#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_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_EVS_AA	i_EVS_All	i_EVS_EA	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_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains_WU	i_amino_acid_change_WU	i_annotation_transcript	i_build	i_c_position_WU	i_ccds_id	i_chromosome_name_WU	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_default_gene_name_WU	i_deletion_substructures_WU	i_domain_WU	i_ensembl_gene_id	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_WU	i_gene_name_source_WU	i_gene_type	i_havana_transcript	i_normal_ref_reads	i_normal_vaf	i_normal_var_reads	i_reference_WU	i_refseq_mrna_id	i_secondary_variant_classification	i_start_WU	i_stop_WU	i_strand_WU	i_transcript_error_WU	i_transcript_name_WU	i_transcript_source_WU	i_transcript_species_WU	i_transcript_status_WU	i_transcript_version_WU	i_trv_type_WU	i_tumor_ref_reads	i_tumor_vaf	i_tumors_var_reads	i_type_WU	i_ucsc_cons_WU	i_variant_WU
APPL2	55198	genome.wustl.edu	37	12	105570747	105570747	+	Missense_Mutation	SNP	C	C	G			TCGA-AN-A0XP-01A-11D-A117-09	TCGA-AN-A0XP-10A-01D-A10G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	6179b498-2cea-4f7a-82a8-b7ec71431ea8	6c4eee86-8839-4a74-a786-b37e7dd35b21	g.chr12:105570747C>G	ENST00000258530.3	-	19	1944	c.1719G>C	c.(1717-1719)aaG>aaC	p.K573N	APPL2_ENST00000546731.1_5'Flank|APPL2_ENST00000539978.2_Missense_Mutation_p.K530N|APPL2_ENST00000551662.1_Missense_Mutation_p.K579N	NM_001251904.1|NM_018171.3	NP_001238833.1|NP_060641.2	Q06481	APLP2_HUMAN	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 2	0					cellular copper ion homeostasis (GO:0006878)|cholesterol metabolic process (GO:0008203)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|midbrain development (GO:0030901)|neuromuscular process controlling balance (GO:0050885)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of protein binding (GO:0043393)|suckling behavior (GO:0001967)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|serine-type endopeptidase inhibitor activity (GO:0004867)|transition metal ion binding (GO:0046914)	p.K573N(1)		breast(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						CAACCAGTCTCTTGTTTTCTT	0.398																																						dbGAP											1	Substitution - Missense(1)	breast(1)											94.0	92.0	93.0					12																	105570747		2203	4300	6503	-	-	-	SO:0001583	missense	0			AY113704	CCDS9101.1, CCDS58275.1, CCDS58276.1	12q23.3	2014-08-12			ENSG00000136044	ENSG00000136044		"""Pleckstrin homology (PH) domain containing"""	18242	protein-coding gene	gene with protein product		606231				11431708, 17030088	Standard	NM_001251904		Approved	FLJ10659, DIP13B	uc010swu.1	Q8NEU8	OTTHUMG00000169853	ENST00000258530.3:c.1719G>C	12.37:g.105570747C>G	ENSP00000258530:p.Lys573Asn	Somatic		WXS	Illumina GAIIx	Phase_IV	B3KXX9|H7BXI4|Q13861|Q14594|Q14662|Q71U10|Q7M4L3|Q9BT36	Missense_Mutation	SNP	pfam_PTyr_interaction_dom,pfam_Pleckstrin_homology,pfam_PTB,smart_Pleckstrin_homology,smart_PTyr_interaction_dom,pfscan_Pleckstrin_homology,pfscan_PTyr_interaction_dom	p.K579N	ENST00000258530.3	37	c.1737	CCDS9101.1	12	.	.	.	.	.	.	.	.	.	.	C	15.69	2.906580	0.52333	.	.	ENSG00000136044	ENST00000258530;ENST00000539978;ENST00000551662;ENST00000553109	T;T;T;T	0.19532	2.14;2.14;2.14;2.14	5.69	3.85	0.44370	Phosphotyrosine interaction domain (1);Pleckstrin homology-type (1);	0.197325	0.50627	D	0.000107	T	0.19805	0.0476	L	0.49126	1.545	0.41833	D	0.990089	P;P	0.43392	0.767;0.805	B;B	0.38458	0.193;0.274	T	0.01904	-1.1250	10	0.51188	T	0.08	-29.6515	11.8921	0.52635	0.0:0.8695:0.0:0.1305	.	579;573	F8W1P5;Q8NEU8	.;DP13B_HUMAN	N	573;530;579;104	ENSP00000258530:K573N;ENSP00000444472:K530N;ENSP00000446917:K579N;ENSP00000446510:K104N	ENSP00000258530:K573N	K	-	3	2	APPL2	104094877	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	1.116000	0.31221	0.743000	0.32719	0.650000	0.86243	AAG	APPL2	-	pfam_PTyr_interaction_dom,pfam_PTB,smart_PTyr_interaction_dom	ENSG00000136044		0.398	APPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	APPL2	HGNC	protein_coding	OTTHUMT00000406238.3	192	0.00	0	C	NM_018171		105570747	105570747	-1	no_errors	ENST00000551662	ensembl	human	known	69_37n	missense	91	44.17	72	SNP	1.000	G
CAMSAP1	157922	genome.wustl.edu	37	9	138714311	138714311	+	Silent	SNP	A	A	T			TCGA-AN-A0XP-01A-11D-A117-09	TCGA-AN-A0XP-10A-01D-A10G-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	6179b498-2cea-4f7a-82a8-b7ec71431ea8	6c4eee86-8839-4a74-a786-b37e7dd35b21	g.chr9:138714311A>T	ENST00000389532.4	-	11	2260	c.2196T>A	c.(2194-2196)acT>acA	p.T732T	CAMSAP1_ENST00000312405.6_Silent_p.T454T|CAMSAP1_ENST00000483991.1_5'UTR|CAMSAP1_ENST00000409386.3_Silent_p.T743T	NM_015447.3	NP_056262.3	Q5T5Y3	CAMP1_HUMAN	calmodulin regulated spectrin-associated protein 1	732					cytoskeleton organization (GO:0007010)|neuron projection development (GO:0031175)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|spectrin binding (GO:0030507)	p.T732T(1)		breast(3)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(11)|lung(16)|ovary(3)|pancreas(1)|skin(1)	47				OV - Ovarian serous cystadenocarcinoma(145;1.4e-06)|Epithelial(140;1.11e-05)		GCCTGAGGAGAGTCCACGGCT	0.517																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											86.0	78.0	81.0					9																	138714311		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AJ519841	CCDS35176.2	9q34.3	2008-02-05			ENSG00000130559	ENSG00000130559			19946	protein-coding gene	gene with protein product		613774				12477932	Standard	NM_015447		Approved	FLJ31228, DKFZp434F195	uc004cgr.4	Q5T5Y3	OTTHUMG00000020918	ENST00000389532.4:c.2196T>A	9.37:g.138714311A>T		Somatic		WXS	Illumina GAIIx	Phase_IV	A1L4L2|B2REB2|B2REB3|Q70W33|Q8NCY0|Q96E80|Q96FM3|Q9UFJ5	Silent	SNP	pfam_CKK_domain,pfam_CAMSAP_CH,pfam_CH-domain,superfamily_PRC_barrell-like,superfamily_CH-domain	p.T743	ENST00000389532.4	37	c.2229	CCDS35176.2	9																																																																																			CAMSAP1	-	NULL	ENSG00000130559		0.517	CAMSAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CAMSAP1	HGNC	protein_coding	OTTHUMT00000055024.2	81	0.00	0	A	XM_351857		138714311	138714311	-1	no_errors	ENST00000409386	ensembl	human	known	69_37n	silent	69	31.00	31	SNP	0.000	T
CAPN1	823	genome.wustl.edu	37	11	64953422	64953422	+	Missense_Mutation	SNP	T	T	C			TCGA-AN-A0XP-01A-11D-A117-09	TCGA-AN-A0XP-10A-01D-A10G-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	6179b498-2cea-4f7a-82a8-b7ec71431ea8	6c4eee86-8839-4a74-a786-b37e7dd35b21	g.chr11:64953422T>C	ENST00000527323.1	+	4	731	c.491T>C	c.(490-492)gTg>gCg	p.V164A	CAPN1_ENST00000279247.6_Missense_Mutation_p.V164A|CAPN1_ENST00000533129.1_Missense_Mutation_p.V164A|CAPN1_ENST00000524773.1_Missense_Mutation_p.V164A|CAPN1_ENST00000533820.1_Missense_Mutation_p.V164A			P07384	CAN1_HUMAN	calpain 1, (mu/I) large subunit	164	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of cell proliferation (GO:0008284)|proteolysis (GO:0006508)|receptor catabolic process (GO:0032801)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)	p.V164A(1)		breast(2)|endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	13		Lung NSC(402;0.094)|Melanoma(852;0.16)		Lung(977;0.00168)|LUSC - Lung squamous cell carcinoma(976;0.00813)		GACGTGGTCGTGGATGACCTG	0.607																																						dbGAP											1	Substitution - Missense(1)	breast(1)											46.0	53.0	51.0					11																	64953422		2166	4276	6442	-	-	-	SO:0001583	missense	0			X04366	CCDS44644.1	11q13	2013-01-10			ENSG00000014216	ENSG00000014216	3.4.22.52	"""EF-hand domain containing"""	1476	protein-coding gene	gene with protein product		114220				3017764, 2209092	Standard	NM_005186		Approved	muCANP, muCL, CANP, CANPL1	uc009yqd.2	P07384	OTTHUMG00000165614	ENST00000527323.1:c.491T>C	11.37:g.64953422T>C	ENSP00000431984:p.Val164Ala	Somatic		WXS	Illumina GAIIx	Phase_IV	Q2TTR0|Q6DHV4	Missense_Mutation	SNP	pfam_Peptidase_C2_calpain_cat,pfam_Calpain_domain_III,superfamily_Calpain_domain_III,smart_Peptidase_C2_calpain_cat,smart_Calpain_III,pfscan_EF_HAND_2,pfscan_Peptidase_C2_calpain_cat,prints_Calpain_cysteine_protease	p.V164A	ENST00000527323.1	37	c.491	CCDS44644.1	11	.	.	.	.	.	.	.	.	.	.	T	28.3	4.910702	0.92107	.	.	ENSG00000014216	ENST00000529133;ENST00000533820;ENST00000530571;ENST00000533129;ENST00000524773;ENST00000279247;ENST00000259755;ENST00000527323;ENST00000526468	T;T;T;T;T;T;T	0.27256	1.68;1.68;1.68;1.68;1.68;1.68;1.68	4.82	4.82	0.62117	Peptidase C2, calpain, catalytic domain (3);	0.230380	0.39274	N	0.001418	T	0.63212	0.2492	H	0.99169	4.455	0.46222	D	0.998932	B	0.27068	0.167	P	0.45998	0.5	T	0.71659	-0.4526	10	0.87932	D	0	.	12.3551	0.55171	0.0:0.0:0.0:1.0	.	164	P07384	CAN1_HUMAN	A	164;164;164;164;164;164;110;164;59	ENSP00000432512:V164A;ENSP00000435272:V164A;ENSP00000431686:V164A;ENSP00000434176:V164A;ENSP00000279247:V164A;ENSP00000431984:V164A;ENSP00000433366:V59A	ENSP00000259755:V110A	V	+	2	0	CAPN1	64709998	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.967000	0.87967	1.811000	0.52892	0.533000	0.62120	GTG	CAPN1	-	pfam_Peptidase_C2_calpain_cat,smart_Peptidase_C2_calpain_cat,pfscan_Peptidase_C2_calpain_cat,prints_Calpain_cysteine_protease	ENSG00000014216		0.607	CAPN1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	CAPN1	HGNC	protein_coding	OTTHUMT00000385325.1	87	0.00	0	T			64953422	64953422	+1	no_errors	ENST00000279247	ensembl	human	known	69_37n	missense	78	30.36	34	SNP	1.000	C
