	28682	protein-coding gene	gene with protein product			"""zinc finger protein 545"", ""zinc finger protein 82 homolog (mouse)"", ""zinc finger protein 82"""	ZNF545		11853319	Standard	NM_133466		Approved	MGC45380, KIAA1948	uc002ody.1	Q8N141		ENST00000392161.3:c.230-67A>G	19.37:g.36885079T>C			41576919	Q8NC63|Q8TF53	Missense_Mutation	SNP	superfamily_Krueppel-associated_box,HMMPfam_KRAB,HMMSmart_KRAB,superfamily_SSF57667,HMMPfam_zf-C2H2,HMMSmart_ZnF_C2H2,PatternScan_ZINC_FINGER_C2H2_1	p.T55A	ENST00000392161.3	37	c.163	CCDS12493.1	19	.	.	.	.	.	.	.	.	.	.	T	0.939	-0.710050	0.03230	.	.	ENSG00000181007	ENST00000392171	T	0.07114	3.22	4.27	-3.42	0.04825	.	.	.	.	.	T	0.08403	0.0209	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.33599	-0.9862	6	0.44086	T	0.13	.	7.1653	0.25687	0.0:0.5295:0.1635:0.307	.	.	.	.	A	55	ENSP00000446080:T55A	ENSP00000446080:T55A	T	-	1	0	ZFP82	41576919	0.000000	0.05858	0.000000	0.03702	0.121000	0.20230	-0.261000	0.08694	-0.984000	0.03507	-0.408000	0.06270	ACA	-	HMMSmart_KRAB		0.284	ZFP82-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ZFP82	protein_coding	OTTHUMT00000109552.2	T	NM_133466		41576919	-1	no_errors	ENST00000392171	ensembl	human	known	54_36p	missense	SNP	0.000	C
DOK5	55816	genome.wustl.edu	37	20	53171519	53171519	+	Silent	SNP	T	T	C			TCGA-09-1664-01A-01W-0639-09	TCGA-09-1664-11A-01W-0639-09	T	T					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	8364585f-d532-4c26-9e0e-22cbfaeaf683	396c481e-d6ec-456f-a9dc-5740e9bfb22c	g.chr20:53171519T>C	ENST00000262593.5	+	2	464	c.114T>C	c.(112-114)ggT>ggC	p.G38G	DOK5_ENST00000395939.1_5'UTR	NM_018431.3	NP_060901.2	Q9P104	DOK5_HUMAN	docking protein 5	38	PH.				MAPK cascade (GO:0000165)|nervous system development (GO:0007399)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)		receptor signaling protein activity (GO:0005057)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(2)|skin(1)	19			Colorectal(105;0.202)			CAAGCAAAGGTCCAAAAAGAC	0.393																																																0			20											124.0	122.0	123.0					20																	53171519		2203	4300	6503	52604926	SO:0001819	synonymous_variant	55816			AF132732	CCDS13446.1, CCDS13447.1	20q13.2	2013-01-10	2002-11-28	2002-11-29	ENSG00000101134	ENSG00000101134		"""Pleckstrin homology (PH) domain containing"""	16173	protein-coding gene	gene with protein product		608334	"""chromosome 20 open reading frame 180"""	C20orf180		11470823	Standard	XM_005260451		Approved	dJ805C22.1	uc002xwy.3	Q9P104	OTTHUMG00000032778	ENST00000262593.5:c.114T>C	20.37:g.53171519T>C			52604926	Q5T7Y0|Q5TE53|Q8TEW7|Q96H13|Q9BZ24|Q9NQF4|Q9Y411	Silent	SNP	superfamily_PH domain-like,HMMPfam_PH,HMMSmart_SM00233,HMMSmart_SM00310,HMMPfam_IRS	p.G38	ENST00000262593.5	37	c.114	CCDS13446.1	20																																																																																			-	superfamily_PH domain-like,HMMPfam_PH,HMMSmart_SM00233		0.393	DOK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DOK5	protein_coding	OTTHUMT00000079777.2	T			52604926	+1	no_errors	NM_018431	genbank	human	reviewed	54_36p	silent	SNP	0.965	C
