#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
ANKRD36B	57730	genome.wustl.edu	37	2	98165911	98165911	+	RNA	SNP	T	T	C	rs1839230|rs112877086	byFrequency	TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr2:98165911T>C	ENST00000443455.1	-	0	1558							Q8N2N9	AN36B_HUMAN	ankyrin repeat domain 36B																		ATCCTTTTTTTCTCTGGCTAT	0.308													.|||	980	0.195687	0.5703	0.1239	5008	,	,		38822	0.0069		0.1004	False		,,,				2504	0.0327					dbGAP											0													45.0	18.0	26.0					2																	98165911		1759	3782	5541	-	-	-			0			AK024934	CCDS74543.1	2q11.2	2013-01-11	2008-03-25	2008-03-25	ENSG00000196912	ENSG00000196912		"""Ankyrin repeat domain containing"""	29333	protein-coding gene	gene with protein product	"""melanoma-associated antigen"", ""CLL-associated antigen KW-1"""		"""KIAA1641"""	KIAA1641		10997877	Standard	NM_025190		Approved	FLJ21281	uc010yvc.1	Q8N2N9	OTTHUMG00000130547		2.37:g.98165911T>C		Somatic		WXS	Illumina GAIIx	Phase_IV	Q08AK5|Q6IPR0|Q6PI49|Q8IZM7|Q8TDH6|Q96N30|Q9H759	RNA	SNP	-	NULL	ENST00000443455.1	37	NULL		2																																																																																			ANKRD36B	-	-	ENSG00000196912		0.308	ANKRD36B-003	KNOWN	basic	processed_transcript	ANKRD36B	HGNC	pseudogene	OTTHUMT00000328967.2	113	0.88	1	T	NM_025190		98165911	98165911	-1	no_errors	ENST00000443455	ensembl	human	known	69_37n	rna	73	13.10	11	SNP	0.003	C
BAIAP2	10458	genome.wustl.edu	37	17	79006850	79006850	+	5'Flank	SNP	T	T	C	rs11870986	byFrequency	TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr17:79006850T>C	ENST00000321300.6	+	0	0				BAIAP2_ENST00000575712.1_5'Flank|BAIAP2_ENST00000435091.3_5'Flank|BAIAP2_ENST00000392411.3_5'Flank|BAIAP2-AS1_ENST00000577066.1_lincRNA|BAIAP2_ENST00000321280.7_5'Flank|BAIAP2_ENST00000428708.2_5'Flank|BAIAP2_ENST00000575245.1_5'Flank	NM_001144888.1|NM_017451.2	NP_001138360.1|NP_059345.1	Q9UQB8	BAIP2_HUMAN	BAI1-associated protein 2						actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|axonogenesis (GO:0007409)|dendrite development (GO:0016358)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|filopodium assembly (GO:0046847)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of synaptic plasticity (GO:0048167)|response to bacterium (GO:0009617)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	cytoskeletal adaptor activity (GO:0008093)|identical protein binding (GO:0042802)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|skin(1)	18	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			GCAGGCCAGCTCAGGAAGTAA	0.607													C|||	2656	0.530351	0.6286	0.5893	5008	,	,		19577	0.377		0.673	False		,,,				2504	0.3671					dbGAP											0																																										-	-	-	SO:0001631	upstream_gene_variant	0			AB015019	CCDS11775.1, CCDS11776.1, CCDS11777.1, CCDS45806.1	17q25.3	2014-09-11			ENSG00000175866				947	protein-coding gene	gene with protein product		605475				10343108	Standard	NM_017451		Approved	BAP2	uc002jzg.2	Q9UQB8	OTTHUMG00000177698		17.37:g.79006850T>C	Exception_encountered	Somatic		WXS	Illumina GAIIx	Phase_IV	O43858|Q53HB1|Q86WC1|Q8N5C0|Q96CR7|Q9UBR3|Q9UQ43	RNA	SNP	-	NULL	ENST00000321300.6	37	NULL	CCDS11775.1	17																																																																																			BAIAP2-AS1	-	-	ENSG00000226137		0.607	BAIAP2-003	KNOWN	basic|CCDS	protein_coding	BAIAP2-AS1	HGNC	protein_coding	OTTHUMT00000438553.1	44	0.00	0	T			79006850	79006850	-1	no_errors	ENST00000573167	ensembl	human	known	69_37n	rna	32	11.11	4	SNP	0.035	C
