#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_NormalRefReads_WU	i_NormalVAF_WU	i_NormalVarReads_WU	i_ORegAnno_bin	i_RNARefReads_WU	i_RNAVAF_WU	i_RNAVarReads_WU	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_Start_position_hg18	i_TumorRefReads_WU	i_TumorVAF_WU	i_TumorVarReads_WU	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_deletion_substructures	i_domain	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_name	i_gene_type	i_havana_transcript	i_reference	i_refseq_mrna_id	i_secondary_variant_classification	i_stop	i_strand	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_type	i_ucsc_cons	i_variant
SOS1	6654	genome.wustl.edu	37	2	39249914	39249914	+	Missense_Mutation	SNP	C	C	T	rs397517154		TCGA-AB-2990-03A-01D-0739-09	TCGA-AB-2990-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	8b0e6903-5e1e-4f8b-8f17-8c2442507379	7ff43be0-1381-4220-a165-9a9e17909534	g.chr2:39249914C>T	ENST00000426016.1	-	11	1741	c.1655G>A	c.(1654-1656)aGg>aAg	p.R552K	SOS1_ENST00000402219.2_Missense_Mutation_p.R552K|SOS1_ENST00000395038.2_Missense_Mutation_p.R552K|SOS1_ENST00000472480.1_5'Flank			Q07889	SOS1_HUMAN	son of sevenless homolog 1 (Drosophila)	552			R -> G (in NS4; increases the basal level of active RAS; prolonges RAS activation after EGF stimulation and enhances ERK activation; dbSNP:rs137852814). {ECO:0000269|PubMed:17143282, ECO:0000269|PubMed:17143285, ECO:0000269|PubMed:19953625, ECO:0000269|PubMed:21387466}.|R -> K (in NS4). {ECO:0000269|PubMed:17143282, ECO:0000269|PubMed:21387466}.|R -> M (in NS4). {ECO:0000269|PubMed:21387466}.|R -> S (in NS4). {ECO:0000269|PubMed:17143282, ECO:0000269|PubMed:21387466}.|R -> T (in NS4). {ECO:0000269|PubMed:21387466}.		apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|Ras protein signal transduction (GO:0007265)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	DNA binding (GO:0003677)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R552K(2)|p.R552M(1)		autonomic_ganglia(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(29)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	75		all_hematologic(82;0.21)				ATCAAGCATCCTTTCCAGTGT	0.403									Noonan syndrome																													dbGAP											3	Substitution - Missense(3)	endometrium(2)|haematopoietic_and_lymphoid_tissue(1)	2	GRCh37	CM070273	SOS1	M							156.0	147.0	150.0					2																	39249914		2203	4300	6503	39103418	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	L13857	CCDS1802.1	2p21	2014-09-17	2002-11-05		ENSG00000115904	ENSG00000115904		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11187	protein-coding gene	gene with protein product		182530	"""gingival fibromatosis, hereditary, 1"""	GINGF		8276400, 10995566	Standard	NM_005633		Approved	HGF, GF1	uc002rrk.4	Q07889	OTTHUMG00000102109	ENST00000426016.1:c.1655G>A	2.37:g.39249914C>T	ENSP00000387784:p.Arg552Lys	Somatic	436	6.64	31		16	36.00	9	WXS	Illumina HiSeq	Phase_IV	39103418	630	41.01	438	A8K2G3|B4DXG2	Missense_Mutation	SNP	HMMPfam_RhoGEF,HMMSmart_SM00325,superfamily_DBL homology domain (DH-domain),HMMPfam_RasGEF_N,HMMSmart_SM00229,HMMPfam_PH,HMMSmart_SM00233,HMMPfam_RasGEF,HMMSmart_SM00147,HMMPfam_Histone,superfamily_Ras GEF,superfamily_Histone-fold,PatternScan_RASGEF,superfamily_PH domain-like	p.R552K	ENST00000426016.1	37	c.1655	CCDS1802.1	2	.	