#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_NormalRefReads_WU	i_NormalVAF_WU	i_NormalVarReads_WU	i_ORegAnno_bin	i_RNARefReads_WU	i_RNAVAF_WU	i_RNAVarReads_WU	i_Start_position_hg18	i_TumorRefReads_WU	i_TumorVAF_WU	i_TumorVarReads_WU	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_deletion_substructures	i_domain	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_name	i_gene_type	i_havana_transcript	i_reference	i_refseq_mrna_id	i_secondary_variant_classification	i_stop	i_strand	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_type	i_ucsc_cons	i_variant
GJA4	2701	genome.wustl.edu	37	1	35260717	35260717	+	Silent	SNP	G	G	A	rs113974864	byFrequency	TCGA-AB-2808-03D-01W-0755-09	TCGA-AB-2808-11D-01W-0755-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	06038210-fb82-4e20-8c82-d6695453eecb	92b4a800-c7d2-4f97-94fc-85d30528c574	g.chr1:35260717G>A	ENST00000342280.4	+	2	991	c.903G>A	c.(901-903)gcG>gcA	p.A301A		NM_002060.2	NP_002051.2	P35212	CXA4_HUMAN	gap junction protein, alpha 4, 37kDa	301					blood vessel development (GO:0001568)|calcium ion transport (GO:0006816)|cell-cell junction assembly (GO:0007043)|cell-cell signaling (GO:0007267)|endothelium development (GO:0003158)|response to pain (GO:0048265)|transport (GO:0006810)	connexon complex (GO:0005922)|gap junction (GO:0005921)|integral component of plasma membrane (GO:0005887)				NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(3)|prostate(4)|stomach(1)	14		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234)				AGAGGCTGGCGTCTTCCAGGC	0.602																																						dbGAP											0			1						G		2,4404	4.2+/-10.8	0,2,2201	46.0	43.0	44.0		903	-1.9	1.0	1	dbSNP_132	44	0,8600		0,0,4300	no	coding-synonymous	GJA4	NM_002060.2		0,2,6501	AA,AG,GG		0.0,0.0454,0.0154		301/334	35260717	2,13004	2203	4300	6503	35033304	SO:0001819	synonymous_variant	0			M96789	CCDS30669.1	1p35.1	2008-02-05	2007-01-16		ENSG00000187513	ENSG00000187513		"""Ion channels / Gap junction proteins (connexins)"""	4278	protein-coding gene	gene with protein product	"""connexin 37"""	121012	"""gap junction protein, alpha 4, 37kD (connexin 37)"", ""gap junction protein, alpha 4, 37kDa (connexin 37)"""			9843209, 7680674	Standard	XM_005270750		Approved	CX37	uc001bya.3	P35212	OTTHUMG00000004050	ENST00000342280.4:c.903G>A	1.37:g.35260717G>A		43	2.27	1		NA	NA	NA	35033304	37	53.16	42	A8K698|D3DPR4|Q9P106|Q9UBL1|Q9UNA9|Q9UNB0|Q9UNB1|Q9Y5N7	Silent	SNP	HMMPfam_Connexin,HMMSmart_SM00037,PatternScan_CONNEXINS_1,PatternScan_CONNEXINS_2,HMMPfam_Connexin_CCC	p.A301	ENST00000342280.4	37	c.903	CCDS30669.1	1																																																																																			-	NULL		0.602	GJA4-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	GJA4	protein_coding	OTTHUMT00000011556.1	G	NM_002060		35033304	+1	no_errors	NM_002060.2	genbank	human	reviewed	54_36p	silent	SNP	0.012	A
CSF3R	1441	genome.wustl.edu	37	1	36933434	36933434	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2808-03D-01W-0755-09	TCGA-AB-2808-11D-01W-0755-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	06038210-fb82-4e20-8c82-d6695453eecb	92b4a800-c7d2-4f97-94fc-85d30528c574	g.chr1:36933434G>A	ENST00000373106.1	-	14	2400	c.1853C>T	c.