#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
AGBL1	123624	genome.wustl.edu	37	15	86768172	86768172	+	Missense_Mutation	SNP	G	G	T			TCGA-E2-A1IL-01A-11D-A14G-09	TCGA-E2-A1IL-10A-01D-A14G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1540ae03-7bb4-418b-afbc-44bf3ad60a31	6a5f0824-3724-42a3-af37-ca7215491e63	g.chr15:86768172G>T	ENST00000441037.2	+	5	473	c.378G>T	c.(376-378)ttG>ttT	p.L126F	AGBL1_ENST00000421325.2_Missense_Mutation_p.L126F	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	126					C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytoplasm (GO:0005737)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(3)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(2)|lung(28)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	62						TGGCAGCATTGCTGAAATCCA	0.438																																						dbGAP											0													204.0	197.0	199.0					15																	86768172		1894	4113	6007	-	-	-	SO:0001583	missense	0			AK056872	CCDS58398.1	15q25.3	2014-06-23			ENSG00000166748	ENSG00000166748			26504	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase 4"""	615496				21074048, 24094747	Standard	NM_152336		Approved	FLJ32310, CCP4	uc002blz.1	Q96MI9	OTTHUMG00000149978	ENST00000441037.2:c.378G>T	15.37:g.86768172G>T	ENSP00000413001:p.Leu126Phe	Somatic		WXS	Illumina GAIIx	Phase_IV	A1A4X5|A6NJH6|C9JHL5	Missense_Mutation	SNP	pfam_Peptidase_M14,superfamily_ARM-type_fold	p.L126F	ENST00000441037.2	37	c.378	CCDS58398.1	15	.	.	.	.	.	.	.	.	.	.	G	18.12	3.552628	0.65425	.	.	ENSG00000166748	ENST00000441037;ENST00000421325	T	0.73469	-0.75	5.18	5.18	0.71444	Armadillo-like helical (1);Armadillo-type fold (1);	.	.	.	.	D	0.85940	0.5814	M	0.77313	2.365	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.86561	0.1841	9	0.52906	T	0.07	-8.567	15.8104	0.78557	0.0:0.0:1.0:0.0	.	126	Q96MI9	CBPC4_HUMAN	F	155;126	ENSP00000397173:L126F	ENSP00000397173:L126F	L	+	3	2	AGBL1	84569176	1.000000	0.71417	0.996000	0.52242	0.918000	0.54935	3.110000	0.50352	2.579000	0.87056	0.555000	0.69702	TTG	AGBL1	-	superfamily_ARM-type_fold	ENSG00000166748		0.438	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	AGBL1	HGNC	protein_coding	OTTHUMT00000314929.5	103	0.00	0	G	NM_152336		86768172	86768172	+1	no_errors	ENST00000441037	ensembl	human	known	69_37n	missense	100	26.47	36	SNP	1.000	T
ANKRD17	26057	genome.wustl.edu	37	4	73942663	73942663	+	Silent	SNP	A	A	C			TCGA-E2-A1IL-01A-11D-A14G-09	TCGA-E2-A1IL-10A-01D-A14G-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1540ae03-7bb4-418b-afbc-44bf3ad60a31	6a5f0824-3724-42a3-af37-ca7215491e63	g.chr4:73942663A>C	ENST00000358602.4	-	33	7862	c.7746T>G	c.(7744-7746)ccT>ccG	p.P2582P	ANKRD17_ENST00000509867.2_Silent_p.P2469P|ANKRD17_ENST00000330838.6_Silent_p.P2331P	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	2582					blood vessel maturation (GO:0001955)|negative regulation of smooth muscle cell differentiation (GO:0051151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(39)|ovary(6)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)	96	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TCACCGTTTGAGGGCCATTAT	0.423																																						dbGAP											0													135.0	134.0	135.0					4																	73942663		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AB014597	CCDS34003.1, CCDS34004.1, CCDS68721.1	4q21.1-q21.21	2013-01-10			ENSG00000132466	ENSG00000132466		"""Ankyrin repeat domain containing"""	23575	protein-coding gene	gene with protein product		615929				11165478	Standard	NM_032217		Approved	GTAR, KIAA0697, FLJ22206, NY-BR-16	uc003hgp.3	O75179	OTTHUMG00000160826	ENST00000358602.4:c.7746T>G	4.37:g.73942663A>C		Somatic		WXS	Illumina GAIIx	Phase_IV	E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Missense_Mutation	SNP	pfam_Ankyrin_rpt,pfam_KH_dom_type_1,superfamily_Ankyrin_rpt-contain_dom,smart_Ankyrin_rpt,smart_KH_dom,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom,pfscan_KH_dom_type_1,prints_Ankyrin_rpt	p.L2466R	ENST00000358602.4	37	c.7397	CCDS34004.1	4																																																																																			ANKRD17	-	NULL	ENSG00000132466		0.423	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ANKRD17	HGNC	protein_coding	OTTHUMT00000362475.1	55	0.00	0	A	NM_032217		73942663	73942663	-1	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000558247	ensembl	human	known	69_37n	missense	40	21.57	11	SNP	1.000	C
APOBR	55911	genome.wustl.edu	37	16	28507424	28507424	+	Intron	SNP	C	C	T	rs148114931|rs441214	byFrequency	TCGA-E2-A1IL-01A-11D-A14G-09	TCGA-E2-A1IL-10A-01D-A14G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1540ae03-7bb4-418b-afbc-44bf3ad60a31	6a5f0824-3724-42a3-af37-ca7215491e63	g.chr16:28507424C>T	ENST00000431282.1	+	3	1058				APOBR_ENST00000564831.1_Silent_p.A354A|CLN3_ENST00000567160.1_5'Flank|CLN3_ENST00000569430.1_5'Flank|APOBR_ENST00000328423.5_Intron			Q0VD83	APOBR_HUMAN	apolipoprotein B receptor						cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|triglyceride metabolic process (GO:0006641)	chylomicron (GO:0042627)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	very-low-density lipoprotein particle receptor activity (GO:0030229)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|skin(2)|stomach(1)	29						GGGAGGAGGCCGGGACAGCCT	0.711																																						dbGAP											0													8.0	11.0	10.0					16																	28507424		1858	4004	5862	-	-	-	SO:0001627	intron_variant	0			AK025123	CCDS58442.1	16p11.2	2011-02-14			ENSG00000184730	ENSG00000184730			24087	protein-coding gene	gene with protein product	"""apolipoprotein B48 receptor"", ""apolipoprotein B100 receptor"""	605220				10852956	Standard	NM_018690		Approved	APOB48R, APOB100R	uc002dqb.2	Q0VD83		ENST00000431282.1:c.1049-14C>T	16.37:g.28507424C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	H3BU97|Q0VD81|Q8NC15|Q9NPJ9	Silent	SNP	NULL	p.A354	ENST00000431282.1	37	c.1062		16																																																																																			APOBR	-	NULL	ENSG00000184730		0.711	APOBR-202	KNOWN	basic|appris_candidate	protein_coding	APOBR	HGNC	protein_coding		16	0.00	0	C	NM_182804		28507424	28507424	+1	no_errors	ENST00000564831	ensembl	human	known	69_37n	silent	30	26.83	11	SNP	0.000	T
