#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
ABT1	29777	genome.wustl.edu	37	6	26598210	26598210	+	Missense_Mutation	SNP	G	G	T			TCGA-AN-A0XS-01A-22D-A10G-09	TCGA-AN-A0XS-10A-01D-A10G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f1b5268d-556f-404f-a956-770df4a1e7aa	3a722354-b991-44cf-9ab8-f276b4a38701	g.chr6:26598210G>T	ENST00000274849.1	+	2	341	c.310G>T	c.(310-312)Gac>Tac	p.D104Y		NM_013375.3	NP_037507.1	Q9ULW3	ABT1_HUMAN	activator of basal transcription 1	104	RRM.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|spinal cord motor neuron differentiation (GO:0021522)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)	p.D104Y(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|urinary_tract(1)	11						CTACACCAAGGACTACACCGA	0.622																																						dbGAP											1	Substitution - Missense(1)	breast(1)											58.0	53.0	55.0					6																	26598210		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB027258	CCDS4616.1	6p21.31	2008-07-07			ENSG00000146109	ENSG00000146109			17369	protein-coding gene	gene with protein product						10648625	Standard	NM_013375		Approved		uc003nii.3	Q9ULW3	OTTHUMG00000016319	ENST00000274849.1:c.310G>T	6.37:g.26598210G>T	ENSP00000274849:p.Asp104Tyr	Somatic		WXS	Illumina GAIIx	Phase_IV		Missense_Mutation	SNP	NULL	p.D104Y	ENST00000274849.1	37	c.310	CCDS4616.1	6	.	.	.	.	.	.	.	.	.	.	G	22.4	4.290207	0.80914	.	.	ENSG00000146109	ENST00000274849	T	0.56444	0.46	5.23	5.23	0.72850	Nucleotide-binding, alpha-beta plait (1);	0.147192	0.64402	D	0.000012	T	0.58509	0.2127	L	0.45581	1.43	0.50632	D	0.999886	D	0.71674	0.998	D	0.65443	0.935	T	0.60156	-0.7318	10	0.59425	D	0.04	-16.1942	16.6701	0.85263	0.0:0.0:1.0:0.0	.	104	Q9ULW3	ABT1_HUMAN	Y	104	ENSP00000274849:D104Y	ENSP00000274849:D104Y	D	+	1	0	ABT1	26706189	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.006000	0.57083	2.629000	0.89072	0.563000	0.77884	GAC	ABT1	-	NULL	ENSG00000146109		0.622	ABT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ABT1	HGNC	protein_coding	OTTHUMT00000043698.1	28	0.00	0	G			26598210	26598210	+1	no_errors	ENST00000274849	ensembl	human	known	69_37n	missense	21	34.38	11	SNP	1.000	T
ACVR2A	92	genome.wustl.edu	37	2	148680662	148680662	+	Missense_Mutation	SNP	C	C	T			TCGA-AN-A0XS-01A-22D-A10G-09	TCGA-AN-A0XS-10A-01D-A10G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f1b5268d-556f-404f-a956-770df4a1e7aa	3a722354-b991-44cf-9ab8-f276b4a38701	g.chr2:148680662C>T	ENST00000241416.7	+	9	1834	c.1198C>T	c.(1198-1200)Cgc>Tgc	p.R400C	ACVR2A_ENST00000404590.1_Missense_Mutation_p.R400C|ACVR2A_ENST00000535787.1_Missense_Mutation_p.R292C	NM_001278579.1|NM_001278580.1|NM_001616.3	NP_001265508.1|NP_001265509.1|NP_001607.1	P27037	AVR2A_HUMAN	activin A receptor, type IIA	400	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|gastrulation with mouth forming second (GO:0001702)|mesoderm development (GO:0007498)|penile erection (GO:0043084)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|regulation of BMP signaling pathway (GO:0030510)|regulation of nitric-oxide synthase activity (GO:0050999)|Sertoli cell proliferation (GO:0060011)|sperm ejaculation (GO:0042713)|spermatogenesis (GO:0007283)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|coreceptor activity (GO:0015026)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)	p.R400C(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(5)|large_intestine(14)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(8)	45				BRCA - Breast invasive adenocarcinoma(221;0.0969)		ACTGGCTTCTCGCTGTACTGC	0.388																																						dbGAP											1	Substitution - Missense(1)	breast(1)											148.0	152.0	151.0					2																	148680662		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS33301.1, CCDS63030.1	2q22.2-q23.3	2008-02-05	2005-05-10	2005-05-10	ENSG00000121989	ENSG00000121989			173	protein-coding gene	gene with protein product		102581	"""activin A receptor, type II"""	ACVR2		1314589, 10702675	Standard	NM_001278579		Approved	ACTRII	uc002twh.3	P27037	OTTHUMG00000150603	ENST00000241416.7:c.1198C>T	2.37:g.148680662C>T	ENSP00000241416:p.Arg400Cys	Somatic		WXS	Illumina GAIIx	Phase_IV	B2RAB8|B4DWQ2|D3DP85|Q53TH4|Q6NWV2|Q92474	Missense_Mutation	SNP	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Activin_rcpt,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom,prints_Activin_II/TGFBeta-II_recpt	p.R400C	ENST00000241416.7	37	c.1198	CCDS33301.1	2	.	.	.	.	.	.	.	.	.	.	C	29.9	5.041929	0.93685	.	.	ENSG00000121989	ENST00000241416;ENST00000535787;ENST00000404590	D;D;D	0.93811	-3.29;-3.29;-3.29	5.65	5.65	0.86999	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.97278	0.9110	M	0.86573	2.825	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.97318	0.9942	10	0.87932	D	0	.	19.9142	0.97043	0.0:1.0:0.0:0.0	.	400	P27037	AVR2A_HUMAN	C	400;292;400	ENSP00000241416:R400C;ENSP00000439988:R292C;ENSP00000384338:R400C	ENSP00000241416:R400C	R	+	1	0	ACVR2A	148397132	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.752000	0.68728	2.941000	0.99782	0.655000	0.94253	CGC	ACVR2A	-	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	ENSG00000121989		0.388	ACVR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ACVR2A	HGNC	protein_coding	OTTHUMT00000319051.1	86	0.00	0	C	NM_001616		148680662	148680662	+1	no_errors	ENST00000241416	ensembl	human	known	69_37n	missense	100	35.48	55	SNP	1.000	T
AOX1	316	genome.wustl.edu	37	2	201523988	201523988	+	Missense_Mutation	SNP	T	T	A			TCGA-AN-A0XS-01A-22D-A10G-09	TCGA-AN-A0XS-10A-01D-A10G-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f1b5268d-556f-404f-a956-770df4a1e7aa	3a722354-b991-44cf-9ab8-f276b4a38701	g.chr2:201523988T>A	ENST00000374700.2	+	28	3513	c.3272T>A	c.(3271-3273)gTg>gAg	p.V1091E	AOX1_ENST00000485106.1_3'UTR	NM_001159.3	NP_001150.3	Q06278	AOXA_HUMAN	aldehyde oxidase 1	1091					inflammatory response (GO:0006954)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	2 iron, 2 sulfur cluster binding (GO:0051537)|aldehyde oxidase activity (GO:0004031)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|NAD binding (GO:0051287)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)	p.V1091E(1)		breast(5)|endometrium(3)|kidney(4)|large_intestine(13)|lung(38)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	81					Allopurinol(DB00437)|Aminocaproic Acid(DB00513)|Brimonidine(DB00484)|Famciclovir(DB00426)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Pyrazinamide(DB00339)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	GGTTCTGTGGTGGCAGATCTC	0.502																																						dbGAP											1	Substitution - Missense(1)	breast(1)											165.0	150.0	155.0					2																	201523988		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF017060	CCDS33360.1	2q33	2008-05-20			ENSG00000138356	ENSG00000138356			553	protein-coding gene	gene with protein product		602841				7570184	Standard	NM_001159		Approved	AO, AOH1	uc002uvx.3	Q06278	OTTHUMG00000154536	ENST00000374700.2:c.3272T>A	2.37:g.201523988T>A	ENSP00000363832:p.Val1091Glu	Somatic		WXS	Illumina GAIIx	Phase_IV	O14765|Q53RR8|Q53TV3|Q9BYF0|Q9UPG6	Missense_Mutation	SNP	pfam_AldOxase/xan_DH_Mopterin-bd,pfam_Mopterin_DH_FAD-bd,pfam_Ald_Oxase/Xan_DH_a/b,pfam_2Fe-2S-bd,pfam_CO_DH_flav_C,pfam_2Fe-2S_ferredoxin-type,superfamily_AldOxase/xan_DH_Mopterin-bd,superfamily_FAD-bd_2,superfamily_Ald_Oxase/Xan_DH_a/b,superfamily_2Fe-2S-bd,superfamily_CO_DH_flav_C,superfamily_2Fe-2S_ferredoxin-type,pirsf_Ald_Oxase/xanthine_DH,pfscan_2Fe-2S_ferredoxin-type,tigrfam_Aldehyde_oxidase	p.V1091E	ENST00000374700.2	37	c.3272	CCDS33360.1	2	.	.	.	.	.	.	.	.	.	.	T	17.43	3.387561	0.61956	.	.	ENSG00000138356	ENST00000374700	T	0.42513	0.97	4.97	1.34	0.21922	Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding (3);	0.232670	0.42964	D	0.000626	T	0.34193	0.0889	L	0.40543	1.245	0.30427	N	0.777538	P	0.34864	0.473	B	0.41135	0.348	T	0.34477	-0.9827	10	0.87932	D	0	-14.8327	5.4195	0.16392	0.0:0.2486:0.2634:0.488	.	1091	Q06278	ADO_HUMAN	E	1091	ENSP00000363832:V1091E	ENSP00000363832:V1091E	V	+	2	0	AOX1	201232233	1.000000	0.71417	0.737000	0.30932	0.937000	0.57800	1.740000	0.38228	0.078000	0.16900	0.459000	0.35465	GTG	AOX1	-	pfam_AldOxase/xan_DH_Mopterin-bd,superfamily_AldOxase/xan_DH_Mopterin-bd,pirsf_Ald_Oxase/xanthine_DH,tigrfam_Aldehyde_oxidase	ENSG00000138356		0.502	AOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	AOX1	HGNC	protein_coding	OTTHUMT00000335844.1	105	0.00	0	T	NM_001159		201523988	201523988	+1	no_errors	ENST00000374700	ensembl	human	known	69_37n	missense	79	31.30	36	SNP	0.997	A
