#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
ASCC2	84164	genome.wustl.edu	37	22	30210708	30210708	+	Missense_Mutation	SNP	T	T	G			TCGA-D8-A1XS-01A-11D-A14K-09	TCGA-D8-A1XS-10A-01D-A14K-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	5d302c04-302e-4040-9429-37cd672e8d53	9b6db1ae-c8eb-4b02-9913-76070077fedf	g.chr22:30210708T>G	ENST00000397771.2	-	8	835	c.658A>C	c.(658-660)Aat>Cat	p.N220H	ASCC2_ENST00000307790.3_Missense_Mutation_p.N220H|ASCC2_ENST00000478812.1_5'UTR|ASCC2_ENST00000542393.1_Missense_Mutation_p.N144H			Q9H1I8	ASCC2_HUMAN	activating signal cointegrator 1 complex subunit 2	220					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					endometrium(3)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(5;0.000103)|Epithelial(10;0.0169)|all cancers(5;0.0259)			GGTGTGGTATTGGCCCCGTCC	0.572																																						dbGAP											0													88.0	73.0	78.0					22																	30210708		2203	4300	6503	-	-	-	SO:0001583	missense	0			AY013289	CCDS13869.1, CCDS56226.1	22q12.1	2004-07-27			ENSG00000100325	ENSG00000100325			24103	protein-coding gene	gene with protein product	"""ASC 1 complex subunit P100"""	614216				12077347, 9847074	Standard	NM_032204		Approved	ASC1p100, FLJ21588, DKFZp586O0223	uc003agr.3	Q9H1I8	OTTHUMG00000067658	ENST00000397771.2:c.658A>C	22.37:g.30210708T>G	ENSP00000380877:p.Asn220His	Somatic		WXS	Illumina GAIIx	Phase_IV	B7Z8E0|F5H6J9|Q4TT54|Q8TAZ0|Q9H711|Q9H9D6	Missense_Mutation	SNP	pfam_CUE,superfamily_UBA-like,smart_CUE,pfscan_CUE	p.N220H	ENST00000397771.2	37	c.658	CCDS13869.1	22	.	.	.	.	.	.	.	.	.	.	T	14.24	2.476163	0.44044	.	.	ENSG00000100325	ENST00000307790;ENST00000397771;ENST00000542393;ENST00000431535	T;T;T;T	0.30182	1.54;1.54;1.54;1.54	5.33	3.2	0.36748	.	0.390200	0.31020	N	0.008417	T	0.18882	0.0453	N	0.14661	0.345	0.09310	N	1	B;B	0.32939	0.221;0.391	B;B	0.40101	0.319;0.155	T	0.26744	-1.0094	10	0.15499	T	0.54	-2.7557	8.2542	0.31746	0.5585:0.0:0.0:0.4415	.	144;220	F5H6J9;Q9H1I8	.;ASCC2_HUMAN	H	220;220;144;220	ENSP00000305502:N220H;ENSP00000380877:N220H;ENSP00000437570:N144H;ENSP00000412382:N220H	ENSP00000305502:N220H	N	-	1	0	ASCC2	28540708	0.788000	0.28762	0.269000	0.24586	0.888000	0.51559	1.105000	0.31086	0.455000	0.26910	0.533000	0.62120	AAT	ASCC2	-	NULL	ENSG00000100325		0.572	ASCC2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	ASCC2	HGNC	protein_coding	OTTHUMT00000322127.1	65	0.00	0	T	NM_032204		30210708	30210708	-1	no_errors	ENST00000307790	ensembl	human	known	69_37n	missense	36	30.77	16	SNP	0.755	G
BEST1	7439	genome.wustl.edu	37	11	61725644	61725644	+	Silent	SNP	C	C	T			TCGA-D8-A1XS-01A-11D-A14K-09	TCGA-D8-A1XS-10A-01D-A14K-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	5d302c04-302e-4040-9429-37cd672e8d53	9b6db1ae-c8eb-4b02-9913-76070077fedf	g.chr11:61725644C>T	ENST00000378043.4	+	7	1384	c.741C>T	c.(739-741)ttC>ttT	p.F247F	BEST1_ENST00000301774.9_Intron|BEST1_ENST00000449131.2_Silent_p.F187F|BEST1_ENST00000378042.3_Silent_p.F187F|BEST1_ENST00000526988.1_Silent_p.F141F|BEST1_ENST00000534553.1_Intron|BEST1_ENST00000435278.2_Intron	NM_004183.3	NP_004174.1	O76090	BEST1_HUMAN	bestrophin 1	247					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|detection of light stimulus involved in visual perception (GO:0050908)|ion transmembrane transport (GO:0034220)|regulation of calcium ion transport (GO:0051924)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	basolateral plasma membrane (GO:0016323)|chloride channel complex (GO:0034707)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(9)|prostate(1)|skin(2)|urinary_tract(2)	25						TGTACAGCTTCTTCCTGACTT	0.592																																						dbGAP											0													171.0	139.0	150.0					11																	61725644		2202	4299	6501	-	-	-	SO:0001819	synonymous_variant	0			AF057170	CCDS31580.1, CCDS44623.1	11q12	2013-02-14	2006-10-18	2006-10-18	ENSG00000167995	ENSG00000167995		"""Ion channels / Chloride channels : Calcium activated : Bestrophins"""	12703	protein-coding gene	gene with protein product	"""Best disease"""	607854	"""vitelliform macular dystrophy 2"""	VMD2		1302019, 17003041	Standard	NM_004183		Approved	BMD, BEST, RP50	uc001nsr.2	O76090	OTTHUMG00000167469	ENST00000378043.4:c.741C>T	11.37:g.61725644C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	A8K0W6|B7Z3J8|B7Z736|O75904|Q53YQ9|Q8IUR9|Q8IZ80	Silent	SNP	pfam_Bestrophin/UPF0187	p.F187	ENST00000378043.4	37	c.561	CCDS31580.1	11																																																																																			BEST1	-	pfam_Bestrophin/UPF0187	ENSG00000167995		0.592	BEST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	BEST1	HGNC	protein_coding	OTTHUMT00000394715.1	89	0.00	0	C	NM_004183		61725644	61725644	+1	no_errors	ENST00000449131	ensembl	human	known	69_37n	silent	57	21.92	16	SNP	1.000	T
C5orf52	100190949	genome.wustl.edu	37	5	157098676	157098676	+	Silent	SNP	C	C	A			TCGA-D8-A1XS-01A-11D-A14K-09	TCGA-D8-A1XS-10A-01D-A14K-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	5d302c04-302e-4040-9429-37cd672e8d53	9b6db1ae-c8eb-4b02-9913-76070077fedf	g.chr5:157098676C>A	ENST00000409999.3	+	1	116	c.54C>A	c.(52-54)atC>atA	p.I18I	SOX30_ENST00000519442.1_5'Flank	NM_001145132.1	NP_001138604.1	A6NGY3	CE052_HUMAN	chromosome 5 open reading frame 52	18										endometrium(2)|lung(1)	3						CCTCCACGATCGGCGGGACCG	0.647																																						dbGAP											0													10.0	18.0	15.0					5																	157098676		688	1580	2268	-	-	-	SO:0001819	synonymous_variant	0			BG721329	CCDS47329.1	5q33.3	2012-02-24			ENSG00000187658	ENSG00000187658			35121	protein-coding gene	gene with protein product							Standard	NM_001145132		Approved		uc011ddt.2	A6NGY3	OTTHUMG00000154518	ENST00000409999.3:c.54C>A	5.37:g.157098676C>A		Somatic		WXS	Illumina GAIIx	Phase_IV		Silent	SNP	NULL	p.I18	ENST00000409999.3	37	c.54	CCDS47329.1	5																																																																																			C5orf52	-	NULL	ENSG00000187658		0.647	C5orf52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	C5orf52	HGNC	protein_coding	OTTHUMT00000335664.1	12	0.00	0	C	NM_001145132		157098676	157098676	+1	no_errors	ENST00000409999	ensembl	human	known	69_37n	silent	3	66.67	6	SNP	0.000	A