C16orf96	342346	genome.wustl.edu	37	16	4626109	4626109	+	Missense_Mutation	SNP	T	T	C			TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr16:4626109T>C	ENST00000444310.4	+	5	1628	c.1628T>C	c.(1627-1629)gTt>gCt	p.V543A		NM_001145011.1	NP_001138483.1			chromosome 16 open reading frame 96											NS(1)|breast(1)|endometrium(6)|kidney(1)|skin(3)	12						AAGGATAGAGTTGGCAAGGAT	0.592																																						dbGAP											0													79.0	90.0	87.0					16																	4626109		692	1591	2283	-	-	-	SO:0001583	missense	0				CCDS53986.1	16p13.3	2012-10-10			ENSG00000205832	ENSG00000205832			40031	protein-coding gene	gene with protein product							Standard	NM_001145011		Approved		uc010uxn.2	A6NNT2	OTTHUMG00000176519	ENST00000444310.4:c.1628T>C	16.37:g.4626109T>C	ENSP00000415027:p.Val543Ala	Somatic		WXS	Illumina GAIIx	Phase_IV		Missense_Mutation	SNP	NULL	p.V543A	ENST00000444310.4	37	c.1628	CCDS53986.1	16	.	.	.	.	.	.	.	.	.	.	T	1.131	-0.652310	0.03480	.	.	ENSG00000205832	ENST00000444310	.	.	.	1.09	-2.18	0.07037	.	.	.	.	.	T	0.14700	0.0355	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.31530	-0.9940	8	0.07644	T	0.81	.	4.1404	0.10191	0.0:0.5615:0.2379:0.2006	.	543	A6NNT2	CP096_HUMAN	A	543	.	ENSP00000415027:V543A	V	+	2	0	C16orf96	4566110	0.000000	0.05858	0.000000	0.03702	0.037000	0.13140	-3.316000	0.00515	-0.814000	0.04352	-1.015000	0.02457	GTT	C16orf96	-	NULL	ENSG00000205832		0.592	C16orf96-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	C16orf96	HGNC	protein_coding	OTTHUMT00000432384.1	23	0.00	0	T	NM_001145011		4626109	4626109	+1	no_errors	ENST00000444310	ensembl	human	known	69_37n	missense	23	25.81	8	SNP	0.002	C
PRR31	101928638	genome.wustl.edu	37	9	139863841	139863841	+	Missense_Mutation	SNP	C	C	T	rs11787585	byFrequency	TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr9:139863841C>T	ENST00000371629.1	+	1	147	c.22C>T	c.(22-24)Ctc>Ttc	p.L8F				Q5SQ13	PRR31_HUMAN		8			L -> F (in dbSNP:rs11787585).							lung(1)	1						ACAGTGGACTCTCGCACGGTG	0.692													C|||	670	0.133786	0.1029	0.1657	5008	,	,		15895	0.0417		0.2624	False		,,,				2504	0.1155					dbGAP											0																																										-	-	-	SO:0001583	missense	0																														ENST00000371629.1:c.22C>T	9.37:g.139863841C>T	ENSP00000360692:p.Leu8Phe	Somatic		WXS	Illumina GAIIx	Phase_IV		Missense_Mutation	SNP	superfamily_Calycin-like	p.L8F	ENST00000371629.1	37	c.22		9	351	0.16071428571428573	48	0.0975609756097561	68	0.1878453038674033	27	0.0472027972027972	208	0.27440633245382584	C	7.553	0.663136	0.14710	.	.	ENSG00000198454	ENST00000371629	T	0.33216	1.42	1.26	0.308	0.15815	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	.	.	.	.	.	.	T	0.29488	-1.0010	5	0.87932	D	0	.	5.3236	0.15895	0.0:0.6343:0.3657:0.0	rs11787585	.	.	.	F	8	ENSP00000360692:L8F	ENSP00000360692:L8F	L	+	1	0	C9orf141	138983662	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-0.662000	0.05305	0.101000	0.17610	-1.038000	0.02383	CTC	C9orf141	-	NULL	ENSG00000198454		0.692	C9orf141-001	KNOWN	basic|appris_principal	protein_coding	C9orf141	HGNC	protein_coding	OTTHUMT00000055250.1	44	0.00	0	C			139863841	139863841	+1	no_errors	ENST00000371629	ensembl	human	known	69_37n	missense	39	13.33	6	SNP	0.000	T