ATIC	471	genome.wustl.edu	37	2	216177253	216177253	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A0XS-01A-22D-A10G-09	TCGA-AN-A0XS-10A-01D-A10G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f1b5268d-556f-404f-a956-770df4a1e7aa	3a722354-b991-44cf-9ab8-f276b4a38701	g.chr2:216177253G>A	ENST00000236959.9	+	2	378	c.52G>A	c.(52-54)Gtg>Atg	p.V18M	ATIC_ENST00000435675.1_Missense_Mutation_p.V17M|ATIC_ENST00000540518.1_5'UTR	NM_004044.6	NP_004035.2	P31939	PUR9_HUMAN	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	18					'de novo' IMP biosynthetic process (GO:0006189)|brainstem development (GO:0003360)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|dihydrofolate metabolic process (GO:0046452)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|organ regeneration (GO:0031100)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to inorganic substance (GO:0010035)|small molecule metabolic process (GO:0044281)|tetrahydrofolate biosynthetic process (GO:0046654)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	IMP cyclohydrolase activity (GO:0003937)|phosphoribosylaminoimidazolecarboxamide formyltransferase activity (GO:0004643)|protein homodimerization activity (GO:0042803)	p.V18M(1)	ATIC/ALK(24)	large_intestine(2)|lung(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	8		Renal(323;0.229)		Epithelial(149;2.02e-06)|all cancers(144;0.000316)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.0097)	Methotrexate(DB00563)|Pemetrexed(DB00642)|Tetrahydrofolic acid(DB00116)	AACCGGCCTTGTGGAATTTGC	0.493			T	ALK	ALCL																																	dbGAP		Dom	yes		2	2q35	471	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase		L	1	Substitution - Missense(1)	breast(1)											133.0	129.0	130.0					2																	216177253		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS2398.1	2q35	2010-04-27			ENSG00000138363	ENSG00000138363	2.1.2.3, 3.5.4.10		794	protein-coding gene	gene with protein product	"""phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase"""	601731				8567683, 9378707	Standard	NM_004044		Approved	PURH, AICARFT, IMPCHASE	uc002vex.4	P31939	OTTHUMG00000133023	ENST00000236959.9:c.52G>A	2.37:g.216177253G>A	ENSP00000236959:p.Val18Met	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K202|E9PBU3|Q13856|Q53S28	Missense_Mutation	SNP	pfam_AICARFT_IMPCHas,pfam_MGS-like_dom,superfamily_Cytidine_deaminase-like,superfamily_MGS-like_dom,smart_MGS-like_dom,smart_AICARFT_IMPCHas,pirsf_AICARFT_IMPCHas,tigrfam_AICARFT_IMPCHas	p.V18M	ENST00000236959.9	37	c.52	CCDS2398.1	2	.	.	.	.	.	.	.	.	.	.	G	24.8	4.567610	0.86439	.	.	ENSG00000138363	ENST00000236959;ENST00000435675	D;D	0.83992	-1.79;-1.79	5.65	1.48	0.22813	Methylglyoxal synthase-like domain (4);	0.063436	0.64402	D	0.000007	D	0.87128	0.6100	M	0.92784	3.345	0.80722	D	1	P;P	0.46578	0.88;0.878	B;P	0.45660	0.319;0.489	D	0.88671	0.3195	10	0.87932	D	0	-14.4988	11.3487	0.49575	0.0:0.2187:0.5565:0.2248	.	17;18	E9PBU3;P31939	.;PUR9_HUMAN	M	18;17	ENSP00000236959:V18M;ENSP00000415935:V17M	ENSP00000236959:V18M	V	+	1	0	ATIC	215885498	0.995000	0.38212	0.921000	0.36526	0.989000	0.77384	2.058000	0.41374	0.691000	0.31592	0.655000	0.94253	GTG	ATIC	-	pfam_MGS-like_dom,superfamily_MGS-like_dom,smart_MGS-like_dom,pirsf_AICARFT_IMPCHas,tigrfam_AICARFT_IMPCHas	ENSG00000138363		0.493	ATIC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ATIC	HGNC	protein_coding	OTTHUMT00000256610.1	150	0.00	0	G	NM_004044		216177253	216177253	+1	no_errors	ENST00000236959	ensembl	human	known	69_37n	missense	90	35.71	50	SNP	0.994	A
ATP9A	10079	genome.wustl.edu	37	20	50287755	50287755	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AN-A0XS-01A-22D-A10G-09	TCGA-AN-A0XS-10A-01D-A10G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f1b5268d-556f-404f-a956-770df4a1e7aa	3a722354-b991-44cf-9ab8-f276b4a38701	g.chr20:50287755C>T	ENST00000338821.5	-	12	1343	c.1079G>A	c.(1078-1080)tGg>tAg	p.W360*	ATP9A_ENST00000311637.5_Nonsense_Mutation_p.W224*|ATP9A_ENST00000402822.1_Nonsense_Mutation_p.W239*	NM_006045.1	NP_006036.1	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	360					phospholipid translocation (GO:0045332)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.W360*(1)		breast(2)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(10)|lung(18)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						TCGAATCACCCAGCTGTACAC	0.517																																						dbGAP											1	Substitution - Nonsense(1)	breast(1)											96.0	81.0	86.0					20																	50287755		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0			AB014511	CCDS33489.1	20q13.2	2010-04-20	2007-09-19		ENSG00000054793	ENSG00000054793		"""ATPases / P-type"""	13540	protein-coding gene	gene with protein product		609126	"""ATPase, Class II, type 9A"""			9734811, 11015572	Standard	NM_006045		Approved	KIAA0611, ATPIIA	uc002xwg.1	O75110	OTTHUMG00000032751	ENST00000338821.5:c.1079G>A	20.37:g.50287755C>T	ENSP00000342481:p.Trp360*	Somatic		WXS	Illumina GAIIx	Phase_IV	E1P5Y3|E1P5Y4|Q5TFW5|Q5TFW6|Q5TFW9|Q6ZMF3|Q9NQK6|Q9NQK7	Nonsense_Mutation	SNP	pfam_ATPase_P-typ_ATPase-assoc-dom,pfam_Dehalogen-like_hydro,superfamily_HAD-like_dom,superfamily_ATPase_cation_domN,prints_ATPase_P-typ_ion-transptr,tigrfam_ATPase_P-typ_Plipid-transl,tigrfam_ATPase_P-typ_ion-transptr	p.W360*	ENST00000338821.5	37	c.1079	CCDS33489.1	20	.	.	.	.	.	.	.	.	.	.	C	40	8.489354	0.98834	.	.	ENSG00000054793	ENST00000311637;ENST00000338821;ENST00000402822	.	.	.	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-24.1321	18.985	0.92766	0.0:1.0:0.0:0.0	.	.	.	.	X	224;360;239	.	ENSP00000309086:W224X	W	-	2	0	ATP9A	49721162	1.000000	0.71417	1.000000	0.80357	0.837000	0.47467	7.436000	0.80404	2.478000	0.83669	0.313000	0.20887	TGG	ATP9A	-	tigrfam_ATPase_P-typ_Plipid-transl,tigrfam_ATPase_P-typ_ion-transptr	ENSG00000054793		0.517	ATP9A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	ATP9A	HGNC	protein_coding	OTTHUMT00000106494.1	84	0.00	0	C	NM_006045		50287755	50287755	-1	no_errors	ENST00000338821	ensembl	human	known	69_37n	nonsense	74	30.19	32	SNP	1.000	T
BRAT1	221927	genome.wustl.edu	37	7	2578238	2578238	+	Missense_Mutation	SNP	C	C	T	rs71531463|rs374879575|rs4719553	byFrequency	TCGA-AN-A0XS-01A-22D-A10G-09	TCGA-AN-A0XS-10A-01D-A10G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f1b5268d-556f-404f-a956-770df4a1e7aa	3a722354-b991-44cf-9ab8-f276b4a38701	g.chr7:2578238C>T	ENST00000340611.4	-	14	2187	c.1931G>A	c.(1930-1932)cGa>cAa	p.R644Q	BRAT1_ENST00000473879.1_5'UTR	NM_152743.3	NP_689956.2	Q6PJG6	BRAT1_HUMAN	BRCA1-associated ATM activator 1	644				R -> Q (in Ref. 6; CAB61405). {ECO:0000305}.	response to ionizing radiation (GO:0010212)	membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	23						GTCCAGGTCTCGGCTCGCCGC	0.706													C|||	345	0.0688898	0.0076	0.1628	5008	,	,		14670	0.006		0.1431	False		,,,				2504	0.0736					dbGAP											0													10.0	12.0	11.0					7																	2578238		2148	4184	6332	-	-	-	SO:0001583	missense	0			BC015632	CCDS5334.1	7p22.3	2011-03-22	2011-02-28	2011-03-22	ENSG00000106009	ENSG00000106009			21701	protein-coding gene	gene with protein product	"""BRCA1-associated protein required for ATM activation protein 1"""	614506	"""chromosome 7 open reading frame 27"""	C7orf27, BAAT1		16452482	Standard	NM_152743		Approved	MGC22916	uc003smi.3	Q6PJG6	OTTHUMG00000119091	ENST00000340611.4:c.1931G>A	7.37:g.2578238C>T	ENSP00000339637:p.Arg644Gln	Somatic		WXS	Illumina GAIIx	Phase_IV	A4D200|C9JY24|Q8IW85|Q8IZ43|Q8WVR8|Q96IV9|Q9H7J8|Q9UFA3	Missense_Mutation	SNP	pfam_HEAT,superfamily_ARM-type_fold	p.R644Q	ENST00000340611.4	37	c.1931	CCDS5334.1	7	177	0.08104395604395605	8	0.016260162601626018	56	0.15469613259668508	2	0.0034965034965034965	111	0.14643799472295516	C	7.277	0.608294	0.14002	.	.	ENSG00000106009	ENST00000340611	T	0.68181	-0.31	5.32	1.39	0.22231	Armadillo-like helical (1);Armadillo-type fold (1);	0.648012	0.16891	N	0.195304	T	0.00328	0.0010	L	0.31294	0.92	0.80722	P	0.0	B	0.25312	0.123	B	0.12837	0.008	T	0.06197	-1.0840	9	0.18710	T	0.47	-25.966	9.3037	0.37863	0.0:0.5147:0.0:0.4853	rs62907961	644	Q6PJG6	BRAT1_HUMAN	Q	644	ENSP00000339637:R644Q	ENSP00000339637:R644Q	R	-	2	0	BRAT1	2544764	0.000000	0.05858	0.906000	0.35671	0.312000	0.27988	-1.134000	0.03228	-0.025000	0.13918	-0.258000	0.10820	CGA	BRAT1	-	superfamily_ARM-type_fold	ENSG00000106009		0.706	BRAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	BRAT1	HGNC	protein_coding	OTTHUMT00000239305.2	8	0.00	0	C	NM_152743		2578238	2578238	-1	no_errors	ENST00000340611	ensembl	human	known	69_37n	missense	6	45.45	5	SNP	0.045	T