KDM5C	8242	genome.wustl.edu	37	X	53222193	53222193	+	Silent	SNP	G	G	A			TCGA-09-1664-01A-01W-0639-09	TCGA-09-1664-11A-01W-0639-09	G	G					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	8364585f-d532-4c26-9e0e-22cbfaeaf683	396c481e-d6ec-456f-a9dc-5740e9bfb22c	g.chrX:53222193G>A	ENST00000375401.3	-	26	5171	c.4639C>T	c.(4639-4641)Ctg>Ttg	p.L1547L	KDM5C_ENST00000452825.3_Intron|KDM5C_ENST00000404049.3_Silent_p.L1546L|KDM5C_ENST00000375383.3_Silent_p.L1503L|KDM5C_ENST00000375379.3_Silent_p.L1544L	NM_001282622.1|NM_004187.3	NP_001269551.1|NP_004178.2	P41229	KDM5C_HUMAN	lysine (K)-specific demethylase 5C	1547					histone H3-K4 demethylation (GO:0034720)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-K4 specific) (GO:0032453)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(30)|large_intestine(9)|lung(17)|oesophagus(1)|ovary(6)|prostate(1)|salivary_gland(1)|skin(1)|upper_aerodigestive_tract(2)	82						GGCAGATGCAGCCGGGGAGTC	0.647			"""N, F, S"""		clear cell renal carcinoma																																		Rec	yes		X	Xp11.22-p11.21	8242	lysine (K)-specific demethylase 5C (JARID1C)		E	0			X											23.0	24.0	23.0					X																	53222193		2202	4298	6500	53238918	SO:0001819	synonymous_variant	8242			Z29650	CCDS14351.1, CCDS55417.1, CCDS65269.1	Xp11.22-p11.21	2014-01-31	2009-04-06	2009-04-06	ENSG00000126012	ENSG00000126012		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	11114	protein-coding gene	gene with protein product		314690	"""Jumonji, AT rich interactive domain 1C (RBP2-like)"", ""Smcy homolog, X-linked (mouse)"", ""jumonji, AT rich interactive domain 1C"", ""mental retardation, X-linked 13"""	SMCX, JARID1C, MRX13		7951230, 8162017, 19826449	Standard	NM_004187		Approved	DXS1272E, XE169	uc004drz.3	P41229	OTTHUMG00000021606	ENST00000375401.3:c.4639C>T	X.37:g.53222193G>A			53238918	B0QZ44|B4E3I2|F5H3T1|Q5JUX3|Q5JUX4|Q5JUX5|Q7Z5S5	Silent	SNP	HMMSmart_SM00545,HMMPfam_JmjN,superfamily_ARID-like,HMMPfam_ARID,HMMSmart_SM00501,superfamily_FYVE/PHD zinc finger,HMMSmart_SM00249,HMMPfam_PHD,PatternScan_ZF_PHD_1,HMMSmart_SM00558,HMMPfam_JmjC,HMMPfam_zf-C5HC2,HMMPfam_PLU-1	p.L1547	ENST00000375401.3	37	c.4639	CCDS14351.1	X																																																																																			-	NULL		0.647	KDM5C-005	KNOWN	basic|CCDS	protein_coding	JARID1C	protein_coding	OTTHUMT00000056737.2	G	NM_004187		53238918	-1	no_errors	NM_004187	genbank	human	reviewed	54_36p	silent	SNP	0.012	A
RB1CC1	9821	genome.wustl.edu	37	8	53570293	53570293	+	Missense_Mutation	SNP	G	G	A			TCGA-09-1664-01A-01W-0639-09	TCGA-09-1664-11A-01W-0639-09	G	G					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	8364585f-d532-4c26-9e0e-22cbfaeaf683	396c481e-d6ec-456f-a9dc-5740e9bfb22c	g.chr8:53570293G>A	ENST00000025008.5	-	15	2619	c.2096C>T	c.(2095-2097)aCg>aTg	p.T699M	RB1CC1_ENST00000435644.2_Missense_Mutation_p.T699M|RB1CC1_ENST00000521611.1_Intron|RB1CC1_ENST00000539297.1_Missense_Mutation_p.T699M	NM_014781.4	NP_055596.3	Q8TDY2	RBCC1_HUMAN	RB1-inducible coiled-coil 1	699					autophagic vacuole assembly (GO:0000045)|cell cycle (GO:0007049)|heart development (GO:0007507)|JNK cascade (GO:0007254)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell size (GO:0045793)|positive regulation of protein phosphorylation (GO:0001934)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)				NS(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(19)|ovary(8)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	60		all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023)				AAAATCAAACGTATGTGCATC	0.398																																					GBM(180;1701 2102 13475 42023 52570)											0			8											110.0	111.0	110.0					8																	53570293		2203	4300	6503	53732846	SO:0001583	missense	9821			AB059622	CCDS34892.1, CCDS47856.1	8q11	2014-06-13				ENSG00000023287			15574	protein-coding gene	gene with protein product	"""200 kDa FAK family kinase-interacting protein"", ""phosphatase 1, regulatory subunit 131"""	606837				11850849, 7724523, 18443221	Standard	NM_014781		Approved	KIAA0203, Cc1, DRAGOU14, FIP200, ATG17, PPP1R131	uc003xre.4	Q8TDY2		ENST00000025008.5:c.2096C>T	8.37:g.53570293G>A	ENSP00000025008:p.Thr699Met		53732846	Q86YR4|Q8WVU9|Q92601	Missense_Mutation	SNP	superfamily_SSF54236,HMMPfam_ATG11	p.T699M	ENST00000025008.5	37	c.2096	CCDS34892.1	8	.	