CCDC120	90060	genome.wustl.edu	37	X	48924824	48924824	+	Missense_Mutation	SNP	C	C	T			TCGA-AN-A0XP-01A-11D-A117-09	TCGA-AN-A0XP-10A-01D-A10G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	6179b498-2cea-4f7a-82a8-b7ec71431ea8	6c4eee86-8839-4a74-a786-b37e7dd35b21	g.chrX:48924824C>T	ENST00000376396.3	+	10	1288	c.1069C>T	c.(1069-1071)Cgc>Tgc	p.R357C	CCDC120_ENST00000536628.2_Missense_Mutation_p.R345C|CCDC120_ENST00000597275.1_Missense_Mutation_p.R357C|CCDC120_ENST00000422185.2_Missense_Mutation_p.R357C|CCDC120_ENST00000496529.2_Missense_Mutation_p.R357C|CCDC120_ENST00000603986.1_Missense_Mutation_p.R392C	NM_001271835.1|NM_001271836.1|NM_033626.2	NP_001258764.1|NP_001258765.1|NP_296375.1	Q96HB5	CC120_HUMAN	coiled-coil domain containing 120	357								p.R357C(1)		breast(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	14						TCGCACCCGCCGCAGCAACAG	0.711																																						dbGAP											1	Substitution - Missense(1)	breast(1)											15.0	17.0	16.0					X																	48924824		2173	4204	6377	-	-	-	SO:0001583	missense	0			BC008769	CCDS14316.1, CCDS55413.1, CCDS55414.1, CCDS55414.2	Xp11.23	2008-02-05			ENSG00000147144	ENSG00000147144			28910	protein-coding gene	gene with protein product						12477932	Standard	NM_033626		Approved	JM11	uc011mmr.3	Q96HB5	OTTHUMG00000021509	ENST00000376396.3:c.1069C>T	X.37:g.48924824C>T	ENSP00000365577:p.Arg357Cys	Somatic		WXS	Illumina GAIIx	Phase_IV	B4DFC1|B4DTU2|F5GZU4	Missense_Mutation	SNP	pfam_DUF3338	p.R357C	ENST00000376396.3	37	c.1069	CCDS14316.1	X	.	.	.	.	.	.	.	.	.	.	C	17.81	3.481552	0.63849	.	.	ENSG00000147144	ENST00000376396;ENST00000422185;ENST00000536628	.	.	.	5.28	3.52	0.40303	.	0.060951	0.64402	N	0.000002	T	0.68805	0.3041	L	0.58810	1.83	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.982;0.996;0.996;0.993	T	0.67688	-0.5606	9	0.87932	D	0	-27.3508	8.5406	0.33390	0.0:0.8122:0.0:0.1878	.	345;392;345;357	B4DTU2;B4DFC1;B4DF24;Q96HB5	.;.;.;CC120_HUMAN	C	357;357;345	.	ENSP00000365577:R357C	R	+	1	0	CCDC120	48811768	1.000000	0.71417	0.978000	0.43139	0.979000	0.70002	2.440000	0.44855	0.450000	0.26774	0.529000	0.55759	CGC	CCDC120	-	NULL	ENSG00000147144		0.711	CCDC120-001	KNOWN	basic|CCDS	protein_coding	CCDC120	HGNC	protein_coding	OTTHUMT00000056528.1	8	0.00	0	C	NM_033626		48924824	48924824	+1	no_errors	ENST00000422185	ensembl	human	known	69_37n	missense	9	35.71	5	SNP	1.000	T
CD2	914	genome.wustl.edu	37	1	117311091	117311091	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AN-A0XP-01A-11D-A117-09	TCGA-AN-A0XP-10A-01D-A10G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	6179b498-2cea-4f7a-82a8-b7ec71431ea8	6c4eee86-8839-4a74-a786-b37e7dd35b21	g.chr1:117311091G>T	ENST00000369478.3	+	5	850	c.742G>T	c.(742-744)Gag>Tag	p.E248*		NM_001767.3	NP_001758.2	P06729	CD2_HUMAN	CD2 molecule	248					apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|heterotypic cell-cell adhesion (GO:0034113)|leukocyte migration (GO:0050900)|membrane raft polarization (GO:0001766)|natural killer cell activation (GO:0030101)|positive regulation of interferon-gamma secretion (GO:1902715)|positive regulation of interleukin-8 secretion (GO:2000484)|positive regulation of myeloid dendritic cell activation (GO:0030887)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of T cell differentiation (GO:0045580)|single organismal cell-cell adhesion (GO:0016337)|T cell activation (GO:0042110)	anchored component of plasma membrane (GO:0046658)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)	p.E248*(1)		NS(1)|breast(2)|large_intestine(3)|liver(1)|lung(8)|skin(2)|stomach(1)	18	Lung SC(450;0.225)	all_cancers(81;3.15e-06)|Acute lymphoblastic leukemia(138;1.7e-08)|all_epithelial(167;8.38e-07)|all_lung(203;3.37e-06)|Lung NSC(69;2.31e-05)		Epithelial(280;6.71e-26)|OV - Ovarian serous cystadenocarcinoma(397;4.74e-24)|all cancers(265;1.93e-22)|Lung(183;0.0543)|Kidney(133;0.0813)|Colorectal(144;0.174)|KIRC - Kidney renal clear cell carcinoma(1967;0.176)|LUSC - Lung squamous cell carcinoma(189;0.189)|BRCA - Breast invasive adenocarcinoma(282;0.201)	Alefacept(DB00092)	TGCAGATGAGGAGCTGGAGAC	0.478																																					NSCLC(14;263 555 26380 43512 51332)	dbGAP											1	Substitution - Nonsense(1)	breast(1)											45.0	47.0	47.0					1																	117311091		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0			BC033583	CCDS889.1	1p13	2013-01-11	2006-03-28		ENSG00000116824	ENSG00000116824		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"""	1639	protein-coding gene	gene with protein product		186990	"""CD2 antigen (p50), sheep red blood cell receptor"""	SRBC		2437578	Standard	NM_001767		Approved		uc001egu.4	P06729	OTTHUMG00000022750	ENST00000369478.3:c.742G>T	1.37:g.117311091G>T	ENSP00000358490:p.Glu248*	Somatic		WXS	Illumina GAIIx	Phase_IV	Q96TE5	Nonsense_Mutation	SNP	pfam_Ig_C2-set,pfam_Ig_V-set,prints_T-cell_sdhesion_molc_CD2	p.E248*	ENST00000369478.3	37	c.742	CCDS889.1	1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.690259	0.88735	.	.	ENSG00000116824	ENST00000369478	.	.	.	5.05	2.13	0.27403	.	0.196373	0.42172	D	0.000760	.	.	.	.	.	.	0.52501	D	0.999956	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-13.394	4.8784	0.13667	0.1894:0.1766:0.634:0.0	.	.	.	.	X	248	.	ENSP00000358490:E248X	E	+	1	0	CD2	117112614	0.073000	0.21202	0.871000	0.34182	0.795000	0.44927	1.248000	0.32827	0.805000	0.34159	0.655000	0.94253	GAG	CD2	-	NULL	ENSG00000116824		0.478	CD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CD2	HGNC	protein_coding	OTTHUMT00000059039.2	42	0.00	0	G	NM_001767		117311091	117311091	+1	no_errors	ENST00000369478	ensembl	human	known	69_37n	nonsense	47	11.32	6	SNP	0.823	T
CD34	947	genome.wustl.edu	37	1	208063100	208063101	+	Intron	INS	-	-	AA	rs546561927|rs3043874|rs5780411|rs397861623|rs397751524	byFrequency	TCGA-AN-A0XP-01A-11D-A117-09	TCGA-AN-A0XP-10A-01D-A10G-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	6179b498-2cea-4f7a-82a8-b7ec71431ea8	6c4eee86-8839-4a74-a786-b37e7dd35b21	g.chr1:208063100_208063101insAA	ENST00000310833.7	-	5	919				CD34_ENST00000537704.1_Intron|CD34_ENST00000367036.3_Frame_Shift_Ins_p.S28fs|CD34_ENST00000356522.4_Intron|CD34_ENST00000485761.1_Intron	NM_001025109.1	NP_001020280.1	P28906	CD34_HUMAN	CD34 molecule						cell motility (GO:0048870)|cell proliferation (GO:0008283)|endothelial cell proliferation (GO:0001935)|endothelium development (GO:0003158)|extracellular vesicular exosome assembly (GO:0071971)|glomerular endothelium development (GO:0072011)|glomerular filtration (GO:0003094)|glutamate metabolic process (GO:0006536)|hematopoietic stem cell proliferation (GO:0071425)|hemopoiesis (GO:0030097)|leukocyte migration (GO:0050900)|mesangial cell-matrix adhesion (GO:0035759)|metanephric glomerular mesangial cell differentiation (GO:0072254)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cellular response to heat (GO:1900035)|negative regulation of cellular response to hypoxia (GO:1900038)|negative regulation of gene expression (GO:0010629)|negative regulation of interleukin-2 secretion (GO:1900041)|negative regulation of neuron death (GO:1901215)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of tumor necrosis factor production (GO:0032720)|paracrine signaling (GO:0038001)|positive regulation of angiogenesis (GO:0045766)|positive regulation of gene expression (GO:0010628)|positive regulation of glial cell line-derived neurotrophic factor secretion (GO:1900168)|positive regulation of granulocyte colony-stimulating factor production (GO:0071657)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of odontogenesis (GO:0042482)|positive regulation of transforming growth factor beta production (GO:0071636)|positive regulation of vasculogenesis (GO:2001214)|regulation of blood pressure (GO:0008217)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|stem cell proliferation (GO:0072089)|tissue homeostasis (GO:0001894)|transdifferentiation (GO:0060290)|vascular wound healing (GO:0061042)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|glomerular endothelium fenestra (GO:0036053)|integral component of plasma membrane (GO:0005887)|intercellular bridge (GO:0045171)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|sulfate binding (GO:0043199)|transcription factor binding (GO:0008134)			kidney(2)|large_intestine(2)|lung(8)|ovary(1)	13						AATTCCAACAGAAAAAAAAAAA	0.366																																						dbGAP											0																																										-	-	-	SO:0001627	intron_variant	0			M81104	CCDS31011.1, CCDS31012.1	1q32	2008-02-05	2006-03-28		ENSG00000174059	ENSG00000174059		"""CD molecules"""	1662	protein-coding gene	gene with protein product		142230	"""CD34 antigen"""			1370171, 1374051	Standard	NM_001025109		Approved		uc001hgw.1	P28906	OTTHUMG00000036565	ENST00000310833.7:c.598-134->TT	1.37:g.208063109_208063110dupAA		Somatic		WXS	Illumina GAIIx	Phase_IV	A8K664|Q15970|Q15971|Q5JTA3|Q5JTA4|Q9UJB1	Frame_Shift_Ins	INS	pfam_CD34/Podocalyxin,prints_CD34	p.S28fs	ENST00000310833.7	37	c.83_82	CCDS31011.1	1																																																																																			CD34	-	NULL	ENSG00000174059		0.366	CD34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CD34	HGNC	protein_coding	OTTHUMT00000088933.1	15	0.00	0	-	NM_001773		208063100	208063101	-1	no_errors	ENST00000367036	ensembl	human	known	69_37n	frame_shift_ins	12	20.00	3	INS	0.000:0.000	AA