C18orf54	162681	genome.wustl.edu	37	18	51889197	51889197	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A0XS-01A-22D-A10G-09	TCGA-AN-A0XS-10A-01D-A10G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f1b5268d-556f-404f-a956-770df4a1e7aa	3a722354-b991-44cf-9ab8-f276b4a38701	g.chr18:51889197G>A	ENST00000300091.5	+	4	978	c.646G>A	c.(646-648)Gaa>Aaa	p.E216K	C18orf54_ENST00000382911.4_Missense_Mutation_p.E377K|C18orf54_ENST00000578138.1_5'UTR	NM_173529.4	NP_775800.3	Q8IYD9	LAS2_HUMAN	chromosome 18 open reading frame 54	216						extracellular region (GO:0005576)		p.E216K(1)		breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	15				Colorectal(16;0.0206)|READ - Rectum adenocarcinoma(59;0.186)		GCAGTGTACTGAAGAATTACC	0.328																																						dbGAP											1	Substitution - Missense(1)	breast(1)											81.0	80.0	81.0					18																	51889197		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK126503	CCDS11956.1, CCDS74223.1	18q21	2012-10-24			ENSG00000166845	ENSG00000166845			13796	protein-coding gene	gene with protein product	"""lung adenoma susceptibility protein 2"""	613258					Standard	XM_005258201		Approved	MGC33382, LAS2	uc031rij.1	Q8IYD9	OTTHUMG00000132703	ENST00000300091.5:c.646G>A	18.37:g.51889197G>A	ENSP00000300091:p.Glu216Lys	Somatic		WXS	Illumina GAIIx	Phase_IV	I7HFJ6|Q6MZU3|Q6ZTL6	Missense_Mutation	SNP	NULL	p.E216K	ENST00000300091.5	37	c.646	CCDS11956.1	18	.	.	.	.	.	.	.	.	.	.	G	0.938	-0.710563	0.03230	.	.	ENSG00000166845	ENST00000300091;ENST00000382911	T;T	0.16743	2.32;2.32	4.97	3.15	0.36227	.	0.669254	0.15508	N	0.258687	T	0.12050	0.0293	L	0.37561	1.115	0.09310	N	0.999998	B;B	0.12013	0.001;0.005	B;B	0.17433	0.003;0.018	T	0.37686	-0.9695	10	0.06236	T	0.91	6.0E-4	10.9181	0.47148	0.1611:0.0:0.8389:0.0	.	377;216	Q8IYD9-2;Q8IYD9	.;CR054_HUMAN	K	216;377	ENSP00000300091:E216K;ENSP00000372368:E377K	ENSP00000300091:E216K	E	+	1	0	C18orf54	50143195	0.106000	0.21978	0.058000	0.19502	0.184000	0.23303	0.583000	0.23849	0.472000	0.27344	-0.424000	0.05967	GAA	C18orf54	-	NULL	ENSG00000166845		0.328	C18orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	C18orf54	HGNC	protein_coding	OTTHUMT00000256001.1	161	0.00	0	G	NM_173529		51889197	51889197	+1	no_errors	ENST00000300091	ensembl	human	known	69_37n	missense	125	25.15	42	SNP	0.811	A
CRHR2	1395	genome.wustl.edu	37	7	30704716	30704716	+	Silent	SNP	G	G	A			TCGA-AN-A0XS-01A-22D-A10G-09	TCGA-AN-A0XS-10A-01D-A10G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f1b5268d-556f-404f-a956-770df4a1e7aa	3a722354-b991-44cf-9ab8-f276b4a38701	g.chr7:30704716G>A	ENST00000471646.1	-	5	930	c.513C>T	c.(511-513)ctC>ctT	p.L171L	CRHR2_ENST00000506074.2_Silent_p.L171L|CRHR2_ENST00000341843.4_Silent_p.L157L|CRHR2_ENST00000348438.4_Silent_p.L198L	NM_001202482.1|NM_001202483.1|NM_001883.4	NP_001189411.1|NP_001189412.1|NP_001874.2	Q13324	CRFR2_HUMAN	corticotropin releasing hormone receptor 2	171					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cAMP-mediated signaling (GO:0043951)|positive regulation of cAMP-mediated signaling (GO:0043950)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	corticotrophin-releasing factor receptor activity (GO:0015056)	p.L171L(1)|p.L157L(1)		breast(2)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						CATGGTCAACGAGCTGCAGCA	0.577																																						dbGAP											2	Substitution - coding silent(2)	breast(2)											105.0	84.0	91.0					7																	30704716		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0				CCDS5429.1, CCDS56477.1, CCDS56478.1, CCDS75576.1	7p21-p15	2012-08-10			ENSG00000106113	ENSG00000106113		"""GPCR / Class B : Corticotropin-releasing factor receptors"""	2358	protein-coding gene	gene with protein product		602034				8536644	Standard	NM_001883		Approved	CRF2, CRF-RB, HM-CRF	uc003tbp.3	Q13324	OTTHUMG00000023218	ENST00000471646.1:c.513C>T	7.37:g.30704716G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	B2R967|B3SXS6|B3SXS7|B3SXS8|B3SXT0|F8WA81|O43461|Q4QRJ4|Q99431	Silent	SNP	pfam_GPCR_2_secretin-like,pfam_GPCR_2_extracellular_dom,smart_GPCR_2_extracellular_dom,pfscan_GPCR_2_extracellular_dom,pfscan_GPCR_2-like,prints_GPCR_2_CRF_rcpt,prints_GPCR_2_secretin-like,prints_GPCR_2_CRF2_rcpt,prints_GPCR_2_diuretic_rcpt	p.L198	ENST00000471646.1	37	c.594	CCDS5429.1	7																																																																																			CRHR2	-	pfam_GPCR_2_secretin-like,pfscan_GPCR_2-like,prints_GPCR_2_secretin-like,prints_GPCR_2_CRF2_rcpt	ENSG00000106113		0.577	CRHR2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	CRHR2	HGNC	protein_coding	OTTHUMT00000250448.3	65	0.00	0	G			30704716	30704716	-1	no_errors	ENST00000348438	ensembl	human	known	69_37n	silent	53	32.05	25	SNP	1.000	A
INO80	54617	genome.wustl.edu	37	15	41275191	41275191	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A0XS-01A-22D-A10G-09	TCGA-AN-A0XS-10A-01D-A10G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f1b5268d-556f-404f-a956-770df4a1e7aa	3a722354-b991-44cf-9ab8-f276b4a38701	g.chr15:41275191G>A	ENST00000361937.3	-	35	4746	c.4322C>T	c.(4321-4323)gCc>gTc	p.A1441V	INO80_ENST00000561244.1_5'Flank|INO80_ENST00000401393.3_Missense_Mutation_p.A1441V			Q9ULG1	INO80_HUMAN	INO80 complex subunit	1441	Assembles INO80 complex module consisting of conserved components INO80B, INO80C, ACTR5, RVBL1, RVBL2.				ATP catabolic process (GO:0006200)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|mitotic sister chromatid segregation (GO:0000070)|positive regulation of cell growth (GO:0030307)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|spindle assembly (GO:0051225)|UV-damage excision repair (GO:0070914)	Ino80 complex (GO:0031011)|microtubule (GO:0005874)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)	p.A1441V(2)		NS(1)|breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						TGCTCCTTTGGCTGTGCTTCC	0.627																																						dbGAP											2	Substitution - Missense(2)	breast(2)											46.0	44.0	45.0					15																	41275191		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB033085	CCDS10071.1	15q15.1	2013-08-21	2013-08-21	2008-08-07	ENSG00000128908	ENSG00000128908	3.6.1.3	"""INO80 complex subunits"""	26956	protein-coding gene	gene with protein product	"""INO80 complex subunit A"""	610169	"""INO80 complex homolog 1 (S. cerevisiae)"", ""INO80 homolog (S. cerevisiae)"""	INOC1		16298340, 16230350, 20237820	Standard	NM_017553		Approved	KIAA1259, Ino80, hINO80, INO80A	uc001zni.3	Q9ULG1	OTTHUMG00000130209	ENST00000361937.3:c.4322C>T	15.37:g.41275191G>A	ENSP00000355205:p.Ala1441Val	Somatic		WXS	Illumina GAIIx	Phase_IV	A6H8X4|Q9NTG6	Missense_Mutation	SNP	pfam_SNF2_N,pfam_Helicase_C,smart_Helicase_ATP-bd,smart_Helicase_C,pfscan_Helicase_ATP-bd,pfscan_Helicase_C	p.A1441V	ENST00000361937.3	37	c.4322	CCDS10071.1	15	.	.	.	.	.	.	.	.	.	.	G	16.99	3.274729	0.59649	.	.	ENSG00000128908	ENST00000361937;ENST00000401393	D;D	0.91180	-2.8;-2.8	5.55	5.55	0.83447	.	0.315746	0.33875	N	0.004475	D	0.85513	0.5714	N	0.19112	0.55	0.41978	D	0.990787	B	0.06786	0.001	B	0.04013	0.001	T	0.79645	-0.1717	10	0.52906	T	0.07	.	19.6982	0.96039	0.0:0.0:1.0:0.0	.	1441	Q9ULG1	INO80_HUMAN	V	1441	ENSP00000355205:A1441V;ENSP00000384686:A1441V	ENSP00000355205:A1441V	A	-	2	0	INO80	39062483	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.305000	0.65750	2.894000	0.99253	0.655000	0.94253	GCC	INO80	-	NULL	ENSG00000128908		0.627	INO80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	INO80	HGNC	protein_coding	OTTHUMT00000252527.2	25	0.00	0	G	NM_017553		41275191	41275191	-1	no_errors	ENST00000361937	ensembl	human	known	69_37n	missense	32	30.43	14	SNP	1.000	A