ARFGEF2	10564	genome.wustl.edu	37	20	47607613	47607613	+	Missense_Mutation	SNP	T	T	C			TCGA-E2-A1IL-01A-11D-A14G-09	TCGA-E2-A1IL-10A-01D-A14G-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1540ae03-7bb4-418b-afbc-44bf3ad60a31	6a5f0824-3724-42a3-af37-ca7215491e63	g.chr20:47607613T>C	ENST00000371917.4	+	21	2851	c.2851T>C	c.(2851-2853)Ttc>Ctc	p.F951L		NM_006420.2	NP_006411.2	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	951					endomembrane system organization (GO:0010256)|endosome organization (GO:0007032)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of tumor necrosis factor production (GO:0032760)|protein transport (GO:0015031)|receptor recycling (GO:0001881)|regulation of ARF protein signal transduction (GO:0032012)|vesicle-mediated transport (GO:0016192)	asymmetric synapse (GO:0032279)|axonemal microtubule (GO:0005879)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|recycling endosome (GO:0055037)|symmetric synapse (GO:0032280)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|GABA receptor binding (GO:0050811)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase A regulatory subunit binding (GO:0034237)			breast(7)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	63			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			TCTTGCTCGCTTCTCCCTACT	0.488																																					Esophageal Squamous(176;1738 1974 26285 33069 35354)	dbGAP											0													161.0	125.0	137.0					20																	47607613		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF084521	CCDS13411.1	20q13.13	2010-08-20			ENSG00000124198	ENSG00000124198		"""A-kinase anchor proteins"""	15853	protein-coding gene	gene with protein product	"""Brefeldin A-inhibited guanine nucleotide-exchange protein 2"""	605371				10212200	Standard	NM_006420		Approved	BIG2	uc002xtx.4	Q9Y6D5	OTTHUMG00000032687	ENST00000371917.4:c.2851T>C	20.37:g.47607613T>C	ENSP00000360985:p.Phe951Leu	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5TFT9|Q9NTS1	Missense_Mutation	SNP	pfam_Sec7,pfam_DUF1981_SEC7_assoc,superfamily_Sec7,superfamily_ARM-type_fold,smart_Sec7,pfscan_Sec7	p.F951L	ENST00000371917.4	37	c.2851	CCDS13411.1	20	.	.	.	.	.	.	.	.	.	.	T	21.8	4.208795	0.79240	.	.	ENSG00000124198	ENST00000371917	T	0.66099	-0.19	5.86	5.86	0.93980	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.80628	0.4659	M	0.79693	2.465	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.83332	-0.0012	10	0.87932	D	0	.	16.2669	0.82588	0.0:0.0:0.0:1.0	.	951	Q9Y6D5	BIG2_HUMAN	L	951	ENSP00000360985:F951L	ENSP00000360985:F951L	F	+	1	0	ARFGEF2	47041020	1.000000	0.71417	1.000000	0.80357	0.094000	0.18550	8.040000	0.89188	2.240000	0.73641	0.533000	0.62120	TTC	ARFGEF2	-	superfamily_ARM-type_fold	ENSG00000124198		0.488	ARFGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ARFGEF2	HGNC	protein_coding	OTTHUMT00000079627.1	100	0.00	0	T	NM_006420		47607613	47607613	+1	no_errors	ENST00000371917	ensembl	human	known	69_37n	missense	52	38.10	32	SNP	1.000	C
AVL9	23080	genome.wustl.edu	37	7	32598971	32598971	+	Missense_Mutation	SNP	T	T	G			TCGA-E2-A1IL-01A-11D-A14G-09	TCGA-E2-A1IL-10A-01D-A14G-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1540ae03-7bb4-418b-afbc-44bf3ad60a31	6a5f0824-3724-42a3-af37-ca7215491e63	g.chr7:32598971T>G	ENST00000318709.4	+	10	1331	c.1110T>G	c.(1108-1110)atT>atG	p.I370M	AVL9_ENST00000409301.1_Missense_Mutation_p.I370M|AVL9_ENST00000404479.1_Missense_Mutation_p.I370M	NM_015060.1	NP_055875.1	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)	370					cell migration (GO:0016477)	integral component of membrane (GO:0016021)|recycling endosome (GO:0055037)				endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						GTCTTCCAATTACTGTACAAC	0.488																																						dbGAP											0													48.0	48.0	48.0					7																	32598971		2201	4295	6496	-	-	-	SO:0001583	missense	0			D87682	CCDS34613.1	7p14.3	2013-05-01	2008-10-03	2008-10-03	ENSG00000105778	ENSG00000105778			28994	protein-coding gene	gene with protein product		612927	"""KIAA0241"""	KIAA0241		17229886, 22595670	Standard	XM_005249668		Approved		uc003tcv.1	Q8NBF6	OTTHUMG00000152929	ENST00000318709.4:c.1110T>G	7.37:g.32598971T>G	ENSP00000315568:p.Ile370Met	Somatic		WXS	Illumina GAIIx	Phase_IV	Q92573	Missense_Mutation	SNP	pfam_Secretory_pathway_prot_Avl9,pfam_DUF2347	p.I370M	ENST00000318709.4	37	c.1110	CCDS34613.1	7	.	.	.	.	.	.	.	.	.	.	T	15.93	2.978106	0.53720	.	.	ENSG00000105778	ENST00000318709;ENST00000409301;ENST00000329714;ENST00000404479;ENST00000446718	T;T;T;T	0.58940	0.65;0.64;0.3;0.5	5.41	2.98	0.34508	.	0.000000	0.85682	D	0.000000	T	0.65281	0.2676	L	0.57536	1.79	0.46028	D	0.998825	D;P;D	0.89917	0.999;0.627;1.0	D;B;D	0.91635	0.989;0.216;0.999	T	0.61023	-0.7146	10	0.35671	T	0.21	-19.6736	4.4202	0.11477	0.1376:0.2365:0.0:0.626	.	370;370;370	Q8N6Z3;Q8NBF6-2;Q8NBF6	.;.;AVL9_HUMAN	M	370;370;370;370;301	ENSP00000315568:I370M;ENSP00000387011:I370M;ENSP00000385242:I370M;ENSP00000395134:I301M	ENSP00000315568:I370M	I	+	3	3	AVL9	32565496	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	0.699000	0.25586	0.474000	0.27392	0.533000	0.62120	ATT	AVL9	-	pfam_Secretory_pathway_prot_Avl9	ENSG00000105778		0.488	AVL9-003	NOVEL	basic|appris_principal|CCDS	protein_coding	AVL9	HGNC	protein_coding	OTTHUMT00000328643.1	13	0.00	0	T	NM_015060		32598971	32598971	+1	no_errors	ENST00000404479	ensembl	human	known	69_37n	missense	9	40.00	6	SNP	1.000	G