CHD1L	9557	genome.wustl.edu	37	1	146724328	146724328	+	Missense_Mutation	SNP	C	C	T			TCGA-AN-A0XP-01A-11D-A117-09	TCGA-AN-A0XP-10A-01D-A10G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	6179b498-2cea-4f7a-82a8-b7ec71431ea8	6c4eee86-8839-4a74-a786-b37e7dd35b21	g.chr1:146724328C>T	ENST00000369258.4	+	2	198	c.178C>T	c.(178-180)Cgc>Tgc	p.R60C	CHD1L_ENST00000431239.1_Missense_Mutation_p.R60C|RP11-337C18.10_ENST00000606856.1_RNA|CHD1L_ENST00000361293.5_Intron|CHD1L_ENST00000369259.3_Intron|CHD1L_ENST00000467213.1_3'UTR	NM_001256336.1|NM_004284.4|NM_024568.2	NP_001243265.1|NP_004275.4|NP_078844.2	Q86WJ1	CHD1L_HUMAN	chromodomain helicase DNA binding protein 1-like	60	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|nucleotide binding (GO:0000166)	p.R60C(1)		breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(15)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33	all_hematologic(923;0.0487)					GCTCGCCCAGCGCTTCCATTG	0.517																																						dbGAP											1	Substitution - Missense(1)	breast(1)											124.0	110.0	115.0					1																	146724328		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF054177	CCDS927.1, CCDS58021.1, CCDS58022.1, CCDS72882.1	1q21.1	2008-02-05			ENSG00000131778	ENSG00000131778			1916	protein-coding gene	gene with protein product		613039				9653160	Standard	NM_004284		Approved	ALC1	uc001epm.5	Q86WJ1	OTTHUMG00000150271	ENST00000369258.4:c.178C>T	1.37:g.146724328C>T	ENSP00000358262:p.Arg60Cys	Somatic		WXS	Illumina GAIIx	Phase_IV	A5YM64|B4DDE1|B5MDZ7|Q53EZ3|Q5VXX7|Q6DD94|Q6PK83|Q86XH3|Q96HF7|Q96SP3|Q9BVJ1|Q9NVV8	Missense_Mutation	SNP	pfam_SNF2_N,pfam_Helicase_C,pfam_HDA_complex_subunit-2/3,pfam_Helicase/UvrB_dom,pfam_DNA/RNA_helicase_DEAD/DEAH_N,smart_Helicase_ATP-bd,smart_Helicase_C,pfscan_A1pp,pfscan_Helicase_ATP-bd,pfscan_Helicase_C	p.R60C	ENST00000369258.4	37	c.178	CCDS927.1	1	.	.	.	.	.	.	.	.	.	.	C	13.87	2.366613	0.41902	.	.	ENSG00000131778	ENST00000431239;ENST00000369258;ENST00000254086	D;D	0.94723	-3.5;-3.5	5.23	-2.56	0.06268	DEAD-like helicase (2);SNF2-related (1);	0.612195	0.18756	N	0.132023	T	0.72366	0.3451	N	0.04043	-0.29	0.58432	D	0.999991	B;B	0.06786	0.001;0.001	B;B	0.08055	0.001;0.003	T	0.54596	-0.8270	10	0.87932	D	0	.	6.049	0.19775	0.0:0.3668:0.1347:0.4984	.	60;60	Q86WJ1-2;Q86WJ1	.;CHD1L_HUMAN	C	60;60;22	ENSP00000389031:R60C;ENSP00000358262:R60C	ENSP00000254086:R22C	R	+	1	0	CHD1L	145190952	0.304000	0.24472	0.850000	0.33497	0.944000	0.59088	-0.582000	0.05814	-0.931000	0.03746	-0.749000	0.03505	CGC	CHD1L	-	pfam_SNF2_N,pfam_Helicase/UvrB_dom,pfam_DNA/RNA_helicase_DEAD/DEAH_N,smart_Helicase_ATP-bd,pfscan_Helicase_ATP-bd	ENSG00000131778		0.517	CHD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CHD1L	HGNC	protein_coding	OTTHUMT00000040377.1	181	0.00	0	C	NM_004284		146724328	146724328	+1	no_errors	ENST00000369258	ensembl	human	known	69_37n	missense	248	22.01	70	SNP	0.777	T
CSNK1A1L	122011	genome.wustl.edu	37	13	37678520	37678520	+	Missense_Mutation	SNP	A	A	G			TCGA-AN-A0XP-01A-11D-A117-09	TCGA-AN-A0XP-10A-01D-A10G-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	6179b498-2cea-4f7a-82a8-b7ec71431ea8	6c4eee86-8839-4a74-a786-b37e7dd35b21	g.chr13:37678520A>G	ENST00000379800.3	-	1	1283	c.874T>C	c.(874-876)Tat>Cat	p.Y292H		NM_145203.5	NP_660204.2	Q8N752	KC1AL_HUMAN	casein kinase 1, alpha 1-like	292					cell morphogenesis (GO:0000902)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.Y292H(1)		NS(1)|breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	37		Lung NSC(96;7.97e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.109)		all cancers(112;3.58e-07)|Epithelial(112;1.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00695)|BRCA - Breast invasive adenocarcinoma(63;0.0117)|GBM - Glioblastoma multiforme(144;0.0407)		GTGTAGTCATATTGGTGGTTC	0.507																																						dbGAP											1	Substitution - Missense(1)	breast(1)											176.0	160.0	165.0					13																	37678520		2203	4300	6503	-	-	-	SO:0001583	missense	0			BC028723	CCDS9363.1	13q13.2	2008-02-05			ENSG00000180138	ENSG00000180138			20289	protein-coding gene	gene with protein product							Standard	NM_145203		Approved	MGC33182	uc001uwm.1	Q8N752	OTTHUMG00000016748	ENST00000379800.3:c.874T>C	13.37:g.37678520A>G	ENSP00000369126:p.Tyr292His	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5T2N2	Missense_Mutation	SNP	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom	p.Y292H	ENST00000379800.3	37	c.874	CCDS9363.1	13	.	.	.	.	.	.	.	.	.	.	A	12.30	1.897611	0.33535	.	.	ENSG00000180138	ENST00000379800	T	0.10099	2.91	1.01	1.01	0.19927	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.18299	0.0439	M	0.91972	3.26	0.42902	D	0.994233	B	0.20550	0.046	B	0.26202	0.067	T	0.05500	-1.0881	10	0.87932	D	0	.	6.1608	0.20364	1.0:0.0:0.0:0.0	.	292	Q8N752	KC1AL_HUMAN	H	292	ENSP00000369126:Y292H	ENSP00000369126:Y292H	Y	-	1	0	CSNK1A1L	36576520	1.000000	0.71417	0.944000	0.38274	0.970000	0.65996	6.335000	0.72949	0.688000	0.31529	0.459000	0.35465	TAT	CSNK1A1L	-	superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom	ENSG00000180138		0.507	CSNK1A1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CSNK1A1L	HGNC	protein_coding	OTTHUMT00000044563.1	260	0.00	0	A	NM_145203		37678520	37678520	-1	no_errors	ENST00000379800	ensembl	human	known	69_37n	missense	239	28.57	96	SNP	1.000	G
CYP24A1	1591	genome.wustl.edu	37	20	52789446	52789446	+	Splice_Site	SNP	A	A	T			TCGA-AN-A0XP-01A-11D-A117-09	TCGA-AN-A0XP-10A-01D-A10G-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	6179b498-2cea-4f7a-82a8-b7ec71431ea8	6c4eee86-8839-4a74-a786-b37e7dd35b21	g.chr20:52789446A>T	ENST00000216862.3	-	2	843		c.e2+1		CYP24A1_ENST00000395955.3_Splice_Site|CYP24A1_ENST00000395954.3_5'Flank	NM_000782.4	NP_000773.2	Q07973	CP24A_HUMAN	cytochrome P450, family 24, subfamily A, polypeptide 1						osteoblast differentiation (GO:0001649)|oxidation-reduction process (GO:0055114)|response to vitamin D (GO:0033280)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D catabolic process (GO:0042369)|vitamin D metabolic process (GO:0042359)|vitamin D receptor signaling pathway (GO:0070561)|vitamin metabolic process (GO:0006766)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)	1-alpha,25-dihydroxyvitamin D3 24-hydroxylase activity (GO:0030342)|25-hydroxycholecalciferol-24-hydroxylase activity (GO:0008403)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity (GO:0016491)	p.?(1)		breast(2)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Lung NSC(4;1.08e-05)|all_lung(4;2.7e-05)		STAD - Stomach adenocarcinoma(23;0.206)		Calcidiol(DB00146)|Calcipotriol(DB02300)|Calcitriol(DB00136)|Corticotropin(DB01285)|Ergocalciferol(DB00153)|Paricalcitol(DB00910)	GATTGGACTCACAGGATCAGC	0.612																																						dbGAP											1	Unknown(1)	breast(1)											85.0	78.0	80.0					20																	52789446		2203	4300	6503	-	-	-	SO:0001630	splice_region_variant	0			U60669	CCDS33491.1, CCDS46616.1	20q13.2-q13.3	2003-02-28	2003-02-14	2003-02-28	ENSG00000019186	ENSG00000019186		"""Cytochrome P450s"""	2602	protein-coding gene	gene with protein product		126065	"""cytochrome P450, subfamily XXIV (vitamin D 24-hydroxylase)"""	CYP24			Standard	NM_000782		Approved	CP24, P450-CC24	uc002xwv.2	Q07973	OTTHUMG00000032773	ENST00000216862.3:c.449+1T>A	20.37:g.52789446A>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q15807|Q32ML3|Q5I2W7	Splice_Site	SNP	-	e2+2	ENST00000216862.3	37	c.449+2	CCDS33491.1	20	.	.	.	.	.	.	.	.	.	.	A	22.0	4.225817	0.79576	.	.	ENSG00000019186	ENST00000216862;ENST00000395955	.	.	.	5.21	5.21	0.72293	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.9028	0.63815	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CYP24A1	52222853	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	8.809000	0.91944	1.955000	0.56771	0.459000	0.35465	.	CYP24A1	-	-	ENSG00000019186		0.612	CYP24A1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	CYP24A1	HGNC	protein_coding	OTTHUMT00000079769.2	60	0.00	0	A		Intron	52789446	52789446	-1	no_errors	ENST00000216862	ensembl	human	known	69_37n	splice_site	81	22.86	24	SNP	1.000	T