MAP3K1	4214	genome.wustl.edu	37	5	56155725	56155726	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-AN-A0XS-01A-22D-A10G-09	TCGA-AN-A0XS-10A-01D-A10G-09	AG	AG					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f1b5268d-556f-404f-a956-770df4a1e7aa	3a722354-b991-44cf-9ab8-f276b4a38701	g.chr5:56155725_56155726delAG	ENST00000399503.3	+	3	817_818	c.817_818delAG	c.(817-819)agafs	p.R273fs	AC008937.2_ENST00000415589.1_RNA|snoU13_ENST00000459264.1_RNA	NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	273					activation of MAPKK activity (GO:0000186)|apoptotic mitochondrial changes (GO:0008637)|cellular response to mechanical stimulus (GO:0071260)|epithelial cell morphogenesis (GO:0003382)|eyelid development in camera-type eye (GO:0061029)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of actin filament polymerization (GO:0030838)|protein phosphorylation (GO:0006468)|regulation of cell migration (GO:0030334)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cytosol (GO:0005829)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			NS(1)|breast(19)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(11)|ovary(1)|skin(3)|urinary_tract(1)	57		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		AAGGAGAAAAAGAGTTTCCCCA	0.431																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			U29671, AF042838	CCDS43318.1	5q11.2	2012-02-23	2012-02-23		ENSG00000095015	ENSG00000095015		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6848	protein-coding gene	gene with protein product		600982	"""mitogen-activated protein kinase kinase kinase 1"""	MEKK1		8597633	Standard	NM_005921		Approved	MEKK, MAPKKK1	uc003jqw.4	Q13233	OTTHUMG00000059486	ENST00000399503.3:c.817_818delAG	5.37:g.56155727_56155728delAG	ENSP00000382423:p.Arg273fs	Somatic		WXS	Illumina GAIIx	Phase_IV		Frame_Shift_Del	DEL	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,superfamily_ARM-type_fold,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Znf_RING,pfscan_Znf_SWIM,pfscan_Prot_kinase_cat_dom	p.R273fs	ENST00000399503.3	37	c.817_818	CCDS43318.1	5																																																																																			MAP3K1	-	NULL	ENSG00000095015		0.431	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	MAP3K1	HGNC	protein_coding	OTTHUMT00000132309.2	49	0.00	0	AG	XM_042066		56155725	56155726	+1	no_errors	ENST00000399503	ensembl	human	novel	69_37n	frame_shift_del	42	30.00	18	DEL	0.959:0.996	-
NT5DC3	51559	genome.wustl.edu	37	12	104208866	104208866	+	Missense_Mutation	SNP	T	T	A			TCGA-AN-A0XS-01A-22D-A10G-09	TCGA-AN-A0XS-10A-01D-A10G-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f1b5268d-556f-404f-a956-770df4a1e7aa	3a722354-b991-44cf-9ab8-f276b4a38701	g.chr12:104208866T>A	ENST00000392876.3	-	2	282	c.242A>T	c.(241-243)aAt>aTt	p.N81I		NM_001031701.2	NP_001026871.1	Q86UY8	NT5D3_HUMAN	5'-nucleotidase domain containing 3	81						cytosol (GO:0005829)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)	p.N81I(1)|p.N6I(1)		NS(1)|breast(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(15)|ovary(2)|skin(1)|stomach(2)	30						GGCATCTGGATTCAACAAGTT	0.323																																						dbGAP											2	Substitution - Missense(2)	breast(2)											74.0	69.0	70.0					12																	104208866		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB032786	CCDS41824.1	12q22-q23.1	2006-02-03			ENSG00000111696	ENSG00000111696			30826	protein-coding gene	gene with protein product		611076					Standard	NM_001031701		Approved	TU12B1-TY, FLJ11266	uc010swe.1	Q86UY8	OTTHUMG00000157017	ENST00000392876.3:c.242A>T	12.37:g.104208866T>A	ENSP00000376615:p.Asn81Ile	Somatic		WXS	Illumina GAIIx	Phase_IV	Q9NUM7|Q9P2T2|Q9P2T3	Missense_Mutation	SNP	pfam_HAD-SF_hydro_IG_5-nucl,superfamily_HAD-like_dom,pirsf_Pur_nucleotidase,tigrfam_HAD-SF_hydro_IG_5-nucl	p.N81I	ENST00000392876.3	37	c.242	CCDS41824.1	12	.	.	.	.	.	.	.	.	.	.	T	25.1	4.600288	0.87055	.	.	ENSG00000111696	ENST00000392876	T	0.24538	1.85	5.87	5.87	0.94306	HAD-like domain (1);	0.040499	0.85682	D	0.000000	T	0.39410	0.1077	L	0.36672	1.1	0.58432	D	0.999999	D	0.63880	0.993	P	0.60345	0.873	T	0.15925	-1.0420	10	0.87932	D	0	-42.6078	16.5764	0.84681	0.0:0.0:0.0:1.0	.	81	Q86UY8	NT5D3_HUMAN	I	81	ENSP00000376615:N81I	ENSP00000376615:N81I	N	-	2	0	NT5DC3	102732996	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.861000	0.69553	2.371000	0.80710	0.533000	0.62120	AAT	NT5DC3	-	superfamily_HAD-like_dom,pirsf_Pur_nucleotidase	ENSG00000111696		0.323	NT5DC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NT5DC3	HGNC	protein_coding	OTTHUMT00000347118.2	125	0.00	0	T	NM_016575		104208866	104208866	-1	no_errors	ENST00000392876	ensembl	human	known	69_37n	missense	120	30.23	52	SNP	1.000	A
PDZRN3	23024	genome.wustl.edu	37	3	73433946	73433946	+	Missense_Mutation	SNP	C	C	T			TCGA-AN-A0XS-01A-22D-A10G-09	TCGA-AN-A0XS-10A-01D-A10G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f1b5268d-556f-404f-a956-770df4a1e7aa	3a722354-b991-44cf-9ab8-f276b4a38701	g.chr3:73433946C>T	ENST00000263666.4	-	10	1885	c.1771G>A	c.(1771-1773)Gac>Aac	p.D591N	PDZRN3_ENST00000466780.1_Missense_Mutation_p.D248N|PDZRN3_ENST00000462146.2_Missense_Mutation_p.D248N|PDZRN3_ENST00000466348.1_5'Flank|PDZRN3_ENST00000535920.1_Missense_Mutation_p.D313N|PDZRN3_ENST00000479530.1_Missense_Mutation_p.D308N	NM_015009.1	NP_055824.1	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	591					neuromuscular junction development (GO:0007528)|protein ubiquitination (GO:0016567)	neuromuscular junction (GO:0031594)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.G590fs*73(1)|p.D591N(1)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(31)|ovary(4)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		GTGGCGTCGTCGCCATTGTTC	0.642																																						dbGAP											2	Substitution - Missense(1)|Deletion - Frameshift(1)	ovary(1)|breast(1)											82.0	74.0	77.0					3																	73433946		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB029018	CCDS33789.1	3p14.1	2013-01-09	2008-08-14		ENSG00000121440	ENSG00000121440		"""RING-type (C3HC4) zinc fingers"""	17704	protein-coding gene	gene with protein product	"""likely ortholog of mouse semaF cytoplasmic domain associated protein 3"""	609729				10470851	Standard	XM_005264718		Approved	KIAA1095, SEMACAP3, LNX3	uc003dpl.1	Q9UPQ7	OTTHUMG00000158865	ENST00000263666.4:c.1771G>A	3.37:g.73433946C>T	ENSP00000263666:p.Asp591Asn	Somatic		WXS	Illumina GAIIx	Phase_IV	A7MCZ6|Q8N2N7|Q96CC2|Q9NSQ2	Missense_Mutation	SNP	pfam_PDZ,pfam_Znf_C3HC4_RING-type,superfamily_PDZ,superfamily_TRAF-like,smart_Znf_RING,smart_PDZ,pfscan_PDZ,pfscan_Znf_RING,pfscan_Znf_TRAF	p.D591N	ENST00000263666.4	37	c.1771	CCDS33789.1	3	.	.	.	.	.	.	.	.	.	.	C	16.30	3.085606	0.55861	.	.	ENSG00000121440	ENST00000263666;ENST00000535920;ENST00000462146;ENST00000466780;ENST00000479530;ENST00000416926;ENST00000492909	T;T;T;T;T;T	0.12569	2.67;3.38;3.27;3.27;3.38;3.34	4.77	4.77	0.60923	.	1.169940	0.06737	U	0.777761	T	0.37461	0.1004	M	0.76328	2.33	0.80722	D	1	D;P;D;P	0.57257	0.979;0.772;0.964;0.483	P;B;P;B	0.55222	0.771;0.242;0.595;0.142	T	0.14364	-1.0475	10	0.87932	D	0	.	17.5919	0.87999	0.0:1.0:0.0:0.0	.	313;308;308;591	F5H8I9;B7ZAG0;B7Z5X9;Q9UPQ7	.;.;.;PZRN3_HUMAN	N	591;313;248;248;308;591;289	ENSP00000263666:D591N;ENSP00000442026:D313N;ENSP00000418168:D248N;ENSP00000418484:D248N;ENSP00000418624:D308N;ENSP00000419250:D289N	ENSP00000263666:D591N	D	-	1	0	PDZRN3	73516636	1.000000	0.71417	0.877000	0.34402	0.535000	0.34838	7.461000	0.80834	2.464000	0.83262	0.655000	0.94253	GAC	PDZRN3	-	NULL	ENSG00000121440		0.642	PDZRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PDZRN3	HGNC	protein_coding	OTTHUMT00000352460.1	51	0.00	0	C	XM_041363		73433946	73433946	-1	no_errors	ENST00000263666	ensembl	human	known	69_37n	missense	68	32.00	32	SNP	1.000	T