CNTD1	124817	genome.wustl.edu	37	17	40956304	40956305	+	Frame_Shift_Del	DEL	AA	AA	-			TCGA-E2-A1IL-01A-11D-A14G-09	TCGA-E2-A1IL-10A-01D-A14G-09	AA	AA					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1540ae03-7bb4-418b-afbc-44bf3ad60a31	6a5f0824-3724-42a3-af37-ca7215491e63	g.chr17:40956304_40956305delAA	ENST00000588408.1	+	3	583_584	c.307_308delAA	c.(307-309)aagfs	p.K103fs	CNTD1_ENST00000588527.1_Frame_Shift_Del_p.K20fs	NM_173478.2	NP_775749.2	Q8N815	CNTD1_HUMAN	cyclin N-terminal domain containing 1	103	Cyclin N-terminal.									central_nervous_system(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	10		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0749)		AAGAGATAATAAGAGAGAGTCT	0.47																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AK097456	CCDS11440.1	17q21.31	2014-07-03	2006-03-31	2006-03-31	ENSG00000176563	ENSG00000176563			26847	protein-coding gene	gene with protein product			"""cyclin N-terminal domain containing"""	CNTD		24891606	Standard	NM_173478		Approved	FLJ40137	uc002ibm.4	Q8N815		ENST00000588408.1:c.307_308delAA	17.37:g.40956304_40956305delAA	ENSP00000465204:p.Lys103fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q658Q6|Q8NEP1	Frame_Shift_Del	DEL	pfam_Cyclin_N,superfamily_Cyclin-like	p.K103fs	ENST00000588408.1	37	c.307_308	CCDS11440.1	17																																																																																			CNTD1	-	superfamily_Cyclin-like	ENSG00000176563		0.470	CNTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CNTD1	HGNC	protein_coding	OTTHUMT00000452398.1	64	0.00	0	AA	NM_173478		40956304	40956305	+1	no_errors	ENST00000588408	ensembl	human	known	69_37n	frame_shift_del	28	41.18	21	DEL	0.061:0.074	-
FMN2	56776	genome.wustl.edu	37	1	240370352	240370352	+	Missense_Mutation	SNP	C	C	T			TCGA-E2-A1IL-01A-11D-A14G-09	TCGA-E2-A1IL-10A-01D-A14G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1540ae03-7bb4-418b-afbc-44bf3ad60a31	6a5f0824-3724-42a3-af37-ca7215491e63	g.chr1:240370352C>T	ENST00000319653.9	+	5	2470	c.2240C>T	c.(2239-2241)tCc>tTc	p.S747F		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	747					cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			ATACAGACTTCCCCCACGGAA	0.572																																						dbGAP											0													47.0	47.0	47.0					1																	240370352		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.2240C>T	1.37:g.240370352C>T	ENSP00000318884:p.Ser747Phe	Somatic		WXS	Illumina GAIIx	Phase_IV	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	pfam_FH2_actin-bd,pfam_Formin_homology_1,superfamily_FH2_actin-bd,smart_Actin-bd_FH2/DRF_autoreg,pfscan_DEP_dom	p.S747F	ENST00000319653.9	37	c.2240	CCDS31069.2	1	.	.	.	.	.	.	.	.	.	.	C	10.69	1.420442	0.25639	.	.	ENSG00000155816	ENST00000447095;ENST00000319653	T	0.52295	0.67	5.59	4.68	0.58851	.	0.000000	0.64402	D	0.000011	T	0.51736	0.1692	M	0.72894	2.215	0.80722	D	1	P	0.47106	0.89	B	0.43623	0.425	T	0.60078	-0.7333	10	0.87932	D	0	.	14.3165	0.66454	0.0:0.9286:0.0:0.0714	.	747	Q9NZ56	FMN2_HUMAN	F	184;747	ENSP00000318884:S747F	ENSP00000318884:S747F	S	+	2	0	FMN2	238436975	1.000000	0.71417	0.975000	0.42487	0.088000	0.18126	6.848000	0.75409	1.368000	0.46115	0.655000	0.94253	TCC	FMN2	-	NULL	ENSG00000155816		0.572	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FMN2	HGNC	protein_coding	OTTHUMT00000096217.2	36	0.00	0	C	XM_371352		240370352	240370352	+1	no_errors	ENST00000319653	ensembl	human	known	69_37n	missense	20	45.95	17	SNP	0.999	T
NEUROD6	63974	genome.wustl.edu	37	7	31378167	31378167	+	Missense_Mutation	SNP	G	G	A			TCGA-E2-A1IL-01A-11D-A14G-09	TCGA-E2-A1IL-10A-01D-A14G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1540ae03-7bb4-418b-afbc-44bf3ad60a31	6a5f0824-3724-42a3-af37-ca7215491e63	g.chr7:31378167G>A	ENST00000297142.3	-	2	1038	c.716C>T	c.(715-717)gCg>gTg	p.A239V		NM_022728.2	NP_073565.2	Q96NK8	NDF6_HUMAN	neuronal differentiation 6	239					cell differentiation (GO:0030154)|dentate gyrus development (GO:0021542)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	32						GGATTCATACGCACTGCAATA	0.483																																						dbGAP											0													86.0	79.0	81.0					7																	31378167		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF248954	CCDS5434.1	7p15.1	2013-05-21	2012-02-22		ENSG00000164600	ENSG00000164600		"""Basic helix-loop-helix proteins"""	13804	protein-coding gene	gene with protein product		611513	"""neurogenic differentiation 6"""			12357074	Standard	NM_022728		Approved	Atoh2, NEX1M, Math-2, bHLHa2, Nex1	uc003tch.4	Q96NK8	OTTHUMG00000022865	ENST00000297142.3:c.716C>T	7.37:g.31378167G>A	ENSP00000297142:p.Ala239Val	Somatic		WXS	Illumina GAIIx	Phase_IV	Q548T9|Q9H3H6	Missense_Mutation	SNP	pfam_Neurogenic_DUF,pfam_HLH_DNA-bd,superfamily_HLH_DNA-bd,smart_HLH_DNA-bd,pirsf_TF_bHLH_NeuroD,pfscan_HLH_DNA-bd	p.A239V	ENST00000297142.3	37	c.716	CCDS5434.1	7	.	.	.	.	.	.	.	.	.	.	G	10.23	1.292531	0.23564	.	.	ENSG00000164600	ENST00000297142	T	0.64618	-0.11	5.32	4.43	0.53597	Neurogenic differentiation factor, domain of unknown function (1);	0.106309	0.64402	D	0.000006	T	0.51702	0.1690	L	0.28556	0.865	0.45056	D	0.99807	B	0.18610	0.029	B	0.15870	0.014	T	0.46275	-0.9203	10	0.44086	T	0.13	-21.3163	15.9382	0.79734	0.0:0.1355:0.8645:0.0	.	239	Q96NK8	NDF6_HUMAN	V	239	ENSP00000297142:A239V	ENSP00000297142:A239V	A	-	2	0	NEUROD6	31344692	1.000000	0.71417	0.949000	0.38748	0.792000	0.44763	7.541000	0.82084	1.219000	0.43474	-0.181000	0.13052	GCG	NEUROD6	-	pfam_Neurogenic_DUF,pirsf_TF_bHLH_NeuroD	ENSG00000164600		0.483	NEUROD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NEUROD6	HGNC	protein_coding	OTTHUMT00000215050.1	31	0.00	0	G	NM_022728		31378167	31378167	-1	no_errors	ENST00000297142	ensembl	human	known	69_37n	missense	26	46.94	23	SNP	0.992	A
NME8	51314	genome.wustl.edu	37	7	37896882	37896882	+	Missense_Mutation	SNP	G	G	C			TCGA-E2-A1IL-01A-11D-A14G-09	TCGA-E2-A1IL-10A-01D-A14G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1540ae03-7bb4-418b-afbc-44bf3ad60a31	6a5f0824-3724-42a3-af37-ca7215491e63	g.chr7:37896882G>C	ENST00000199447.4	+	6	577	c.205G>C	c.