FAM86DP	692099	genome.wustl.edu	37	3	75471725	75471725	+	RNA	SNP	A	A	G	rs58659934	byFrequency	TCGA-AN-A0XP-01A-11D-A117-09	TCGA-AN-A0XP-10A-01D-A10G-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	6179b498-2cea-4f7a-82a8-b7ec71431ea8	6c4eee86-8839-4a74-a786-b37e7dd35b21	g.chr3:75471725A>G	ENST00000459803.1	-	0	1416					NR_024241.1				family with sequence similarity 86, member D, pseudogene																		CAGGGATGTGACAGCTGCAGC	0.567													.|||	1269	0.253395	0.4803	0.2305	5008	,	,		15334	0.0536		0.2117	False		,,,				2504	0.2117					dbGAP											0																																										-	-	-			0			BC016686		3p12.3	2010-06-04	2010-06-04	2010-06-04	ENSG00000244026	ENSG00000244026			32659	pseudogene	pseudogene			"""family with sequence similarity 86, member D"""	FAM86D			Standard	NR_024241		Approved		uc003dpp.4		OTTHUMG00000158855		3.37:g.75471725A>G		Somatic		WXS	Illumina GAIIx	Phase_IV		RNA	SNP	-	NULL	ENST00000459803.1	37	NULL		3																																																																																			FAM86DP	-	-	ENSG00000244026		0.567	FAM86DP-003	KNOWN	basic	processed_transcript	FAM86DP	HGNC	pseudogene	OTTHUMT00000352425.1	12	0.00	0	A	NR_024241		75471725	75471725	-1	no_errors	ENST00000459803	ensembl	human	known	69_37n	rna	6	36.36	4	SNP	0.000	G
FAT1	2195	genome.wustl.edu	37	4	187524066	187524066	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AN-A0XP-01A-11D-A117-09	TCGA-AN-A0XP-10A-01D-A10G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	6179b498-2cea-4f7a-82a8-b7ec71431ea8	6c4eee86-8839-4a74-a786-b37e7dd35b21	g.chr4:187524066G>A	ENST00000441802.2	-	20	11682	c.11473C>T	c.(11473-11475)Cag>Tag	p.Q3825*		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	3825	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.Q3828*(1)|p.Q3825*(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						CCTGGGCACTGACCAAACCTG	0.443										HNSCC(5;0.00058)																											Colon(197;1040 2055 4143 4984 49344)	dbGAP											2	Substitution - Nonsense(2)	breast(2)											51.0	53.0	52.0					4																	187524066		1894	4113	6007	-	-	-	SO:0001587	stop_gained	0			X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.11473C>T	4.37:g.187524066G>A	ENSP00000406229:p.Gln3825*	Somatic		WXS	Illumina GAIIx	Phase_IV		Nonsense_Mutation	SNP	pfam_Cadherin,pfam_Laminin_G,pfam_EGF-like_dom,pfam_EGF-like_Ca-bd,superfamily_ConA-like_lec_gl,superfamily_Cadherin-like,smart_Cadherin,smart_EGF-like,smart_Laminin_G,smart_EGF-like_Ca-bd,prints_Cadherin,pfscan_EG-like_dom,pfscan_Laminin_G,pfscan_Cadherin	p.Q3825*	ENST00000441802.2	37	c.11473	CCDS47177.1	4	.	.	.	.	.	.	.	.	.	.	G	52	19.601280	0.99921	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	.	.	.	5.39	2.58	0.30949	.	0.230618	0.45126	D	0.000399	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05436	T	0.98	.	11.8657	0.52493	0.0:0.2348:0.6342:0.131	.	.	.	.	X	3825;3827	.	ENSP00000260147:Q3827X	Q	-	1	0	FAT1	187761060	0.997000	0.39634	0.277000	0.24703	0.424000	0.31475	2.355000	0.44107	0.284000	0.22305	0.508000	0.49915	CAG	FAT1	-	smart_EGF-like,pfscan_EG-like_dom	ENSG00000083857		0.443	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FAT1	HGNC	protein_coding	OTTHUMT00000360209.3	45	0.00	0	G	NM_005245		187524066	187524066	-1	no_errors	ENST00000441802	ensembl	human	known	69_37n	nonsense	16	52.94	18	SNP	0.685	A
GTF2IRD2	84163	genome.wustl.edu	37	7	74234113	74234113	+	Missense_Mutation	SNP	T	T	C			TCGA-AN-A0XP-01A-11D-A117-09	TCGA-AN-A0XP-10A-01D-A10G-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	6179b498-2cea-4f7a-82a8-b7ec71431ea8	6c4eee86-8839-4a74-a786-b37e7dd35b21	g.chr7:74234113T>C	ENST00000405086.2	-	8	830	c.641A>G	c.(640-642)aAt>aGt	p.N214S	GTF2IRD2_ENST00000453619.2_Intron|GTF2IRD2_ENST00000361071.5_Missense_Mutation_p.N214S	NM_173537.2	NP_775808	Q86UP8	GTD2A_HUMAN	GTF2I repeat domain containing 2	214					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.N214S(1)		breast(1)|endometrium(3)|large_intestine(2)|lung(2)|ovary(2)|skin(1)	11						AGTTTTCACATTGATGGGGCC	0.547																																					NSCLC(40;560 1096 7501 40315 49546)	dbGAP											1	Substitution - Missense(1)	breast(1)											1.0	1.0	1.0					7																	74234113		28	46	74	-	-	-	SO:0001583	missense	0			BC047706	CCDS5576.1, CCDS64682.1	7q11.23	2014-05-06			ENSG00000196275	ENSG00000196275			30775	protein-coding gene	gene with protein product	"""transcription factor GTF2IRD2"""	608899				15243160	Standard	NM_173537		Approved	FLJ37938, GTF2IRD2A	uc003ubd.1	Q86UP8	OTTHUMG00000181527	ENST00000405086.2:c.641A>G	7.37:g.74234113T>C	ENSP00000385491:p.Asn214Ser	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K5W6|B3KUZ2|Q69G40|Q6EKI8|Q6EKI9|Q6NVW2|Q6P7N8|Q86WX4|Q8ND85|Q8NDE5	Missense_Mutation	SNP	pfam_GTF2I,superfamily_GTF2I,superfamily_RNaseH-like_dom,pfscan_GTF2I	p.N214S	ENST00000405086.2	37	c.641	CCDS5576.1	7	.	.	.	.	.	.	.	.	.	.	T	3.175	-0.169132	0.06461	.	.	ENSG00000196275	ENST00000405086;ENST00000361071	T;T	0.40756	3.02;1.02	2.61	-5.22	0.02806	.	.	.	.	.	T	0.12178	0.0296	N	0.01576	-0.805	0.21627	N	0.999612	B;B;B	0.10296	0.003;0.002;0.0	B;B;B	0.09377	0.002;0.004;0.0	T	0.26985	-1.0087	9	0.14656	T	0.56	-0.0074	5.7218	0.17990	0.0:0.455:0.1607:0.3844	.	214;214;214	Q86UP8-3;Q86UP8-5;Q86UP8	.;.;GTD2A_HUMAN	S	214	ENSP00000385491:N214S;ENSP00000354362:N214S	ENSP00000354362:N214S	N	-	2	0	GTF2IRD2	73872049	0.000000	0.05858	0.068000	0.19968	0.987000	0.75469	-0.629000	0.05508	-1.580000	0.01644	0.315000	0.21342	AAT	GTF2IRD2	-	NULL	ENSG00000196275		0.547	GTF2IRD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GTF2IRD2	HGNC	protein_coding	OTTHUMT00000252712.3	22	0.00	0	T	NM_173537		74234113	74234113	-1	no_errors	ENST00000405086	ensembl	human	known	69_37n	missense	12	42.86	9	SNP	0.131	C
HIST2H2AC	8338	genome.wustl.edu	37	1	149858866	149858866	+	Silent	SNP	C	C	G			TCGA-AN-A0XP-01A-11D-A117-09	TCGA-AN-A0XP-10A-01D-A10G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	6179b498-2cea-4f7a-82a8-b7ec71431ea8	6c4eee86-8839-4a74-a786-b37e7dd35b21	g.chr1:149858866C>G	ENST00000331380.2	+	1	342	c.342C>G	c.(340-342)gcC>gcG	p.A114A	HIST2H2BE_ENST00000369155.2_5'Flank|BOLA1_ENST00000369153.2_5'Flank	NM_003517.2	NP_003508.1	Q16777	H2A2C_HUMAN	histone cluster 2, H2ac	114						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.A114A(1)		NS(1)|breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(11)|ovary(1)|skin(1)	20	Breast(34;0.0124)|all_hematologic(923;0.127)		STAD - Stomach adenocarcinoma(528;0.133)|LUSC - Lung squamous cell carcinoma(543;0.221)			ACATCCAGGCCGTTCTGTTAC	0.507																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											83.0	84.0	84.0					1																	149858866		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AY131973	CCDS937.1	1q21.2	2011-01-27	2006-10-11	2003-02-21	ENSG00000184260	ENSG00000184260		"""Histones / Replication-dependent"""	4738	protein-coding gene	gene with protein product		602797	"""H2A histone family, member Q"", ""histone 2, H2ac"""	H2A, H2AFQ		1469070, 9439656, 12408966	Standard	NM_003517		Approved	H2A/q	uc001etd.3	Q16777	OTTHUMG00000035825	ENST00000331380.2:c.342C>G	1.37:g.149858866C>G		Somatic		WXS	Illumina GAIIx	Phase_IV	Q6DRA7|Q8IUE5	Silent	SNP	pfam_Histone_core_D,pfam_CBFA_NFYB_domain,superfamily_Histone-fold,smart_Histone_H2A,prints_Histone_H2A	p.A114	ENST00000331380.2	37	c.342	CCDS937.1	1																																																																																			HIST2H2AC	-	superfamily_Histone-fold,smart_Histone_H2A,prints_Histone_H2A	ENSG00000184260		0.507	HIST2H2AC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HIST2H2AC	HGNC	protein_coding	OTTHUMT00000087128.1	65	0.00	0	C	NM_003517		149858866	149858866	+1	no_errors	ENST00000331380	ensembl	human	known	69_37n	silent	104	18.60	24	SNP	0.990	G
HSD17B4	3295	genome.wustl.edu	37	5	118860980	118860980	+	Splice_Site	DEL	G	G	-			TCGA-AN-A0XP-01A-11D-A117-09	TCGA-AN-A0XP-10A-01D-A10G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	6179b498-2cea-4f7a-82a8-b7ec71431ea8	6c4eee86-8839-4a74-a786-b37e7dd35b21	g.chr5:118860980delG	ENST00000256216.6	+	18	1706	c.1573delG	c.(1573-1575)ggt>gt	p.G525fs	HSD17B4_ENST00000504811.1_Splice_Site_p.G550fs|HSD17B4_ENST00000513628.1_Splice_Site_p.G388fs|HSD17B4_ENST00000509514.1_Splice_Site_p.G263fs|HSD17B4_ENST00000515320.1_Splice_Site_p.G507fs|HSD17B4_ENST00000510025.1_Splice_Site_p.G501fs|HSD17B4_ENST00000522415.1_3'UTR|HSD17B4_ENST00000414835.2_Splice_Site_p.G385fs	NM_000414.3	NP_000405.1	P51659	DHB4_HUMAN	hydroxysteroid (17-beta) dehydrogenase 4	525	Enoyl-CoA hydratase 2.