(1852-1854)aCc>aTc	p.T618I	CSF3R_ENST00000361632.4_Missense_Mutation_p.T618I|CSF3R_ENST00000331941.5_Missense_Mutation_p.T618I|CSF3R_ENST00000487540.2_5'UTR|CSF3R_ENST00000338937.5_Missense_Mutation_p.T618I|CSF3R_ENST00000373104.1_Missense_Mutation_p.T618I|CSF3R_ENST00000373103.1_Missense_Mutation_p.T618I|CSF3R_ENST00000440588.2_Missense_Mutation_p.T618I|CSF3R_ENST00000418048.2_Missense_Mutation_p.T618I	NM_000760.3	NP_000751.1	Q99062	CSF3R_HUMAN	colony stimulating factor 3 receptor (granulocyte)	618	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|defense response (GO:0006952)|neutrophil chemotaxis (GO:0030593)|odontogenesis of dentin-containing tooth (GO:0042475)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)			central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(9)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)			Filgrastim(DB00099)|Pegfilgrastim(DB00019)	TGGGGTCAAGGTCATCAGGGT	0.597																																						dbGAP											0			1											91.0	100.0	97.0					1																	36933434		2203	4300	6503	36706021	SO:0001583	missense	0			M59820	CCDS412.1, CCDS413.1, CCDS414.1	1p35-p34.3	2014-09-17			ENSG00000119535	ENSG00000119535		"""CD molecules"", ""Fibronectin type III domain containing"""	2439	protein-coding gene	gene with protein product		138971		CD114		1371413	Standard	NM_000760		Approved	GCSFR	uc001cax.2	Q99062	OTTHUMG00000008010	ENST00000373106.1:c.1853C>T	1.37:g.36933434G>A	ENSP00000362198:p.Thr618Ile	61	0.00	0		250	27.54	95	36706021	184	17.33	39		Missense_Mutation	SNP	PatternScan_HEMATOPO_REC_L_F2,HMMPfam_fn3,HMMSmart_FN3,superfamily_FN_III-like,HMMPfam_Lep_receptor_Ig	p.T618I	ENST00000373106.1	37	c.1853	CCDS413.1	1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.56|15.56	2.869935|2.869935	0.51588|0.51588	.|.	.|.	ENSG00000119535|ENSG00000119535	ENST00000464465|ENST00000373106;ENST00000373104;ENST00000373103;ENST00000361632;ENST00000331941;ENST00000418048;ENST00000338937;ENST00000440588	.|T;T;T;T;T;T;T;T	.|0.61627	.|0.09;0.09;0.09;0.09;0.09;0.09;0.09;0.09	5.59|5.59	4.67|4.67	0.58626|0.58626	.|Fibronectin, type III (2);Immunoglobulin-like fold (1);	.|0.255320	.|0.45606	.|D	.|0.000357	T|T	0.73583|0.73583	0.3605|0.3605	M|M	0.69823|0.69823	2.125|2.125	0.33207|0.33207	D|D	0.552964|0.552964	.|D;D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;0.999;1.0	.|D;D;D;D;D;D	.|0.91635	.|0.997;0.997;0.999;0.997;0.969;0.996	T|T	0.81711|0.81711	-0.0808|-0.0808	5|10	.|0.54805	.|T	.|0.06	-27.5191|-27.5191	13.1782|13.1782	0.59639|0.59639	0.0:0.0:0.8403:0.1597|0.0:0.0:0.8403:0.1597	.|.	.|618;618;618;618;618;618	.|Q1ZYL6;E1B6W6;Q99062-3;Q99062;Q99062-4;Q99062-2	.|.;.;.;CSF3R_HUMAN;.;.	S|I	170|618	.|ENSP00000362198:T618I;ENSP00000362196:T618I;ENSP00000362195:T618I;ENSP00000355406:T618I;ENSP00000332180:T618I;ENSP00000401588:T618I;ENSP00000345013:T618I;ENSP00000397568:T618I	.|ENSP00000332180:T618I	P|T	-|-	1|2	0|0	CSF3R|CSF3R	36706021|36706021	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.414000|0.414000	0.31173|0.31173	5.794000|5.794000	0.69067|0.69067	1.337000|1.337000	0.45525|0.45525	0.655000|0.655000	0.94253|0.94253	CCT|ACC	-	superfamily_FN_III-like		0.597	CSF3R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CSF3R	protein_coding	OTTHUMT00000021997.2	G	NM_156039		36706021	-1	no_errors	NM_156039.2	genbank	human	reviewed	54_36p	missense	SNP	0.989	A
NRAS	4893	genome.wustl.edu	37	1	115258744	115258744	+	Missense_Mutation	SNP	C	C	T	rs121434596		TCGA-AB-2808-03D-01W-0755-09	TCGA-AB-2808-11D-01W-0755-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	06038210-fb82-4e20-8c82-d6695453eecb	92b4a800-c7d2-4f97-94fc-85d30528c574	g.chr1:115258744C>T	ENST00000369535.4	-	2	291	c.38G>A	c.(37-39)gGt>gAt	p.G13D	CSDE1_ENST00000483407.1_5'Flank	NM_002524.4	NP_002515.1	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	13			G -> D (in ALPS4). {ECO:0000269|PubMed:17517660}.