CBFB	865	genome.wustl.edu	37	16	67116170	67116170	+	Frame_Shift_Del	DEL	G	G	-			TCGA-D8-A1XS-01A-11D-A14K-09	TCGA-D8-A1XS-10A-01D-A14K-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	5d302c04-302e-4040-9429-37cd672e8d53	9b6db1ae-c8eb-4b02-9913-76070077fedf	g.chr16:67116170delG	ENST00000290858.6	+	5	715	c.454delG	c.(454-456)gaafs	p.E152fs	CBFB_ENST00000412916.2_Frame_Shift_Del_p.E152fs|CBFB_ENST00000561924.2_Frame_Shift_Del_p.E52fs	NM_001755.2|NM_022845.2	NP_001746.1|NP_074036.1	Q13951	PEBB_HUMAN	core-binding factor, beta subunit	152					cell maturation (GO:0048469)|definitive hemopoiesis (GO:0060216)|lymphocyte differentiation (GO:0030098)|myeloid cell differentiation (GO:0030099)|osteoblast differentiation (GO:0001649)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)	p.E152K(3)|p.E152*(2)		breast(3)|large_intestine(1)	4		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00189)|Epithelial(162;0.00755)|all cancers(182;0.066)		AAGGACACGCGAATTTGAAGA	0.438			T	MYH11	AML																																	dbGAP		Dom	yes		16	16q22	865	"""core-binding factor, beta subunit"""		L	5	Substitution - Missense(3)|Substitution - Nonsense(2)	large_intestine(3)|breast(2)											101.0	93.0	96.0					16																	67116170		2200	4300	6500	-	-	-	SO:0001589	frameshift_variant	0			BC018509	CCDS10827.1, CCDS45508.1	16q22.1	2008-02-05			ENSG00000067955	ENSG00000067955			1539	protein-coding gene	gene with protein product		121360				8351518, 7587111	Standard	NM_001755		Approved	PEBP2B	uc002erb.3	Q13951	OTTHUMG00000137520	ENST00000290858.6:c.454delG	16.37:g.67116170delG	ENSP00000290858:p.Glu152fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K347|Q13124|Q9HCT2	Frame_Shift_Del	DEL	pfam_CBF_beta,superfamily_CBF_beta	p.E152fs	ENST00000290858.6	37	c.454	CCDS10827.1	16																																																																																			CBFB	-	pfam_CBF_beta	ENSG00000067955		0.438	CBFB-001	KNOWN	basic|CCDS	protein_coding	CBFB	HGNC	protein_coding	OTTHUMT00000268843.2	60	0.00	0	G	NM_001755		67116170	67116170	+1	no_errors	ENST00000290858	ensembl	human	known	69_37n	frame_shift_del	16	50.00	17	DEL	1.000	-
COL15A1	1306	genome.wustl.edu	37	9	101767249	101767249	+	Missense_Mutation	SNP	G	G	T			TCGA-D8-A1XS-01A-11D-A14K-09	TCGA-D8-A1XS-10A-01D-A14K-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	5d302c04-302e-4040-9429-37cd672e8d53	9b6db1ae-c8eb-4b02-9913-76070077fedf	g.chr9:101767249G>T	ENST00000375001.3	+	9	1693	c.1270G>T	c.(1270-1272)Ggg>Tgg	p.G424W		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	424	4 X tandem repeats.|Nonhelical region 1 (NC1).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|signal transduction (GO:0007165)	collagen type XV trimer (GO:0005582)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(20)|liver(1)|lung(42)|ovary(6)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	107		Acute lymphoblastic leukemia(62;0.0562)				CAGCATGCCTGGGGAAGTGGA	0.612																																						dbGAP											0													81.0	78.0	79.0					9																	101767249		2203	4300	6503	-	-	-	SO:0001583	missense	0			L25286	CCDS35081.1	9q21-q22	2013-01-16			ENSG00000204291	ENSG00000204291		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2192	protein-coding gene	gene with protein product	"""collagen type XV proteoglycan"""	120325				1427836	Standard	NM_001855		Approved		uc004azb.2	P39059	OTTHUMG00000020351	ENST00000375001.3:c.1270G>T	9.37:g.101767249G>T	ENSP00000364140:p.Gly424Trp	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5T6J4|Q9UDC5|Q9Y4W4	Missense_Mutation	SNP	pfam_Collagenase_NC10/endostatin,pfam_Collagen,superfamily_C-type_lectin_fold,superfamily_ConA-like_lec_gl,smart_Laminin_G	p.G424W	ENST00000375001.3	37	c.1270	CCDS35081.1	9	.	.	.	.	.	.	.	.	.	.	g	7.397	0.632024	0.14322	.	.	ENSG00000204291	ENST00000375001;ENST00000536083	D	0.89617	-2.54	3.21	-2.15	0.07102	.	14.645300	0.00166	N	0.000000	D	0.85031	0.5604	L	0.27053	0.805	0.09310	N	1	D	0.55172	0.97	P	0.50049	0.629	T	0.73770	-0.3878	10	0.59425	D	0.04	5.8175	3.8583	0.08985	0.2882:0.0:0.4283:0.2835	.	424	P39059	COFA1_HUMAN	W	424;394	ENSP00000364140:G424W	ENSP00000364140:G424W	G	+	1	0	COL15A1	100807070	0.001000	0.12720	0.000000	0.03702	0.022000	0.10575	-0.555000	0.05999	-0.899000	0.03901	-1.611000	0.00801	GGG	COL15A1	-	NULL	ENSG00000204291		0.612	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	COL15A1	HGNC	protein_coding	OTTHUMT00000053386.3	34	0.00	0	G	NM_001855		101767249	101767249	+1	no_errors	ENST00000375001	ensembl	human	known	69_37n	missense	26	13.33	4	SNP	0.000	T
FCGBP	8857	genome.wustl.edu	37	19	40383905	40383905	+	Silent	SNP	G	G	A	rs145218790		TCGA-D8-A1XS-01A-11D-A14K-09	TCGA-D8-A1XS-10A-01D-A14K-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	5d302c04-302e-4040-9429-37cd672e8d53	9b6db1ae-c8eb-4b02-9913-76070077fedf	g.chr19:40383905G>A	ENST00000221347.6	-	21	9712	c.9705C>T	c.(9703-9705)tgC>tgT	p.C3235C		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	3235						extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			CCCCAGGCCCGCAGCGACACC	0.677																																						dbGAP											0													1.0	1.0	1.0					19																	40383905		234	700	934	-	-	-	SO:0001819	synonymous_variant	0			D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.9705C>T	19.37:g.40383905G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	O95784	Silent	SNP	pfam_VWF_type-D,pfam_Unchr_dom_Cys-rich,pfam_TIL_dom,superfamily_TIL_dom,smart_Fol_N,smart_VWF_type-D,smart_Unchr_dom_Cys-rich,smart_EGF-like,smart_VWF_C,smart_VWC_out	p.C3235	ENST00000221347.6	37	c.9705	CCDS12546.1	19																																																																																			FCGBP	-	smart_VWC_out	ENSG00000090920		0.677	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FCGBP	HGNC	protein_coding	OTTHUMT00000462507.1	12	0.00	0	G	NM_003890		40383905	40383905	-1	no_errors	ENST00000221347	ensembl	human	known	69_37n	silent	12	36.84	7	SNP	0.488	A