|MaoC-like.				alpha-linolenic acid metabolic process (GO:0036109)|androgen metabolic process (GO:0008209)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|estrogen metabolic process (GO:0008210)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|medium-chain fatty-acyl-CoA metabolic process (GO:0036112)|metabolic process (GO:0008152)|osteoblast differentiation (GO:0001649)|oxidation-reduction process (GO:0055114)|Sertoli cell development (GO:0060009)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)|very long-chain fatty-acyl-CoA metabolic process (GO:0036111)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	17-beta-hydroxysteroid dehydrogenase (NAD+) activity (GO:0044594)|3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase activity (GO:0033989)|isomerase activity (GO:0016853)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.G525fs*107(1)		breast(2)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(2)	25		all_cancers(142;0.0206)|Prostate(80;0.0322)		OV - Ovarian serous cystadenocarcinoma(64;0.000247)|Epithelial(69;0.000849)|all cancers(49;0.0122)		TAGTCTAGCAGGTGAGTTGTC	0.353																																					Colon(35;490 801 34689 41394 43344)	dbGAP											1	Deletion - Frameshift(1)	breast(1)											109.0	100.0	103.0					5																	118860980		2202	4299	6501	-	-	-	SO:0001630	splice_region_variant	0				CCDS4126.1, CCDS56378.1, CCDS56379.1	5q2	2011-09-20			ENSG00000133835	ENSG00000133835	4.2.1.107, 1.1.1.35	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	5213	protein-coding gene	gene with protein product	"""17beta-estradiol dehydrogenase type IV"", ""peroxisomal multifunctional protein 2"", ""17-beta-HSD IV"", ""17-beta-hydroxysteroid dehydrogenase 4"", ""D-bifunctional protein, peroxisomal"", ""D-3-hydroxyacyl-CoA dehydratase"", ""3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholest-24-enoyl-CoA hydratase"", ""beta-keto-reductase"", ""beta-hydroxyacyl dehydrogenase"", ""short chain dehydrogenase/reductase family 8C, member 1"""	601860				8938456, 19027726	Standard	NM_000414		Approved	MFE-2, DBP, SDR8C1	uc003ksj.3	P51659	OTTHUMG00000128899	ENST00000256216.6:c.1573+1G>-	5.37:g.118860980delG		Somatic		WXS	Illumina GAIIx	Phase_IV	B4DNV1|B4DVS5|E9PB82|F5HE57	Frame_Shift_Del	DEL	pfam_MaoC_deHydtase,pfam_DH_sc/Rdtase_SDR,pfam_SCP2_sterol-bd_dom,pfam_PKS_KR,superfamily_SCP2_sterol-bd_dom,smart_PKS/FAS_KR,prints_Glc/ribitol_DH,prints_DH_sc/Rdtase_SDR,prints_DHB_DH	p.G525fs	ENST00000256216.6	37	c.1573	CCDS4126.1	5																																																																																			HSD17B4	-	pfam_MaoC_deHydtase	ENSG00000133835		0.353	HSD17B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HSD17B4	HGNC	protein_coding	OTTHUMT00000250863.3	202	0.00	0	G	NM_000414	Frame_Shift_Del	118860980	118860980	+1	no_errors	ENST00000256216	ensembl	human	known	69_37n	frame_shift_del	157	28.89	65	DEL	1.000	-
ICE1	23379	genome.wustl.edu	37	5	5457514	5457514	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A0XP-01A-11D-A117-09	TCGA-AN-A0XP-10A-01D-A10G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	6179b498-2cea-4f7a-82a8-b7ec71431ea8	6c4eee86-8839-4a74-a786-b37e7dd35b21	g.chr5:5457514G>A	ENST00000296564.7	+	12	983	c.761G>A	c.(760-762)gGc>gAc	p.G254D		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		254					positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)	p.G254D(2)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						CCAACACAGGGCAGCCCTCTC	0.483																																						dbGAP											2	Substitution - Missense(2)	breast(2)											44.0	46.0	45.0					5																	5457514		2045	4207	6252	-	-	-	SO:0001583	missense	0																														ENST00000296564.7:c.761G>A	5.37:g.5457514G>A	ENSP00000296564:p.Gly254Asp	Somatic		WXS	Illumina GAIIx	Phase_IV	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Missense_Mutation	SNP	superfamily_Vitellinogen_superhlx	p.G254D	ENST00000296564.7	37	c.761	CCDS47187.1	5	.	.	.	.	.	.	.	.	.	.	G	10.31	1.314342	0.23908	.	.	ENSG00000164151	ENST00000296564	T	0.10288	2.89	5.38	2.33	0.28932	.	1.542790	0.03614	N	0.235225	T	0.08223	0.0205	N	0.24115	0.695	0.09310	N	1	B	0.14012	0.009	B	0.16722	0.016	T	0.36696	-0.9737	10	0.20046	T	0.44	-0.7011	4.9896	0.14207	0.2068:0.1677:0.6255:0.0	.	254	Q9Y2F5	K0947_HUMAN	D	254	ENSP00000296564:G254D	ENSP00000296564:G254D	G	+	2	0	KIAA0947	5510514	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	0.162000	0.16501	0.553000	0.29044	0.555000	0.69702	GGC	KIAA0947	-	NULL	ENSG00000164151		0.483	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KIAA0947	HGNC	protein_coding	OTTHUMT00000365575.1	84	0.00	0	G			5457514	5457514	+1	no_errors	ENST00000296564	ensembl	human	known	69_37n	missense	71	34.26	37	SNP	0.000	A
LBR	3930	genome.wustl.edu	37	1	225592382	225592382	+	Missense_Mutation	SNP	C	C	T			TCGA-AN-A0XP-01A-11D-A117-09	TCGA-AN-A0XP-10A-01D-A10G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	6179b498-2cea-4f7a-82a8-b7ec71431ea8	6c4eee86-8839-4a74-a786-b37e7dd35b21	g.chr1:225592382C>T	ENST00000338179.2	-	12	1635	c.1510G>A	c.(1510-1512)Gca>Aca	p.A504T	LBR_ENST00000272163.4_Missense_Mutation_p.A504T	NM_194442.2	NP_919424.1	Q14739	LBR_HUMAN	lamin B receptor	504					cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|integral component of nuclear inner membrane (GO:0005639)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|lamin binding (GO:0005521)|oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor (GO:0016628)|poly(A) RNA binding (GO:0044822)	p.A504T(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22	Breast(184;0.165)			GBM - Glioblastoma multiforme(131;0.117)		TGAGAATTTGCACCTCGGAAG	0.294																																						dbGAP											1	Substitution - Missense(1)	breast(1)											60.0	63.0	62.0					1																	225592382		2200	4297	6497	-	-	-	SO:0001583	missense	0			L25931	CCDS1545.1	1q42.1	2013-01-23			ENSG00000143815	ENSG00000143815		"""Tudor domain containing"""	6518	protein-coding gene	gene with protein product	"""tudor domain containing 18"""	600024				8157663, 9878250	Standard	NM_194442		Approved	DHCR14B, TDRD18	uc001hoy.3	Q14739	OTTHUMG00000037520	ENST00000338179.2:c.1510G>A	1.37:g.225592382C>T	ENSP00000339883:p.Ala504Thr	Somatic		WXS	Illumina GAIIx	Phase_IV	B2R5P3|Q14740|Q53GU7|Q59FE6	Missense_Mutation	SNP	pfam_Ergosterol_biosynth_ERG4_ERG24,pfam_Lamin-B_rcpt_of_tudor,pfam_DUF1295,smart_Tudor	p.A504T	ENST00000338179.2	37	c.1510	CCDS1545.1	1	.	.	.	.	.	.	.	.	.	.	C	19.14	3.770644	0.69992	.	.	ENSG00000143815	ENST00000272163;ENST00000338179	D;D	0.98512	-4.97;-4.97	5.36	4.44	0.53790	.	0.051016	0.85682	D	0.000000	D	0.98457	0.9486	M	0.73372	2.23	0.54753	D	0.999988	D	0.67145	0.996	D	0.66351	0.943	D	0.98352	1.0544	10	0.39692	T	0.17	-15.6391	14.1045	0.65080	0.2736:0.7264:0.0:0.0	.	504	Q14739	LBR_HUMAN	T	504	ENSP00000272163:A504T;ENSP00000339883:A504T	ENSP00000272163:A504T	A	-	1	0	LBR	223659005	1.000000	0.71417	1.000000	0.80357	0.488000	0.33401	3.559000	0.53756	1.356000	0.45884	0.655000	0.94253	GCA	LBR	-	pfam_Ergosterol_biosynth_ERG4_ERG24,pfam_DUF1295	ENSG00000143815		0.294	LBR-201	KNOWN	basic|appris_principal|CCDS	protein_coding	LBR	HGNC	protein_coding	OTTHUMT00000091398.1	199	0.00	0	C	NM_002296		225592382	225592382	-1	no_errors	ENST00000272163	ensembl	human	known	69_37n	missense	205	18.97	48	SNP	1.000	T
KMT2C	58508	genome.wustl.edu	37	7	151845282	151845283	+	Frame_Shift_Del	DEL	GG	GG	-			TCGA-AN-A0XP-01A-11D-A117-09	TCGA-AN-A0XP-10A-01D-A10G-09	GG	GG					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	6179b498-2cea-4f7a-82a8-b7ec71431ea8	6c4eee86-8839-4a74-a786-b37e7dd35b21	g.chr7:151845282_151845283delGG	ENST00000262189.6	-	52	13947_13948	c.13729_13730delCC	c.(13729-13731)cctfs	p.P4577fs	KMT2C_ENST00000355193.2_Frame_Shift_Del_p.P4634fs	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	4577	FYR N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00875}.				histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.P4577fs*4(1)|p.P4634fs*4(1)									ATAGCCCACAGGGAAGAGTGCT	0.564																																						dbGAP											2	Deletion - Frameshift(2)	breast(2)																																								-	-	-	SO:0001589	frameshift_variant	0			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.13729_13730delCC	7.37:g.151845282_151845283delGG	ENSP00000262189:p.Pro4577fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Frame_Shift_Del	DEL	pfam_Znf_PHD-finger,pfam_SET_dom,pfam_FYrich_C,pfam_FYrich_N,superfamily_Znf_FYVE_PHD,superfamily_HMG_superfamily,smart_Znf_PHD,smart_Znf_RING,smart_HMG_superfamily,smart_FYrich_N,smart_FYrich_C,smart_SET_dom,smart_Post-SET_dom,pfscan_SET_dom,pfscan_Post-SET_dom,pfscan_Znf_DHHC_palmitoyltrfase,pfscan_Znf_PHD-finger,pfscan_Znf_RING	p.P4634fs	ENST00000262189.6	37	c.13901_13900	CCDS5931.1	7																																																																																			MLL3	-	pfam_FYrich_N,smart_FYrich_N	ENSG00000055609		0.564	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	MLL3	HGNC	protein_coding	OTTHUMT00000318887.3	51	0.00	0	GG			151845282	151845283	-1	no_errors	ENST00000355193	ensembl	human	known	69_37n	frame_shift_del	58	31.40	27	DEL	1.000:1.000	-