PHLDB1	23187	genome.wustl.edu	37	11	118486807	118486807	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A0XS-01A-22D-A10G-09	TCGA-AN-A0XS-10A-01D-A10G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f1b5268d-556f-404f-a956-770df4a1e7aa	3a722354-b991-44cf-9ab8-f276b4a38701	g.chr11:118486807G>A	ENST00000361417.2	+	5	647	c.236G>A	c.(235-237)gGc>gAc	p.G79D	PHLDB1_ENST00000356063.5_Missense_Mutation_p.G79D	NM_015157.3	NP_055972.1	Q86UU1	PHLB1_HUMAN	pleckstrin homology-like domain, family B, member 1	79	FHA.							p.G79D(1)		breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(10)|liver(3)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(1)	46	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.0735)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)		CAGGGCCCAGGCCTGGCTCCA	0.607																																						dbGAP											1	Substitution - Missense(1)	breast(1)											106.0	100.0	102.0					11																	118486807		2200	4295	6495	-	-	-	SO:0001583	missense	0				CCDS8401.1, CCDS44750.1	11q23.3	2013-01-10			ENSG00000019144	ENSG00000019144		"""Pleckstrin homology (PH) domain containing"""	23697	protein-coding gene	gene with protein product		612834				14532993	Standard	NM_015157		Approved	FLJ00141, LL5a, KIAA0638	uc001pts.3	Q86UU1	OTTHUMG00000166341	ENST00000361417.2:c.236G>A	11.37:g.118486807G>A	ENSP00000354498:p.Gly79Asp	Somatic		WXS	Illumina GAIIx	Phase_IV	B0YJ63|B0YJ64|O75133|Q4KMF8|Q8TEQ2	Missense_Mutation	SNP	pfam_Pleckstrin_homology,superfamily_SMAD_FHA_domain,smart_Pleckstrin_homology,pfscan_Pleckstrin_homology	p.G79D	ENST00000361417.2	37	c.236	CCDS8401.1	11	.	.	.	.	.	.	.	.	.	.	G	34	5.386398	0.95967	.	.	ENSG00000019144	ENST00000361417;ENST00000543207;ENST00000545313;ENST00000356063	T;T	0.56275	0.47;0.47	5.76	5.76	0.90799	Forkhead-associated (FHA) domain (1);SMAD/FHA domain (1);	0.000000	0.85682	D	0.000000	T	0.68970	0.3059	L	0.59967	1.855	0.80722	D	1	P;D;D	0.89917	0.938;1.0;1.0	P;D;D	0.97110	0.849;1.0;0.998	T	0.60234	-0.7303	10	0.20519	T	0.43	-31.0484	18.9014	0.92444	0.0:0.0:1.0:0.0	.	79;79;79	B4DIX4;Q86UU1-2;Q86UU1	.;.;PHLB1_HUMAN	D	79	ENSP00000354498:G79D;ENSP00000348359:G79D	ENSP00000348359:G79D	G	+	2	0	PHLDB1	117992017	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.154000	0.94694	2.882000	0.98803	0.655000	0.94253	GGC	PHLDB1	-	superfamily_SMAD_FHA_domain	ENSG00000019144		0.607	PHLDB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PHLDB1	HGNC	protein_coding	OTTHUMT00000389279.1	55	0.00	0	G	NM_015157		118486807	118486807	+1	no_errors	ENST00000361417	ensembl	human	known	69_37n	missense	46	20.69	12	SNP	1.000	A
PIK3CA	5290	genome.wustl.edu	37	3	178936091	178936091	+	Missense_Mutation	SNP	G	G	A	rs104886003		TCGA-AN-A0XS-01A-22D-A10G-09	TCGA-AN-A0XS-10A-01D-A10G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f1b5268d-556f-404f-a956-770df4a1e7aa	3a722354-b991-44cf-9ab8-f276b4a38701	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	117	0.00	0	G			178936091	178936091	+1	no_errors	ENST00000263967	ensembl	human	known	69_37n	missense	104	27.27	39	SNP	1.000	A
PTPRM	5797	genome.wustl.edu	37	18	8088802	8088802	+	Silent	SNP	C	C	T			TCGA-AN-A0XS-01A-22D-A10G-09	TCGA-AN-A0XS-10A-01D-A10G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f1b5268d-556f-404f-a956-770df4a1e7aa	3a722354-b991-44cf-9ab8-f276b4a38701	g.chr18:8088802C>T	ENST00000332175.8	+	11	2846	c.1809C>T	c.(1807-1809)acC>acT	p.T603T	PTPRM_ENST00000400053.4_Silent_p.T541T|PTPRM_ENST00000444013.1_Silent_p.T390T|PTPRM_ENST00000578571.1_3'UTR|PTPRM_ENST00000580170.1_Silent_p.T603T|PTPRM_ENST00000400060.4_Silent_p.T603T	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	603	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.T603T(1)		breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				CTGACAATACCGTGACAGTCA	0.463																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											123.0	108.0	113.0					18																	8088802		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.1809C>T	18.37:g.8088802C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	A7MBN1|D3DUH8|J3QL11	Missense_Mutation	SNP	pfam_Fibronectin_type3,superfamily_Fibronectin_type3,pfscan_Fibronectin_type3	p.P76L	ENST00000332175.8	37	c.227	CCDS11840.1	18																																																																																			PTPRM	-	superfamily_Fibronectin_type3	ENSG00000173482		0.463	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	PTPRM	HGNC	protein_coding	OTTHUMT00000254456.1	148	0.00	0	C			8088802	8088802	+1	no_start_codon:pseudogene:no_stop_codon	ENST00000583289	ensembl	human	novel	69_37n	missense	147	23.04	44	SNP	0.007	T
ROR1	4919	genome.wustl.edu	37	1	64643303	64643303	+	Missense_Mutation	SNP	A	A	C			TCGA-AN-A0XS-01A-22D-A10G-09	TCGA-AN-A0XS-10A-01D-A10G-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f1b5268d-556f-404f-a956-770df4a1e7aa	3a722354-b991-44cf-9ab8-f276b4a38701	g.chr1:64643303A>C	ENST00000371079.1	+	9	1954	c.1579A>C	c.(1579-1581)Atg>Ctg	p.M527L	ROR1_ENST00000545203.1_5'UTR	NM_005012.3	NP_005003.2	Q01973	ROR1_HUMAN	receptor tyrosine kinase-like orphan receptor 1	527	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				peptidyl-tyrosine phosphorylation (GO:0018108)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)	p.M527L(1)		breast(7)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(10)|ovary(6)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	51						AGCCTCCCTAATGGCAGAACT	0.483																																						dbGAP											1	Substitution - Missense(1)	breast(1)											220.0	213.0	215.0					1																	64643303		2203	4300	6503	-	-	-	SO:0001583	missense	0			M97675	CCDS626.1, CCDS41344.1	1p32-p31	2013-01-11			ENSG00000185483	ENSG00000185483		"""Immunoglobulin superfamily / I-set domain containing"""	10256	protein-coding gene	gene with protein product		602336		NTRKR1		1334494, 8875995	Standard	NM_001083592		Approved		uc001dbj.3	Q01973	OTTHUMG00000009022	ENST00000371079.1:c.1579A>C	1.37:g.64643303A>C	ENSP00000360120:p.Met527Leu	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5VVX6|Q66K77|Q92776	Missense_Mutation	SNP	pirsf_Tyr_kinase_rcpt_ROR,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_cat_dom,pfam_Kringle,pfam_Frizzled_dom,pfam_Ig_I-set,pfam_Immunoglobulin,pfam_Ig_V-set,superfamily_Kinase-like_dom,superfamily_Kringle-like,superfamily_Frizzled_dom,smart_Ig_sub,smart_Ig_sub2,smart_Kringle,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,prints_Ser-Thr/Tyr_kinase_cat_dom,pfscan_Frizzled_dom,pfscan_Kringle,pfscan_Prot_kinase_cat_dom,pfscan_Ig-like	p.M527L	ENST00000371079.1	37	c.1579	CCDS626.1	1	.	.	.	.	.	.	.	.	.	.	A	0.250	-1.007086	0.02112	.	.	ENSG00000185483	ENST00000371079;ENST00000544776	D	0.82619	-1.63	5.88	3.48	0.39840	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.52532	D	0.000075	T	0.41604	0.1166	N	0.04320	-0.23	0.80722	D	1	B	0.02656	0.0	B	0.09377	0.004	T	0.36529	-0.9744	10	0.07030	T	0.85	.	12.7547	0.57328	0.7407:0.2593:0.0:0.0	.	527	Q01973	ROR1_HUMAN	L	527;530	ENSP00000360120:M527L	ENSP00000360120:M527L	M	+	1	0	ROR1	64415891	0.997000	0.39634	0.813000	0.32504	0.928000	0.56348	3.623000	0.54224	0.438000	0.26450	0.533000	0.62120	ATG	ROR1	-	pirsf_Tyr_kinase_rcpt_ROR,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom	ENSG00000185483		0.483	ROR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ROR1	HGNC	protein_coding	OTTHUMT00000025002.1	89	0.00	0	A	NM_005012		64643303	64643303	+1	no_errors	ENST00000371079	ensembl	human	known	69_37n	missense	64	36.00	36	SNP	0.865	C