GOLGA2	2801	genome.wustl.edu	37	9	131024001	131024001	+	Silent	SNP	C	C	T			TCGA-D8-A1XS-01A-11D-A14K-09	TCGA-D8-A1XS-10A-01D-A14K-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	5d302c04-302e-4040-9429-37cd672e8d53	9b6db1ae-c8eb-4b02-9913-76070077fedf	g.chr9:131024001C>T	ENST00000421699.2	-	14	1101	c.1089G>A	c.(1087-1089)caG>caA	p.Q363Q	GOLGA2_ENST00000609374.1_Silent_p.Q351Q	NM_004486.4	NP_004477.3	Q08379	GOGA2_HUMAN	golgin A2	363					mitotic cell cycle (GO:0000278)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)				NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	34						GCTGTAACTGCTGGTTAGCAT	0.572																																						dbGAP											0													53.0	54.0	54.0					9																	131024001		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			L06147	CCDS6896.2	9q34.13	2010-06-28	2010-02-12		ENSG00000167110	ENSG00000167110			4425	protein-coding gene	gene with protein product	"""Golgi matrix protein GM130"", ""SY11 protein"""	602580	"""golgi autoantigen, golgin subfamily a, 2"""			8315394	Standard	NM_004486		Approved	GM130, golgin-95	uc011maw.2	Q08379	OTTHUMG00000020732	ENST00000421699.2:c.1089G>A	9.37:g.131024001C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q6GRM9|Q9BRB0|Q9NYF9	Silent	SNP	superfamily_CofA_tubulin-bd	p.Q363	ENST00000421699.2	37	c.1089	CCDS6896.2	9																																																																																			GOLGA2	-	superfamily_CofA_tubulin-bd	ENSG00000167110		0.572	GOLGA2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	GOLGA2	HGNC	protein_coding	OTTHUMT00000054358.2	46	0.00	0	C	NM_004486		131024001	131024001	-1	no_errors	ENST00000421699	ensembl	human	known	69_37n	silent	24	41.46	17	SNP	1.000	T
HMGXB4	10042	genome.wustl.edu	37	22	35661544	35661544	+	Frame_Shift_Del	DEL	A	A	-	rs76572304		TCGA-D8-A1XS-01A-11D-A14K-09	TCGA-D8-A1XS-10A-01D-A14K-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	5d302c04-302e-4040-9429-37cd672e8d53	9b6db1ae-c8eb-4b02-9913-76070077fedf	g.chr22:35661544delA	ENST00000216106.5	+	5	1291	c.1163delA	c.(1162-1164)gaafs	p.E388fs	HMGXB4_ENST00000444518.2_Frame_Shift_Del_p.E279fs	NM_001003681.2	NP_001003681.1	Q9UGU5	HMGX4_HUMAN	HMG box domain containing 4	388					endosome to lysosome transport (GO:0008333)|negative regulation of Wnt signaling pathway (GO:0030178)|Wnt signaling pathway (GO:0016055)	NURF complex (GO:0016589)	DNA binding (GO:0003677)			breast(1)|endometrium(1)|large_intestine(6)|liver(1)|lung(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						GGGCATAGTGAaaaaaaaaag	0.493																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AJ010069	CCDS33641.1	22q13	2011-07-01	2009-01-05	2009-01-05	ENSG00000100281	ENSG00000100281		"""High mobility group / Non-canonical"""	5003	protein-coding gene	gene with protein product		604702	"""high-mobility group protein 2-like 1"""	HMG2L1		10329004, 10591208, 20511232	Standard	NM_001003681		Approved	THC211630	uc003anl.3	Q9UGU5	OTTHUMG00000150439	ENST00000216106.5:c.1163delA	22.37:g.35661544delA	ENSP00000216106:p.Glu388fs	Somatic		WXS	Illumina GAIIx	Phase_IV	O75672|O75673|Q9UMT5	Frame_Shift_Del	DEL	pfam_HMG_superfamily,superfamily_HMG_superfamily,smart_HMG_superfamily,pfscan_HMG_superfamily	p.K391fs	ENST00000216106.5	37	c.1163	CCDS33641.1	22																																																																																			HMGXB4	-	superfamily_HMG_superfamily	ENSG00000100281		0.493	HMGXB4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	HMGXB4	HGNC	protein_coding	OTTHUMT00000318104.2	18	0.00	0	A	NM_005487		35661544	35661544	+1	no_errors	ENST00000216106	ensembl	human	known	69_37n	frame_shift_del	17	10.00	2	DEL	1.000	-
IGSF10	285313	genome.wustl.edu	37	3	151163762	151163762	+	Missense_Mutation	SNP	G	G	T			TCGA-D8-A1XS-01A-11D-A14K-09	TCGA-D8-A1XS-10A-01D-A14K-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	5d302c04-302e-4040-9429-37cd672e8d53	9b6db1ae-c8eb-4b02-9913-76070077fedf	g.chr3:151163762G>T	ENST00000282466.3	-	4	4006	c.4007C>A	c.(4006-4008)aCa>aAa	p.T1336K		NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	1336					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			AGATCTCTCTGTTTGGGTTTC	0.433																																						dbGAP											0													313.0	299.0	304.0					3																	151163762		2203	4300	6503	-	-	-	SO:0001583	missense	0			AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"""Immunoglobulin superfamily / I-set domain containing"""	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.4007C>A	3.37:g.151163762G>T	ENSP00000282466:p.Thr1336Lys	Somatic		WXS	Illumina GAIIx	Phase_IV	Q86YJ9|Q8N772|Q8NA84	Missense_Mutation	SNP	pfam_Ig_I-set,pfam_Immunoglobulin,pfam_Ig_V-set,smart_LRR-contain_N,smart_Leu-rich_rpt_typical-subtyp,smart_Cys-rich_flank_reg_C,smart_Ig_sub,smart_Ig_sub2,smart_Ig_V-set_subgr,pfscan_Ig-like	p.T1336K	ENST00000282466.3	37	c.4007	CCDS3160.1	3	.	.	.	.	.	.	.	.	.	.	G	0.090	-1.168237	0.01660	.	.	ENSG00000152580	ENST00000282466	T	0.68331	-0.32	4.62	-1.01	0.10169	.	1.104600	0.07043	N	0.830445	T	0.43033	0.1229	N	0.19112	0.55	0.09310	N	1	B	0.26002	0.139	B	0.19946	0.027	T	0.17471	-1.0368	10	0.22109	T	0.4	.	1.9184	0.03302	0.4011:0.1299:0.3393:0.1297	.	1336	Q6WRI0	IGS10_HUMAN	K	1336	ENSP00000282466:T1336K	ENSP00000282466:T1336K	T	-	2	0	IGSF10	152646452	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.317000	0.08060	-0.163000	0.10946	-0.218000	0.12543	ACA	IGSF10	-	NULL	ENSG00000152580		0.433	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	IGSF10	HGNC	protein_coding	OTTHUMT00000357782.1	101	0.98	1	G	NM_178822		151163762	151163762	-1	no_errors	ENST00000282466	ensembl	human	known	69_37n	missense	55	36.36	32	SNP	0.000	T