(205-207)Gct>Cct	p.A69P	NME8_ENST00000440017.1_Missense_Mutation_p.A69P|EPDR1_ENST00000476620.1_5'UTR	NM_016616.4	NP_057700.3	Q8N427	TXND3_HUMAN	NME/NM23 family member 8	69	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|CTP biosynthetic process (GO:0006241)|GTP biosynthetic process (GO:0006183)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)|UTP biosynthetic process (GO:0006228)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)										CCAGGCAGAAGCTGACAACAT	0.274																																						dbGAP											0													95.0	95.0	95.0					7																	37896882		2203	4298	6501	-	-	-	SO:0001583	missense	0			AF202051	CCDS5452.1	7p15.2	2012-05-18	2012-05-18	2012-05-18	ENSG00000086288	ENSG00000086288			16473	protein-coding gene	gene with protein product	"""sperm-specific thioredoxin 2"""	607421	"""thioredoxin domain containing 3 (spermatozoa)"""	TXNDC3		11737268, 11768308, 19852809	Standard	NM_016616		Approved	CILD6, SPTRX2, NM23-H8	uc003tfn.3	Q8N427	OTTHUMG00000023716	ENST00000199447.4:c.205G>C	7.37:g.37896882G>C	ENSP00000199447:p.Ala69Pro	Somatic		WXS	Illumina GAIIx	Phase_IV	Q9NZH1	Missense_Mutation	SNP	pfam_Nucleoside_diP_kinase,pfam_Thioredoxin_domain,superfamily_Nucleoside_diP_kinase,superfamily_Thioredoxin-like_fold,smart_Nucleoside_diP_kinase	p.A69P	ENST00000199447.4	37	c.205	CCDS5452.1	7	.	.	.	.	.	.	.	.	.	.	G	20.4	3.980132	0.74474	.	.	ENSG00000086288	ENST00000199447;ENST00000455500;ENST00000444718;ENST00000440017	T;T	0.22134	1.97;1.97	5.65	5.65	0.86999	Thioredoxin domain (1);Thioredoxin-like fold (3);	0.000000	0.50627	D	0.000112	T	0.50120	0.1597	M	0.85373	2.75	0.39103	D	0.961314	D	0.76494	0.999	D	0.78314	0.991	T	0.57923	-0.7727	10	0.72032	D	0.01	-17.5899	13.4629	0.61237	0.0:0.0:0.8431:0.1569	.	69	Q8N427	TXND3_HUMAN	P	69;14;14;69	ENSP00000199447:A69P;ENSP00000397063:A69P	ENSP00000199447:A69P	A	+	1	0	TXNDC3	37863407	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.490000	0.60319	2.654000	0.90174	0.585000	0.79938	GCT	NME8	-	pfam_Thioredoxin_domain,superfamily_Thioredoxin-like_fold	ENSG00000086288		0.274	NME8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NME8	HGNC	protein_coding	OTTHUMT00000219946.1	119	0.00	0	G	NM_016616		37896882	37896882	+1	no_errors	ENST00000199447	ensembl	human	known	69_37n	missense	103	16.80	21	SNP	1.000	C
PGPEP1	54858	genome.wustl.edu	37	19	18474258	18474258	+	Silent	SNP	C	C	T			TCGA-E2-A1IL-01A-11D-A14G-09	TCGA-E2-A1IL-10A-01D-A14G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1540ae03-7bb4-418b-afbc-44bf3ad60a31	6a5f0824-3724-42a3-af37-ca7215491e63	g.chr19:18474258C>T	ENST00000269919.6	+	5	590	c.495C>T	c.(493-495)gcC>gcT	p.A165A	PGPEP1_ENST00000604499.2_Missense_Mutation_p.P152L|PGPEP1_ENST00000597431.2_Missense_Mutation_p.L88F|PGPEP1_ENST00000252813.5_Silent_p.A88A	NM_017712.2	NP_060182.1	Q9NXJ5	PGPI_HUMAN	pyroglutamyl-peptidase I	165						cytosol (GO:0005829)	cysteine-type peptidase activity (GO:0008234)|pyroglutamyl-peptidase activity (GO:0016920)										GTCGATCAGCCTTCGTCCACG	0.582																																						dbGAP											0													89.0	71.0	77.0					19																	18474258		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AJ278828	CCDS12375.1, CCDS74314.1	19p13.11	2012-07-25				ENSG00000130517	3.4.19.3		13568	protein-coding gene	gene with protein product	"""pyroglutamyl aminopeptidase"""	610694					Standard	XM_006722783		Approved	PGP-I, Pcp, PGP, PGPI	uc002nis.1	Q9NXJ5		ENST00000269919.6:c.495C>T	19.37:g.18474258C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	A8K1Q3|Q8IVT1	Silent	SNP	pfam_Peptidase_C15,superfamily_Peptidase_C15-like,pirsf_Peptidase_C15,prints_Peptidase_C15	p.A165	ENST00000269919.6	37	c.495	CCDS12375.1	19																																																																																			PGPEP1	-	pfam_Peptidase_C15,superfamily_Peptidase_C15-like,pirsf_Peptidase_C15	ENSG00000130517		0.582	PGPEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PGPEP1	HGNC	protein_coding	OTTHUMT00000466327.3	57	0.00	0	C	NM_017712		18474258	18474258	+1	no_errors	ENST00000269919	ensembl	human	known	69_37n	silent	36	35.71	20	SNP	0.964	T
PHLDB3	653583	genome.wustl.edu	37	19	44005930	44005930	+	Missense_Mutation	SNP	G	G	T			TCGA-E2-A1IL-01A-11D-A14G-09	TCGA-E2-A1IL-10A-01D-A14G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1540ae03-7bb4-418b-afbc-44bf3ad60a31	6a5f0824-3724-42a3-af37-ca7215491e63	g.chr19:44005930G>T	ENST00000292140.5	-	4	850	c.490C>A	c.(490-492)Cag>Aag	p.Q164K	PHLDB3_ENST00000599242.1_Missense_Mutation_p.Q164K	NM_198850.3	NP_942147.3	Q6NSJ2	PHLB3_HUMAN	pleckstrin homology-like domain, family B, member 3	164							enzyme binding (GO:0019899)			breast(1)|central_nervous_system(1)|lung(5)	7		Prostate(69;0.0153)				GCCGCCTGCTGCTCCAGCAGC	0.682																																						dbGAP											0													9.0	11.0	11.0					19																	44005930		2167	4208	6375	-	-	-	SO:0001583	missense	0				CCDS12621.2	19q13.31	2013-01-10			ENSG00000176531	ENSG00000176531		"""Pleckstrin homology (PH) domain containing"""	30499	protein-coding gene	gene with protein product							Standard	NM_198850		Approved	FLJ40193	uc002own.4	Q6NSJ2	OTTHUMG00000150693	ENST00000292140.5:c.490C>A	19.37:g.44005930G>T	ENSP00000292140:p.Gln164Lys	Somatic		WXS	Illumina GAIIx	Phase_IV	Q8N7Z4	Missense_Mutation	SNP	pfam_Pleckstrin_homology,smart_Pleckstrin_homology,pfscan_Pleckstrin_homology	p.Q164K	ENST00000292140.5	37	c.490	CCDS12621.2	19	.	.	.	.	.	.	.	.	.	.	G	7.304	0.613620	0.14066	.	.	ENSG00000176531	ENST00000292140	T	0.39229	1.09	4.93	4.93	0.64822	.	0.443317	0.20427	N	0.092548	T	0.24890	0.0604	N	0.16743	0.435	0.24421	N	0.994619	B;B	0.32101	0.356;0.131	B;B	0.33454	0.164;0.035	T	0.12785	-1.0534	10	0.02654	T	1	.	14.075	0.64885	0.0:0.0:1.0:0.0	.	164;164	Q6NSJ2-2;Q6NSJ2	.;PHLB3_HUMAN	K	164	ENSP00000292140:Q164K	ENSP00000292140:Q164K	Q	-	1	0	PHLDB3	48697770	0.930000	0.31532	0.806000	0.32338	0.818000	0.46254	3.259000	0.51515	2.470000	0.83445	0.306000	0.20318	CAG	PHLDB3	-	NULL	ENSG00000176531		0.682	PHLDB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PHLDB3	HGNC	protein_coding	OTTHUMT00000319643.2	12	0.00	0	G			44005930	44005930	-1	no_errors	ENST00000292140	ensembl	human	known	69_37n	missense	12	25.00	4	SNP	0.972	T