.	.	.	.	.	.	.	.	.	C	25.9	4.686644	0.88639	.	.	ENSG00000115904	ENST00000426016;ENST00000402219;ENST00000543698;ENST00000395038;ENST00000263879	D;D;D	0.87029	-2.2;-2.2;-2.2	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	D	0.94401	0.8199	M	0.85859	2.78	0.80722	D	1	D;D	0.69078	0.996;0.997	D;D	0.87578	0.998;0.992	D	0.93719	0.7031	10	0.48119	T	0.1	.	20.0039	0.97428	0.0:1.0:0.0:0.0	.	284;552	F5GX06;Q07889	.;SOS1_HUMAN	K	552;552;284;552;552	ENSP00000387784:R552K;ENSP00000384675:R552K;ENSP00000378479:R552K	ENSP00000263879:R552K	R	-	2	0	SOS1	39103418	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.711000	0.84669	2.722000	0.93159	0.557000	0.71058	AGG	-	NULL		0.403	SOS1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	SOS1	protein_coding	OTTHUMT00000219948.3	C	NM_005633		39103418	-1	no_errors	NM_005633.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
EPB41L5	57669	genome.wustl.edu	37	2	120849220	120849220	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2990-03A-01D-0739-09	TCGA-AB-2990-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	8b0e6903-5e1e-4f8b-8f17-8c2442507379	7ff43be0-1381-4220-a165-9a9e17909534	g.chr2:120849220G>A	ENST00000263713.5	+	13	1347	c.1133G>A	c.(1132-1134)cGa>cAa	p.R378Q	EPB41L5_ENST00000443902.2_Missense_Mutation_p.R378Q|EPB41L5_ENST00000331393.4_Missense_Mutation_p.R378Q|EPB41L5_ENST00000452780.1_Missense_Mutation_p.R378Q|EPB41L5_ENST00000443124.1_Missense_Mutation_p.R378Q	NM_020909.3	NP_065960.2	Q9HCM4	E41L5_HUMAN	erythrocyte membrane protein band 4.1 like 5	378					actomyosin structure organization (GO:0031032)|apical constriction (GO:0003383)|axial mesoderm morphogenesis (GO:0048319)|cellular response to transforming growth factor beta stimulus (GO:0071560)|ectoderm development (GO:0007398)|embryonic foregut morphogenesis (GO:0048617)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|in utero embryonic development (GO:0001701)|left/right axis specification (GO:0070986)|mesoderm migration involved in gastrulation (GO:0007509)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of protein binding (GO:0032091)|neural plate morphogenesis (GO:0001839)|paraxial mesoderm development (GO:0048339)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein binding (GO:0032092)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of establishment of protein localization (GO:0070201)|somite rostral/caudal axis specification (GO:0032525)|substrate-dependent cell migration, cell attachment to substrate (GO:0006931)|unidimensional cell growth (GO:0009826)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)		p.R378Q(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(5)|lung(12)|ovary(1)	26						TATTCTAGACGAACTCTACAA	0.383																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	2											104.0	90.0	95.0					2																	120849220		2203	4300	6503	120565690	SO:0001583	missense	0			AK023019	CCDS2130.1, CCDS54392.1, CCDS54393.1	2q14.2	2009-07-28			ENSG00000115109	ENSG00000115109			19819	protein-coding gene	gene with protein product		611730					Standard	NM_001184937		Approved	KIAA1548, FLJ12957, BE37, YMO1	uc002tmg.3	Q9HCM4	OTTHUMG00000131433	ENST00000263713.5:c.1133G>A	2.37:g.120849220G>A	ENSP00000263713:p.Arg378Gln	Somatic	443	9.22	45		2	60.00	3	WXS	Illumina HiSeq	Phase_IV	120565690	921	34.91	494	Q7Z5S1|Q8IZ12|Q9H975	Missense_Mutation	SNP	HMMPfam_FA,HMMPfam_FERM_N,HMMPfam_FERM_C,PatternScan_FERM_1,PatternScan_FERM_2,HMMPfam_FERM_M,superfamily_Second domain of FERM,HMMSmart_SM00295,superfamily_PH domain-like,superfamily_Ubiquitin-like	p.R378Q	ENST00000263713.5	37	c.1133	CCDS2130.1	2	.	