IRF8	3394	genome.wustl.edu	37	16	85952387	85952387	+	Silent	SNP	C	C	T			TCGA-D8-A1XS-01A-11D-A14K-09	TCGA-D8-A1XS-10A-01D-A14K-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	5d302c04-302e-4040-9429-37cd672e8d53	9b6db1ae-c8eb-4b02-9913-76070077fedf	g.chr16:85952387C>T	ENST00000268638.5	+	7	1388	c.966C>T	c.(964-966)ttC>ttT	p.F322F	IRF8_ENST00000562492.1_Silent_p.F118F	NM_002163.2	NP_002154.1	Q02556	IRF8_HUMAN	interferon regulatory factor 8	322					cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|myeloid cell differentiation (GO:0030099)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phagocytosis (GO:0006909)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	24		Prostate(104;0.0771)				TCCAGGTCTTCGACACCAGCC	0.607																																						dbGAP											0													37.0	39.0	38.0					16																	85952387		2198	4299	6497	-	-	-	SO:0001819	synonymous_variant	0			M91196	CCDS10956.1	16q24.1	2014-09-17	2004-11-12	2004-11-12	ENSG00000140968	ENSG00000140968			5358	protein-coding gene	gene with protein product		601565	"""interferon consensus sequence binding protein 1"""	ICSBP1		1460054, 11997525	Standard	NM_002163		Approved	IRF-8, ICSBP	uc002fjh.3	Q02556	OTTHUMG00000137648	ENST00000268638.5:c.966C>T	16.37:g.85952387C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	A0AV82	Silent	SNP	pfam_Interferon_reg_factor-3,pfam_Interferon_reg_fact_DNA-bd_dom,superfamily_SMAD_FHA_domain,smart_Interferon_reg_fact_DNA-bd_dom,prints_Interferon_reg_fact_DNA-bd_dom	p.F322	ENST00000268638.5	37	c.966	CCDS10956.1	16																																																																																			IRF8	-	pfam_Interferon_reg_factor-3,superfamily_SMAD_FHA_domain	ENSG00000140968		0.607	IRF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	IRF8	HGNC	protein_coding	OTTHUMT00000269100.2	24	0.00	0	C	NM_002163		85952387	85952387	+1	no_errors	ENST00000268638	ensembl	human	known	69_37n	silent	3	72.73	8	SNP	0.990	T
MYLIP	29116	genome.wustl.edu	37	6	16145378	16145378	+	Missense_Mutation	SNP	T	T	A			TCGA-D8-A1XS-01A-11D-A14K-09	TCGA-D8-A1XS-10A-01D-A14K-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	5d302c04-302e-4040-9429-37cd672e8d53	9b6db1ae-c8eb-4b02-9913-76070077fedf	g.chr6:16145378T>A	ENST00000356840.3	+	6	1276	c.1078T>A	c.(1078-1080)Tgc>Agc	p.C360S	MYLIP_ENST00000349606.4_Missense_Mutation_p.C179S	NM_013262.3	NP_037394.2	Q8WY64	MYLIP_HUMAN	myosin regulatory light chain interacting protein	360					cellular component movement (GO:0006928)|cholesterol homeostasis (GO:0042632)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|nervous system development (GO:0007399)|positive regulation of protein catabolic process (GO:0045732)|protein destabilization (GO:0031648)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of low-density lipoprotein particle receptor catabolic process (GO:0032803)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	cytoskeletal protein binding (GO:0008092)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28	Breast(50;0.0799)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.241)			CAGCATGAACTGCAGCAGCTG	0.582																																						dbGAP											0													75.0	77.0	77.0					6																	16145378		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF187016	CCDS4536.1	6p23-p22.3	2011-11-17			ENSG00000007944	ENSG00000007944			21155	protein-coding gene	gene with protein product	"""E3 ubiquitin ligase-inducible degrader of the low density lipoprotein receptor"""	610082				10593918, 11162443, 19688294	Standard	NM_013262		Approved	MIR, IDOL	uc003nbq.3	Q8WY64	OTTHUMG00000016405	ENST00000356840.3:c.1078T>A	6.37:g.16145378T>A	ENSP00000349298:p.Cys360Ser	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5TIA4|Q9BU73|Q9NRL9|Q9UHE7	Missense_Mutation	SNP	pfam_FERM_N,pfam_FERM_central,superfamily_FERM_central,smart_Band_41_domain,pfscan_FERM_domain,pfscan_Znf_RING,prints_Band_41_fam,prints_Ez/rad/moesin	p.C360S	ENST00000356840.3	37	c.1078	CCDS4536.1	6	.	.	.	.	.	.	.	.	.	.	T	14.84	2.654629	0.47467	.	.	ENSG00000007944	ENST00000356840;ENST00000349606	T;T	0.80304	-1.36;1.36	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.60353	0.2262	L	0.50333	1.59	0.58432	D	0.999999	P	0.34662	0.462	B	0.28553	0.091	T	0.65146	-0.6239	10	0.08599	T	0.76	.	16.5764	0.84681	0.0:0.0:0.0:1.0	.	360	Q8WY64	MYLIP_HUMAN	S	360;179	ENSP00000349298:C360S;ENSP00000008686:C179S	ENSP00000008686:C179S	C	+	1	0	MYLIP	16253357	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	7.405000	0.80007	2.371000	0.80710	0.533000	0.62120	TGC	MYLIP	-	NULL	ENSG00000007944		0.582	MYLIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MYLIP	HGNC	protein_coding	OTTHUMT00000043864.1	37	0.00	0	T	NM_013262		16145378	16145378	+1	no_errors	ENST00000356840	ensembl	human	known	69_37n	missense	22	26.67	8	SNP	1.000	A
NLRC3	197358	genome.wustl.edu	37	16	3598192	3598192	+	RNA	DEL	C	C	-			TCGA-D8-A1XS-01A-11D-A14K-09	TCGA-D8-A1XS-10A-01D-A14K-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	5d302c04-302e-4040-9429-37cd672e8d53	9b6db1ae-c8eb-4b02-9913-76070077fedf	g.chr16:3598192delC	ENST00000301749.7	-	0	3119				LA16c-390H2.4_ENST00000573820.1_RNA|NLRC3_ENST00000448023.2_RNA|NLRC3_ENST00000419350.2_RNA|NLRC3_ENST00000359128.5_RNA|NLRC3_ENST00000603507.1_RNA	NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN	NLR family, CARD domain containing 3						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of protein ubiquitination (GO:0031396)|response to lipopolysaccharide (GO:0032496)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						CTGGGCAGCGCCGGCCTGGAT	0.612																																						dbGAP											0													27.0	31.0	29.0					16																	3598192		1978	4148	6126	-	-	-			0			BK001112	CCDS73817.1	16p13.3	2014-03-25			ENSG00000167984	ENSG00000167984		"""Nucleotide-binding domain and leucine rich repeat containing"""	29889	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3"", ""NOD-like receptor C3"""	615648				15705585, 12766759	Standard	NM_178844		Approved	CLR16.2, FLJ00348, NOD3	uc010btn.3	Q7RTR2	OTTHUMG00000177561		16.37:g.3598192delC		Somatic		WXS	Illumina GAIIx	Phase_IV	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Frame_Shift_Del	DEL	smart_Leu-rich_rpt_RNase_inh_sub-typ,pfscan_NACHT_NTPase	p.G951fs	ENST00000301749.7	37	c.2852		16																																																																																			NLRC3	-	smart_Leu-rich_rpt_RNase_inh_sub-typ	ENSG00000167984		0.612	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	NLRC3	HGNC	polymorphic_pseudogene		49	0.00	0	C	NM_178844		3598192	3598192	-1	no_errors	ENST00000448023	ensembl	human	known	69_37n	frame_shift_del	55	24.66	18	DEL	0.023	-