NCR2	9436	genome.wustl.edu	37	6	41304105	41304105	+	Silent	SNP	C	C	A			TCGA-AN-A0XP-01A-11D-A117-09	TCGA-AN-A0XP-10A-01D-A10G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	6179b498-2cea-4f7a-82a8-b7ec71431ea8	6c4eee86-8839-4a74-a786-b37e7dd35b21	g.chr6:41304105C>A	ENST00000373089.5	+	2	421	c.333C>A	c.(331-333)atC>atA	p.I111I	NCR2_ENST00000373083.4_Silent_p.I111I|NCR2_ENST00000373086.3_Silent_p.I111I	NM_004828.3	NP_004819.2	O95944	NCTR2_HUMAN	natural cytotoxicity triggering receptor 2	111	Ig-like.				cellular defense response (GO:0006968)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)	p.I111I(1)		NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	14	Ovarian(28;0.0327)|Colorectal(47;0.196)					GGTGTAGAATCTACCGCCCTT	0.522																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											100.0	91.0	94.0					6																	41304105		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AJ225109	CCDS4855.1, CCDS56428.1, CCDS56429.1	6p21.1	2013-01-11	2002-11-13	2002-11-15	ENSG00000096264	ENSG00000096264		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	6732	protein-coding gene	gene with protein product		604531	"""lymphocyte antigen 95 (activating NK-receptor; NK-p44)"""	LY95		10049942	Standard	NM_004828		Approved	NK-p44, CD336	uc003oqh.2	O95944	OTTHUMG00000014678	ENST00000373089.5:c.333C>A	6.37:g.41304105C>A		Somatic		WXS	Illumina GAIIx	Phase_IV	Q9H562|Q9H563|Q9H564|Q9UMT1|Q9UMT2	Silent	SNP	pfam_Ig_V-set,smart_Ig_sub,pfscan_Ig-like	p.I111	ENST00000373089.5	37	c.333	CCDS4855.1	6																																																																																			NCR2	-	pfam_Ig_V-set,smart_Ig_sub,pfscan_Ig-like	ENSG00000096264		0.522	NCR2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NCR2	HGNC	protein_coding	OTTHUMT00000040511.3	60	0.00	0	C			41304105	41304105	+1	no_errors	ENST00000373089	ensembl	human	known	69_37n	silent	50	36.71	29	SNP	0.001	A
OR4K14	122740	genome.wustl.edu	37	14	20482985	20482985	+	Missense_Mutation	SNP	C	C	G			TCGA-AN-A0XP-01A-11D-A117-09	TCGA-AN-A0XP-10A-01D-A10G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	6179b498-2cea-4f7a-82a8-b7ec71431ea8	6c4eee86-8839-4a74-a786-b37e7dd35b21	g.chr14:20482985C>G	ENST00000305045.2	-	1	367	c.368G>C	c.(367-369)aGa>aCa	p.R123T		NM_001004712.1	NP_001004712.1	Q8NGD5	OR4KE_HUMAN	olfactory receptor, family 4, subfamily K, member 14	123						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R123T(1)		breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(20)|skin(6)	37	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2e-06)	GBM - Glioblastoma multiforme(265;0.00124)		GGCCACATATCTGTCATAGGC	0.478																																						dbGAP											1	Substitution - Missense(1)	breast(1)											95.0	92.0	93.0					14																	20482985		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS32027.1	14q11.2	2013-09-23			ENSG00000169484	ENSG00000169484		"""GPCR / Class A : Olfactory receptors"""	15352	protein-coding gene	gene with protein product							Standard	NM_001004712		Approved		uc010tky.2	Q8NGD5	OTTHUMG00000170780	ENST00000305045.2:c.368G>C	14.37:g.20482985C>G	ENSP00000305011:p.Arg123Thr	Somatic		WXS	Illumina GAIIx	Phase_IV	Q6IEU1|Q96R71	Missense_Mutation	SNP	pfam_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam,prints_Olfact_rcpt,prints_7TM_GPCR_Rhodpsn	p.R123T	ENST00000305045.2	37	c.368	CCDS32027.1	14	.	.	.	.	.	.	.	.	.	.	.	19.50	3.839197	0.71373	.	.	ENSG00000169484	ENST00000305045	T	0.77489	-1.1	4.04	4.04	0.47022	GPCR, rhodopsin-like superfamily (1);	0.000000	0.43919	D	0.000519	D	0.93058	0.7790	H	0.99475	4.585	0.31070	N	0.713077	D	0.89917	1.0	D	0.74674	0.984	D	0.93324	0.6695	10	0.87932	D	0	.	15.1214	0.72447	0.0:1.0:0.0:0.0	.	123	Q8NGD5	OR4KE_HUMAN	T	123	ENSP00000305011:R123T	ENSP00000305011:R123T	R	-	2	0	OR4K14	19552825	1.000000	0.71417	1.000000	0.80357	0.853000	0.48598	5.029000	0.64121	2.086000	0.62901	0.505000	0.49811	AGA	OR4K14	-	pfam_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam,prints_7TM_GPCR_Rhodpsn	ENSG00000169484		0.478	OR4K14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR4K14	HGNC	protein_coding	OTTHUMT00000410343.1	105	0.00	0	C			20482985	20482985	-1	no_errors	ENST00000305045	ensembl	human	known	69_37n	missense	84	29.41	35	SNP	0.999	G
PIK3CA	5290	genome.wustl.edu	37	3	178936091	178936091	+	Missense_Mutation	SNP	G	G	A	rs104886003		TCGA-AN-A0XP-01A-11D-A117-09	TCGA-AN-A0XP-10A-01D-A10G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	6179b498-2cea-4f7a-82a8-b7ec71431ea8	6c4eee86-8839-4a74-a786-b37e7dd35b21	g.chr3:178936091G>A	ENST00000263967.3	+	10	1790	c.1633G>A	c.(1633-1635)Gag>Aag	p.E545K		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	545	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.		E -> A (in CWS5 and HCC; also found in a glioblastoma multiforme sample). {ECO:0000269|PubMed:15608678, ECO:0000269|PubMed:15924253, ECO:0000269|PubMed:23246288}.|E -> G (in KERSEB; also found in an endometrial carcinoma sample). {ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:17673550}.|E -> K (in MCAP, KERSEB, CRC and BC; shows an increase in lipid kinase activity; oncogenic in vivo; occurs in the interface between the PI3K helical domain and the nSH2 (N-terminal SH2) region of the p85 regulatory subunit and may reduce the inhibitory effect of p85; requires interaction with RAS to induce cellular transformation; enhances invadopodia-mediated extracellular matrix degradation and invasion in breast cancer cells). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15712344, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.E545K(881)|p.E545Q(18)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TGAAATCACTGAGCAGGAGAA	0.353	E545K(BC3C_URINARY_TRACT)|E545K(BFTC909_KIDNEY)|E545K(DLD1_LARGE_INTESTINE)|E545K(ESS1_ENDOMETRIUM)|E545K(HCC202_BREAST)|E545K(HCT15_LARGE_INTESTINE)|E545K(HSC4_UPPER_AERODIGESTIVE_TRACT)|E545K(HT1197_URINARY_TRACT)|E545K(HUH28_BILIARY_TRACT)|E545K(KYSE510_OESOPHAGUS)|E545K(L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|E545K(MCF7_BREAST)|E545K(MDAMB361_BREAST)|E545K(MKN1_STOMACH)|E545K(NCIH460_LUNG)|E545K(NCIH508_LARGE_INTESTINE)|E545K(NCIH596_LUNG)|E545K(RERFLCSQ1_LUNG)|E545K(TCCSUP_URINARY_TRACT)|E545K(TE5_OESOPHAGUS)	57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)	dbGAP		Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	899	Substitution - Missense(899)	breast(308)|large_intestine(286)|urinary_tract(97)|lung(44)|endometrium(37)|ovary(25)|stomach(17)|upper_aerodigestive_tract(16)|skin(14)|central_nervous_system(13)|cervix(13)|thyroid(7)|oesophagus(7)|penis(4)|kidney(3)|soft_tissue(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(1)|biliary_tract(1)|NS(1)|pituitary(1)											61.0	60.0	60.0					3																	178936091		1813	4072	5885	-	-	-	SO:0001583	missense	0				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1633G>A	3.37:g.178936091G>A	ENSP00000263967:p.Glu545Lys	Somatic		WXS	Illumina GAIIx	Phase_IV	Q14CW1|Q99762	Missense_Mutation	SNP	pfam_PInositide-3_kin_accessory_dom,pfam_PI3/4_kinase_cat_dom,pfam_PI3K_Ras-bd_dom,pfam_PI3K_C2_dom,pfam_PI3K_adapt-bd_dom,superfamily_Kinase-like_dom,superfamily_ARM-type_fold,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_PI3K_adapt-bd_dom,smart_PI3K_Ras-bd_dom,smart_PI3K_C2_dom,smart_PInositide-3_kin_accessory_dom,smart_PI3/4_kinase_cat_dom,pfscan_PI3/4_kinase_cat_dom	p.E545K	ENST00000263967.3	37	c.1633	CCDS43171.1	3	.	.	.	.	.	.	.	.	.	.	G	36	5.703347	0.96812	.	.	ENSG00000121879	ENST00000263967	T	0.63255	-0.03	5.78	5.78	0.91487	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.73822	0.3636	L	0.51914	1.62	0.80722	D	1	D	0.62365	0.991	D	0.62955	0.909	T	0.68872	-0.5294	10	0.32370	T	0.25	-25.7963	20.0024	0.97423	0.0:0.0:1.0:0.0	.	545	P42336	PK3CA_HUMAN	K	545	ENSP00000263967:E545K	ENSP00000263967:E545K	E	+	1	0	PIK3CA	180418785	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	9.476000	0.97823	2.722000	0.93159	0.467000	0.42956	GAG	PIK3CA	-	pfam_PInositide-3_kin_accessory_dom,superfamily_ARM-type_fold,smart_PInositide-3_kin_accessory_dom	ENSG00000121879		0.353	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	PIK3CA	HGNC	protein_coding	OTTHUMT00000348409.2	136	0.00	0	G			178936091	178936091	+1	no_errors	ENST00000263967	ensembl	human	known	69_37n	missense	67	45.53	56	SNP	1.000	A
RTN4RL1	146760	genome.wustl.edu	37	17	1839853	1839853	+	Silent	SNP	C	C	T			TCGA-AN-A0XP-01A-11D-A117-09	TCGA-AN-A0XP-10A-01D-A10G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	6179b498-2cea-4f7a-82a8-b7ec71431ea8	6c4eee86-8839-4a74-a786-b37e7dd35b21	g.chr17:1839853C>T	ENST00000331238.6	-	2	1742	c.1263G>A	c.(1261-1263)tcG>tcA	p.S421S		NM_178568.2	NP_848663.1			reticulon 4 receptor-like 1									p.S421S(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|prostate(2)|skin(1)	11						GGGAACTGGCCGAGGAGGCCT	0.687																																					GBM(68;949 1139 14865 32798 38342)	dbGAP											1	Substitution - coding silent(1)	breast(1)											8.0	10.0	9.0					17																	1839853		1916	4106	6022	-	-	-	SO:0001819	synonymous_variant	0			AF532859	CCDS45569.1	17p13.3	2008-02-05				ENSG00000185924			21329	protein-coding gene	gene with protein product	"""nogo-66 receptor homolog 2"""	610461					Standard	NM_178568		Approved	NGRH2, NgR3, DKFZp547J144	uc002ftp.3	Q86UN2		ENST00000331238.6:c.1263G>A	17.37:g.1839853C>T		Somatic		WXS	Illumina GAIIx	Phase_IV		Silent	SNP	pfam_Leu-rich_rpt,smart_Leu-rich_rpt_typical-subtyp,smart_Cys-rich_flank_reg_C	p.S421	ENST00000331238.6	37	c.1263	CCDS45569.1	17																																																																																			RTN4RL1	-	NULL	ENSG00000185924		0.687	RTN4RL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RTN4RL1	HGNC	protein_coding	OTTHUMT00000450155.2	14	0.00	0	C	NM_178568		1839853	1839853	-1	no_errors	ENST00000331238	ensembl	human	known	69_37n	silent	6	66.67	12	SNP	0.858	T