.	.	.	.	.	.	.	.	.	G	32	5.154222	0.94645	.	.	ENSG00000115109	ENST00000263713;ENST00000443902;ENST00000331393;ENST00000443124;ENST00000452780	D;D;D;D;D	0.88586	-2.4;-2.4;-2.4;-2.4;-2.4	5.82	5.82	0.92795	FERM adjacent (FA) (1);	0.000000	0.64402	D	0.000004	D	0.95004	0.8383	M	0.80028	2.48	0.80722	D	1	D;D;D;D	0.89917	0.998;1.0;1.0;1.0	P;D;D;D	0.97110	0.886;1.0;0.994;1.0	D	0.94825	0.7990	10	0.72032	D	0.01	.	20.1142	0.97922	0.0:0.0:1.0:0.0	.	378;378;378;378	Q9HCM4-3;Q9HCM4-4;Q9HCM4-2;Q9HCM4	.;.;.;E41L5_HUMAN	Q	378	ENSP00000263713:R378Q;ENSP00000393856:R378Q;ENSP00000329687:R378Q;ENSP00000393722:R378Q;ENSP00000390439:R378Q	ENSP00000263713:R378Q	R	+	2	0	EPB41L5	120565690	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	9.728000	0.98792	2.765000	0.95021	0.650000	0.86243	CGA	-	HMMPfam_FA		0.383	EPB41L5-001	KNOWN	basic|CCDS	protein_coding	EPB41L5	protein_coding	OTTHUMT00000254230.2	G	NM_020909		120565690	+1	no_errors	NM_020909.2	genbank	human	provisional	54_36p	missense	SNP	0.995	A
IDH1	3417	genome.wustl.edu	37	2	209113113	209113113	+	Missense_Mutation	SNP	G	G	C	rs121913499		TCGA-AB-2990-03A-01D-0739-09	TCGA-AB-2990-11A-01D-0739-09	G	G	G	C	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	8b0e6903-5e1e-4f8b-8f17-8c2442507379	7ff43be0-1381-4220-a165-9a9e17909534	g.chr2:209113113G>C	ENST00000415913.1	-	4	775	c.394C>G	c.(394-396)Cgt>Ggt	p.R132G	IDH1_ENST00000446179.1_Missense_Mutation_p.R132G|IDH1_ENST00000345146.2_Missense_Mutation_p.R132G	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132C(446)|p.R132G(125)|p.R132S(106)|p.G131_R132>VL(1)|p.R132V(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		TAAGCATGACGACCTATGATG	0.398			Mis		gliobastoma																																Pancreas(158;264 1958 3300 35450 36047)	dbGAP		Dom	yes		2	2q33.3	3417	"""isocitrate dehydrogenase 1 (NADP+), soluble"""		O	679	Substitution - Missense(678)|Complex - compound substitution(1)	haematopoietic_and_lymphoid_tissue(280)|central_nervous_system(181)|bone(177)|biliary_tract(21)|soft_tissue(12)|large_intestine(2)|skin(2)|autonomic_ganglia(1)|endometrium(1)|NS(1)|prostate(1)	2											81.0	74.0	76.0					2																	209113113		2203	4300	6503	208821358	SO:0001583	missense	0				CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.394C>G	2.37:g.209113113G>C	ENSP00000390265:p.Arg132Gly	Somatic	441	10.18	50		35	50.70	36	WXS	Illumina HiSeq	Phase_IV	208821358	580	41.12	405	Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like	p.R132G	ENST00000415913.1	37	c.394	CCDS2381.1	2	.	.	.	.	.	.	.	.	.	.	G	22.4	4.286370	0.80803	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	5.57	5.57	0.84162	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.96636	0.8902	H	0.99379	4.54	0.80722	D	1	D	0.57899	0.981	P	0.62813	0.907	D	0.98312	1.0524	10	0.87932	D	0	-20.0399	19.5341	0.95242	0.0:0.0:1.0:0.0	.	