P2RY1	5028	genome.wustl.edu	37	3	152554180	152554180	+	Silent	SNP	C	C	T			TCGA-D8-A1XS-01A-11D-A14K-09	TCGA-D8-A1XS-10A-01D-A14K-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	5d302c04-302e-4040-9429-37cd672e8d53	9b6db1ae-c8eb-4b02-9913-76070077fedf	g.chr3:152554180C>T	ENST00000305097.3	+	1	1445	c.609C>T	c.(607-609)taC>taT	p.Y203Y	RP11-38P22.2_ENST00000460407.1_lincRNA	NM_002563.3	NP_002554.1	P47900	P2RY1_HUMAN	purinergic receptor P2Y, G-protein coupled, 1	203					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|aging (GO:0007568)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cell surface receptor signaling pathway (GO:0007166)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of binding (GO:0051100)|negative regulation of norepinephrine secretion (GO:0010700)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of hormone secretion (GO:0046887)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of ion transport (GO:0043270)|positive regulation of penile erection (GO:0060406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to plasma membrane (GO:0072659)|regulation of receptor activity (GO:0010469)|regulation of vasodilation (GO:0042312)|relaxation of muscle (GO:0090075)|response to growth factor (GO:0070848)|response to mechanical stimulus (GO:0009612)|sensory perception of pain (GO:0019233)|signal transduction involved in regulation of gene expression (GO:0023019)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell body (GO:0044297)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ADP binding (GO:0043531)|ADP-activated nucleotide receptor activity (GO:0045032)|ATP binding (GO:0005524)|ATP-activated nucleotide receptor activity (GO:0045031)|G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|receptor activity (GO:0004872)|scaffold protein binding (GO:0097110)			breast(1)|endometrium(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)	23			LUSC - Lung squamous cell carcinoma(72;0.0628)|Lung(72;0.11)			TCACCTGTTACGACACCACCT	0.537																																						dbGAP											0													178.0	160.0	167.0					3																	152554180		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			U42029	CCDS3169.1	3q25.2	2012-08-08			ENSG00000169860	ENSG00000169860		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	8539	protein-coding gene	gene with protein product		601167				8579591	Standard	NM_002563		Approved	P2Y1	uc003ezq.3	P47900	OTTHUMG00000159694	ENST00000305097.3:c.609C>T	3.37:g.152554180C>T		Somatic		WXS	Illumina GAIIx	Phase_IV		Silent	SNP	pfam_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam,prints_P2Y_purnocptor,prints_7TM_GPCR_Rhodpsn,prints_P2_purnocptor	p.Y203	ENST00000305097.3	37	c.609	CCDS3169.1	3																																																																																			P2RY1	-	pfam_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam	ENSG00000169860		0.537	P2RY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	P2RY1	HGNC	protein_coding	OTTHUMT00000356943.1	111	0.00	0	C	NM_002563		152554180	152554180	+1	no_errors	ENST00000305097	ensembl	human	known	69_37n	silent	60	40.00	40	SNP	0.467	T
PIK3CA	5290	genome.wustl.edu	37	3	178936091	178936091	+	Missense_Mutation	SNP	G	G	A	rs104886003		TCGA-D8-A1XS-01A-11D-A14K-09	TCGA-D8-A1XS-10A-01D-A14K-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	5d302c04-302e-4040-9429-37cd672e8d53	9b6db1ae-c8eb-4b02-9913-76070077fedf	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	48	0.00	0	G			178936091	178936091	+1	no_errors	ENST00000263967	ensembl	human	known	69_37n	missense	27	46.00	23	SNP	1.000	A
PLEKHA2	59339	genome.wustl.edu	37	8	38775523	38775523	+	Silent	SNP	C	C	T			TCGA-D8-A1XS-01A-11D-A14K-09	TCGA-D8-A1XS-10A-01D-A14K-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	5d302c04-302e-4040-9429-37cd672e8d53	9b6db1ae-c8eb-4b02-9913-76070077fedf	g.chr8:38775523C>T	ENST00000521746.1	+	2	310	c.76C>T	c.(76-78)Ctg>Ttg	p.L26L	PLEKHA2_ENST00000388745.4_3'UTR|PLEKHA2_ENST00000420274.1_Silent_p.L26L			Q9HB19	PKHA2_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 2	26	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				positive regulation of cell-matrix adhesion (GO:0001954)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	fibronectin binding (GO:0001968)|laminin binding (GO:0043236)|lipid binding (GO:0008289)			breast(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	13		all_lung(54;0.0413)|Lung NSC(58;0.115)|Hepatocellular(245;0.152)	LUSC - Lung squamous cell carcinoma(45;4.68e-08)|COAD - Colon adenocarcinoma(9;0.235)			CGGCAAGTTTCTGCGGAGGTA	0.567																																						dbGAP											0													113.0	116.0	115.0					8																	38775523		2060	4218	6278	-	-	-	SO:0001819	synonymous_variant	0			AF286164	CCDS75732.1	8p11.21	2013-01-10	2002-01-14			ENSG00000169499		"""Pleckstrin homology (PH) domain containing"""	14336	protein-coding gene	gene with protein product	"""tandem PH Domain containing protein-2"""	607773	"""pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 2"""			11001876	Standard	NM_021623		Approved	TAPP2	uc003xmi.4	Q9HB19		ENST00000521746.1:c.76C>T	8.37:g.38775523C>T		Somatic		WXS	Illumina GAIIx	Phase_IV		Silent	SNP	pfam_Pleckstrin_homology,smart_Pleckstrin_homology,pfscan_Pleckstrin_homology	p.L26	ENST00000521746.1	37	c.76		8																																																																																			PLEKHA2	-	pfam_Pleckstrin_homology,smart_Pleckstrin_homology,pfscan_Pleckstrin_homology	ENSG00000169499		0.567	PLEKHA2-002	PUTATIVE	basic	protein_coding	PLEKHA2	HGNC	protein_coding	OTTHUMT00000377068.1	86	0.00	0	C	NM_021623		38775523	38775523	+1	no_errors	ENST00000420274	ensembl	human	known	69_37n	silent	68	36.45	39	SNP	1.000	T