PIK3CA	5290	genome.wustl.edu	37	3	178952085	178952085	+	Missense_Mutation	SNP	A	A	G	rs121913279		TCGA-E2-A1IL-01A-11D-A14G-09	TCGA-E2-A1IL-10A-01D-A14G-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1540ae03-7bb4-418b-afbc-44bf3ad60a31	6a5f0824-3724-42a3-af37-ca7215491e63	g.chr3:178952085A>G	ENST00000263967.3	+	21	3297	c.3140A>G	c.(3139-3141)cAt>cGt	p.H1047R	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1047	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		H -> L (in BC; unknown pathological significance). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16353168}.|H -> R (in CLOVE, KERSEB, CRC, BC and OC; also found in an endometrial carcinoma sample; shows an increase in lipid kinase activity; oncogenic in vivo; requires binding to p85 regulatory subunit to induce cellular transformation but not interaction with RAS; may mimic the conformatitonal change triggered by the interaction with RAS; enhances invadopodia-mediated extracellular matrix degradation and invasion in breast cancer cells; increases lipid kinase activity; may alter the interaction of the PI3K/ PI4K kinase domain with the cell membrane). {ECO:0000269|PubMed:15016963, ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15712344, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16114017, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22658544}.|H -> Y (in MCAP; also found in an endometrial carcinoma sample). {ECO:0000269|PubMed:16322209, 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.H1047R(1387)|p.H1047L(194)|p.H1047P(1)		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)	AATGATGCACATCATGGTGGC	0.378	H1047L(EFM19_BREAST)|H1047R(BT20_BREAST)|H1047R(CAL29_URINARY_TRACT)|H1047R(CAL33_UPPER_AERODIGESTIVE_TRACT)|H1047R(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|H1047R(HCC1954_BREAST)|H1047R(HCT116_LARGE_INTESTINE)|H1047R(HSC2_UPPER_AERODIGESTIVE_TRACT)|H1047R(LS180_LARGE_INTESTINE)|H1047R(MCAS_OVARY)|H1047R(MDAMB453_BREAST)|H1047R(NCIH1048_LUNG)|H1047R(RKO_LARGE_INTESTINE)|H1047R(SKOV3_OVARY)|H1047R(T47D_BREAST)	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"""	1582	Substitution - Missense(1582)	breast(961)|large_intestine(245)|endometrium(114)|ovary(77)|urinary_tract(36)|upper_aerodigestive_tract(26)|lung(19)|central_nervous_system(19)|stomach(19)|haematopoietic_and_lymphoid_tissue(11)|thyroid(10)|NS(9)|liver(7)|kidney(6)|soft_tissue(6)|skin(4)|prostate(4)|pituitary(3)|pancreas(3)|meninges(1)|cervix(1)|bone(1)											99.0	89.0	92.0					3																	178952085		1912	4130	6042	-	-	-	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.3140A>G	3.37:g.178952085A>G	ENSP00000263967:p.His1047Arg	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.H1047R	ENST00000263967.3	37	c.3140	CCDS43171.1	3	.	.	.	.	.	.	.	.	.	.	A	14.34	2.506328	0.44558	.	.	ENSG00000121879	ENST00000263967	T	0.80214	-1.35	6.08	6.08	0.98989	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	T	0.62466	0.2430	N	0.08118	0	0.80722	D	1	P	0.38597	0.639	B	0.28011	0.085	T	0.67526	-0.5648	10	0.40728	T	0.16	-21.2893	16.6512	0.85203	1.0:0.0:0.0:0.0	.	1047	P42336	PK3CA_HUMAN	R	1047	ENSP00000263967:H1047R	ENSP00000263967:H1047R	H	+	2	0	PIK3CA	180434779	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	8.859000	0.92264	2.333000	0.79357	0.482000	0.46254	CAT	PIK3CA	-	superfamily_Kinase-like_dom,smart_PI3/4_kinase_cat_dom,pfscan_PI3/4_kinase_cat_dom	ENSG00000121879		0.378	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	PIK3CA	HGNC	protein_coding	OTTHUMT00000348409.2	55	0.00	0	A			178952085	178952085	+1	no_errors	ENST00000263967	ensembl	human	known	69_37n	missense	26	50.00	26	SNP	1.000	G
PLEKHB2	55041	genome.wustl.edu	37	2	131883435	131883435	+	Missense_Mutation	SNP	G	G	A			TCGA-E2-A1IL-01A-11D-A14G-09	TCGA-E2-A1IL-10A-01D-A14G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1540ae03-7bb4-418b-afbc-44bf3ad60a31	6a5f0824-3724-42a3-af37-ca7215491e63	g.chr2:131883435G>A	ENST00000403716.1	+	3	707	c.147G>A	c.(145-147)atG>atA	p.M49I	PLEKHB2_ENST00000303908.3_Missense_Mutation_p.M49I|PLEKHB2_ENST00000234115.6_Missense_Mutation_p.M49I|PLEKHB2_ENST00000438882.2_Missense_Mutation_p.M49I|PLEKHB2_ENST00000439822.2_Missense_Mutation_p.M49I|PLEKHB2_ENST00000409612.1_Missense_Mutation_p.M49I|PLEKHB2_ENST00000538982.1_Start_Codon_SNP_p.M1I|PLEKHB2_ENST00000409158.1_Missense_Mutation_p.M49I|PLEKHB2_ENST00000404460.1_Missense_Mutation_p.M49I|PLEKHB2_ENST00000409279.1_Missense_Mutation_p.M49I	NM_001100623.1|NM_001267062.1|NM_001267063.1|NM_001267064.1|NM_001267065.1|NM_001267066.1|NM_017958.2	NP_001094093.1|NP_001253991.1|NP_001253992.1|NP_001253993.1|NP_001253994.1|NP_001253995.1|NP_060428.2	Q96CS7	PKHB2_HUMAN	pleckstrin homology domain containing, family B (evectins) member 2	49	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.					endosome (GO:0005768)|membrane (GO:0016020)				large_intestine(1)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				BRCA - Breast invasive adenocarcinoma(221;0.0828)		AGGTCCACATGCCAATGGACT	0.522																																						dbGAP											0													131.0	116.0	121.0					2																	131883435		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS2166.1, CCDS46413.1, CCDS58729.1, CCDS58730.1, CCDS74576.1, CCDS74577.1	2q22.1	2013-01-10			ENSG00000115762	ENSG00000115762		"""Pleckstrin homology (PH) domain containing"""	19236	protein-coding gene	gene with protein product						10200314	Standard	NM_017958		Approved	EVT2, FLJ20783	uc031rpd.1	Q96CS7	OTTHUMG00000131656	ENST00000403716.1:c.147G>A	2.37:g.131883435G>A	ENSP00000385892:p.Met49Ile	Somatic		WXS	Illumina GAIIx	Phase_IV	B4DF08|B4DZ66|B8ZZN1|Q53FF1|Q53TH7|Q86W37|Q9BV75|Q9NWK1	Missense_Mutation	SNP	pfam_Pleckstrin_homology,smart_Pleckstrin_homology,pfscan_Pleckstrin_homology	p.M49I	ENST00000403716.1	37	c.147	CCDS46413.1	2	.	.	.	.	.	.	.	.	.	.	G	19.34	3.808586	0.70797	.	.	ENSG00000115762	ENST00000409158;ENST00000403716;ENST00000234115;ENST00000439822;ENST00000438882;ENST00000538982;ENST00000404460;ENST00000409612;ENST00000409279;ENST00000303908	T;T;T;T;T;T;T;T;T	0.75050	-0.9;-0.9;-0.9;-0.9;-0.9;-0.9;-0.9;-0.9;-0.9	4.93	3.98	0.46160	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	U	0.000000	T	0.59362	0.2188	N	0.19112	0.55	0.37270	D	0.907355	B;B;B;B;P;B;P	0.36768	0.276;0.357;0.004;0.014;0.569;0.004;0.569	B;B;B;B;B;B;B	0.39840	0.219;0.229;0.008;0.017;0.311;0.008;0.311	T	0.59789	-0.7388	10	0.15952	T	0.53	-0.1974	12.0272	0.53377	0.0:0.0:0.8267:0.1733	.	49;49;49;49;49;49;49	B4DZ66;B4DF08;Q53FF1;Q96CS7-3;B7WPA5;Q96CS7;B8ZZN1	.;.;.;.;.;PKHB2_HUMAN;.	I	49;49;49;49;49;1;49;49;49;49	ENSP00000386410:M49I;ENSP00000385892:M49I;ENSP00000234115:M49I;ENSP00000389629:M49I;ENSP00000401193:M49I;ENSP00000385609:M49I;ENSP00000386662:M49I;ENSP00000386666:M49I;ENSP00000306852:M49I	ENSP00000234115:M49I	M	+	3	0	PLEKHB2	131599905	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	6.837000	0.75354	2.443000	0.82685	0.462000	0.41574	ATG	PLEKHB2	-	pfam_Pleckstrin_homology,smart_Pleckstrin_homology,pfscan_Pleckstrin_homology	ENSG00000115762		0.522	PLEKHB2-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PLEKHB2	HGNC	protein_coding	OTTHUMT00000331304.2	45	0.00	0	G	NM_017958		131883435	131883435	+1	no_errors	ENST00000303908	ensembl	human	known	69_37n	missense	36	30.77	16	SNP	1.000	A