132	O75874	IDHC_HUMAN	G	132	ENSP00000260985:R132G;ENSP00000410513:R132G;ENSP00000390265:R132G;ENSP00000391075:R132G	ENSP00000260985:R132G	R	-	1	0	IDH1	208821358	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	7.074000	0.76791	2.616000	0.88540	0.555000	0.69702	CGT	-	HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like		0.398	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	IDH1	protein_coding	OTTHUMT00000336672.1	G			208821358	-1	no_errors	NM_005896.2	genbank	human	reviewed	54_36p	missense	SNP	1.000	C
CADM2	253559	genome.wustl.edu	37	3	86114833	86114833	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2990-03A-01D-0739-09	TCGA-AB-2990-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	8b0e6903-5e1e-4f8b-8f17-8c2442507379	7ff43be0-1381-4220-a165-9a9e17909534	g.chr3:86114833C>T	ENST00000407528.2	+	9	1204	c.1142C>T	c.(1141-1143)aCg>aTg	p.T381M	CADM2_ENST00000405615.2_Missense_Mutation_p.T383M|CADM2_ENST00000383699.3_Missense_Mutation_p.T350M	NM_001167674.1	NP_001161146.1	Q8N3J6	CADM2_HUMAN	cell adhesion molecule 2	381					adherens junction organization (GO:0034332)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|synapse (GO:0045202)		p.T383M(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(1)|prostate(1)|skin(4)	38		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)		GTATTTGTCACGCTGTGTTCT	0.423																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	3											200.0	171.0	181.0					3																	86114833		2203	4300	6503	86197523	SO:0001583	missense	0			AF538973	CCDS33792.1, CCDS54613.1, CCDS54614.1	3p12.2	2013-01-11	2007-02-07	2007-02-07	ENSG00000175161	ENSG00000175161		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"""	29849	protein-coding gene	gene with protein product	"""nectin-like 3"""	609938	"""immunoglobulin superfamily, member 4D"""	IGSF4D			Standard	NM_153184		Approved	NECL3, Necl-3, SynCAM2	uc003dqj.3	Q8N3J6	OTTHUMG00000158990	ENST00000407528.2:c.1142C>T	3.37:g.86114833C>T	ENSP00000384575:p.Thr381Met	Somatic	433	7.46	35		1	0.00	0	WXS	Illumina HiSeq	Phase_IV	86197523	428	41.45	303	G3XHN7|G3XHN8|Q3KQY9|Q658Q7|Q8IZP8	Missense_Mutation	SNP	HMMSmart_4.1m,HMMSmart_IGc2,HMMSmart_IG,HMMPfam_V-set,HMMPfam_ig,HMMPfam_C2-set_2,superfamily_SSF48726	p.T383M	ENST00000407528.2	37	c.1148	CCDS54614.1	3	.	.	.	.	.	.	.	.	.	.	C	13.50	2.255425	0.39896	.	.	ENSG00000175161	ENST00000383699;ENST00000407528;ENST00000405615	T;T;T	0.63417	1.03;-0.04;-0.03	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.61837	0.2379	N	0.04043	-0.29	0.80722	D	1	P;D;D	0.89917	0.949;1.0;1.0	P;D;D	0.87578	0.674;0.998;0.997	T	0.64385	-0.6420	10	0.22109	T	0.4	.	19.964	0.97260	0.0:1.0:0.0:0.0	.	383;350;381	Q8N3J6-3;G3XHN4;Q8N3J6	.;.;CADM2_HUMAN	M	350;381;383	ENSP00000373200:T350M;ENSP00000384575:T381M;ENSP00000384193:T383M	ENSP00000373200:T350M	T	+	2	0	CADM2	86197523	1.000000	0.71417	0.995000	0.50966	0.995000	0.86356	7.818000	0.86416	2.721000	0.93114	0.650000	0.86243	ACG	-	NULL		0.423	CADM2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	CADM2	protein_coding	OTTHUMT00000352822.1	C	NM_153184		86197523	+1	no_errors	NM_153184.2	genbank	human	validated	54_36p	missense	SNP	1.000	T