|G -> R (in CMNS and colorectal cancer; somatic mutation). {ECO:0000269|PubMed:18633438, ECO:0000269|PubMed:3102434}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of skeletal muscle tissue development (GO:0048642)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|small GTPase mediated signal transduction (GO:0007264)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G13D(188)|p.G13V(56)|p.G13A(16)|p.G13N(1)|p.G13Y(1)		NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		TTTCCCAACACCACCTGCTCC	0.498	G13D(HDMYZ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G13D(KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G13D(MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G13D(NCIH929_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G13V(AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	50	Mis		"""melanoma, MM, AML, thyroid"""				Noonan syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)																												dbGAP		Dom	yes		1	1p13.2	4893	neuroblastoma RAS viral (v-ras) oncogene homolog		"""L, E"""	262	Substitution - Missense(262)	haematopoietic_and_lymphoid_tissue(217)|skin(36)|thyroid(2)|large_intestine(2)|soft_tissue(2)|central_nervous_system(1)|endometrium(1)|NS(1)	1	GRCh37	CM071907	NRAS	M	rs121434596						208.0	185.0	193.0					1																	115258744		2203	4300	6503	115060267	SO:0001583	missense	0	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	BC005219	CCDS877.1	1p13.2	2014-09-17			ENSG00000213281	ENSG00000213281			7989	protein-coding gene	gene with protein product		164790					Standard	NM_002524		Approved	N-ras	uc009wgu.3	P01111	OTTHUMG00000012059	ENST00000369535.4:c.38G>A	1.37:g.115258744C>T	ENSP00000358548:p.Gly13Asp	74	0.00	0		26	16.13	5	115060267	153	16.85	31	Q14971|Q15104|Q15282	Missense_Mutation	SNP	HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases	p.G13D	ENST00000369535.4	37	c.38	CCDS877.1	1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.048221	0.93740	.	.	ENSG00000213281	ENST00000369535	T	0.72942	-0.7	5.58	5.58	0.84498	Small GTP-binding protein domain (1);	0.000000	0.56097	U	0.000022	T	0.79644	0.4481	M	0.92604	3.325	0.80722	D	1	B	0.33964	0.434	B	0.42319	0.383	T	0.81673	-0.0826	10	0.62326	D	0.03	.	19.3769	0.94514	0.0:1.0:0.0:0.0	.	13	P01111	RASN_HUMAN	D	13	ENSP00000358548:G13D	ENSP00000358548:G13D	G	-	2	0	NRAS	115060267	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.651000	0.83577	2.906000	0.99361	0.655000	0.94253	GGT	-	HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases		0.498	NRAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NRAS	protein_coding	OTTHUMT00000033395.2	C	NM_002524		115060267	-1	no_errors	NM_002524.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
TSPAN2	10100	genome.wustl.edu	37	1	115596001	115596001	+	Splice_Site	SNP	G	G	A			TCGA-AB-2808-03D-01W-0755-09	TCGA-AB-2808-11D-01W-0755-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	06038210-fb82-4e20-8c82-d6695453eecb	92b4a800-c7d2-4f97-94fc-85d30528c574	g.chr1:115596001G>A	ENST00000369516.2	-	7	630	c.599C>T	c.(598-600)aCg>aTg	p.T200M	TSPAN2_ENST00000491992.1_5'UTR|TSPAN2_ENST00000369515.2_Splice_Site_p.T175M|TSPAN2_ENST00000369514.2_Intron	NM_005725.4	NP_005716.2	O60636	TSN2_HUMAN	tetraspanin 2	200					astrocyte development (GO:0014002)|axon development (GO:0061564)|brain development (GO:0007420)|inflammatory response (GO:0006954)|microglia development (GO:0014005)|myelination (GO:0042552)|oligodendrocyte differentiation (GO:0048709)	integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)|plasma membrane (GO:0005886)				central_nervous_system(1)|large_intestine(4)|lung(3)|pancreas(1)|prostate(1)	10	Lung SC(450;0.211)	all_cancers(81;2.9e-07)|all_epithelial(167;1.42e-06)|all_lung(203;6.72e-06)|Lung NSC(69;1.13e-05)|Acute lymphoblastic leukemia(138;0.191)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|all cancers(265;0.159)|Epithelial(280;0.179)		CTTTCTCACCGTCAGACCTGC	0.363																																						dbGAP											