.	.	.	.	.	.	.	.	.	G	19.32	3.805846	0.70682	.	.	ENSG00000023287	ENST00000025008;ENST00000435644;ENST00000539297	T;T;T	0.25579	1.8;1.79;1.79	5.35	5.35	0.76521	.	0.049824	0.85682	D	0.000000	T	0.44519	0.1297	L	0.36672	1.1	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.35699	-0.9778	10	0.72032	D	0.01	-16.7894	19.4123	0.94679	0.0:0.0:1.0:0.0	.	699;699	Q8TDY2-2;Q8TDY2	.;RBCC1_HUMAN	M	699	ENSP00000025008:T699M;ENSP00000396067:T699M;ENSP00000445960:T699M	ENSP00000025008:T699M	T	-	2	0	RB1CC1	53732846	1.000000	0.71417	0.992000	0.48379	0.993000	0.82548	9.416000	0.97383	2.649000	0.89929	0.655000	0.94253	ACG	-	NULL		0.398	RB1CC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	RB1CC1	protein_coding	OTTHUMT00000378011.1	G	NM_014781		53732846	-1	no_errors	NM_014781	genbank	human	validated	54_36p	missense	SNP	1.000	A
MAGT1	84061	genome.wustl.edu	37	X	77112371	77112371	+	Splice_Site	SNP	C	C	A			TCGA-09-1664-01A-01W-0639-09	TCGA-09-1664-11A-01W-0639-09	C	C					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	8364585f-d532-4c26-9e0e-22cbfaeaf683	396c481e-d6ec-456f-a9dc-5740e9bfb22c	g.chrX:77112371C>A	ENST00000358075.6	-	5	714		c.e5-1			NM_032121.5	NP_115497.4	Q9H0U3	MAGT1_HUMAN	magnesium transporter 1						cellular protein metabolic process (GO:0044267)|cognition (GO:0050890)|magnesium ion transport (GO:0015693)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	magnesium ion transmembrane transporter activity (GO:0015095)			cervix(1)|kidney(2)|large_intestine(3)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	17						TCACTCTAATCTAATGGAAAG	0.323																																																0			X											62.0	61.0	61.0					X																	77112371		2203	4296	6499	76999027	SO:0001630	splice_region_variant	84061				CCDS14436.2	Xq21.1	2014-09-17			ENSG00000102158	ENSG00000102158			28880	protein-coding gene	gene with protein product	"""oligosaccharyltransferase 3 homolog B (S. cerevisiae)"""	300715				15804357	Standard	NM_032121		Approved	DKFZp564K142, IAP, OST3B, MRX95	uc004fof.3	Q9H0U3	OTTHUMG00000021882	ENST00000358075.6:c.628-1G>T	X.37:g.77112371C>A			76999027	B2RAR4|D3DTE3|Q53G00|Q6P577|Q8NBN6	Splice_Site	SNP	-	e5-1	ENST00000358075.6	37	c.532-1	CCDS14436.2	X	.	.	.	.	.	.	.	.	.	.	C	19.83	3.899346	0.72754	.	.	ENSG00000102158	ENST00000358075;ENST00000453109	.	.	.	4.42	4.42	0.53409	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9804	0.80105	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MAGT1	76999027	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.358000	0.79466	1.772000	0.52199	0.600000	0.82982	.	-	-		0.323	MAGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MAGT1	protein_coding	OTTHUMT00000057301.2	C	NM_032121	Intron	76999027	-1	no_errors	NM_032121	genbank	human	validated	54_36p	splice_site	SNP	1.000	A