ZNF462	58499	genome.wustl.edu	37	9	109691231	109691231	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2990-03A-01D-0739-09	TCGA-AB-2990-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	8b0e6903-5e1e-4f8b-8f17-8c2442507379	7ff43be0-1381-4220-a165-9a9e17909534	g.chr9:109691231C>T	ENST00000277225.5	+	3	5327	c.5038C>T	c.(5038-5040)Cgc>Tgc	p.R1680C	ZNF462_ENST00000441147.2_Missense_Mutation_p.R525C|ZNF462_ENST00000457913.1_Missense_Mutation_p.R1680C			Q96JM2	ZN462_HUMAN	zinc finger protein 462	1680					chromatin organization (GO:0006325)|negative regulation of DNA binding (GO:0043392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R1680C(1)		NS(2)|autonomic_ganglia(2)|breast(5)|central_nervous_system(4)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(20)|lung(32)|ovary(5)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	119						CAGGCACTACCGCATCAAGCA	0.567																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	9											143.0	124.0	130.0					9																	109691231		2203	4300	6503	108731052	SO:0001583	missense	0			AB058706	CCDS35096.1	9q31.3	2008-02-05			ENSG00000148143	ENSG00000148143		"""Zinc fingers, C2H2-type"""	21684	protein-coding gene	gene with protein product							Standard	NM_021224		Approved	DKFZP762N2316, KIAA1803, Zfp462	uc004bcz.3	Q96JM2	OTTHUMG00000020438	ENST00000277225.5:c.5038C>T	9.37:g.109691231C>T	ENSP00000277225:p.Arg1680Cys	Somatic	567	9.71	61		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	108731052	582	38.63	367	Q5T0T4|Q8N408	Missense_Mutation	SNP	HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers,superfamily_beta-sandwich domain of Sec23/24	p.R1680C	ENST00000277225.5	37	c.5038	CCDS35096.1	9	.	.	.	.	.	.	.	.	.	.	C	19.72	3.879503	0.72294	.	.	ENSG00000148143	ENST00000277225;ENST00000457913;ENST00000374686;ENST00000441147	T;T;T;T	0.11604	2.76;3.2;3.15;3.21	6.03	6.03	0.97812	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);	0.000000	0.85682	D	0.000000	T	0.24198	0.0586	N	0.24115	0.695	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.01198	-1.1421	10	0.72032	D	0.01	-21.9171	20.5568	0.99304	0.0:1.0:0.0:0.0	.	1680;1680	Q96JM2-3;Q96JM2	.;ZN462_HUMAN	C	1680;1680;563;525	ENSP00000277225:R1680C;ENSP00000414570:R1680C;ENSP00000363818:R563C;ENSP00000397306:R525C	ENSP00000277225:R1680C	R	+	1	0	ZNF462	108731052	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.456000	0.80751	2.861000	0.98227	0.655000	0.94253	CGC	-	PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers,superfamily_beta-sandwich domain of Sec23/24		0.567	ZNF462-001	KNOWN	basic|CCDS	protein_coding	ZNF462	protein_coding	OTTHUMT00000053532.2	C	NM_021224		108731052	+1	no_errors	NM_021224.4	genbank	human	validated	54_36p	missense	SNP	1.000	T
CALB2	794	genome.wustl.edu	37	16	71419500	71419500	+	Silent	SNP	C	C	T			TCGA-AB-2990-03A-01D-0739-09	TCGA-AB-2990-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	8b0e6903-5e1e-4f8b-8f17-8c2442507379	7ff43be0-1381-4220-a165-9a9e17909534	g.chr16:71419500C>T	ENST00000302628.4	+	10	725	c.648C>T	c.(646-648)gaC>gaT	p.D216D	CALB2_ENST00000349553.5_Missense_Mutation_p.T185M	NM_001740.4	NP_001731.2	P22676	CALB2_HUMAN	calbindin 2	216	EF-hand 5. {ECO:0000255|PROSITE- ProRule:PRU00448}.				