SERPINB6	5269	genome.wustl.edu	37	6	2955880	2955880	+	Missense_Mutation	SNP	C	C	T			TCGA-E2-A1IL-01A-11D-A14G-09	TCGA-E2-A1IL-10A-01D-A14G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1540ae03-7bb4-418b-afbc-44bf3ad60a31	6a5f0824-3724-42a3-af37-ca7215491e63	g.chr6:2955880C>T	ENST00000380520.1	-	2	2184	c.190G>A	c.(190-192)Ggt>Agt	p.G64S	SERPINB6_ENST00000380539.1_Missense_Mutation_p.G64S|SERPINB6_ENST00000380524.1_Missense_Mutation_p.G64S|SERPINB6_ENST00000380546.3_Missense_Mutation_p.G64S|SERPINB6_ENST00000335686.5_Missense_Mutation_p.G64S|SERPINB6_ENST00000380529.1_Missense_Mutation_p.G64S			P35237	SPB6_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 6	64					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(8)|stomach(1)|upper_aerodigestive_tract(2)	17	Ovarian(93;0.0412)	all_hematologic(90;0.0895)			Drotrecogin alfa(DB00055)	TCTCCACCACCGCCACTTTTA	0.463																																						dbGAP											0													46.0	50.0	49.0					6																	2955880		2203	4300	6503	-	-	-	SO:0001583	missense	0			Z22658	CCDS4479.1, CCDS75386.1, CCDS75387.1	6p25.2	2014-02-18	2005-08-18		ENSG00000124570	ENSG00000124570		"""Serine (or cysteine) peptidase inhibitors"""	8950	protein-coding gene	gene with protein product	"""cytoplasmic antiproteinase"""	173321	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 6"", ""deafness, autosomal recessive 91"""	PI6, DFNB91		8415716, 9858835, 20451170, 24172014	Standard	NM_004568		Approved	PTI, CAP	uc031smo.1	P35237	OTTHUMG00000016170	ENST00000380520.1:c.190G>A	6.37:g.2955880C>T	ENSP00000369891:p.Gly64Ser	Somatic		WXS	Illumina GAIIx	Phase_IV	B2RBA8|Q59F97|Q5TD06|Q7Z2Y7|Q96J44|Q9UDI7	Missense_Mutation	SNP	pfam_Sepin_dom,superfamily_Sepin_dom,smart_Sepin_dom	p.G64S	ENST00000380520.1	37	c.190	CCDS4479.1	6	.	.	.	.	.	.	.	.	.	.	C	7.634	0.679525	0.14907	.	.	ENSG00000124570	ENST00000380524;ENST00000380520;ENST00000335686;ENST00000380529;ENST00000380539;ENST00000380546;ENST00000440670	T;T;T;T;T;T	0.81078	-1.45;-1.45;-1.45;-1.45;-1.45;-1.45	3.29	3.29	0.37713	Serpin domain (3);	1.019050	0.07807	N	0.957539	T	0.42245	0.1194	N	0.05574	-0.02	0.23559	N	0.997417	P	0.39157	0.662	B	0.29176	0.099	T	0.14200	-1.0481	10	0.34782	T	0.22	.	10.3589	0.43980	0.0:1.0:0.0:0.0	.	64	P35237	SPB6_HUMAN	S	64	ENSP00000369896:G64S;ENSP00000369891:G64S;ENSP00000338358:G64S;ENSP00000369901:G64S;ENSP00000369912:G64S;ENSP00000369919:G64S	ENSP00000338358:G64S	G	-	1	0	SERPINB6	2900879	0.000000	0.05858	0.118000	0.21660	0.021000	0.10359	-0.477000	0.06583	2.163000	0.67991	0.561000	0.74099	GGT	SERPINB6	-	pfam_Sepin_dom,superfamily_Sepin_dom,smart_Sepin_dom	ENSG00000124570		0.463	SERPINB6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	SERPINB6	HGNC	protein_coding	OTTHUMT00000043422.1	38	0.00	0	C			2955880	2955880	-1	no_errors	ENST00000335686	ensembl	human	known	69_37n	missense	37	27.45	14	SNP	0.452	T
SIT1	27240	genome.wustl.edu	37	9	35649944	35649944	+	Silent	SNP	G	G	A			TCGA-E2-A1IL-01A-11D-A14G-09	TCGA-E2-A1IL-10A-01D-A14G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1540ae03-7bb4-418b-afbc-44bf3ad60a31	6a5f0824-3724-42a3-af37-ca7215491e63	g.chr9:35649944G>A	ENST00000259608.3	-	5	578	c.492C>T	c.(490-492)ccC>ccT	p.P164P	RP11-331F9.4_ENST00000428948.1_RNA|SIT1_ENST00000474403.1_5'UTR	NM_014450.2	NP_055265.1	Q9Y3P8	SIT1_HUMAN	signaling threshold regulating transmembrane adaptor 1	164					immune system process (GO:0002376)|regulation of T cell activation (GO:0050863)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	kinase binding (GO:0019900)|SH2 domain binding (GO:0042169)			endometrium(2)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	9			Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			GCTCCGGCTCGGGGCCCGAGG	0.677																																						dbGAP											0													10.0	12.0	11.0					9																	35649944		2195	4281	6476	-	-	-	SO:0001819	synonymous_variant	0				CCDS6582.1	9p13-p12	2008-02-05	2005-04-26		ENSG00000137078	ENSG00000137078			17710	protein-coding gene	gene with protein product	"""SHP2 interacting transmembrane adaptor"""	604964	"""suppression inducing transmembrane adaptor 1"""			11491537, 10209036	Standard	NM_014450		Approved	SIT	uc003zxe.1	Q9Y3P8	OTTHUMG00000019867	ENST00000259608.3:c.492C>T	9.37:g.35649944G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	B2RBP9	Silent	SNP	NULL	p.P164	ENST00000259608.3	37	c.492	CCDS6582.1	9																																																																																			SIT1	-	NULL	ENSG00000137078		0.677	SIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SIT1	HGNC	protein_coding	OTTHUMT00000052322.1	30	0.00	0	G	NM_014450		35649944	35649944	-1	no_errors	ENST00000259608	ensembl	human	known	69_37n	silent	12	42.86	9	SNP	0.000	A