SCN8A	6334	genome.wustl.edu	37	12	52115519	52115519	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A0XP-01A-11D-A117-09	TCGA-AN-A0XP-10A-01D-A10G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	6179b498-2cea-4f7a-82a8-b7ec71431ea8	6c4eee86-8839-4a74-a786-b37e7dd35b21	g.chr12:52115519G>A	ENST00000354534.6	+	12	2003	c.1825G>A	c.(1825-1827)Gag>Aag	p.E609K	SCN8A_ENST00000550891.1_Missense_Mutation_p.E609K|SCN8A_ENST00000545061.1_Missense_Mutation_p.E609K	NM_001177984.2|NM_014191.3	NP_001171455.1|NP_055006.1	Q9UQD0	SCN8A_HUMAN	sodium channel, voltage gated, type VIII, alpha subunit	609					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|membrane depolarization during action potential (GO:0086010)|muscle organ development (GO:0007517)|myelination (GO:0042552)|nervous system development (GO:0007399)|neuromuscular process (GO:0050905)|neuronal action potential (GO:0019228)|peripheral nervous system development (GO:0007422)|response to toxic substance (GO:0009636)|sensory perception of sound (GO:0007605)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	ATP binding (GO:0005524)|voltage-gated sodium channel activity (GO:0005248)	p.E609K(2)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(19)|ovary(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55				BRCA - Breast invasive adenocarcinoma(357;0.181)	Valproic Acid(DB00313)	CCGGGCCCGCGAGCGCCGGAG	0.697																																						dbGAP											2	Substitution - Missense(2)	breast(2)											7.0	12.0	10.0					12																	52115519		1968	4091	6059	-	-	-	SO:0001583	missense	0			AB027567	CCDS44891.1, CCDS53794.1	12q13.1	2012-02-26	2007-01-23			ENSG00000196876		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10596	protein-coding gene	gene with protein product		600702	"""sodium channel, voltage gated, type VIII, alpha polypeptide"""	MED		7670495, 9828131, 16382098	Standard	NM_014191		Approved	Nav1.6, NaCh6, PN4, CerIII	uc001ryw.4	Q9UQD0		ENST00000354534.6:c.1825G>A	12.37:g.52115519G>A	ENSP00000346534:p.Glu609Lys	Somatic		WXS	Illumina GAIIx	Phase_IV	B9VWG8|O95788|Q9NYX2|Q9UPB2	Missense_Mutation	SNP	pfam_Ion_trans_dom,pfam_DUF3451,pfam_Na_trans_assoc,pfam_PKD1_2_channel,pfam_IQ_motif_EF-hand-BS,smart_IQ_motif_EF-hand-BS,prints_Na_channel_a8su,prints_Na_channel_asu,prints_PKD_2,pfscan_IQ_motif_EF-hand-BS	p.E609K	ENST00000354534.6	37	c.1825	CCDS44891.1	12	.	.	.	.	.	.	.	.	.	.	G	16.50	3.142036	0.57044	.	.	ENSG00000196876	ENST00000550891;ENST00000354534;ENST00000545061;ENST00000355133;ENST00000357961;ENST00000551216	D;D;D;D;D	0.90504	-2.68;-2.68;-2.68;-2.68;-2.68	3.93	3.04	0.35103	Domain of unknown function DUF3451 (1);	0.348482	0.30260	N	0.010028	D	0.87767	0.6260	L	0.55990	1.75	0.32547	N	0.532824	P;B;B;P	0.43750	0.665;0.072;0.021;0.816	B;B;B;B	0.41332	0.247;0.011;0.011;0.354	D	0.89704	0.3907	10	0.72032	D	0.01	.	11.74	0.51788	0.0872:0.0:0.9128:0.0	.	609;609;609;609	F8VWM7;Q9UQD0-3;F8VRN5;Q9UQD0	.;.;.;SCN8A_HUMAN	K	609;609;609;609;522;407	ENSP00000448415:E609K;ENSP00000346534:E609K;ENSP00000440360:E609K;ENSP00000347255:E609K;ENSP00000447567:E407K	ENSP00000346534:E609K	E	+	1	0	SCN8A	50401786	0.998000	0.40836	1.000000	0.80357	0.995000	0.86356	3.364000	0.52328	1.004000	0.39156	0.467000	0.42956	GAG	SCN8A	-	pfam_DUF3451	ENSG00000196876		0.697	SCN8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SCN8A	HGNC	protein_coding	OTTHUMT00000404372.3	14	0.00	0	G	NM_014191		52115519	52115519	+1	no_errors	ENST00000354534	ensembl	human	known	69_37n	missense	11	35.29	6	SNP	0.999	A
SH3BP1	23616	genome.wustl.edu	37	22	38037425	38037425	+	Missense_Mutation	SNP	C	C	G			TCGA-AN-A0XP-01A-11D-A117-09	TCGA-AN-A0XP-10A-01D-A10G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	6179b498-2cea-4f7a-82a8-b7ec71431ea8	6c4eee86-8839-4a74-a786-b37e7dd35b21	g.chr22:38037425C>G	ENST00000357436.4	+	3	460	c.147C>G	c.(145-147)atC>atG	p.I49M	SH3BP1_ENST00000599616.1_5'Flank|SH3BP1_ENST00000336738.5_Missense_Mutation_p.I49M|Z83844.1_ENST00000456099.1_RNA|SH3BP1_ENST00000495174.1_3'UTR|SH3BP1_ENST00000442465.2_Missense_Mutation_p.I49M	NM_018957.3	NP_061830.3	Q9Y3L3	3BP1_HUMAN	SH3-domain binding protein 1	49	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)	p.I49M(1)		breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	Melanoma(58;0.0574)					CCCACAACATCCACAAGCGGC	0.657																																						dbGAP											1	Substitution - Missense(1)	breast(1)											11.0	14.0	13.0					22																	38037425		2023	3981	6004	-	-	-	SO:0001583	missense	0				CCDS13952.2	22q13.1	2011-07-04			ENSG00000100092	ENSG00000100092		"""Rho GTPase activating proteins"""	10824	protein-coding gene	gene with protein product						10591208, 12029088	Standard	NM_018957		Approved	ARHGAP43	uc003ati.3	Q9Y3L3	OTTHUMG00000030996	ENST00000357436.4:c.147C>G	22.37:g.38037425C>G	ENSP00000350018:p.Ile49Met	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5R3N0|Q6IBZ2|Q6ZVL9|Q96HQ5|Q9NSQ9	Missense_Mutation	SNP	pfam_RhoGAP_dom,pfam_BAR_dom,superfamily_Rho_GTPase_activation_prot,smart_BAR_dom,smart_RhoGAP_dom,pfscan_BAR_dom,pfscan_RhoGAP_dom	p.I49M	ENST00000357436.4	37	c.147	CCDS13952.2	22	.	.	.	.	.	.	.	.	.	.	C	8.240	0.806648	0.16467	.	.	ENSG00000100092	ENST00000357436;ENST00000336738;ENST00000442465	T;T;T	0.35605	1.3;1.3;1.3	5.54	-1.04	0.10068	BAR (2);	0.000000	0.48767	D	0.000172	T	0.22044	0.0531	N	0.14661	0.345	0.20821	N	0.999844	B;P	0.45634	0.029;0.863	B;P	0.47206	0.062;0.541	T	0.15607	-1.0431	10	0.46703	T	0.11	.	6.2725	0.20963	0.1168:0.2577:0.542:0.0835	.	49;49	F5GZA8;Q9Y3L3	.;3BP1_HUMAN	M	49	ENSP00000350018:I49M;ENSP00000337213:I49M;ENSP00000395126:I49M	ENSP00000337213:I49M	I	+	3	3	SH3BP1	36367371	0.962000	0.33011	0.990000	0.47175	0.008000	0.06430	-0.026000	0.12392	-0.031000	0.13781	-0.175000	0.13238	ATC	SH3BP1	-	pfam_BAR_dom,smart_BAR_dom,pfscan_BAR_dom	ENSG00000100092		0.657	SH3BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SH3BP1	HGNC	protein_coding	OTTHUMT00000075884.4	25	0.00	0	C	NM_018957		38037425	38037425	+1	no_errors	ENST00000357436	ensembl	human	known	69_37n	missense	19	36.67	11	SNP	0.940	G
SHARPIN	81858	genome.wustl.edu	37	8	145154196	145154196	+	Silent	SNP	A	A	C			TCGA-AN-A0XP-01A-11D-A117-09	TCGA-AN-A0XP-10A-01D-A10G-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	6179b498-2cea-4f7a-82a8-b7ec71431ea8	6c4eee86-8839-4a74-a786-b37e7dd35b21	g.chr8:145154196A>C	ENST00000398712.2	-	6	1342	c.906T>G	c.(904-906)gcT>gcG	p.A302A	SHARPIN_ENST00000533948.1_5'Flank	NM_030974.3	NP_112236.3	Q9H0F6	SHRPN_HUMAN	SHANK-associated RH domain interactor	302	Interaction with SHANK1. {ECO:0000250}.				apoptotic nuclear changes (GO:0030262)|brain development (GO:0007420)|keratinization (GO:0031424)|mitochondrion organization (GO:0007005)|negative regulation of inflammatory response (GO:0050728)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein homooligomerization (GO:0051260)|protein linear polyubiquitination (GO:0097039)|regulation of CD40 signaling pathway (GO:2000348)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)	cell junction (GO:0030054)|cytosol (GO:0005829)|dendrite (GO:0030425)|LUBAC complex (GO:0071797)|postsynaptic density (GO:0014069)	polyubiquitin binding (GO:0031593)|zinc ion binding (GO:0008270)	p.A302A(1)		breast(1)|endometrium(1)|kidney(1)|lung(2)|ovary(2)	7	all_cancers(97;2.87e-11)|all_epithelial(106;2.16e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;4.1e-42)|Epithelial(56;1.58e-40)|all cancers(56;6.12e-36)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CTTCTCGAGGAGCTGACAGCA	0.652																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											49.0	57.0	54.0					8																	145154196		2070	4206	6276	-	-	-	SO:0001819	synonymous_variant	0			AL136816	CCDS43777.1	8q24.3	2005-08-09				ENSG00000179526			25321	protein-coding gene	gene with protein product		611885				11178875, 12753155	Standard	NM_030974		Approved	DKFZP434N1923, SIPL1	uc003zba.3	Q9H0F6		ENST00000398712.2:c.906T>G	8.37:g.145154196A>C		Somatic		WXS	Illumina GAIIx	Phase_IV	A6NEG3|C0L3L2|D3DWL3|Q8IXF5|Q8IXF6|Q8N2E7|Q8TB25|Q9BUE4	Silent	SNP	pfam_Znf_RanBP2,smart_Znf_RanBP2,pfscan_Znf_RanBP2	p.A302	ENST00000398712.2	37	c.906	CCDS43777.1	8																																																																																			SHARPIN	-	NULL	ENSG00000179526		0.652	SHARPIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SHARPIN	HGNC	protein_coding	OTTHUMT00000382901.1	27	0.00	0	A	NM_030974		145154196	145154196	-1	no_errors	ENST00000398712	ensembl	human	known	69_37n	silent	35	27.08	13	SNP	0.896	C