CDH1	999	genome.wustl.edu	37	16	68862155	68862155	+	Frame_Shift_Del	DEL	C	C	-			TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr16:68862155delC	ENST00000261769.5	+	14	2434	c.2243delC	c.(2242-2244)accfs	p.T748fs	CDH1_ENST00000562836.1_3'UTR|CDH1_ENST00000422392.2_Frame_Shift_Del_p.T687fs	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	748					adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)			NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		GAGGATGACACCCGGGACAAC	0.517			"""Mis, N, F, S"""		"""lobular breast, gastric"""	gastric			Hereditary Diffuse Gastric Cancer																													dbGAP	yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"""cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"""		E	0													107.0	100.0	103.0					16																	68862155		2198	4300	6498	-	-	-	SO:0001589	frameshift_variant	0	Familial Cancer Database	HDGC	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"""CD molecules"", ""Cadherins / Major cadherins"""	1748	protein-coding gene	gene with protein product	"""E-Cadherin"""	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.2243delC	16.37:g.68862155delC	ENSP00000261769:p.Thr748fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Frame_Shift_Del	DEL	pfam_Cadherin,pfam_Cadherin_cytoplasmic-dom,pfam_Cadherin_pro_dom,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	p.R749fs	ENST00000261769.5	37	c.2243	CCDS10869.1	16																																																																																			CDH1	-	pfam_Cadherin_cytoplasmic-dom	ENSG00000039068		0.517	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CDH1	HGNC	protein_coding	OTTHUMT00000268897.2	75	0.00	0	C	NM_004360		68862155	68862155	+1	no_errors	ENST00000261769	ensembl	human	known	69_37n	frame_shift_del	41	20.75	11	DEL	0.997	-
CXorf22	170063	genome.wustl.edu	37	X	35989851	35989851	+	Missense_Mutation	SNP	G	G	T			TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chrX:35989851G>T	ENST00000297866.5	+	12	2185	c.2119G>T	c.(2119-2121)Ggt>Tgt	p.G707C		NM_152632.3	NP_689845.2	Q6ZTR5	CX022_HUMAN	chromosome X open reading frame 22	707										breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(3)	44						AACCACCAGGGGTATAGCATC	0.413																																						dbGAP											0													56.0	50.0	52.0					X																	35989851		2202	4300	6502	-	-	-	SO:0001583	missense	0			BC027936	CCDS14237.2	Xp21.1	2014-08-07			ENSG00000165164	ENSG00000165164			28546	protein-coding gene	gene with protein product						12477932	Standard	NM_152632		Approved	MGC34831	uc004ddj.3	Q6ZTR5	OTTHUMG00000021350	ENST00000297866.5:c.2119G>T	X.37:g.35989851G>T	ENSP00000297866:p.Gly707Cys	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5JRM8|Q8N6X8	Missense_Mutation	SNP	superfamily_PapD-like	p.G707C	ENST00000297866.5	37	c.2119	CCDS14237.2	X	.	.	.	.	.	.	.	.	.	.	A	3.937	-0.014942	0.07681	.	.	ENSG00000165164	ENST00000297866	T	0.14640	2.49	5.84	-1.04	0.10068	.	0.791726	0.12448	N	0.468037	T	0.06142	0.0159	N	0.08118	0	0.09310	N	1	B	0.23490	0.086	B	0.15052	0.012	T	0.30966	-0.9960	10	0.45353	T	0.12	-10.5692	7.7756	0.29035	0.3052:0.542:0.1528:0.0	.	707	Q6ZTR5	CX022_HUMAN	C	707	ENSP00000297866:G707C	ENSP00000297866:G707C	G	+	1	0	CXorf22	35899772	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	0.342000	0.19926	-0.980000	0.03524	-2.635000	0.00153	GGT	CXorf22	-	NULL	ENSG00000165164		0.413	CXorf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CXorf22	HGNC	protein_coding	OTTHUMT00000056216.2	36	0.00	0	G	NM_152632		35989851	35989851	+1	no_errors	ENST00000297866	ensembl	human	known	69_37n	missense	23	32.35	11	SNP	0.000	T