0			1											111.0	107.0	108.0					1																	115596001		2203	4300	6503	115397524	SO:0001630	splice_region_variant	0			AF054839	CCDS881.1	1p13.1	2013-02-14			ENSG00000134198	ENSG00000134198		"""Tetraspanins"""	20659	protein-coding gene	gene with protein product		613133				9714763, 11739647	Standard	NM_005725		Approved	TSPAN-2, TSN2, FLJ12082	uc001eft.3	O60636	OTTHUMG00000011878	ENST00000369516.2:c.600+1C>T	1.37:g.115596001G>A		63	5.97	4		21	8.70	2	115397524	215	35.61	120	D6PTH4|Q5TET2|Q8WU05	Missense_Mutation	SNP	superfamily_Tetraspanin,HMMPfam_Tetraspannin,PatternScan_TM4_1	p.T200M	ENST00000369516.2	37	c.599	CCDS881.1	1	.	.	.	.	.	.	.	.	.	.	G	6.664	0.491141	0.12702	.	.	ENSG00000134198	ENST00000369516;ENST00000369515	T;T	0.78595	-1.19;-1.19	5.7	4.78	0.61160	.	0.128334	0.64402	N	0.000001	T	0.33000	0.0848	N	0.01277	-0.915	0.80722	D	1	P	0.45240	0.854	B	0.41946	0.371	T	0.50996	-0.8761	10	0.11182	T	0.66	.	13.1714	0.59599	0.0774:0.0:0.9226:0.0	.	200	O60636	TSN2_HUMAN	M	200;175	ENSP00000358529:T200M;ENSP00000358528:T175M	ENSP00000358528:T175M	T	-	2	0	TSPAN2	115397524	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	4.468000	0.60162	1.414000	0.47017	0.467000	0.42956	ACG	-	HMMPfam_Tetraspannin		0.363	TSPAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TSPAN2	protein_coding	OTTHUMT00000032828.1	G	NM_005725	Missense_Mutation	115397524	-1	no_errors	NM_005725.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
CTNNA2	1496	genome.wustl.edu	37	2	80085262	80085262	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2808-03D-01W-0755-09	TCGA-AB-2808-11D-01W-0755-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	06038210-fb82-4e20-8c82-d6695453eecb	92b4a800-c7d2-4f97-94fc-85d30528c574	g.chr2:80085262C>T	ENST00000402739.4	+	3	427	c.422C>T	c.(421-423)gCg>gTg	p.A141V	CTNNA2_ENST00000541047.1_Missense_Mutation_p.A141V|CTNNA2_ENST00000496558.1_Missense_Mutation_p.A141V|CTNNA2_ENST00000361291.4_Missense_Mutation_p.A175V|CTNNA2_ENST00000540488.1_Missense_Mutation_p.A141V|CTNNA2_ENST00000466387.1_Missense_Mutation_p.A141V	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2	141					axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|dendrite morphogenesis (GO:0048813)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|prepulse inhibition (GO:0060134)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of synapse structural plasticity (GO:0051823)|single organismal cell-cell adhesion (GO:0016337)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	structural constituent of cytoskeleton (GO:0005200)	p.A141V(2)		breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(49)|pancreas(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	78						CTCATCCTGGCGGACATGGCA	0.498																																						dbGAP											2	Substitution - Missense(2)	lung(2)	2											73.0	72.0	73.0					2																	80085262		2045	4190	6235	79938770	SO:0001583	missense	0				CCDS42703.2, CCDS62944.1, CCDS62945.1, CCDS74531.1	2p12-p11.1	2010-05-04			ENSG00000066032	ENSG00000066032			2510	protein-coding gene	gene with protein product	"""cadherin-associated protein, related"", ""cancer/testis antigen 114"""	114025				8432524	Standard	NM_004389		Approved	CAP-R, CT114	uc010ysf.2	P26232	OTTHUMG00000152903	ENST00000402739.4:c.422C>T	2.37:g.80085262C>T	ENSP00000384638:p.Ala141Val	41	6.82	3		NA	NA	NA	79938770	44	53.68	51	B3KXE5|B7Z2W7|B7Z352|B7Z898|Q4ZFW1|Q53R26|Q53R33|Q53T67|Q53T71|Q53TM8|Q7Z3L1|Q7Z3Y0	Missense_Mutation	SNP	PatternScan_VINCULIN_1,HMMPfam_Vinculin,superfamily_alpha-catenin/vinculin	p.A141V	ENST00000402739.4	37	c.422		2	.	.	.	.	.	.	.	.	.	.	C	36	5.968190	0.97156	.	.	