RCSD1	92241	genome.wustl.edu	37	1	167667018	167667018	+	Missense_Mutation	SNP	G	G	T			TCGA-AN-A0XS-01A-22D-A10G-09	TCGA-AN-A0XS-10A-01D-A10G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f1b5268d-556f-404f-a956-770df4a1e7aa	3a722354-b991-44cf-9ab8-f276b4a38701	g.chr1:167667018G>T	ENST00000367854.3	+	6	1488	c.1157G>T	c.(1156-1158)gGc>gTc	p.G386V	RCSD1_ENST00000537350.1_Missense_Mutation_p.G356V	NM_052862.3	NP_443094.3	Q6JBY9	CPZIP_HUMAN	RCSD domain containing 1	386					cellular hyperosmotic response (GO:0071474)|skeletal muscle contraction (GO:0003009)	actin filament (GO:0005884)	actin filament binding (GO:0051015)	p.G386V(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(2)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	24	all_hematologic(923;0.215)					CCCCAGACCGGCCCTGCCCAG	0.642																																						dbGAP											1	Substitution - Missense(1)	breast(1)											15.0	19.0	18.0					1																	167667018		2187	4273	6460	-	-	-	SO:0001583	missense	0			BC072399	CCDS1263.1	1q24.2	2008-02-05			ENSG00000198771	ENSG00000198771			28310	protein-coding gene	gene with protein product		610579				12477932	Standard	NM_052862		Approved	MK2S4, MGC21854	uc001gem.3	Q6JBY9	OTTHUMG00000035318	ENST00000367854.3:c.1157G>T	1.37:g.167667018G>T	ENSP00000356828:p.Gly386Val	Somatic		WXS	Illumina GAIIx	Phase_IV	B1AK48|Q4G0E7|Q6IN93|Q8IZM2|Q96DX0|Q9NST4	Missense_Mutation	SNP	pfam_RCSD	p.G386V	ENST00000367854.3	37	c.1157	CCDS1263.1	1	.	.	.	.	.	.	.	.	.	.	G	5.918	0.353352	0.11182	.	.	ENSG00000198771	ENST00000367854;ENST00000537350	T;T	0.47177	0.85;0.85	4.22	-2.58	0.06228	.	0.941555	0.08776	N	0.895502	T	0.10294	0.0252	N	0.08118	0	0.21878	N	0.999495	P;B	0.44877	0.845;0.005	B;B	0.43478	0.421;0.003	T	0.04522	-1.0945	9	0.27082	T	0.32	0.0402	6.259	0.20889	0.4564:0.1315:0.4121:0.0	.	356;386	B7ZKW8;Q6JBY9	.;CPZIP_HUMAN	V	386;356	ENSP00000356828:G386V;ENSP00000439409:G356V	ENSP00000356828:G386V	G	+	2	0	RCSD1	165933642	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.253000	0.08794	-0.977000	0.03537	-2.484000	0.00197	GGC	RCSD1	-	NULL	ENSG00000198771		0.642	RCSD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	RCSD1	HGNC	protein_coding	OTTHUMT00000085451.1	24	0.00	0	G	NM_052862		167667018	167667018	+1	no_errors	ENST00000367854	ensembl	human	known	69_37n	missense	25	19.35	6	SNP	0.000	T
SLC25A2	83884	genome.wustl.edu	37	5	140682837	140682837	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A0XS-01A-22D-A10G-09	TCGA-AN-A0XS-10A-01D-A10G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f1b5268d-556f-404f-a956-770df4a1e7aa	3a722354-b991-44cf-9ab8-f276b4a38701	g.chr5:140682837G>A	ENST00000239451.4	-	1	775	c.596C>T	c.(595-597)gCg>gTg	p.A199V		NM_031947.2	NP_114153.1	Q9BXI2	ORNT2_HUMAN	solute carrier family 25 (mitochondrial carrier; ornithine transporter) member 2	199					cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)|urea cycle (GO:0000050)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)		p.A199V(1)		breast(3)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	19		all_lung(500;0.000249)|Lung NSC(810;0.0011)|Ovarian(839;0.00556)|Breast(839;0.0173)|all_hematologic(541;0.152)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.00204)	L-Ornithine(DB00129)	TCTCCCTGACGCAAAAAACGA	0.468																																						dbGAP											1	Substitution - Missense(1)	breast(1)											98.0	100.0	99.0					5																	140682837		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF332005	CCDS4258.1	5q31.3	2013-05-22			ENSG00000120329	ENSG00000120329		"""Solute carriers"""	22921	protein-coding gene	gene with protein product		608157				11004451	Standard	NM_031947		Approved	ORNT2	uc003ljf.3	Q9BXI2	OTTHUMG00000129604	ENST00000239451.4:c.596C>T	5.37:g.140682837G>A	ENSP00000239451:p.Ala199Val	Somatic		WXS	Illumina GAIIx	Phase_IV	Q496C1|Q6XUI0|Q8NFZ2	Missense_Mutation	SNP	pfam_Mitochondrial_sb/sol_carrier,superfamily_Mt_carrier_dom,pfscan_Mitochondrial_sb/sol_carrier	p.A199V	ENST00000239451.4	37	c.596	CCDS4258.1	5	.	.	.	.	.	.	.	.	.	.	G	11.44	1.639682	0.29157	.	.	ENSG00000120329	ENST00000239451	T	0.77750	-1.12	3.78	2.9	0.33743	Mitochondrial carrier domain (2);	0.234464	0.33438	U	0.004908	T	0.70029	0.3177	L	0.58510	1.815	0.43632	D	0.996024	P	0.36633	0.562	B	0.32465	0.146	T	0.70000	-0.4992	10	0.42905	T	0.14	-19.0874	10.9392	0.47264	0.0:0.0:0.8115:0.1885	.	199	Q9BXI2	ORNT2_HUMAN	V	199	ENSP00000239451:A199V	ENSP00000239451:A199V	A	-	2	0	SLC25A2	140663021	1.000000	0.71417	0.649000	0.29536	0.205000	0.24178	8.070000	0.89493	1.169000	0.42739	0.650000	0.86243	GCG	SLC25A2	-	pfam_Mitochondrial_sb/sol_carrier,superfamily_Mt_carrier_dom	ENSG00000120329		0.468	SLC25A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC25A2	HGNC	protein_coding	OTTHUMT00000251799.2	117	0.00	0	G	NM_031947		140682837	140682837	-1	no_errors	ENST00000239451	ensembl	human	known	69_37n	missense	98	31.47	45	SNP	0.995	A
SH3PXD2B	285590	genome.wustl.edu	37	5	171766645	171766645	+	Missense_Mutation	SNP	C	C	A			TCGA-AN-A0XS-01A-22D-A10G-09	TCGA-AN-A0XS-10A-01D-A10G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f1b5268d-556f-404f-a956-770df4a1e7aa	3a722354-b991-44cf-9ab8-f276b4a38701	g.chr5:171766645C>A	ENST00000311601.5	-	13	1634	c.1464G>T	c.(1462-1464)tgG>tgT	p.W488C	SH3PXD2B_ENST00000519643.1_Intron	NM_001017995.2	NP_001017995.1	A1X283	SPD2B_HUMAN	SH3 and PX domains 2B	488					adipose tissue development (GO:0060612)|bone development (GO:0060348)|cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|eye development (GO:0001654)|heart development (GO:0007507)|podosome assembly (GO:0071800)|positive regulation of fat cell differentiation (GO:0045600)|protein localization to membrane (GO:0072657)|skeletal system development (GO:0001501)|superoxide metabolic process (GO:0006801)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|podosome (GO:0002102)	phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)|SH2 domain binding (GO:0042169)	p.W488C(1)		NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(12)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	36	Renal(175;0.000159)|Lung NSC(126;0.011)|all_lung(126;0.0175)	Medulloblastoma(196;0.0207)|all_neural(177;0.0625)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TACTGCCCTTCCAGTCTTTAG	0.612																																						dbGAP											1	Substitution - Missense(1)	breast(1)											103.0	91.0	95.0					5																	171766645		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK095834	CCDS34291.1	5q35.2	2008-02-05	2006-02-13	2006-02-13	ENSG00000174705	ENSG00000174705			29242	protein-coding gene	gene with protein product		613293	"""KIAA1295"""	KIAA1295		10718198	Standard	NM_001017995		Approved	FLJ20831	uc003mbr.3	A1X283	OTTHUMG00000163280	ENST00000311601.5:c.1464G>T	5.37:g.171766645C>A	ENSP00000309714:p.Trp488Cys	Somatic		WXS	Illumina GAIIx	Phase_IV	B6F0V2|Q9P2Q1	Missense_Mutation	SNP	pfam_SH3_domain,pfam_SH3_2,pfam_Phox,pfam_SH3-like_bac,pfam_DUF1058,superfamily_Phox,superfamily_SH3_domain,smart_Phox,smart_SH3_domain,pfscan_Phox,pfscan_SH3_domain	p.W488C	ENST00000311601.5	37	c.1464	CCDS34291.1	5	.	.	.	.	.	.	.	.	.	.	C	13.15	2.150368	0.37923	.	.	ENSG00000174705	ENST00000311601	T	0.63417	-0.04	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.68210	0.2976	L	0.59436	1.845	0.80722	D	1	D	0.65815	0.995	P	0.51193	0.662	T	0.67971	-0.5532	9	.	.	.	-14.2308	16.9496	0.86240	0.0:1.0:0.0:0.0	.	488	A1X283	SPD2B_HUMAN	C	488	ENSP00000309714:W488C	.	W	-	3	0	SH3PXD2B	171699250	1.000000	0.71417	1.000000	0.80357	0.417000	0.31264	6.748000	0.74877	2.596000	0.87737	0.561000	0.74099	TGG	SH3PXD2B	-	NULL	ENSG00000174705		0.612	SH3PXD2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SH3PXD2B	HGNC	protein_coding	OTTHUMT00000372449.1	62	0.00	0	C	NM_017963		171766645	171766645	-1	no_errors	ENST00000311601	ensembl	human	known	69_37n	missense	49	37.97	30	SNP	1.000	A
SLC44A2	57153	genome.wustl.edu	37	19	10742416	10742416	+	Missense_Mutation	SNP	A	A	G			TCGA-AN-A0XS-01A-22D-A10G-09	TCGA-AN-A0XS-10A-01D-A10G-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f1b5268d-556f-404f-a956-770df4a1e7aa	3a722354-b991-44cf-9ab8-f276b4a38701	g.chr19:10742416A>G	ENST00000335757.5	+	8	993	c.617A>G	c.(616-618)gAg>gGg	p.E206G	SLC44A2_ENST00000586078.1_Missense_Mutation_p.E206G|SLC44A2_ENST00000407327.4_Missense_Mutation_p.E204G			Q8IWA5	CTL2_HUMAN	solute carrier family 44 (choline transporter), member 2	206					choline transport (GO:0015871)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	choline transmembrane transporter activity (GO:0015220)|signal transducer activity (GO:0004871)	p.E206G(1)		NS(1)|breast(3)|endometrium(5)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	27			Epithelial(33;8.7e-06)|all cancers(31;2.77e-05)		Choline(DB00122)	GACCTGGTGGAGGGCGCCAAG	0.592																																						dbGAP											1	Substitution - Missense(1)	breast(1)											57.0	55.0	56.0					19																	10742416		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF070636	CCDS12245.1, CCDS54216.1	19p13.2	2014-08-12	2013-07-17		ENSG00000129353	ENSG00000129353		"""Solute carriers"""	17292	protein-coding gene	gene with protein product		606106				10677542, 15715662	Standard	NM_001145056		Approved	CTL2	uc002mpf.3	Q8IWA5	OTTHUMG00000180585	ENST00000335757.5:c.617A>G	19.37:g.10742416A>G	ENSP00000336888:p.Glu206Gly	Somatic		WXS	Illumina GAIIx	Phase_IV	B2RBB1|B3KNH3|B4DFJ0|F2Q9D7|Q658V1|Q658Z2|Q6PJV7|Q8N2F0|Q9NY68	Missense_Mutation	SNP	pfam_Choline_transptr-like	p.E206G	ENST00000335757.5	37	c.617	CCDS12245.1	19	.	