DMBT1	1755	genome.wustl.edu	37	10	124339284	124339284	+	Silent	SNP	C	C	T			TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr10:124339284C>T	ENST00000338354.3	+	10	976	c.870C>T	c.(868-870)ggC>ggT	p.G290G	DMBT1_ENST00000368955.3_Silent_p.G290G|DMBT1_ENST00000359586.6_Intron|DMBT1_ENST00000330163.4_Silent_p.G290G|DMBT1_ENST00000368956.2_Silent_p.G290G|DMBT1_ENST00000368909.3_Silent_p.G290G|DMBT1_ENST00000344338.3_Silent_p.G290G			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	290	SRCR 2. {ECO:0000255|PROSITE- ProRule:PRU00196}.				defense response to virus (GO:0051607)|epithelial cell differentiation (GO:0030855)|induction of bacterial agglutination (GO:0043152)|innate immune response (GO:0045087)|inner cell mass cell proliferation (GO:0001833)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of epithelial cell differentiation (GO:0030858)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|phagocytic vesicle membrane (GO:0030670)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	calcium-dependent protein binding (GO:0048306)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|zymogen binding (GO:0035375)			breast(2)|central_nervous_system(7)|cervix(3)|endometrium(8)|kidney(1)|large_intestine(1)|lung(46)|prostate(1)|urinary_tract(3)	72		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				CCCAGTTTGGCCAGGGCTCAG	0.597																																					Ovarian(182;93 2026 18125 22222 38972)	dbGAP											0													94.0	94.0	94.0					10																	124339284		1908	4098	6006	-	-	-	SO:0001819	synonymous_variant	0				CCDS44490.1, CCDS44491.1, CCDS44492.1	10q25.3-q26.1	2008-08-01			ENSG00000187908	ENSG00000187908			2926	protein-coding gene	gene with protein product		601969				9288095, 17548659	Standard	NM_004406		Approved	GP340, muclin	uc001lgk.1	Q9UGM3	OTTHUMG00000019185	ENST00000338354.3:c.870C>T	10.37:g.124339284C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Silent	SNP	pfam_Srcr_rcpt,pfam_CUB,pfam_Zona_pellucida_Endoglin/CD105,superfamily_Srcr_rcpt-rel,superfamily_CUB,smart_Srcr_rcpt-rel,smart_CUB,smart_Zona_pellucida_Endoglin/CD105,pfscan_CUB,pfscan_Srcr_rcpt,pfscan_Zona_pellucida_Endoglin/CD105,prints_Srcr_rcpt	p.G290	ENST00000338354.3	37	c.870		10																																																																																			DMBT1	-	pfam_Srcr_rcpt,superfamily_Srcr_rcpt-rel,smart_Srcr_rcpt-rel,pfscan_Srcr_rcpt	ENSG00000187908		0.597	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	DMBT1	HGNC	protein_coding	OTTHUMT00000050792.2	136	0.00	0	C	NM_004406		124339284	124339284	+1	no_errors	ENST00000368915	ensembl	human	known	69_37n	silent	91	18.02	20	SNP	0.019	T
DNPEP	23549	genome.wustl.edu	37	2	220250745	220250745	+	Missense_Mutation	SNP	T	T	A			TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr2:220250745T>A	ENST00000273075.4	-	6	755	c.535A>T	c.(535-537)Atc>Ttc	p.I179F	DNPEP_ENST00000523282.1_Missense_Mutation_p.I187F|AC053503.4_ENST00000420563.1_RNA|DNPEP_ENST00000373972.1_Missense_Mutation_p.I104F	NM_012100.2	NP_036232	Q9ULA0	DNPEP_HUMAN	aspartyl aminopeptidase	169					peptide metabolic process (GO:0006518)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(3)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Renal(207;0.0474)		Epithelial(149;1.09e-06)|all cancers(144;0.000179)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TGCAGATGGATGGCCAGGTGT	0.617																																						dbGAP											0													92.0	103.0	100.0					2																	220250745		2113	4242	6355	-	-	-	SO:0001583	missense	0				CCDS42823.1	2q36.1	2008-05-22			ENSG00000123992	ENSG00000123992			2981	protein-coding gene	gene with protein product		611367				9632644	Standard	NM_012100		Approved	DAP, ASPEP	uc002vle.2	Q9ULA0	OTTHUMG00000058919	ENST00000273075.4:c.535A>T	2.37:g.220250745T>A	ENSP00000273075:p.Ile179Phe	Somatic		WXS	Illumina GAIIx	Phase_IV	Q9BW44|Q9NUV5	Missense_Mutation	SNP	pfam_Peptidase_M18,pfam_Peptidase_M42,prints_Peptidase_M18	p.I179F	ENST00000273075.4	37	c.535	CCDS42823.1	2	.	