PM20D1	148811	genome.wustl.edu	37	1	205813220	205813220	+	Silent	SNP	G	G	A			TCGA-D8-A1XS-01A-11D-A14K-09	TCGA-D8-A1XS-10A-01D-A14K-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	5d302c04-302e-4040-9429-37cd672e8d53	9b6db1ae-c8eb-4b02-9913-76070077fedf	g.chr1:205813220G>A	ENST00000367136.4	-	5	746	c.702C>T	c.(700-702)atC>atT	p.I234I	PM20D1_ENST00000460624.1_5'UTR	NM_152491.4	NP_689704.4	Q6GTS8	P20D1_HUMAN	peptidase M20 domain containing 1	234					negative regulation of neuron death (GO:1901215)|regulation of defense response to virus by host (GO:0050691)|regulation of viral process (GO:0050792)	extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|peptidase activity (GO:0008233)			breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)	28	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0252)			CTCACAAGGCGATGGGCTTCT	0.532																																						dbGAP											0													101.0	99.0	99.0					1																	205813220		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0				CCDS1460.1	1q32.1	2008-02-05			ENSG00000162877	ENSG00000162877			26518	protein-coding gene	gene with protein product							Standard	NM_152491		Approved	FLJ32569, Cps1	uc001hdj.3	Q6GTS8	OTTHUMG00000035999	ENST00000367136.4:c.702C>T	1.37:g.205813220G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	Q6P4E3|Q96DM4	Silent	SNP	pfam_Peptidase_M20,pfam_Peptidase_M20_dimer,superfamily_Peptidase_M20_dimer	p.I234	ENST00000367136.4	37	c.702	CCDS1460.1	1																																																																																			PM20D1	-	pfam_Peptidase_M20	ENSG00000162877		0.532	PM20D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PM20D1	HGNC	protein_coding	OTTHUMT00000087736.1	41	0.00	0	G	NM_152491		205813220	205813220	-1	no_errors	ENST00000367136	ensembl	human	known	69_37n	silent	30	46.43	26	SNP	0.994	A
POTEF	728378	genome.wustl.edu	37	2	130832873	130832873	+	Silent	SNP	G	G	A	rs62165872	byFrequency	TCGA-D8-A1XS-01A-11D-A14K-09	TCGA-D8-A1XS-10A-01D-A14K-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	5d302c04-302e-4040-9429-37cd672e8d53	9b6db1ae-c8eb-4b02-9913-76070077fedf	g.chr2:130832873G>A	ENST00000409914.2	-	17	2571	c.2172C>T	c.(2170-2172)gaC>gaT	p.D724D	POTEF_ENST00000357462.5_Silent_p.D724D	NM_001099771.2	NP_001093241.1	A5A3E0	POTEF_HUMAN	POTE ankyrin domain family, member F	724	Actin-like.				retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(28)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	53						GGGGGGCATCGTCGCCCGCAA	0.592													.|||	130	0.0259585	0.0174	0.0331	5008	,	,		19488	0.0139		0.0437	False		,,,				2504	0.0266					dbGAP											0																																										-	-	-	SO:0001819	synonymous_variant	0			EF523384	CCDS46409.1	2q21.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000196604	ENSG00000196604		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33905	protein-coding gene	gene with protein product			"""ANKRD26-like family C, member 1B"""	A26C1B		17101985	Standard	NM_001099771		Approved	POTEACTIN, POTE2alpha	uc010fmh.2	A5A3E0	OTTHUMG00000153628	ENST00000409914.2:c.2172C>T	2.37:g.130832873G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	A6NC34	Silent	SNP	pfam_Actin-like,pfam_Ankyrin_rpt,superfamily_Ankyrin_rpt-contain_dom,smart_Ankyrin_rpt,smart_Actin-like,prints_Actin-like,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom	p.D724	ENST00000409914.2	37	c.2172	CCDS46409.1	2																																																																																			POTEF	-	pfam_Actin-like,smart_Actin-like	ENSG00000196604		0.592	POTEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	POTEF	HGNC	protein_coding	OTTHUMT00000331889.2	35	0.00	0	G	NM_001099771		130832873	130832873	-1	no_errors	ENST00000357462	ensembl	human	known	69_37n	silent	44	13.73	7	SNP	1.000	A
RIF1	55183	genome.wustl.edu	37	2	152320011	152320011	+	Missense_Mutation	SNP	A	A	G			TCGA-D8-A1XS-01A-11D-A14K-09	TCGA-D8-A1XS-10A-01D-A14K-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	5d302c04-302e-4040-9429-37cd672e8d53	9b6db1ae-c8eb-4b02-9913-76070077fedf	g.chr2:152320011A>G	ENST00000243326.5	+	29	4460	c.3977A>G	c.(3976-3978)aAt>aGt	p.N1326S	RIF1_ENST00000444746.2_Missense_Mutation_p.N1326S|RIF1_ENST00000430328.2_Missense_Mutation_p.N1326S|RIF1_ENST00000453091.2_Missense_Mutation_p.N1326S|RIF1_ENST00000428287.2_Missense_Mutation_p.N1326S			Q9Y581	INSL6_HUMAN	replication timing regulatory factor 1	0					fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			NS(2)|breast(8)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(19)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	97				BRCA - Breast invasive adenocarcinoma(221;0.0429)		GTCTTAGAAAATAACCCACCT	0.378																																						dbGAP											0													73.0	80.0	77.0					2																	152320011		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK022932	CCDS2194.1, CCDS54406.1	2q23.3	2014-06-02	2014-06-02		ENSG00000080345	ENSG00000080345			23207	protein-coding gene	gene with protein product		608952	"""RAP1 interacting factor homolog (yeast)"""			15342490, 15042697, 22850674	Standard	NM_018151		Approved	FLJ12870, FLJ10599	uc002txm.3	Q5UIP0	OTTHUMG00000131886	ENST00000243326.5:c.3977A>G	2.37:g.152320011A>G	ENSP00000243326:p.Asn1326Ser	Somatic		WXS	Illumina GAIIx	Phase_IV	A0AVS0|Q9NS16	Missense_Mutation	SNP	pfam_Rif1_N,superfamily_ARM-type_fold	p.N1326S	ENST00000243326.5	37	c.3977	CCDS2194.1	2	.	