cytosolic calcium ion homeostasis (GO:0051480)	cytoplasm (GO:0005737)|gap junction (GO:0005921)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.D216D(2)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	18		Ovarian(137;0.125)				GCTACATTGACGAGCATGAGC	0.567																																						dbGAP											2	Substitution - coding silent(2)	haematopoietic_and_lymphoid_tissue(1)|prostate(1)	16											58.0	52.0	54.0					16																	71419500		2198	4300	6498	69977001	SO:0001819	synonymous_variant	0			X56667	CCDS10899.1	16q22.2	2013-01-10	2008-05-19		ENSG00000172137	ENSG00000172137		"""EF-hand domain containing"""	1435	protein-coding gene	gene with protein product	"""calretinin"""	114051	"""calbindin 2, 29kDa (calretinin)"""			1906795	Standard	NM_001740		Approved	CAL2	uc002faa.4	P22676	OTTHUMG00000137589	ENST00000302628.4:c.648C>T	16.37:g.71419500C>T		Somatic	1079	9.10	108		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	69977001	909	40.82	629	A8K4Y1|Q53HD2|Q96BK4	Missense_Mutation	SNP	HMMSmart_EFh,PatternScan_EF_HAND_1,HMMPfam_efhand,superfamily_SSF47473	p.T185M	ENST00000302628.4	37	c.554	CCDS10899.1	16	.	.	.	.	.	.	.	.	.	.	C	16.41	3.114761	0.56505	.	.	ENSG00000172137	ENST00000349553	D	0.81821	-1.54	6.15	-2.95	0.05564	.	.	.	.	.	T	0.71592	0.3358	.	.	.	0.24385	N	0.99478	B	0.02656	0.0	B	0.01281	0.0	T	0.60352	-0.7280	8	0.72032	D	0.01	-23.0477	12.6233	0.56616	0.0:0.4879:0.0:0.5121	.	185	A6NER6	.	M	185	ENSP00000340294:T185M	ENSP00000340294:T185M	T	+	2	0	CALB2	69977001	0.994000	0.37717	0.979000	0.43373	0.964000	0.63967	0.102000	0.15272	-0.536000	0.06298	-0.822000	0.03109	ACG	-	NULL		0.567	CALB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CALB2	protein_coding	OTTHUMT00000268988.1	C	NM_001740		69977001	+1	no_errors	NM_007088.3	genbank	human	reviewed	54_36p	missense	SNP	0.999	T
ANKRD24	170961	genome.wustl.edu	37	19	4186441	4186441	+	Nonsense_Mutation	SNP	C	C	T	rs575865153		TCGA-AB-2990-03A-01D-0739-09	TCGA-AB-2990-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	8b0e6903-5e1e-4f8b-8f17-8c2442507379	7ff43be0-1381-4220-a165-9a9e17909534	g.chr19:4186441C>T	ENST00000600132.1	+	2	295	c.19C>T	c.(19-21)Cga>Tga	p.R7*	ANKRD24_ENST00000318934.4_Nonsense_Mutation_p.R7*	NM_133475.1	NP_597732.1	Q8TF21	ANR24_HUMAN	ankyrin repeat domain 24	7								p.R7*(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)	21				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0233)|STAD - Stomach adenocarcinoma(1328;0.181)		TCTCAGGGCGCGATTTAAGAA	0.577											OREG0025160	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1	0.000199681	0.0008	0.0	5008	,	,		18912	0.0		0.0	False		,,,				2504	0.0					dbGAP											1	Substitution - Nonsense(1)	haematopoietic_and_lymphoid_tissue(1)	19											78.0	82.0	81.0					19																	4186441		1976	4145	6121	4137441	SO:0001587	stop_gained	0			AB075861	CCDS45925.1	19p13.3	2013-01-10				ENSG00000089847		"""Ankyrin repeat domain containing"""	29424	protein-coding gene	gene with protein product						11853319	Standard	NM_133475		Approved	KIAA1981	uc010dtt.1	Q8TF21		ENST00000600132.1:c.19C>T	19.37:g.4186441C>T	ENSP00000471252:p.Arg7*	Somatic	447	11.49	58	616	NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	4137441	364	41.38	257	O75268|O95781	Nonsense_Mutation	SNP	HMMPfam_Ank,HMMSmart_SM00248,superfamily_Ankyrin repeat	p.R7*	ENST00000600132.1	37	c.19	CCDS45925.1	19	.	.	.	.	.	.	.	.	.	.	C	37	6.445940	0.97572	.	