MUC17	140453	genome.wustl.edu	37	7	100684392	100684392	+	Missense_Mutation	SNP	C	C	T	rs548952598		TCGA-09-1664-01A-01W-0639-09	TCGA-09-1664-11A-01W-0639-09	C	C					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	8364585f-d532-4c26-9e0e-22cbfaeaf683	396c481e-d6ec-456f-a9dc-5740e9bfb22c	g.chr7:100684392C>T	ENST00000306151.4	+	3	9759	c.9695C>T	c.(9694-9696)aCg>aTg	p.T3232M		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	3232	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					GTCAGCAACACGCCGGTGGCC	0.488													C|||	1	0.000199681	0.0008	0.0	5008	,	,		27118	0.0		0.0	False		,,,				2504	0.0															0			7											260.0	266.0	264.0					7																	100684392		2203	4300	6503	100471112	SO:0001583	missense	140453			AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"""Mucins"""	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.9695C>T	7.37:g.100684392C>T	ENSP00000302716:p.Thr3232Met		100471112	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	superfamily_EGF/Laminin,PatternScan_EGF_1,superfamily_SEA domain,HMMSmart_SM00200,HMMPfam_SEA	p.T3232M	ENST00000306151.4	37	c.9695	CCDS34711.1	7	.	.	.	.	.	.	.	.	.	.	c	5.359	0.251600	0.10185	.	.	ENSG00000169876	ENST00000306151	T	0.02216	4.39	0.976	-0.0482	0.13840	.	.	.	.	.	T	0.04497	0.0123	L	0.27053	0.805	0.09310	N	1	D	0.76494	0.999	D	0.75020	0.985	T	0.46076	-0.9217	9	0.41790	T	0.15	.	5.7193	0.17978	0.0:0.7836:0.0:0.2164	.	3232	Q685J3	MUC17_HUMAN	M	3232	ENSP00000302716:T3232M	ENSP00000302716:T3232M	T	+	2	0	MUC17	100471112	0.000000	0.05858	0.002000	0.10522	0.005000	0.04900	0.168000	0.16622	-0.007000	0.14345	-1.368000	0.01194	ACG	-	NULL		0.488	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MUC17	protein_coding	OTTHUMT00000347161.1	C	NM_001040105		100471112	+1	no_errors	NM_001040105	genbank	human	provisional	54_36p	missense	SNP	0.013	T
KCNH7	90134	genome.wustl.edu	37	2	163236423	163236423	+	Missense_Mutation	SNP	C	C	T			TCGA-09-1664-01A-01W-0639-09	TCGA-09-1664-11A-01W-0639-09	C	C					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	8364585f-d532-4c26-9e0e-22cbfaeaf683	396c481e-d6ec-456f-a9dc-5740e9bfb22c	g.chr2:163236423C>T	ENST00000332142.5	-	14	3170	c.3071G>A	c.(3070-3072)aGc>aAc	p.S1024N		NM_033272.3	NP_150375.2	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 7	1024					circadian rhythm (GO:0007623)|potassium ion transmembrane transport (GO:0071805)|protein heterooligomerization (GO:0051291)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)|signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(22)|lung(53)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	108					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	GGTGAGGTCGCTTTCGGTTTC	0.512																																					GBM(196;1492 2208 17507 24132 45496)											0			2											192.0	180.0	184.0					2																	163236423		2203	4300	6503	162944669	SO:0001583	missense	90134			AF032897	CCDS2219.1, CCDS2220.1	2q24.3	2012-07-05			ENSG00000184611	ENSG00000184611		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	18863	protein-coding gene	gene with protein product		608169				16382104	Standard	NM_173162		Approved	Kv11.3, HERG3, erg3	uc002uch.2	Q9NS40	OTTHUMG00000132069	ENST00000332142.5:c.3071G>A	2.37:g.163236423C>T	ENSP00000331727:p.Ser1024Asn		162944669	Q53QU4|Q53TB7|Q53TP9|Q8IV15	Missense_Mutation	SNP	superfamily_PYP-like sensor domain (PAS domain),superfamily_Voltage-gated potassium channels,HMMPfam_Ion_trans,superfamily_cAMP-binding domain-like,HMMSmart_SM00100,HMMPfam_cNMP_binding	p.S1024N	ENST00000332142.5	37	c.3071	CCDS2219.1	2	.	.	.	.	.	.	.	.	.	.	C	14.85	2.659581	0.47467	.	.	ENSG00000184611	ENST00000332142	D	0.87103	-2.21	5.97	5.97	0.96955	.	0.186437	0.64402	D	0.000017	T	0.76513	0.3998	N	0.12182	0.205	0.80722	D	1	B	0.10296	0.003	B	0.08055	0.003	T	0.70223	-0.4931	10	0.32370	T	0.25	.	13.5933	0.61971	0.0:0.9293:0.0:0.0707	.	1024	Q9NS40	KCNH7_HUMAN	N	1024	ENSP00000331727:S1024N	ENSP00000331727:S1024N	S	-	2	0	KCNH7	162944669	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	4.871000	0.63042	2.835000	0.97688	0.591000	0.81541	AGC	-	NULL		0.512	KCNH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KCNH7	protein_coding	OTTHUMT00000255093.1	C	NM_033272		162944669	-1	no_errors	NM_033272	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