.	.	.	.	.	.	.	.	.	A	13.82	2.349799	0.41599	.	.	ENSG00000080345	ENST00000444746;ENST00000453091;ENST00000428287;ENST00000243326;ENST00000430328	T;T;T;T;T	0.12984	2.63;2.63;2.63;2.63;2.63	4.92	3.73	0.42828	.	0.744850	0.13264	N	0.401041	T	0.29028	0.0721	M	0.66939	2.045	0.80722	D	1	D;D	0.62365	0.991;0.99	P;P	0.58660	0.815;0.843	T	0.00948	-1.1504	10	0.33141	T	0.24	-10.6049	11.4851	0.50348	0.8494:0.1506:0.0:0.0	.	1326;1326	Q5UIP0;Q5UIP0-2	RIF1_HUMAN;.	S	1326	ENSP00000390181:N1326S;ENSP00000414615:N1326S;ENSP00000415691:N1326S;ENSP00000243326:N1326S;ENSP00000416123:N1326S	ENSP00000243326:N1326S	N	+	2	0	RIF1	152028257	0.999000	0.42202	0.997000	0.53966	0.432000	0.31715	0.842000	0.27627	0.868000	0.35678	0.455000	0.32223	AAT	RIF1	-	NULL	ENSG00000080345		0.378	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	RIF1	HGNC	protein_coding	OTTHUMT00000254836.3	41	0.00	0	A			152320011	152320011	+1	no_errors	ENST00000243326	ensembl	human	known	69_37n	missense	48	25.00	16	SNP	1.000	G
RRM1	6240	genome.wustl.edu	37	11	4127418	4127418	+	Missense_Mutation	SNP	C	C	G			TCGA-D8-A1XS-01A-11D-A14K-09	TCGA-D8-A1XS-10A-01D-A14K-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	5d302c04-302e-4040-9429-37cd672e8d53	9b6db1ae-c8eb-4b02-9913-76070077fedf	g.chr11:4127418C>G	ENST00000300738.5	+	3	455	c.251C>G	c.(250-252)tCt>tGt	p.S84C	RRM1_ENST00000423050.2_Intron	NM_001033.3	NP_001024.1	P23921	RIR1_HUMAN	ribonucleotide reductase M1	84	ATP-cone. {ECO:0000255|PROSITE- ProRule:PRU00492}.				cell proliferation in forebrain (GO:0021846)|deoxyribonucleotide biosynthetic process (GO:0009263)|DNA replication (GO:0006260)|male gonad development (GO:0008584)|mitotic cell cycle (GO:0000278)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein heterotetramerization (GO:0051290)|pyrimidine nucleobase metabolic process (GO:0006206)|response to ionizing radiation (GO:0010212)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor (GO:0004748)			breast(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(7)|skin(2)	14		Medulloblastoma(188;0.0025)|Breast(177;0.00502)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0848)|LUSC - Lung squamous cell carcinoma(625;0.205)	Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Hydroxyurea(DB01005)	ATCGCTGTCTCTAACTTGCAC	0.418																																					NSCLC(45;1345 1376 6258 22925)|Ovarian(34;894 1053 6175 12768)	dbGAP											0													67.0	58.0	61.0					11																	4127418		2201	4298	6499	-	-	-	SO:0001583	missense	0			X59543	CCDS7750.1	11p15.5	2009-07-10	2008-03-11		ENSG00000167325	ENSG00000167325	1.17.14.1		10451	protein-coding gene	gene with protein product		180410	"""ribonucleotide reductase M1 polypeptide"""			7557993	Standard	NM_001033		Approved		uc001lyw.4	P23921	OTTHUMG00000133361	ENST00000300738.5:c.251C>G	11.37:g.4127418C>G	ENSP00000300738:p.Ser84Cys	Somatic		WXS	Illumina GAIIx	Phase_IV	Q9UNN2	Missense_Mutation	SNP	pfam_Ribncl_red_lg_C,pfam_Ribncl_Rdtase_lsu_N,pfam_ATP-cone,superfamily_Ribnucl_Rdtase_R1-su_N,pfscan_ATP-cone,prints_Ribncl_red_lg_C,tigrfam_NrdE_NrdA	p.S84C	ENST00000300738.5	37	c.251	CCDS7750.1	11	.	.	.	.	.	.	.	.	.	.	C	28.2	4.901802	0.92035	.	.	ENSG00000167325	ENST00000300738	T	0.34072	1.38	5.77	5.77	0.91146	Ribonucleotide reductase R1 subunit, N-terminal (1);ATP-cone (2);	0.000000	0.85682	D	0.000000	T	0.69504	0.3118	H	0.96576	3.845	0.80722	D	1	D	0.61080	0.989	P	0.55545	0.778	T	0.80430	-0.1386	10	0.87932	D	0	-14.4808	18.9257	0.92544	0.0:1.0:0.0:0.0	.	84	P23921	RIR1_HUMAN	C	84	ENSP00000300738:S84C	ENSP00000300738:S84C	S	+	2	0	RRM1	4083994	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.385000	0.79763	2.885000	0.99019	0.655000	0.94253	TCT	RRM1	-	pfam_ATP-cone,superfamily_Ribnucl_Rdtase_R1-su_N,pfscan_ATP-cone	ENSG00000167325		0.418	RRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RRM1	HGNC	protein_coding	OTTHUMT00000257197.1	39	0.00	0	C	NM_001033		4127418	4127418	+1	no_errors	ENST00000300738	ensembl	human	known	69_37n	missense	20	51.22	21	SNP	1.000	G
SLC7A14	57709	genome.wustl.edu	37	3	170244644	170244644	+	Missense_Mutation	SNP	G	G	A			TCGA-D8-A1XS-01A-11D-A14K-09	TCGA-D8-A1XS-10A-01D-A14K-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	5d302c04-302e-4040-9429-37cd672e8d53	9b6db1ae-c8eb-4b02-9913-76070077fedf	g.chr3:170244644G>A	ENST00000231706.5	-	2	397	c.82C>T	c.(82-84)Cgc>Tgc	p.R28C	CLDN11_ENST00000486975.1_Intron|CLDN11_ENST00000451576.1_Intron	NM_020949.2	NP_066000.2	Q8TBB6	S7A14_HUMAN	solute carrier family 7, member 14	28					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)	amino acid transmembrane transporter activity (GO:0015171)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(23)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(4)	53	all_cancers(22;2.41e-22)|all_epithelial(15;4.2e-27)|all_lung(20;1.17e-16)|Lung NSC(18;4.91e-16)|Ovarian(172;0.000902)|Breast(254;0.137)		Lung(28;6.23e-13)|LUSC - Lung squamous cell carcinoma(14;1.48e-12)			GGTTTGGTGCGTAGGATCCTG	0.587																																						dbGAP											0													158.0	126.0	137.0					3																	170244644		2203	4300	6503	-	-	-	SO:0001583	missense	0			BC022968	CCDS33892.1	3q26.2	2014-06-13	2013-07-19		ENSG00000013293	ENSG00000013293		"""Solute carriers"""	29326	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 142"""	615720					Standard	NM_020949		Approved	KIAA1613, PPP1R142	uc003fgz.2	Q8TBB6	OTTHUMG00000158941	ENST00000231706.5:c.82C>T	3.37:g.170244644G>A	ENSP00000231706:p.Arg28Cys	Somatic		WXS	Illumina GAIIx	Phase_IV	B3KV33|Q9HCF9	Missense_Mutation	SNP	pfam_AA-permease_dom	p.R28C	ENST00000231706.5	37	c.82	CCDS33892.1	3	.	.	.	.	.	.	.	.	.	.	G	20.9	4.059768	0.76074	.	.	ENSG00000013293	ENST00000231706	D	0.90900	-2.75	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	D	0.92331	0.7567	L	0.27053	0.805	0.80722	D	1	D	0.89917	1.0	D	0.75020	0.985	D	0.93528	0.6867	10	0.87932	D	0	.	19.099	0.93266	0.0:0.0:1.0:0.0	.	28	Q8TBB6	S7A14_HUMAN	C	28	ENSP00000231706:R28C	ENSP00000231706:R28C	R	-	1	0	SLC7A14	171727338	1.000000	0.71417	1.000000	0.80357	0.755000	0.42902	7.475000	0.81041	2.579000	0.87056	0.561000	0.74099	CGC	SLC7A14	-	NULL	ENSG00000013293		0.587	SLC7A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC7A14	HGNC	protein_coding	OTTHUMT00000352598.2	77	0.00	0	G	NM_020949		170244644	170244644	-1	no_errors	ENST00000231706	ensembl	human	known	69_37n	missense	66	40.00	44	SNP	1.000	A