ENSG00000066032	ENST00000466387;ENST00000496558;ENST00000361291;ENST00000402739;ENST00000541047;ENST00000540488	T;T;T;T;T;T	0.39997	1.05;1.05;1.05;1.05;1.05;1.05	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	T	0.74336	0.3703	M	0.92649	3.33	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.998	T	0.79169	-0.1914	10	0.54805	T	0.06	.	19.773	0.96379	0.0:1.0:0.0:0.0	.	141;141;141	P26232;P26232-3;P26232-2	CTNA2_HUMAN;.;.	V	141;141;175;141;141;141	ENSP00000418191:A141V;ENSP00000419295:A141V;ENSP00000355398:A175V;ENSP00000384638:A141V;ENSP00000444675:A141V;ENSP00000441705:A141V	ENSP00000355398:A175V	A	+	2	0	CTNNA2	79938770	1.000000	0.71417	0.981000	0.43875	0.994000	0.84299	7.818000	0.86416	2.677000	0.91161	0.655000	0.94253	GCG	-	HMMPfam_Vinculin,superfamily_alpha-catenin/vinculin		0.498	CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	CTNNA2	protein_coding	OTTHUMT00000328511.4	C	NM_004389		79938770	+1	no_errors	NM_004389.2	genbank	human	validated	54_36p	missense	SNP	0.999	T
FILIP1	27145	genome.wustl.edu	37	6	76022883	76022883	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AB-2808-03D-01W-0755-09	TCGA-AB-2808-11D-01W-0755-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	06038210-fb82-4e20-8c82-d6695453eecb	92b4a800-c7d2-4f97-94fc-85d30528c574	g.chr6:76022883G>A	ENST00000237172.7	-	5	2995	c.2665C>T	c.(2665-2667)Cga>Tga	p.R889*	FILIP1_ENST00000393004.2_Nonsense_Mutation_p.R889*|FILIP1_ENST00000498523.1_5'UTR|FILIP1_ENST00000370020.1_Nonsense_Mutation_p.R790*	NM_015687.2	NP_056502.1	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	889										breast(3)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)	80						GAATTTGTTCGGGGCCCTTTC	0.537																																						dbGAP											0			6											72.0	74.0	73.0					6																	76022883		2203	4300	6503	76079603	SO:0001587	stop_gained	0			AB033101	CCDS4984.1, CCDS75480.1	6q14.1	2008-02-05			ENSG00000118407	ENSG00000118407			21015	protein-coding gene	gene with protein product		607307				10574462	Standard	XM_005248713		Approved	FILIP, KIAA1275	uc003pia.3	Q7Z7B0	OTTHUMG00000015056	ENST00000237172.7:c.2665C>T	6.37:g.76022883G>A	ENSP00000237172:p.Arg889*	106	6.19	7		NA	NA	NA	76079603	139	47.15	124	B2RMU6|Q5VUL6|Q86TC3|Q8N8B9|Q96SK6|Q9NVI8|Q9ULE5	Nonsense_Mutation	SNP	HMMPfam_CortBP2	p.R889*	ENST00000237172.7	37	c.2665	CCDS4984.1	6	.	.	.	.	.	.	.	.	.	.	G	42	9.420566	0.99166	.	.	ENSG00000118407	ENST00000393004;ENST00000237172;ENST00000370020	.	.	.	5.67	2.85	0.33270	.	0.290655	0.32868	N	0.005550	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.4341	10.6349	0.45558	0.0:0.1173:0.377:0.5057	.	.	.	.	X	889;889;790	.	ENSP00000237172:R889X	R	-	1	2	FILIP1	76079603	0.986000	0.35501	0.031000	0.17742	0.410000	0.31052	3.024000	0.49674	0.299000	0.22661	0.563000	0.77884	CGA	-	NULL		0.537	FILIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FILIP1	protein_coding	OTTHUMT00000041263.1	G	XM_029179		76079603	-1	no_errors	NM_015687.2	genbank	human	validated	54_36p	nonsense	SNP	0.294	A
SOGA3	387104	genome.wustl.edu	37	6	127796938	127796938	+	Missense_Mutation	SNP	G	G	T			TCGA-AB-2808-03D-01W-0755-09	TCGA-AB-2808-11D-01W-0755-09	G	G	G	T	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	06038210-fb82-4e20-8c82-d6695453eecb	92b4a800-c7d2-4f97-94fc-85d30528c574	g.chr6:127796938G>T	ENST00000525778.1	-	6	2978	c.2233C>A	c.