PDE10A	10846	genome.wustl.edu	37	6	165829727	165829727	+	Silent	SNP	T	T	C			TCGA-09-1664-01A-01W-0639-09	TCGA-09-1664-11A-01W-0639-09	T	T					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	8364585f-d532-4c26-9e0e-22cbfaeaf683	396c481e-d6ec-456f-a9dc-5740e9bfb22c	g.chr6:165829727T>C	ENST00000366882.1	-	13	1165	c.1011A>G	c.(1009-1011)acA>acG	p.T337T	PDE10A_ENST00000354448.4_Silent_p.T337T|PDE10A_ENST00000539869.2_Silent_p.T347T			Q9Y233	PDE10_HUMAN	phosphodiesterase 10A	337	GAF 2.				blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of protein kinase A signaling (GO:0010738)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|metal ion binding (GO:0046872)			breast(4)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(39)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	71		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Caffeine(DB00201)|Dipyridamole(DB00975)|Papaverine(DB01113)|Tofisopam(DB08811)|Triflusal(DB08814)	GGACTTCCCCTGTTCTTGCTA	0.403																																					Esophageal Squamous(22;308 615 5753 12038 40624)											0			6											262.0	237.0	245.0					6																	165829727		2203	4300	6503	165749717	SO:0001819	synonymous_variant	10846			AB020593	CCDS47513.1	6q26	2008-03-18			ENSG00000112541	ENSG00000112541	3.1.4.17	"""Phosphodiesterases"""	8772	protein-coding gene	gene with protein product		610652				10373451	Standard	NM_001130690		Approved		uc003quo.3	Q9Y233	OTTHUMG00000015986	ENST00000366882.1:c.1011A>G	6.37:g.165829727T>C			165749717	Q6FHX1|Q9HCP9|Q9NTV4|Q9ULW9|Q9Y5T1	Silent	SNP	superfamily_GAF domain-like,HMMPfam_GAF,HMMSmart_SM00065,superfamily_HD-domain/PDEase-like,HMMSmart_SM00471,HMMPfam_PDEase_I,PatternScan_PDEASE_I	p.T337	ENST00000366882.1	37	c.1011		6																																																																																			-	superfamily_GAF domain-like,HMMPfam_GAF,HMMSmart_SM00065		0.403	PDE10A-001	PUTATIVE	basic	protein_coding	PDE10A	protein_coding	OTTHUMT00000043031.1	T			165749717	-1	no_errors	NM_006661	genbank	human	validated	54_36p	silent	SNP	0.995	C
COL4A4	1286	genome.wustl.edu	37	2	227914784	227914784	+	Splice_Site	SNP	C	C	A			TCGA-09-1664-01A-01W-0639-09	TCGA-09-1664-11A-01W-0639-09	C	C					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	8364585f-d532-4c26-9e0e-22cbfaeaf683	396c481e-d6ec-456f-a9dc-5740e9bfb22c	g.chr2:227914784C>A	ENST00000396625.3	-	34	3421	c.3214G>T	c.(3214-3216)Gga>Tga	p.G1072*	COL4A4_ENST00000329662.7_Splice_Site_p.G1072*	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	1072	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		CAAACCATACCTTTAGGTCCT	0.408																																																0			2											137.0	127.0	130.0					2																	227914784		1863	4105	5968	227623028	SO:0001630	splice_region_variant	1286				CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"""Collagens"""	2206	protein-coding gene	gene with protein product	"""collagen of basement membrane, alpha-4 chain"""	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.3214+1G>T	2.37:g.227914784C>A			227623028	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Nonsense_Mutation	SNP	HMMPfam_Collagen,HMMPfam_C4,HMMSmart_SM00111,superfamily_C-type lectin-like	p.G1072*	ENST00000396625.3	37	c.3214	CCDS42828.1	2	.	.	.	.	.	.	.	.	.	.	C	43	10.410625	0.99400	.	.	ENSG00000081052	ENST00000396625;ENST00000329662	.	.	.	5.64	5.64	0.86602	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.4868	0.87691	0.0:1.0:0.0:0.0	.	.	.	.	X	1072	.	.	G	-	1	0	COL4A4	227623028	1.000000	0.71417	1.000000	0.80357	0.868000	0.49771	5.384000	0.66225	2.655000	0.90218	0.462000	0.41574	GGA	-	HMMPfam_Collagen		0.408	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	COL4A4	protein_coding	OTTHUMT00000313770.1	C	NM_000092	Nonsense_Mutation	227623028	-1	no_errors	NM_000092	genbank	human	reviewed	54_36p	nonsense	SNP	1.000	A