SOX3	6658	genome.wustl.edu	37	X	139586876	139586876	+	Missense_Mutation	SNP	G	G	T			TCGA-E2-A1IL-01A-11D-A14G-09	TCGA-E2-A1IL-10A-01D-A14G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1540ae03-7bb4-418b-afbc-44bf3ad60a31	6a5f0824-3724-42a3-af37-ca7215491e63	g.chrX:139586876G>T	ENST00000370536.2	-	1	349	c.350C>A	c.(349-351)gCg>gAg	p.A117E		NM_005634.2	NP_005625.2	P41225	SOX3_HUMAN	SRY (sex determining region Y)-box 3	117					central nervous system development (GO:0007417)|face development (GO:0060324)|hypothalamus development (GO:0021854)|negative regulation of neuron differentiation (GO:0045665)|neuron development (GO:0048666)|organ morphogenesis (GO:0009887)|pituitary gland development (GO:0021983)|sensory organ development (GO:0007423)|Sertoli cell development (GO:0060009)|sex determination (GO:0007530)|spermatid differentiation (GO:0048515)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|pancreas(1)|skin(1)	10	Acute lymphoblastic leukemia(192;7.65e-05)					GCCCGAGTTCGCGCCGCCGGC	0.706																																						dbGAP											0													12.0	13.0	13.0					X																	139586876		2189	4276	6465	-	-	-	SO:0001583	missense	0				CCDS14669.1	Xq27.1	2013-10-17			ENSG00000134595	ENSG00000134595		"""SRY (sex determining region Y)-boxes"""	11199	protein-coding gene	gene with protein product		313430	"""panhypopituitarism"""	PHP		15800844	Standard	NM_005634		Approved		uc004fbd.1	P41225	OTTHUMG00000022544	ENST00000370536.2:c.350C>A	X.37:g.139586876G>T	ENSP00000359567:p.Ala117Glu	Somatic		WXS	Illumina GAIIx	Phase_IV	P35714|Q5JWI3|Q9NP49	Missense_Mutation	SNP	pfam_HMG_superfamily,pfam_TF_SOX,superfamily_HMG_superfamily,smart_HMG_superfamily,pfscan_HMG_superfamily	p.A117E	ENST00000370536.2	37	c.350	CCDS14669.1	X	.	.	.	.	.	.	.	.	.	.	g	8.663	0.900905	0.17686	.	.	ENSG00000134595	ENST00000370536	D	0.91631	-2.88	4.19	-0.451	0.12214	.	2.403830	0.04077	U	0.309032	D	0.85314	0.5668	N	0.19112	0.55	0.09310	N	1	P	0.35982	0.531	B	0.36567	0.228	T	0.74850	-0.3524	9	.	.	.	.	7.7661	0.28980	0.122:0.6019:0.2761:0.0	.	117	P41225	SOX3_HUMAN	E	117	ENSP00000359567:A117E	.	A	-	2	0	SOX3	139414542	0.901000	0.30685	0.095000	0.20976	0.473000	0.32948	0.308000	0.19314	-0.199000	0.10317	-0.350000	0.07774	GCG	SOX3	-	NULL	ENSG00000134595		0.706	SOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SOX3	HGNC	protein_coding	OTTHUMT00000058577.1	8	0.00	0	G			139586876	139586876	-1	no_errors	ENST00000370536	ensembl	human	known	69_37n	missense	8	38.46	5	SNP	0.021	T
TBCC	6903	genome.wustl.edu	37	6	42712938	42712938	+	Missense_Mutation	SNP	A	A	G			TCGA-E2-A1IL-01A-11D-A14G-09	TCGA-E2-A1IL-10A-01D-A14G-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1540ae03-7bb4-418b-afbc-44bf3ad60a31	6a5f0824-3724-42a3-af37-ca7215491e63	g.chr6:42712938A>G	ENST00000372876.1	-	1	896	c.874T>C	c.(874-876)Tac>Cac	p.Y292H	TBCC_ENST00000244625.2_Missense_Mutation_p.Y292H	NM_003192.2	NP_003183	Q15814	TBCC_HUMAN	tubulin folding cofactor C	292	C-CAP/cofactor C-like. {ECO:0000255|PROSITE-ProRule:PRU00659}.				'de novo' posttranslational protein folding (GO:0051084)|cell morphogenesis (GO:0000902)|cellular protein metabolic process (GO:0044267)|GTP catabolic process (GO:0006184)|post-chaperonin tubulin folding pathway (GO:0007023)|protein folding (GO:0006457)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)	chaperone binding (GO:0051087)|GTPase activity (GO:0003924)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|urinary_tract(3)	14	Colorectal(47;0.196)		all cancers(41;0.00122)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.125)			CTCCAGGTGTAAGGGGCGAAC	0.537																																						dbGAP											0													103.0	91.0	95.0					6																	42712938		2203	4300	6503	-	-	-	SO:0001583	missense	0			U61234	CCDS4872.1	6p21.1	2008-02-05	2006-11-21		ENSG00000124659	ENSG00000124659			11580	protein-coding gene	gene with protein product		602971	"""tubulin-specific chaperone c"""			8706133, 11847227	Standard	NM_003192		Approved	CFC	uc003osl.3	Q15814	OTTHUMG00000014704	ENST00000372876.1:c.874T>C	6.37:g.42712938A>G	ENSP00000361967:p.Tyr292His	Somatic		WXS	Illumina GAIIx	Phase_IV	Q53Y43|Q5T787	Missense_Mutation	SNP	pfam_Tubulin-bd_cofactor_C,smart_CARP_motif	p.Y292H	ENST00000372876.1	37	c.874	CCDS4872.1	6	.	.	.	.	.	.	.	.	.	.	A	24.0	4.482311	0.84747	.	.	ENSG00000124659	ENST00000372876;ENST00000244625	D;D	0.88046	-2.33;-2.33	5.14	5.14	0.70334	Tubulin binding cofactor C (1);C-CAP/cofactor C-like domain (1);	0.058947	0.64402	D	0.000002	D	0.93207	0.7836	M	0.87827	2.91	0.54753	D	0.999982	D	0.89917	1.0	D	0.91635	0.999	D	0.94498	0.7707	10	0.87932	D	0	-11.4228	15.2658	0.73660	1.0:0.0:0.0:0.0	.	292	Q15814	TBCC_HUMAN	H	292	ENSP00000361967:Y292H;ENSP00000244625:Y292H	ENSP00000244625:Y292H	Y	-	1	0	TBCC	42820916	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	7.387000	0.79785	2.063000	0.61619	0.383000	0.25322	TAC	TBCC	-	pfam_Tubulin-bd_cofactor_C	ENSG00000124659		0.537	TBCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TBCC	HGNC	protein_coding	OTTHUMT00000040559.1	94	0.00	0	A	NM_003192		42712938	42712938	-1	no_errors	ENST00000244625	ensembl	human	known	69_37n	missense	72	27.27	27	SNP	1.000	G
SYNE1	23345	genome.wustl.edu	37	6	152751745	152751745	+	Nonsense_Mutation	SNP	G	G	A			TCGA-E2-A1IL-01A-11D-A14G-09	TCGA-E2-A1IL-10A-01D-A14G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1540ae03-7bb4-418b-afbc-44bf3ad60a31	6a5f0824-3724-42a3-af37-ca7215491e63	g.chr6:152751745G>A	ENST00000367255.5	-	35	5162	c.4561C>T	c.(4561-4563)Cga>Tga	p.R1521*	SYNE1_ENST00000341594.5_Nonsense_Mutation_p.R1591*|SYNE1_ENST00000265368.4_Nonsense_Mutation_p.R1521*|SYNE1_ENST00000423061.1_Nonsense_Mutation_p.R1528*|SYNE1_ENST00000448038.1_Nonsense_Mutation_p.R1528*|SYNE1_ENST00000367253.4_Nonsense_Mutation_p.R1521*	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1521					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GCTTTAATTCGAGCAGATTCT	0.433										HNSCC(10;0.0054)																												dbGAP											0													159.0	159.0	159.0					6																	152751745		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.4561C>T	6.37:g.152751745G>A	ENSP00000356224:p.Arg1521*	Somatic		WXS	Illumina GAIIx	Phase_IV	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Nonsense_Mutation	SNP	pfam_Spectrin_repeat,pfam_CH-domain,pfam_KASH,superfamily_CH-domain,superfamily_Calpain_domain_III,superfamily_ABC_transptrTM_dom_typ1,smart_CH-domain,smart_Spectrin/alpha-actinin,pfscan_CH-domain,pfscan_KASH	p.R1521*	ENST00000367255.5	37	c.4561	CCDS5236.2	6	.	.	.	.	.	.	.	.	.	.	G	47	13.595886	0.99751	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000367253	.	.	.	5.66	3.83	0.44106	.	0.129055	0.35436	N	0.003205	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.0782	0.72093	0.0:0.0:0.7407:0.2593	.	.	.	.	X	1521;1528;1521;1528;1591;1521	.	ENSP00000265368:R1521X	R	-	1	2	SYNE1	152793438	1.000000	0.71417	0.996000	0.52242	0.982000	0.71751	6.677000	0.74503	0.807000	0.34208	-0.181000	0.13052	CGA	SYNE1	-	superfamily_Calpain_domain_III,superfamily_ABC_transptrTM_dom_typ1,smart_Spectrin/alpha-actinin	ENSG00000131018		0.433	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	SYNE1	HGNC	protein_coding	OTTHUMT00000334755.2	98	0.00	0	G	NM_182961		152751745	152751745	-1	no_errors	ENST00000265368	ensembl	human	known	69_37n	nonsense	15	65.12	28	SNP	1.000	A