(2233-2235)Cgc>Agc	p.R745S	SOGA3_ENST00000481848.2_Missense_Mutation_p.R745S|SOGA3_ENST00000368268.2_Missense_Mutation_p.R745S|SOGA3_ENST00000556132.1_Missense_Mutation_p.R745S|SOGA3_ENST00000465909.2_Missense_Mutation_p.R745S|SOGA3_ENST00000474293.2_5'Flank			Q5TF21	SOGA3_HUMAN	SOGA family member 3	745					regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											GGGCTGCCGCGGATGCCCAGG	0.677																																						dbGAP											0			6											50.0	58.0	55.0					6																	127796938		2159	4275	6434	127838631	SO:0001583	missense	0			AK096490	CCDS43505.1	6q22.33	2013-03-28	2012-02-27	2012-02-27	ENSG00000214338	ENSG00000214338			21494	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 174"""	C6orf174			Standard	NM_001012279		Approved	dJ403A15.3	uc003qbd.3	Q5TF21	OTTHUMG00000166438	ENST00000525778.1:c.2233C>A	6.37:g.127796938G>T	ENSP00000434570:p.Arg745Ser	10	0.00	0		NA	NA	NA	127838631	15	51.61	16		Missense_Mutation	SNP	NULL	p.R745S	ENST00000525778.1	37	c.2233	CCDS43505.1	6	.	.	.	.	.	.	.	.	.	.	G	19.88	3.909983	0.72983	.	.	ENSG00000214338	ENST00000556132;ENST00000368268;ENST00000525778;ENST00000465909	T;T;T;T	0.37752	1.18;1.18;1.18;1.18	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.24353	0.0590	L	0.53249	1.67	0.80722	D	1	P	0.38767	0.646	B	0.38020	0.263	T	0.14420	-1.0473	10	0.87932	D	0	-13.309	13.5963	0.61991	0.0:0.0:0.8447:0.1553	.	745	Q5TF21	CF174_HUMAN	S	745	ENSP00000451768:R745S;ENSP00000357251:R745S;ENSP00000434570:R745S;ENSP00000435559:R745S	ENSP00000435559:R745S	R	-	1	0	C6orf174	127838631	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	5.989000	0.70587	2.411000	0.81874	0.462000	0.41574	CGC	-	NULL		0.677	SOGA3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	C6orf174	protein_coding	OTTHUMT00000388246.1	G	NM_001012279		127838631	-1	no_errors	NM_001012279.1	genbank	human	validated	54_36p	missense	SNP	1.000	T
CSMD3	114788	genome.wustl.edu	37	8	113651047	113651047	+	Missense_Mutation	SNP	C	C	T	rs143602091		TCGA-AB-2808-03D-01W-0755-09	TCGA-AB-2808-11D-01W-0755-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	06038210-fb82-4e20-8c82-d6695453eecb	92b4a800-c7d2-4f97-94fc-85d30528c574	g.chr8:113651047C>T	ENST00000297405.5	-	21	3648	c.3404G>A	c.(3403-3405)cGc>cAc	p.R1135H	CSMD3_ENST00000352409.3_Missense_Mutation_p.R1135H|CSMD3_ENST00000343508.3_Missense_Mutation_p.R1095H|CSMD3_ENST00000455883.2_Missense_Mutation_p.R1031H	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1135	CUB 6. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						ACCAGTCAGGCGTGCCAGTGG	0.403										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																												dbGAP											0			8						C	HIS/ARG,HIS/ARG,HIS/ARG	0,4406		0,0,2203	116.0	112.0	114.0		3092,3404,3284	5.4	1.0	8	dbSNP_134	114	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense	CSMD3	NM_052900.2,NM_198123.1,NM_198124.1	29,29,29	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	probably-damaging,probably-damaging,probably-damaging	1031/3539,1135/3708,1095/3668	113651047	3,13003	2203	4300	6503	113720223	SO:0001583	missense	0			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.3404G>A	8.37:g.113651047C>T	ENSP00000297405:p.Arg1135His	74	5.13	4		NA	NA	NA	113720223	95	34.23	51	Q96PZ3	Missense_Mutation	SNP	HMMPfam_Sushi,HMMSmart_SM00032,HMMPfam_CUB,HMMSmart_SM00042,superfamily_Spermadhesin CUB domain,PatternScan_GLYCOSYL_HYDROL_F10,superfamily_Complement control module/SCR domain	p.R1135H	ENST00000297405.5	37	c.3404	CCDS6315.1	8	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	29.1	4.980584	0.92982	0.0	3.49E-4	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.20069	2.1;2.1;2.1;2.1;2.1	5.36	5.36	0.76844	CUB (5);	0.000000	0.64402	D	0.000001	T	0.53158	0.1779	M	0.85462	2.755	0.45621	D	0.998551	D;D;D	0.89917	1.0;1.0;0.981	D;D;D	0.91635	0.999;0.999;0.961	T	0.56565	-0.7958	10	0.48119	T	0.1	.	19.0774	0.93168	0.0:1.0:0.0:0.0	.	1031;1135;1095	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	H	1095;1135;475;1031;1135	ENSP00000345799:R1095H;ENSP00000297405:R1135H;ENSP00000341558:R475H;ENSP00000412263:R1031H;ENSP00000343124:R1135H	ENSP00000297405:R1135H	R	-	2	0	CSMD3	113720223	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.792000	0.85828	2.529000	0.85273	0.491000	0.48974	CGC	-	HMMPfam_CUB,HMMSmart_SM00042,superfamily_Spermadhesin CUB domain		0.403	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CSMD3	protein_coding	OTTHUMT00000347141.1	C	NM_052900		113720223	-1	no_errors	NM_198123.2	genbank	human	validated	54_36p	missense	SNP	1.000	T