.	.	.	.	.	.	.	.	.	A	14.30	2.495663	0.44352	.	.	ENSG00000129353	ENST00000407327;ENST00000335757;ENST00000380614	T;T	0.10668	2.86;2.85	4.73	4.73	0.59995	.	0.286597	0.38492	N	0.001677	T	0.13927	0.0337	M	0.61703	1.905	0.46774	D	0.999193	B;B	0.19583	0.017;0.037	B;B	0.18561	0.006;0.022	T	0.02464	-1.1155	10	0.39692	T	0.17	.	13.3802	0.60762	1.0:0.0:0.0:0.0	.	206;204	Q8IWA5;Q8IWA5-3	CTL2_HUMAN;.	G	204;206;206	ENSP00000385135:E204G;ENSP00000336888:E206G	ENSP00000336888:E206G	E	+	2	0	SLC44A2	10603416	1.000000	0.71417	1.000000	0.80357	0.309000	0.27889	6.395000	0.73228	2.007000	0.58848	0.374000	0.22700	GAG	SLC44A2	-	NULL	ENSG00000129353		0.592	SLC44A2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC44A2	HGNC	protein_coding	OTTHUMT00000452045.1	59	0.00	0	A			10742416	10742416	+1	no_errors	ENST00000335757	ensembl	human	known	69_37n	missense	69	36.70	40	SNP	1.000	G
SLC4A11	83959	genome.wustl.edu	37	20	3214874	3214874	+	Silent	SNP	G	G	A			TCGA-AN-A0XS-01A-22D-A10G-09	TCGA-AN-A0XS-10A-01D-A10G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f1b5268d-556f-404f-a956-770df4a1e7aa	3a722354-b991-44cf-9ab8-f276b4a38701	g.chr20:3214874G>A	ENST00000380056.3	-	4	473	c.426C>T	c.(424-426)aaC>aaT	p.N142N	SLC4A11_ENST00000380059.3_Silent_p.N169N|SLC4A11_ENST00000539553.2_Silent_p.N126N	NM_032034.3	NP_114423.1	Q8NBS3	S4A11_HUMAN	solute carrier family 4, sodium borate transporter, member 11	142					bicarbonate transport (GO:0015701)|borate transmembrane transport (GO:0035445)|borate transport (GO:0046713)|cellular cation homeostasis (GO:0030003)|fluid transport (GO:0042044)|proton transport (GO:0015992)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	bicarbonate transmembrane transporter activity (GO:0015106)|borate transmembrane transporter activity (GO:0046715)|hydrogen ion channel activity (GO:0015252)|inorganic anion exchanger activity (GO:0005452)|protein dimerization activity (GO:0046983)|sodium channel activity (GO:0005272)|symporter activity (GO:0015293)	p.N142N(1)|p.N169N(1)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(4)|soft_tissue(1)|urinary_tract(1)	40						TGGCCGTCTCGTTCAGGACGA	0.597																																					NSCLC(190;922 2139 10266 10292 38692)	dbGAP											2	Substitution - coding silent(2)	breast(2)											126.0	115.0	118.0					20																	3214874		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF336127	CCDS13052.1, CCDS54445.1, CCDS54446.1	20p13	2014-02-14	2007-08-03		ENSG00000088836	ENSG00000088836		"""Solute carriers"""	16438	protein-coding gene	gene with protein product		610206	"""corneal endothelial dystrophy 2 (autosomal recessive)"", ""solute carrier family 4, sodium bicarbonate transporter-like, member 11"", ""corneal dystrophy and perceptive deafness 1"""	CHED2, CDPD1		10843999, 11302728, 16767101	Standard	NM_001174089		Approved	dJ794I6.2, BTR1, NaBC1, FECD4	uc010zqe.2	Q8NBS3	OTTHUMG00000031740	ENST00000380056.3:c.426C>T	20.37:g.3214874G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	B4DKC8|B4DKX9|G3V1M3|Q2TB62|Q2TB63|Q9BXF4|Q9NTW9	Silent	SNP	pfam_HCO3_transpt_C,pfam_PTS_EIIA_2,superfamily_PTrfase/Anion_transptr,prints_HCO3_transpt_euk	p.N169	ENST00000380056.3	37	c.507	CCDS13052.1	20																																																																																			SLC4A11	-	superfamily_PTrfase/Anion_transptr	ENSG00000088836		0.597	SLC4A11-002	KNOWN	basic|CCDS	protein_coding	SLC4A11	HGNC	protein_coding	OTTHUMT00000077728.1	71	0.00	0	G			3214874	3214874	-1	no_errors	ENST00000380059	ensembl	human	known	69_37n	silent	74	35.65	41	SNP	0.722	A
SPDYE2B	100310812	genome.wustl.edu	37	7	102296747	102296747	+	Silent	SNP	G	G	A			TCGA-AN-A0XS-01A-22D-A10G-09	TCGA-AN-A0XS-10A-01D-A10G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f1b5268d-556f-404f-a956-770df4a1e7aa	3a722354-b991-44cf-9ab8-f276b4a38701	g.chr7:102296747G>A	ENST00000507450.1	+	5	1137	c.663G>A	c.(661-663)tcG>tcA	p.S221S	POLR2J2_ENST00000591000.1_Intron|SPDYE2B_ENST00000436228.2_Silent_p.S221S|POLR2J2_ENST00000476151.1_Intron|SPDYE2B_ENST00000455020.2_Silent_p.S77S|POLR2J2_ENST00000333432.6_Intron	NM_001166339.1	NP_001159811.1	A6NHP3	SPE2B_HUMAN	speedy/RINGO cell cycle regulator family member E2B	221																	TGAGGGTGTCGGACAAGGTAA	0.527																																						dbGAP											0																																										-	-	-	SO:0001819	synonymous_variant	0				CCDS59507.1	7q22.1	2013-05-08			ENSG00000173678	ENSG00000173678		"""Speedy homologs"""	48334	protein-coding gene	gene with protein product							Standard	NM_001166339		Approved			A6NHP3	OTTHUMG00000158393	ENST00000507450.1:c.663G>A	7.37:g.102296747G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	D6RBN0	Silent	SNP	pfam_Cell_cycle_regulatory_Spy1	p.S221	ENST00000507450.1	37	c.663	CCDS59507.1	7																																																																																			SPDYE6	-	pfam_Cell_cycle_regulatory_Spy1	ENSG00000173678		0.527	SPDYE2B-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	SPDYE6	HGNC	protein_coding	OTTHUMT00000350899.3	39	0.00	0	G			102296747	102296747	+1	no_errors	ENST00000436228	ensembl	human	known	69_37n	silent	35	10.26	4	SNP	0.086	A
TAF3	83860	genome.wustl.edu	37	10	8006100	8006103	+	Frame_Shift_Del	DEL	ATTG	ATTG	-	rs371658927		TCGA-AN-A0XS-01A-22D-A10G-09	TCGA-AN-A0XS-10A-01D-A10G-09	ATTG	ATTG					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f1b5268d-556f-404f-a956-770df4a1e7aa	3a722354-b991-44cf-9ab8-f276b4a38701	g.chr10:8006100_8006103delATTG	ENST00000344293.5	+	3	833_836	c.627_630delATTG	c.(625-630)ttattgfs	p.LL209fs		NM_031923.3	NP_114129.1	Q5VWG9	TAF3_HUMAN	TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140kDa	209					maintenance of protein location in nucleus (GO:0051457)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	zinc ion binding (GO:0008270)	p.L210fs*9(1)		NS(2)|breast(4)|endometrium(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(3)|prostate(4)|skin(2)	40						ATGTTGTGTTATTGGAAGCTCGAG	0.5																																						dbGAP											1	Deletion - Frameshift(1)	breast(1)																																								-	-	-	SO:0001589	frameshift_variant	0			AJ292190	CCDS41487.1	10p15.1	2013-01-28	2002-08-29		ENSG00000165632	ENSG00000165632		"""Zinc fingers, PHD-type"""	17303	protein-coding gene	gene with protein product		606576	"""TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140 kD"""			11438666, 18549481	Standard	NM_031923		Approved	TAF140, TAFII140	uc010qbd.3	Q5VWG9	OTTHUMG00000017643	ENST00000344293.5:c.627_630delATTG	10.37:g.8006100_8006103delATTG	ENSP00000340271:p.Leu209fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q05DA0|Q6GMS5|Q6P6B5|Q86VY6|Q9BQS9|Q9UFI8	Frame_Shift_Del	DEL	pfam_BTP,pfam_Znf_PHD-finger,superfamily_Znf_FYVE_PHD,superfamily_Histone-fold,smart_BTP,smart_Znf_PHD,pfscan_Znf_PHD-finger	p.L210fs	ENST00000344293.5	37	c.627_630	CCDS41487.1	10																																																																																			TAF3	-	NULL	ENSG00000165632		0.500	TAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TAF3	HGNC	protein_coding	OTTHUMT00000046725.1	50	0.00	0	ATTG	NM_031923		8006100	8006103	+1	no_errors	ENST00000344293	ensembl	human	known	69_37n	frame_shift_del	43	32.88	24	DEL	0.166:0.220:0.877:0.928	-