ST3GAL1	6482	genome.wustl.edu	37	8	134477071	134477071	+	Silent	SNP	G	G	A			TCGA-D8-A1XS-01A-11D-A14K-09	TCGA-D8-A1XS-10A-01D-A14K-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	5d302c04-302e-4040-9429-37cd672e8d53	9b6db1ae-c8eb-4b02-9913-76070077fedf	g.chr8:134477071G>A	ENST00000319914.5	-	6	1660	c.633C>T	c.(631-633)acC>acT	p.T211T	ST3GAL1_ENST00000522652.1_Silent_p.T211T|ST3GAL1_ENST00000521180.1_Silent_p.T211T|ST3GAL1_ENST00000399640.2_Silent_p.T211T			Q11201	SIA4A_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	211					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|N-acetylneuraminate metabolic process (GO:0006054)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein phosphorylation (GO:0006468)|sialylation (GO:0097503)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	beta-galactoside (CMP) alpha-2,3-sialyltransferase activity (GO:0003836)			endometrium(3)|large_intestine(2)|lung(11)|prostate(1)	17	all_epithelial(106;1.53e-23)|Lung NSC(106;3.15e-07)|all_lung(105;1.26e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.00721)			CCAAGTCGATGGTCTTGAAGG	0.602																																						dbGAP											0													161.0	137.0	145.0					8																	134477071		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			L29555	CCDS6373.1	8q24.22	2013-03-01	2003-01-14	2005-02-07	ENSG00000008513	ENSG00000008513	2.4.99.4	"""Sialyltransferases"""	10862	protein-coding gene	gene with protein product	"""ST3Gal I"""	607187	"""sialyltransferase 4A (beta-galactosidase alpha-2,3-sialytransferase)"""	SIAT4A		10504389, 7655169	Standard	NM_003033		Approved	ST3O, SIATFL, ST3GalA.1	uc003yuk.2	Q11201	OTTHUMG00000164534	ENST00000319914.5:c.633C>T	8.37:g.134477071G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	O60677|Q9UN51	Silent	SNP	pfam_Glyco_trans_29,pirsf_Sialyl_trans	p.T211	ENST00000319914.5	37	c.633	CCDS6373.1	8																																																																																			ST3GAL1	-	pfam_Glyco_trans_29,pirsf_Sialyl_trans	ENSG00000008513		0.602	ST3GAL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	ST3GAL1	HGNC	protein_coding	OTTHUMT00000379132.1	42	0.00	0	G	NM_003033		134477071	134477071	-1	no_errors	ENST00000319914	ensembl	human	known	69_37n	silent	104	18.75	24	SNP	0.596	A
THADA	63892	genome.wustl.edu	37	2	43798926	43798926	+	Missense_Mutation	SNP	A	A	C			TCGA-D8-A1XS-01A-11D-A14K-09	TCGA-D8-A1XS-10A-01D-A14K-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	5d302c04-302e-4040-9429-37cd672e8d53	9b6db1ae-c8eb-4b02-9913-76070077fedf	g.chr2:43798926A>C	ENST00000405006.4	-	13	2335	c.1984T>G	c.(1984-1986)Tgg>Ggg	p.W662G	THADA_ENST00000415080.2_Missense_Mutation_p.W372G|THADA_ENST00000330266.7_Missense_Mutation_p.W372G|THADA_ENST00000405975.2_Missense_Mutation_p.W662G|THADA_ENST00000403856.1_Missense_Mutation_p.W662G|THADA_ENST00000402360.2_Missense_Mutation_p.W662G|THADA_ENST00000404790.1_Missense_Mutation_p.W662G	NM_001083953.1|NM_001271643.1	NP_001077422.1|NP_001258572.1	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	662										breast(1)|endometrium(9)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	66		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				AACTGAATCCACTGCATTTCT	0.373																																						dbGAP											0													129.0	133.0	132.0					2																	43798926		1877	4111	5988	-	-	-	SO:0001583	missense	0			AY149629	CCDS46268.1, CCDS62901.1, CCDS62902.1	2p21	2008-02-05			ENSG00000115970	ENSG00000115970			19217	protein-coding gene	gene with protein product		611800				12063398, 11214970	Standard	NM_022065		Approved	FLJ21877, KIAA1767, GITA	uc002rsx.4	Q6YHU6	OTTHUMG00000152398	ENST00000405006.4:c.1984T>G	2.37:g.43798926A>C	ENSP00000385995:p.Trp662Gly	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K1V8|B7WNS6|Q3KR04|Q53RC6|Q53TB2|Q6YHU2|Q6ZU38|Q8IY32|Q8TAU8|Q96I88|Q9BZF7|Q9C096|Q9H6U0|Q9H6W7	Missense_Mutation	SNP	pfam_DUF2428_death-receptor-like,superfamily_ARM-type_fold	p.W662G	ENST00000405006.4	37	c.1984	CCDS46268.1	2	.	.	.	.	.	.	.	.	.	.	A	14.54	2.567268	0.45694	.	.	ENSG00000115970	ENST00000330266;ENST00000405975;ENST00000356975;ENST00000415080;ENST00000405006;ENST00000402360;ENST00000404790;ENST00000403856	T;T;T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.56;1.55;1.54	5.16	2.46	0.29980	Armadillo-type fold (1);	0.272209	0.29737	N	0.011324	T	0.32823	0.0842	L	0.44542	1.39	0.38861	D	0.956477	D;P;P;P;P	0.58268	0.982;0.779;0.813;0.586;0.671	P;B;B;B;B	0.52909	0.713;0.346;0.251;0.191;0.188	T	0.15896	-1.0421	10	0.72032	D	0.01	-5.6784	6.7083	0.23262	0.5415:0.0:0.4585:0.0	.	662;662;662;372;662	B5MC89;Q8IY32;Q6YHU6-5;C9JJB1;Q6YHU6	.;.;.;.;THADA_HUMAN	G	372;662;662;372;662;662;662;662	ENSP00000331105:W372G;ENSP00000386088:W662G;ENSP00000416048:W372G;ENSP00000385995:W662G;ENSP00000385441:W662G;ENSP00000384266:W662G;ENSP00000385469:W662G	ENSP00000331105:W372G	W	-	1	0	THADA	43652430	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.272000	0.58908	0.842000	0.35045	0.482000	0.46254	TGG	THADA	-	superfamily_ARM-type_fold	ENSG00000115970		0.373	THADA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	THADA	HGNC	protein_coding	OTTHUMT00000326070.3	57	0.00	0	A	NM_022065		43798926	43798926	-1	no_errors	ENST00000405006	ensembl	human	known	69_37n	missense	36	36.84	21	SNP	1.000	C