Unknown	0	genome.wustl.edu	37	Unknown	0	0	+	IGR	DEL	CATCCTAGCAATAATCCC	CATCCTAGCAATAATCCC	-			TCGA-09-1664-01A-01W-0639-09	TCGA-09-1664-11A-01W-0639-09	CATCCTAGCAATAATCCC	CATCCTAGCAATAATCCC					Unknown	Invalid:failed_liftOver	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	8364585f-d532-4c26-9e0e-22cbfaeaf683	396c481e-d6ec-456f-a9dc-5740e9bfb22c	g.chrUnknown:0delCATCCTAGCAATAATCCC								None (None upstream) : None (None downstream)																								0.0																																																0			MT																																								15661	SO:0001628	intergenic_variant	4519																															Unknown.37:g.0delCATCCTAGCAATAATCCC			15644		In_Frame_Del	DEL	superfamily_Transmembr_di-haem_cytochrome,HMMPfam_Cytochrom_B_N,HMMPfam_Cytochrom_B_C,superfamily_Cytochrome_b/b6_C	p.AMIPIL302in_frame_del		37	c.897_914		MT																																																																																			(deletion:cds_exon[14748,15882])	HMMPfam_Cytochrom_B_C,superfamily_Cytochrome_b/b6_C	0	0					MT-CYB			CATCCTAGCAATAATCCC			15661	+1	no_stop_codon:bad_bp_length_for_coding_region	ENST00000361789	ensembl	human	known	54_36p	in_frame_del	DEL	NULL	-
NF1	4763	genome.wustl.edu	37	17	29486060	29486061	+	Frame_Shift_Ins	INS	-	-	T			TCGA-09-1664-01A-01W-0639-09	TCGA-09-1664-11A-01W-0639-09	-	-					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	8364585f-d532-4c26-9e0e-22cbfaeaf683	396c481e-d6ec-456f-a9dc-5740e9bfb22c	g.chr17:29486060_29486061insT	ENST00000358273.4	+	3	620_621	c.237_238insT	c.(238-240)tatfs	p.Y80fs	NF1_ENST00000431387.4_Frame_Shift_Ins_p.Y80fs|NF1_ENST00000356175.3_Frame_Shift_Ins_p.Y80fs	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	80			Y -> C. {ECO:0000269|Ref.7}.|Y -> S (in dbSNP:rs4795581).		actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(4)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		AAAAAAATTTATATCTCTCTCA	0.332			"""D, Mis, N, F, S, O"""		"""neurofibroma, glioma"""	"""neurofibroma, glioma"""			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																												yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	12	Whole gene deletion(8)|Unknown(4)	soft_tissue(7)|autonomic_ganglia(3)|central_nervous_system(2)	17																																								26510187	SO:0001589	frameshift_variant	4763	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"""neurofibromatosis"", ""von Recklinghausen disease"", ""Watson disease"""	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.238dupT	17.37:g.29486061_29486061dupT	ENSP00000351015:p.Tyr80fs		26510186	O00662|Q14284|Q14930|Q14931|Q9UMK3	Frame_Shift_Ins	INS	HMMSmart_SM00323,superfamily_GTPase activation domain GAP,HMMPfam_RasGAP,PatternScan_RAS_GTPASE_ACTIV_1,HMMSmart_SM00516	p.Y79fs	ENST00000358273.4	37	c.237_238	CCDS42292.1	17																																																																																			-	NULL		0.332	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NF1	protein_coding	OTTHUMT00000256351.2	-	NM_000267		26510187	+1	no_errors	NM_001042492	genbank	human	reviewed	54_36p	frame_shift_ins	INS	0.988:1.000	T