TNKS1BP1	85456	genome.wustl.edu	37	11	57077320	57077320	+	Silent	SNP	G	G	A			TCGA-E2-A1IL-01A-11D-A14G-09	TCGA-E2-A1IL-10A-01D-A14G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1540ae03-7bb4-418b-afbc-44bf3ad60a31	6a5f0824-3724-42a3-af37-ca7215491e63	g.chr11:57077320G>A	ENST00000532437.1	-	5	3176	c.2865C>T	c.(2863-2865)agC>agT	p.S955S	TNKS1BP1_ENST00000530920.1_5'UTR|TNKS1BP1_ENST00000358252.3_Silent_p.S955S			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	955	Acidic.				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|RNA metabolic process (GO:0016070)|telomere maintenance via telomerase (GO:0007004)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear telomeric heterochromatin (GO:0005724)|nucleus (GO:0005634)	ankyrin binding (GO:0030506)|enzyme binding (GO:0019899)			breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	64		all_epithelial(135;0.21)				TTATCCAAGCGCTCTTCCCAA	0.597																																						dbGAP											0													107.0	117.0	114.0					11																	57077320		2201	4296	6497	-	-	-	SO:0001819	synonymous_variant	0			AB051528	CCDS7951.1	11q12.2	2008-07-21			ENSG00000149115	ENSG00000149115			19081	protein-coding gene	gene with protein product		607104				11854288	Standard	NM_033396		Approved	TAB182, KIAA1741, FLJ45975	uc001njs.3	Q9C0C2	OTTHUMG00000167022	ENST00000532437.1:c.2865C>T	11.37:g.57077320G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	A7E2F8|Q6PJ35|Q6ZV74	Silent	SNP	NULL	p.S955	ENST00000532437.1	37	c.2865	CCDS7951.1	11																																																																																			TNKS1BP1	-	NULL	ENSG00000149115		0.597	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	TNKS1BP1	HGNC	protein_coding	OTTHUMT00000392455.1	63	0.00	0	G	NM_033396		57077320	57077320	-1	no_errors	ENST00000358252	ensembl	human	known	69_37n	silent	34	41.67	25	SNP	0.000	A
ZNF281	23528	genome.wustl.edu	37	1	200378731	200378732	+	In_Frame_Ins	INS	-	-	GCC			TCGA-E2-A1IL-01A-11D-A14G-09	TCGA-E2-A1IL-10A-01D-A14G-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1540ae03-7bb4-418b-afbc-44bf3ad60a31	6a5f0824-3724-42a3-af37-ca7215491e63	g.chr1:200378731_200378732insGCC	ENST00000294740.3	-	2	226_227	c.102_103insGGC	c.(100-105)ggcagc>ggcGGCagc	p.34_35insG	ZNF281_ENST00000367352.3_In_Frame_Ins_p.34_35insG|ZNF281_ENST00000367353.1_In_Frame_Ins_p.34_35insG	NM_001281293.1|NM_001281294.1|NM_012482.4	NP_001268222.1|NP_001268223.1|NP_036614.1	Q9Y2X9	ZN281_HUMAN	zinc finger protein 281	34	Gly-rich.				embryonic body morphogenesis (GO:0010172)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|stem cell differentiation (GO:0048863)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	core promoter binding (GO:0001047)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			breast(4)|endometrium(3)|kidney(3)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	27						CTgccgctgctgccgccgccgc	0.688																																						dbGAP											0																																										-	-	-	SO:0001652	inframe_insertion	0			AF125158	CCDS1402.1, CCDS60384.1	1q32.1	2012-08-08			ENSG00000162702	ENSG00000162702		"""Zinc fingers, C2H2-type"""	13075	protein-coding gene	gene with protein product						10448078	Standard	NM_012482		Approved	ZBP-99	uc001gve.3	Q9Y2X9	OTTHUMG00000035724	ENST00000294740.3:c.100_102dupGGC	1.37:g.200378738_200378740dupGCC	ENSP00000294740:p.Gly34_Gly34dup	Somatic		WXS	Illumina GAIIx	Phase_IV	A6NF48|B3KMX2|Q5RKW5|Q9NY92	In_Frame_Ins	INS	smart_Znf_C2H2-like,pfscan_Znf_C2H2	p.34in_frame_insG	ENST00000294740.3	37	c.103_102	CCDS1402.1	1																																																																																			ZNF281	-	NULL	ENSG00000162702		0.688	ZNF281-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ZNF281	HGNC	protein_coding	OTTHUMT00000086879.2	10	0.00	0	-	NM_012482		200378731	200378732	-1	no_errors	ENST00000294740	ensembl	human	known	69_37n	in_frame_ins	4	33.33	2	INS	0.985:0.997	GCC
ZNF846	162993	genome.wustl.edu	37	19	9868344	9868345	+	Frame_Shift_Del	DEL	CG	CG	-			TCGA-E2-A1IL-01A-11D-A14G-09	TCGA-E2-A1IL-10A-01D-A14G-09	CG	CG					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1540ae03-7bb4-418b-afbc-44bf3ad60a31	6a5f0824-3724-42a3-af37-ca7215491e63	g.chr19:9868344_9868345delCG	ENST00000397902.2	-	6	1821_1822	c.1408_1409delCG	c.(1408-1410)cgafs	p.R470fs	ZNF846_ENST00000588267.1_Intron|ZNF846_ENST00000586293.1_3'UTR|ZNF846_ENST00000592859.1_Intron	NM_001077624.1	NP_001071092.1	Q147U1	ZN846_HUMAN	zinc finger protein 846	470					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	22						TGTGTGCGTTCGCATGTGCATA	0.436																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AK097652	CCDS42496.1	19p13.2	2013-01-08			ENSG00000196605	ENSG00000196605		"""Zinc fingers, C2H2-type"", ""-"""	27260	protein-coding gene	gene with protein product							Standard	NM_001077624		Approved		uc002mmb.1	Q147U1		ENST00000397902.2:c.1408_1409delCG	19.37:g.9868344_9868345delCG	ENSP00000380999:p.Arg470fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K0H1|B3KUP1	Frame_Shift_Del	DEL	pfam_Znf_C2H2,pfam_Krueppel-associated_box,superfamily_Krueppel-associated_box,smart_Krueppel-associated_box,smart_Znf_C2H2-like,smart_Znf_BED_prd,pfscan_Znf_C2H2,pfscan_Krueppel-associated_box	p.R470fs	ENST00000397902.2	37	c.1409_1408	CCDS42496.1	19																																																																																			ZNF846	-	pfam_Znf_C2H2,smart_Znf_BED_prd,smart_Znf_C2H2-like,pfscan_Znf_C2H2	ENSG00000196605		0.436	ZNF846-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ZNF846	HGNC	protein_coding	OTTHUMT00000450253.1	72	0.00	0	CG	NM_001077624		9868344	9868345	-1	no_errors	ENST00000397902	ensembl	human	known	69_37n	frame_shift_del	45	22.03	13	DEL	0.077:0.001	-