Unknown	0	genome.wustl.edu	37	12	127349726	127349726	+	IGR	SNP	G	G	A			TCGA-AB-2808-03D-01W-0755-09	TCGA-AB-2808-11D-01W-0755-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	06038210-fb82-4e20-8c82-d6695453eecb	92b4a800-c7d2-4f97-94fc-85d30528c574	g.chr12:127349726G>A								LINC00944 (92769 upstream) : RP11-983C2.2 (4309 downstream)																							TCTGAGGAGTGCACAACCATG	0.493																																						dbGAP											0			12																																								125915679	SO:0001628	intergenic_variant	0																															12.37:g.127349726G>A		60	0.00	0		NA	NA	NA	125915679	112	12.88	17		RNA	SNP	-	NULL		37	NULL		12																																																																																			-	-	0	0.493					LOC121296			G			125915679	+1	no_errors	XR_016630.1	genbank	human	model	54_36p	rna	SNP	1.000	A
LAMA3	3909	genome.wustl.edu	37	18	21394427	21394427	+	Missense_Mutation	SNP	T	T	C			TCGA-AB-2808-03D-01W-0755-09	TCGA-AB-2808-11D-01W-0755-09	T	T	T	C	T	T	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	06038210-fb82-4e20-8c82-d6695453eecb	92b4a800-c7d2-4f97-94fc-85d30528c574	g.chr18:21394427T>C	ENST00000313654.9	+	15	2090	c.1849T>C	c.(1849-1851)Tat>Cat	p.Y617H	LAMA3_ENST00000399516.3_Missense_Mutation_p.Y617H	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	617	Domain V.|Laminin EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00460}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					CAAACTGTTATATTGGAATCT	0.358																																						dbGAP											0			18											145.0	136.0	139.0					18																	21394427		1822	4089	5911	19648425	SO:0001583	missense	0			L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"""Laminins"""	6483	protein-coding gene	gene with protein product		600805	"""laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"""	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.1849T>C	18.37:g.21394427T>C	ENSP00000324532:p.Tyr617His	53	5.36	3		NA	NA	NA	19648425	101	48.24	96	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Missense_Mutation	SNP	HMMPfam_Laminin_B,HMMSmart_SM00282,HMMPfam_Laminin_EGF,HMMSmart_SM00180,PatternScan_EGF_LAM_1,HMMSmart_SM00181,HMMPfam_Laminin_N,HMMSmart_SM00136,superfamily_Galactose-binding domain-like,superfamily_Concanavalin A-like lectins/glucanases,HMMPfam_Laminin_I,HMMPfam_Laminin_II,HMMPfam_Laminin_G_2,PatternScan_EGF_1,PatternScan_EGF_2,HMMSmart_SM00281,PatternScan_CHAPERONINS_CPN60,superfamily_EGF/Laminin	p.Y617H	ENST00000313654.9	37	c.1849	CCDS42419.1	18	.	.	.	.	.	.	.	.	.	.	T	16.60	3.167289	0.57476	.	.	ENSG00000053747	ENST00000313654;ENST00000399516;ENST00000416669	T;T	0.56103	0.48;0.48	5.64	4.45	0.53987	EGF-like, laminin (3);	.	.	.	.	T	0.67268	0.2875	M	0.61703	1.905	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.76575	0.988;0.969	T	0.66106	-0.6006	9	0.44086	T	0.13	.	11.9406	0.52899	0.1303:0.0:0.0:0.8697	.	617;617	Q6VU67;Q16787	.;LAMA3_HUMAN	H	617;617;615	ENSP00000324532:Y617H;ENSP00000382432:Y617H	ENSP00000324532:Y617H	Y	+	1	0	LAMA3	19648425	1.000000	0.71417	0.875000	0.34327	0.364000	0.29643	5.864000	0.69575	0.912000	0.36772	0.528000	0.53228	TAT	-	HMMPfam_Laminin_EGF,HMMSmart_SM00180,PatternScan_EGF_LAM_1,superfamily_EGF/Laminin		0.358	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LAMA3	protein_coding	OTTHUMT00000254824.3	T	NM_000227, NM_198129		19648425	+1	no_errors	NM_198129.3	genbank	human	reviewed	54_36p	missense	SNP	0.977	C