.	ENSG00000089847	ENST00000318934	.	.	.	3.52	2.43	0.29744	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.0194	0.30400	0.2429:0.7571:0.0:0.0	.	.	.	.	X	7	.	ENSP00000321731:R7X	R	+	1	2	ANKRD24	4137441	0.052000	0.20516	0.969000	0.41365	0.787000	0.44495	1.098000	0.31000	0.777000	0.33496	0.484000	0.47621	CGA	-	NULL		0.577	ANKRD24-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	ANKRD24	protein_coding	OTTHUMT00000458188.1	C	XM_114000		4137441	+1	no_errors	NM_133475.1	genbank	human	provisional	54_36p	nonsense	SNP	0.921	T
LAMA5	3911	genome.wustl.edu	37	20	60900434	60900434	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2990-03A-01D-0739-09	TCGA-AB-2990-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	8b0e6903-5e1e-4f8b-8f17-8c2442507379	7ff43be0-1381-4220-a165-9a9e17909534	g.chr20:60900434C>T	ENST00000252999.3	-	41	5533	c.5467G>A	c.(5467-5469)Gcc>Acc	p.A1823T		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	1823	Laminin IV type A. {ECO:0000255|PROSITE- ProRule:PRU00458}.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)	p.A1823T(1)		breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			CTGGCCAGGGCCCCCTGGCCT	0.672																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	20											29.0	30.0	30.0					20																	60900434		2201	4296	6497	60333829	SO:0001583	missense	0			AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"""Laminins"""	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.5467G>A	20.37:g.60900434C>T	ENSP00000252999:p.Ala1823Thr	Somatic	66	8.22	6		4	20.00	1	WXS	Illumina HiSeq	Phase_IV	60333829	56	41.84	41	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	HMMPfam_Laminin_B,PatternScan_TNFR_NGFR_1,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,superfamily_EGF/Laminin	p.A1823T	ENST00000252999.3	37	c.5467	CCDS33502.1	20	.	.	.	.	.	.	.	.	.	.	C	1.276	-0.611702	0.03690	.	.	ENSG00000130702	ENST00000252999	T	0.35605	1.3	4.84	-1.79	0.07932	Laminin B type IV (2);	0.776649	0.12546	N	0.459469	T	0.15565	0.0375	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.19031	-1.0318	10	0.23891	T	0.37	.	3.1094	0.06352	0.1376:0.3867:0.2549:0.2207	.	1823	O15230	LAMA5_HUMAN	T	1823	ENSP00000252999:A1823T	ENSP00000252999:A1823T	A	-	1	0	LAMA5	60333829	0.020000	0.18652	0.002000	0.10522	0.000000	0.00434	0.183000	0.16919	-0.381000	0.07882	-2.419000	0.00218	GCC	-	HMMPfam_Laminin_B		0.672	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LAMA5	protein_coding	OTTHUMT00000080014.2	C	NM_005560		60333829	-1	no_errors	NM_005560.3	genbank	human	reviewed	54_36p	missense	SNP	0.013	T
NPM1	4869	genome.wustl.edu	37	5	170837547	170837548	+	Frame_Shift_Ins	INS	-	-	TCTG			TCGA-AB-2990-03A-01D-0739-09	TCGA-AB-2990-11A-01D-0739-09	-	-	-	TCTG	-	-	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	8b0e6903-5e1e-4f8b-8f17-8c2442507379	7ff43be0-1381-4220-a165-9a9e17909534	g.chr5:170837547_170837548insTCTG	ENST00000296930.5	+	11	1164_1165	c.863_864insTCTG	c.(862-867)tggcagfs	p.WQ288fs	NPM1_ENST00000351986.6_Frame_Shift_Ins_p.WQ259fs|NPM1_ENST00000517671.1_Frame_Shift_Ins_p.WQ288fs	NM_002520.6	NP_002511.1	P06748	NPM_HUMAN	nucleophosmin (nucleolar phosphoprotein B23, numatrin)	288	Required for nucleolar localization.			WQWRKSL -> CLAVEEVSLRK (in Ref. 6; AAW67752/AAW67755). {ECO:0000305}.