SLC1A4	6509	genome.wustl.edu	37	2	65243809	65243809	+	Splice_Site	SNP	T	T	C			TCGA-AN-A0XP-01A-11D-A117-09	TCGA-AN-A0XP-10A-01D-A10G-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	6179b498-2cea-4f7a-82a8-b7ec71431ea8	6c4eee86-8839-4a74-a786-b37e7dd35b21	g.chr2:65243809T>C	ENST00000234256.3	+	5	1277		c.e5+2		SLC1A4_ENST00000531327.1_Intron	NM_003038.4	NP_003029.2	P43007	SATT_HUMAN	solute carrier family 1 (glutamate/neutral amino acid transporter), member 4						amino acid transport (GO:0006865)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|cognition (GO:0050890)|glutamine transport (GO:0006868)|hydroxyproline transport (GO:0034589)|ion transport (GO:0006811)|L-alanine transport (GO:0015808)|L-cystine transport (GO:0015811)|L-serine transport (GO:0015825)|proline transmembrane transport (GO:0035524)|proline transport (GO:0015824)|synaptic transmission, glutamatergic (GO:0035249)|threonine transport (GO:0015826)|transmembrane transport (GO:0055085)	cell surface (GO:0009986)|centrosome (GO:0005813)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intermediate filament (GO:0005882)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)|L-alanine transmembrane transporter activity (GO:0015180)|L-cystine transmembrane transporter activity (GO:0015184)|L-glutamine transmembrane transporter activity (GO:0015186)|L-hydroxyproline transmembrane transporter activity (GO:0034590)|L-proline transmembrane transporter activity (GO:0015193)|L-serine transmembrane transporter activity (GO:0015194)|L-threonine transmembrane transporter activity (GO:0015195)|sodium:dicarboxylate symporter activity (GO:0017153)	p.?(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)|urinary_tract(1)	13					L-Alanine(DB00160)	CTGCTCCAGGTGAGTGGGTTT	0.473																																						dbGAP											1	Unknown(1)	breast(1)											59.0	58.0	59.0					2																	65243809		2203	4300	6503	-	-	-	SO:0001630	splice_region_variant	0				CCDS1879.1, CCDS54362.1	2p15-p13	2013-05-22			ENSG00000115902	ENSG00000115902		"""Solute carriers"""	10942	protein-coding gene	gene with protein product	"""alanine/serine/cysteine/threonine transporter"""	600229				7896285, 8910405	Standard	NM_003038		Approved	SATT, ASCT1	uc010yqa.2	P43007	OTTHUMG00000129537	ENST00000234256.3:c.1034+2T>C	2.37:g.65243809T>C		Somatic		WXS	Illumina GAIIx	Phase_IV	B7Z3C0|D6W5F0	Splice_Site	SNP	-	e5+2	ENST00000234256.3	37	c.1034+2	CCDS1879.1	2	.	.	.	.	.	.	.	.	.	.	T	27.0	4.790862	0.90367	.	.	ENSG00000115902	ENST00000448784;ENST00000234256	.	.	.	5.87	5.87	0.94306	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.5764	0.84681	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	SLC1A4	65097313	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	7.997000	0.88414	2.371000	0.80710	0.533000	0.62120	.	SLC1A4	-	-	ENSG00000115902		0.473	SLC1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC1A4	HGNC	protein_coding	OTTHUMT00000251726.2	113	0.00	0	T	NM_003038	Intron	65243809	65243809	+1	no_errors	ENST00000234256	ensembl	human	known	69_37n	splice_site	58	41.41	41	SNP	1.000	C
SNRNP200	23020	genome.wustl.edu	37	2	96956114	96956114	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A0XP-01A-11D-A117-09	TCGA-AN-A0XP-10A-01D-A10G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	6179b498-2cea-4f7a-82a8-b7ec71431ea8	6c4eee86-8839-4a74-a786-b37e7dd35b21	g.chr2:96956114G>A	ENST00000323853.5	-	20	2769	c.2692C>T	c.(2692-2694)Cct>Tct	p.P898S	SNRNP200_ENST00000349783.5_Intron	NM_014014.4	NP_054733.2	O75643	U520_HUMAN	small nuclear ribonucleoprotein 200kDa (U5)	898	Helicase C-terminal 1. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|cis assembly of pre-catalytic spliceosome (GO:0000354)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)	p.P898S(1)		breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|lung(37)|ovary(7)|prostate(4)|skin(5)|stomach(1)|urinary_tract(1)	90						AGCATGTCAGGAAGCTTTGAA	0.488																																						dbGAP											1	Substitution - Missense(1)	breast(1)											192.0	178.0	183.0					2																	96956114		2203	4300	6503	-	-	-	SO:0001583	missense	0			AL831994	CCDS2020.1	2q11.2	2013-05-13	2008-10-29	2008-10-29	ENSG00000144028	ENSG00000144028			30859	protein-coding gene	gene with protein product	"""U5 snRNP specific protein, 200 KD"""	601664	"""activating signal cointegrator 1 complex subunit 3-like 1"", ""retinitis pigmentosa 33 (autosomal dominant)"""	ASCC3L1, RP33		9872452, 8670905, 9774689, 9539711, 16612614, 19878916	Standard	NM_014014		Approved	U5-200KD, HELIC2, KIAA0788, BRR2	uc002svu.3	O75643	OTTHUMG00000130455	ENST00000323853.5:c.2692C>T	2.37:g.96956114G>A	ENSP00000317123:p.Pro898Ser	Somatic		WXS	Illumina GAIIx	Phase_IV	O94884|Q6NZY0|Q6PX59|Q8NBE6|Q96IF2|Q9H7S0	Missense_Mutation	SNP	pfam_Sec63-dom,pfam_DNA/RNA_helicase_DEAD/DEAH_N,pfam_Helicase/UvrB_dom,pfam_Helicase_C,smart_Helicase_ATP-bd,smart_Helicase_C,smart_Sec63-dom,pfscan_Helicase_ATP-bd,pfscan_Helicase_C	p.P898S	ENST00000323853.5	37	c.2692	CCDS2020.1	2	.	.	.	.	.	.	.	.	.	.	G	16.80	3.222802	0.58668	.	.	ENSG00000144028	ENST00000323853;ENST00000540328	T	0.40756	1.02	5.74	5.74	0.90152	Helicase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.44435	0.1293	L	0.58969	1.84	0.80722	D	1	B	0.15719	0.014	B	0.11329	0.006	T	0.24404	-1.0161	10	0.44086	T	0.13	-11.5322	18.7061	0.91639	0.0:0.0:1.0:0.0	.	898	O75643	U520_HUMAN	S	898;573	ENSP00000317123:P898S	ENSP00000317123:P898S	P	-	1	0	SNRNP200	96319841	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.458000	0.66679	2.712000	0.92718	0.563000	0.77884	CCT	SNRNP200	-	pfscan_Helicase_C	ENSG00000144028		0.488	SNRNP200-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SNRNP200	HGNC	protein_coding	OTTHUMT00000252846.2	90	0.00	0	G	NM_014014		96956114	96956114	-1	no_errors	ENST00000323853	ensembl	human	known	69_37n	missense	65	29.35	27	SNP	1.000	A
TACC1	6867	genome.wustl.edu	37	8	38684873	38684873	+	Missense_Mutation	SNP	C	C	T			TCGA-AN-A0XP-01A-11D-A117-09	TCGA-AN-A0XP-10A-01D-A10G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	6179b498-2cea-4f7a-82a8-b7ec71431ea8	6c4eee86-8839-4a74-a786-b37e7dd35b21	g.chr8:38684873C>T	ENST00000317827.4	+	5	2019	c.1640C>T	c.(1639-1641)gCg>gTg	p.A547V	TACC1_ENST00000443286.2_Intron|TACC1_ENST00000518415.1_Intron|TACC1_ENST00000520973.1_Intron|TACC1_ENST00000276520.8_Missense_Mutation_p.A137V|TACC1_ENST00000348567.4_Missense_Mutation_p.A109V|TACC1_ENST00000520611.1_5'UTR|TACC1_ENST00000330691.6_Missense_Mutation_p.A121V|TACC1_ENST00000520340.1_Intron|TACC1_ENST00000520615.1_Missense_Mutation_p.A352V|TACC1_ENST00000522752.1_Intron|TACC1_ENST00000519416.1_Missense_Mutation_p.A351V|TACC1_ENST00000379931.3_Missense_Mutation_p.A559V	NM_006283.2	NP_006274.2	O75410	TACC1_HUMAN	transforming, acidic coiled-coil containing protein 1	547					cell cycle (GO:0007049)|cell division (GO:0051301)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)		p.A547V(2)		breast(4)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|skin(3)	17		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.065)	LUSC - Lung squamous cell carcinoma(45;1.7e-09)|COAD - Colon adenocarcinoma(9;0.235)			ATAAATCATGCGTTTTCATCC	0.438																																						dbGAP											2	Substitution - Missense(2)	breast(2)											174.0	134.0	147.0					8																	38684873		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF049910	CCDS6109.1, CCDS47845.1, CCDS55224.1	8p11	2012-12-20			ENSG00000147526	ENSG00000147526			11522	protein-coding gene	gene with protein product		605301					Standard	NM_006283		Approved		uc010lwp.3	O75410	OTTHUMG00000164018	ENST00000317827.4:c.1640C>T	8.37:g.38684873C>T	ENSP00000321703:p.Ala547Val	Somatic		WXS	Illumina GAIIx	Phase_IV	B2RBD9|D3DSX6|Q6Y687|Q86YG7|Q8IUJ2|Q8IUJ3|Q8IUJ4|Q8IZG2|Q8NEY7|Q9UPP9	Missense_Mutation	SNP	pfam_TACC	p.A559V	ENST00000317827.4	37	c.1676	CCDS6109.1	8	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.36|15.36	2.810023|2.810023	0.50421|0.50421	.|.	.|.	ENSG00000147526|ENSG00000147526	ENST00000519416;ENST00000520615;ENST00000443388;ENST00000521642;ENST00000521050;ENST00000330691;ENST00000348567;ENST00000317827;ENST00000379931;ENST00000276520|ENST00000518809	T;T;T;T;T;T;T|.	0.43688|.	2.92;2.92;0.95;0.94;3.09;3.08;0.95|.	5.83|5.83	3.98|3.98	0.46160|0.46160	.|.	0.276961|.	0.31897|.	N|.	0.006892|.	T|T	0.44030|0.44030	0.1274|0.1274	L|L	0.47716|0.47716	1.5|1.5	0.21220|0.21220	N|N	0.999751|0.999751	P;P;P;B;P;B|.	0.47841|.	0.901;0.519;0.84;0.072;0.733;0.384|.	B;B;B;B;B;B|.	0.37601|.	0.254;0.123;0.091;0.039;0.09;0.057|.	T|T	0.25363|0.25363	-1.0134|-1.0134	10|5	0.40728|.	T|.	0.16|.	-0.1244|-0.1244	12.5272|12.5272	0.56093|0.56093	0.3134:0.6866:0.0:0.0|0.3134:0.6866:0.0:0.0	.|.	352;559;547;137;121;351|.	B7Z3G3;O75410-2;O75410;O75410-6;O75410-4;E7ET87|.	.;.;TACC1_HUMAN;.;.;.|.	V|C	351;352;352;109;121;121;109;547;559;137|197	ENSP00000428687:A351V;ENSP00000428450:A352V;ENSP00000332794:A121V;ENSP00000327818:A109V;ENSP00000321703:A547V;ENSP00000369263:A559V;ENSP00000276520:A137V|.	ENSP00000276520:A137V|.	A|R	+|+	2|1	0|0	TACC1|TACC1	38804030|38804030	0.991000|0.991000	0.36638|0.36638	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	0.441000|0.441000	0.21611|0.21611	0.741000|0.741000	0.32674|0.32674	0.655000|0.655000	0.94253|0.94253	GCG|CGT	TACC1	-	NULL	ENSG00000147526		0.438	TACC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	TACC1	HGNC	protein_coding	OTTHUMT00000376768.1	140	0.00	0	C	NM_006283		38684873	38684873	+1	no_errors	ENST00000379931	ensembl	human	known	69_37n	missense	116	35.20	63	SNP	0.998	T