THNSL2	55258	genome.wustl.edu	37	2	88482500	88482500	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AN-A0XS-01A-22D-A10G-09	TCGA-AN-A0XS-10A-01D-A10G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f1b5268d-556f-404f-a956-770df4a1e7aa	3a722354-b991-44cf-9ab8-f276b4a38701	g.chr2:88482500delC	ENST00000324166.5	+	6	2676	c.985delC	c.(985-987)ctcfs	p.L329fs	THNSL2_ENST00000377254.3_Frame_Shift_Del_p.L329fs|THNSL2_ENST00000402102.1_Frame_Shift_Del_p.L329fs|THNSL2_ENST00000358591.2_Frame_Shift_Del_p.L329fs|THNSL2_ENST00000449349.1_Intron|THNSL2_ENST00000496844.1_3'UTR|THNSL2_ENST00000343544.4_Frame_Shift_Del_p.L329fs	NM_018271.4	NP_060741.3	Q86YJ6	THNS2_HUMAN	threonine synthase-like 2 (S. cerevisiae)	329					2-oxobutyrate biosynthetic process (GO:0046360)|dephosphorylation (GO:0016311)|serine family amino acid catabolic process (GO:0009071)	extracellular space (GO:0005615)	lyase activity (GO:0016829)|pyridoxal phosphate binding (GO:0030170)|serine binding (GO:0070905)	p.L329fs*8(1)		breast(4)|lung(17)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)	27						GTTCTGGCTGCTCTCTGGCTC	0.552																																						dbGAP											1	Deletion - Frameshift(1)	breast(1)											82.0	73.0	76.0					2																	88482500		2203	4300	6503	-	-	-	SO:0001589	frameshift_variant	0				CCDS2002.2, CCDS58718.1, CCDS74539.1	2p11.2	2007-06-20			ENSG00000144115	ENSG00000144115			25602	protein-coding gene	gene with protein product		611261				17034760	Standard	NM_018271		Approved	FLJ10916	uc021vkr.1	Q86YJ6	OTTHUMG00000130314	ENST00000324166.5:c.985delC	2.37:g.88482500delC	ENSP00000327323:p.Leu329fs	Somatic		WXS	Illumina GAIIx	Phase_IV	B3KTB1|B5MDX8|B7WPF8|D9ZZB8|Q6P2M7|Q6PI27|Q9NV54	Frame_Shift_Del	DEL	pfam_PyrdxlP-dep_enz_bsu,superfamily_PyrdxlP-dep_enz_bsu,tigrfam_Thr_synthase	p.L329fs	ENST00000324166.5	37	c.985	CCDS2002.2	2																																																																																			THNSL2	-	pfam_PyrdxlP-dep_enz_bsu,superfamily_PyrdxlP-dep_enz_bsu,tigrfam_Thr_synthase	ENSG00000144115		0.552	THNSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	THNSL2	HGNC	protein_coding	OTTHUMT00000252662.1	82	0.00	0	C	NM_018271		88482500	88482500	+1	no_errors	ENST00000324166	ensembl	human	known	69_37n	frame_shift_del	88	22.41	26	DEL	1.000	-
TNFRSF8	943	genome.wustl.edu	37	1	12157238	12157238	+	Missense_Mutation	SNP	G	G	T	rs536232983	byFrequency	TCGA-AN-A0XS-01A-22D-A10G-09	TCGA-AN-A0XS-10A-01D-A10G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f1b5268d-556f-404f-a956-770df4a1e7aa	3a722354-b991-44cf-9ab8-f276b4a38701	g.chr1:12157238G>T	ENST00000263932.2	+	3	454	c.232G>T	c.(232-234)Gcc>Tcc	p.A78S	TNFRSF8_ENST00000417814.2_5'UTR	NM_001243.3|NM_001281430.1	NP_001234.2|NP_001268359.1	P28908	TNR8_HUMAN	tumor necrosis factor receptor superfamily, member 8	78					cellular response to mechanical stimulus (GO:0071260)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of TRAIL biosynthetic process (GO:0045556)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)	p.A78S(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	27	Ovarian(185;0.249)	Lung NSC(185;8.71e-05)|all_lung(284;9.89e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Brentuximab vedotin(DB08870)	CCTGGATGAGGCCGACCGCTG	0.577																																						dbGAP											1	Substitution - Missense(1)	breast(1)											116.0	102.0	107.0					1																	12157238		2203	4300	6503	-	-	-	SO:0001583	missense	0			M83554	CCDS144.1, CCDS59989.1	1p36	2008-02-05			ENSG00000120949	ENSG00000120949		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11923	protein-coding gene	gene with protein product		153243		CD30, D1S166E		1330892, 1310894	Standard	XM_006711049		Approved	KI-1	uc001atq.3	P28908	OTTHUMG00000001827	ENST00000263932.2:c.232G>T	1.37:g.12157238G>T	ENSP00000263932:p.Ala78Ser	Somatic		WXS	Illumina GAIIx	Phase_IV	B1AN79|B9EGD9|D3YTD8|Q6P4D9	Missense_Mutation	SNP	pfam_TNFR/NGFR_Cys_rich_reg,smart_TNFR/NGFR_Cys_rich_reg,pfscan_TNFR/NGFR_Cys_rich_reg,prints_TNFR_8	p.A78S	ENST00000263932.2	37	c.232	CCDS144.1	1	.	.	.	.	.	.	.	.	.	.	.	8.213	0.800685	0.16397	.	.	ENSG00000120949	ENST00000263932	D	0.91894	-2.93	4.06	-1.37	0.09056	TNFR/CD27/30/40/95 cysteine-rich region (4);	1.432500	0.04770	N	0.427893	T	0.79347	0.4430	N	0.14661	0.345	0.09310	N	0.999999	B	0.21606	0.058	B	0.18871	0.023	T	0.68265	-0.5454	10	0.07175	T	0.84	-0.2826	0.6233	0.00782	0.3165:0.1687:0.3421:0.1727	.	78	P28908	TNR8_HUMAN	S	78	ENSP00000263932:A78S	ENSP00000263932:A78S	A	+	1	0	TNFRSF8	12079825	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.391000	0.07323	-0.242000	0.09667	0.655000	0.94253	GCC	TNFRSF8	-	pfam_TNFR/NGFR_Cys_rich_reg,smart_TNFR/NGFR_Cys_rich_reg,pfscan_TNFR/NGFR_Cys_rich_reg	ENSG00000120949		0.577	TNFRSF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TNFRSF8	HGNC	protein_coding	OTTHUMT00000005130.1	115	0.00	0	G			12157238	12157238	+1	no_errors	ENST00000263932	ensembl	human	known	69_37n	missense	95	32.87	47	SNP	0.000	T
XRCC6BP1	91419	genome.wustl.edu	37	12	58339430	58339430	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AN-A0XS-01A-22D-A10G-09	TCGA-AN-A0XS-10A-01D-A10G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f1b5268d-556f-404f-a956-770df4a1e7aa	3a722354-b991-44cf-9ab8-f276b4a38701	g.chr12:58339430delG	ENST00000300145.3	+	2	332	c.207delG	c.(205-207)ctgfs	p.L70fs		NM_033276.2	NP_150592.1	Q9Y6H3	ATP23_HUMAN	XRCC6 binding protein 1	70					double-strand break repair via nonhomologous end joining (GO:0006303)|protein phosphorylation (GO:0006468)	DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)	DNA-dependent protein kinase activity (GO:0004677)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)	p.D71fs*3(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)	11						TCAAACTTCTGCTTGATGCTA	0.343																																						dbGAP											1	Deletion - Frameshift(1)	breast(1)											163.0	152.0	156.0					12																	58339430		1853	4094	5947	-	-	-	SO:0001589	frameshift_variant	0			AF078164	CCDS41802.1	12q14.1	2006-01-09				ENSG00000166896			29452	protein-coding gene	gene with protein product	"""Ku70 binding protein 3"""					10219089	Standard	XM_005269223		Approved	KUB3	uc001sqp.3	Q9Y6H3	OTTHUMG00000170493	ENST00000300145.3:c.207delG	12.37:g.58339430delG	ENSP00000300145:p.Leu70fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q1RLM4|Q96E81	Frame_Shift_Del	DEL	pfam_Peptidase_M76_ATP23	p.D71fs	ENST00000300145.3	37	c.207	CCDS41802.1	12																																																																																			XRCC6BP1	-	pfam_Peptidase_M76_ATP23	ENSG00000166896		0.343	XRCC6BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	XRCC6BP1	HGNC	protein_coding	OTTHUMT00000409390.1	266	0.00	0	G	NM_033276		58339430	58339430	+1	no_errors	ENST00000300145	ensembl	human	known	69_37n	frame_shift_del	231	27.22	89	DEL	0.001	-
XRCC6BP1	91419	genome.wustl.edu	37	12	58339432	58339432	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AN-A0XS-01A-22D-A10G-09	TCGA-AN-A0XS-10A-01D-A10G-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f1b5268d-556f-404f-a956-770df4a1e7aa	3a722354-b991-44cf-9ab8-f276b4a38701	g.chr12:58339432delT	ENST00000300145.3	+	2	334	c.209delT	c.(208-210)cttfs	p.L70fs		NM_033276.2	NP_150592.1	Q9Y6H3	ATP23_HUMAN	XRCC6 binding protein 1	70					double-strand break repair via nonhomologous end joining (GO:0006303)|protein phosphorylation (GO:0006468)	DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)	DNA-dependent protein kinase activity (GO:0004677)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)	p.D71fs*3(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)	11						AAACTTCTGCTTGATGCTATG	0.338																																						dbGAP											1	Deletion - Frameshift(1)	breast(1)											166.0	154.0	158.0					12																	58339432		1852	4093	5945	-	-	-	SO:0001589	frameshift_variant	0			AF078164	CCDS41802.1	12q14.1	2006-01-09				ENSG00000166896			29452	protein-coding gene	gene with protein product	"""Ku70 binding protein 3"""					10219089	Standard	XM_005269223		Approved	KUB3	uc001sqp.3	Q9Y6H3	OTTHUMG00000170493	ENST00000300145.3:c.209delT	12.37:g.58339432delT	ENSP00000300145:p.Leu70fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q1RLM4|Q96E81	Frame_Shift_Del	DEL	pfam_Peptidase_M76_ATP23	p.D71fs	ENST00000300145.3	37	c.209	CCDS41802.1	12																																																																																			XRCC6BP1	-	pfam_Peptidase_M76_ATP23	ENSG00000166896		0.338	XRCC6BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	XRCC6BP1	HGNC	protein_coding	OTTHUMT00000409390.1	270	0.00	0	T	NM_033276		58339432	58339432	+1	no_errors	ENST00000300145	ensembl	human	known	69_37n	frame_shift_del	233	27.05	89	DEL	0.993	-