|WQWRKSL -> CMAVEEVSLRK (in Ref. 6; AAW67753 and 7; ABC40399). {ECO:0000305}.|WQWRKSL -> CVAVEEVSLRK (in Ref. 6; AAW67754). {ECO:0000305}.	cell aging (GO:0007569)|CENP-A containing nucleosome assembly (GO:0034080)|centrosome cycle (GO:0007098)|DNA repair (GO:0006281)|intracellular protein transport (GO:0006886)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of centrosome duplication (GO:0010826)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|nucleocytoplasmic transport (GO:0006913)|nucleosome assembly (GO:0006334)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of translation (GO:0045727)|protein localization (GO:0008104)|protein oligomerization (GO:0051259)|regulation of centriole replication (GO:0046599)|regulation of eIF2 alpha phosphorylation by dsRNA (GO:0060735)|regulation of endodeoxyribonuclease activity (GO:0032071)|regulation of endoribonuclease activity (GO:0060699)|response to stress (GO:0006950)|ribosome assembly (GO:0042255)|signal transduction (GO:0007165)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle pole centrosome (GO:0031616)	histone binding (GO:0042393)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)|ribosomal large subunit binding (GO:0043023)|ribosomal small subunit binding (GO:0043024)|RNA binding (GO:0003723)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|unfolded protein binding (GO:0051082)	p.W288fs*12(2114)|p.W288fs*10(9)|p.Q289fs*11(3)|p.W288*(1)	NPM1/ALK(632)	central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(4261)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	4269	Renal(175;0.000159)|Lung NSC(126;0.00576)|all_lung(126;0.00963)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CAAGATCTCTGGCAGTGGAGGA	0.312			"""T, F """	"""ALK, RARA, MLF1"""	"""NHL, APL, AML"""																																	dbGAP		Dom	yes		5	5q35	4869	"""nucleophosmin (nucleolar phosphoprotein B23, numatrin)"""		L	2127	Insertion - Frameshift(2118)|Complex - frameshift(8)|Substitution - Nonsense(1)	haematopoietic_and_lymphoid_tissue(2127)	5																																								170770153	SO:0001589	frameshift_variant	0			M26697	CCDS4376.1, CCDS4377.1, CCDS43399.1	5q35.1	2014-09-17			ENSG00000181163	ENSG00000181163			7910	protein-coding gene	gene with protein product	"""nucleolar phosphoprotein B23"", ""numatrin"", ""nucleophosmin/nucleoplasmin family, member 1"""	164040				8471164, 8122112	Standard	NM_002520		Approved	B23, NPM	uc003mbi.3	P06748	OTTHUMG00000130465	ENST00000296930.5:c.860_863dupTCTG	5.37:g.170837544_170837547dupTCTG	ENSP00000296930:p.Trp288fs	Somatic	NA	NA	NA		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	170770152	NA	NA	NA	A8K3N7|B5BU00|D3DQL6|P08693|Q12826|Q13440|Q13441|Q14115|Q5EU94|Q5EU95|Q5EU96|Q5EU97|Q5EU98|Q5EU99|Q6V962|Q8WTW5|Q96AT6|Q96DC4|Q96EA5|Q9BYG9|Q9UDJ7	Frame_Shift_Ins	INS	HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain	p.W288fs	ENST00000296930.5	37	c.863_864	CCDS4376.1	5																																																																																			-	NULL		0.312	NPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NPM1	protein_coding	OTTHUMT00000252858.2	-	NM_002520		170770153	+1	no_errors	NM_002520.1	genbank	human	validated	54_36p	frame_shift_ins	INS	1.000:1.000	TCTG