CEBPA	1050	genome.wustl.edu	37	19	33792368	33792369	+	In_Frame_Ins	INS	-	-	TCA			TCGA-AB-2808-03D-01W-0755-09	TCGA-AB-2808-11D-01W-0755-09	-	-	-	TCA	-	-	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	06038210-fb82-4e20-8c82-d6695453eecb	92b4a800-c7d2-4f97-94fc-85d30528c574	g.chr19:33792368_33792369insTCA	ENST00000498907.2	-	1	1101_1102	c.952_953insTGA	c.(952-954)acc>aTGAcc	p.317_318insM	CEBPA-AS1_ENST00000592982.2_RNA|CTD-2540B15.7_ENST00000587312.1_RNA|CTD-2540B15.11_ENST00000589932.1_RNA	NM_004364.3	NP_004355.2	P49715	CEBPA_HUMAN	CCAAT/enhancer binding protein (C/EBP), alpha	317	Leucine-zipper. {ECO:0000255|PROSITE- ProRule:PRU00978}.|bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				acute-phase response (GO:0006953)|brown fat cell differentiation (GO:0050873)|cell maturation (GO:0048469)|cellular response to lithium ion (GO:0071285)|cellular response to organic cyclic compound (GO:0071407)|cholesterol metabolic process (GO:0008203)|cytokine-mediated signaling pathway (GO:0019221)|embryonic placenta development (GO:0001892)|generation of precursor metabolites and energy (GO:0006091)|inner ear development (GO:0048839)|liver development (GO:0001889)|lung development (GO:0030324)|macrophage differentiation (GO:0030225)|mitochondrion organization (GO:0007005)|myeloid cell differentiation (GO:0030099)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ regeneration (GO:0031100)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|response to glucocorticoid (GO:0051384)|response to vitamin B2 (GO:0033274)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|urea cycle (GO:0000050)|viral process (GO:0016032)|white fat cell differentiation (GO:0050872)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|Rb-E2F complex (GO:0035189)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.L317_T318ins13(3)|p.H200_K352>Q(1)|p.?(1)|p.S319fs*11(1)|p.L317_T318insV(1)|p.L317_T318insL(1)|p.L317_T318insKVLEL(1)|p.L317_S319>L(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(912)|lung(5)|prostate(1)|stomach(1)	920	Esophageal squamous(110;0.137)					ATTGTCACTGGTCAGCTCCAGC	0.658			"""Mis, N, F"""		"""AML, MDS"""				Acute Myeloid Leukemia, Familial, associated with CEBPA germline mutation																													dbGAP		Dom	yes		19	19q13.1	1050	"""CCAAT/enhancer binding protein (C/EBP), alpha"""		L	10	Insertion - In frame(6)|Complex - deletion inframe(2)|Unknown(1)|Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(10)	19																																								38484209	SO:0001652	inframe_insertion	0	Familial Cancer Database	Familial AML	M37197	CCDS54243.1	19q13.1	2014-09-17				ENSG00000245848		"""basic leucine zipper proteins"""	1833	protein-coding gene	gene with protein product		116897		CEBP		1535333, 1840554	Standard	NM_004364		Approved	C/EBP-alpha	uc002nun.3	P49715		ENST00000498907.2:c.950_952dupTGA	19.37:g.33792369_33792371dupTCA	ENSP00000427514:p.Leu317_Thr318insMet	1	0.00	0		73	31.78	34	38484208	16	42.86	12	A7LNP2|P78319|Q05CA4	In_Frame_Ins	INS	HMMSmart_BRLZ,PatternScan_BZIP_BASIC,HMMPfam_bZIP_2	p.318in_frame_insM	ENST00000498907.2	37	c.953_952	CCDS54243.1	19																																																																																			-	HMMSmart_BRLZ,HMMPfam_bZIP_2		0.658	CEBPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CEBPA	protein_coding	OTTHUMT00000365012.1	-	NM_004364		38484209	-1	no_errors	NM_004364.3	genbank	human	reviewed	54_36p	in_frame_ins	INS	0.992:0.993	TCA