.	.	.	.	.	.	.	.	.	T	29.6	5.016786	0.93404	.	.	ENSG00000123992	ENST00000273075;ENST00000337010;ENST00000373972;ENST00000523282;ENST00000535056;ENST00000457935;ENST00000429013;ENST00000521459;ENST00000322176;ENST00000434339;ENST00000430206	.	.	.	4.87	4.87	0.63330	Peptidase M18, domain 2 (1);	0.052094	0.85682	D	0.000000	D	0.88250	0.6386	H	0.98068	4.14	0.80722	D	1	D;D;D;D;D	0.89917	0.992;0.998;0.992;1.0;0.992	P;D;P;D;P	0.91635	0.832;0.94;0.832;0.999;0.832	D	0.92502	0.6009	9	0.87932	D	0	-0.0954	14.4812	0.67585	0.0:0.0:0.0:1.0	.	187;179;187;169;179	E7ETB3;B7Z822;B7Z7F0;Q9ULA0;Q53SB6	.;.;.;DNPEP_HUMAN;.	F	179;179;104;187;72;187;165;179;179;104;104	.	ENSP00000273075:I179F	I	-	1	0	DNPEP	219958989	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.449000	0.80643	1.819000	0.53055	0.459000	0.35465	ATC	DNPEP	-	pfam_Peptidase_M18,prints_Peptidase_M18	ENSG00000123992		0.617	DNPEP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	DNPEP	HGNC	protein_coding	OTTHUMT00000130212.1	80	0.00	0	T	NM_012100		220250745	220250745	-1	no_errors	ENST00000273075	ensembl	human	known	69_37n	missense	45	21.05	12	SNP	1.000	A
EPG5	57724	genome.wustl.edu	37	18	43532523	43532523	+	Missense_Mutation	SNP	C	C	A			TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr18:43532523C>A	ENST00000282041.5	-	3	1129	c.1095G>T	c.(1093-1095)aaG>aaT	p.K365N		NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	365					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)					NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						CGAATAGCTTCTTTAGCTCCA	0.438																																						dbGAP											0													100.0	101.0	101.0					18																	43532523		1905	4124	6029	-	-	-	SO:0001583	missense	0			AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"""KIAA1632"""	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.1095G>T	18.37:g.43532523C>A	ENSP00000282041:p.Lys365Asn	Somatic		WXS	Illumina GAIIx	Phase_IV	A2BDF3|Q9H8C8	Missense_Mutation	SNP	NULL	p.K365N	ENST00000282041.5	37	c.1095	CCDS11926.2	18	.	.	.	.	.	.	.	.	.	.	C	14.09	2.432568	0.43224	.	.	ENSG00000152223	ENST00000282041	D	0.81499	-1.5	5.59	3.81	0.43845	.	1.062590	0.07169	N	0.851960	D	0.84079	0.5393	L	0.56769	1.78	0.41335	D	0.98726	D;D	0.53462	0.96;0.96	P;P	0.51229	0.663;0.663	T	0.75213	-0.3397	10	0.49607	T	0.09	-8.1543	12.5437	0.56186	0.0:0.864:0.0:0.136	.	365;365	Q9HCE0-2;Q9HCE0	.;EPG5_HUMAN	N	365	ENSP00000282041:K365N	ENSP00000282041:K365N	K	-	3	2	EPG5	41786521	0.987000	0.35691	0.973000	0.42090	0.055000	0.15305	0.467000	0.22035	0.835000	0.34877	0.563000	0.77884	AAG	EPG5	-	NULL	ENSG00000152223		0.438	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	EPG5	HGNC	protein_coding	OTTHUMT00000445081.1	25	0.00	0	C	NM_020964		43532523	43532523	-1	no_errors	ENST00000282041	ensembl	human	known	69_37n	missense	24	21.88	7	SNP	1.000	A
EPHX1	2052	genome.wustl.edu	37	1	226026576	226026578	+	In_Frame_Del	DEL	AAG	AAG	-			TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	AAG	AAG					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr1:226026576_226026578delAAG	ENST00000366837.4	+	4	782_784	c.586_588delAAG	c.(586-588)aagdel	p.K197del	RP11-285F7.2_ENST00000424332.1_RNA|EPHX1_ENST00000272167.5_In_Frame_Del_p.K197del	NM_000120.3	NP_000111.1	P07099	HYEP_HUMAN	epoxide hydrolase 1, microsomal (xenobiotic)	197					aromatic compound catabolic process (GO:0019439)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	cis-stilbene-oxide hydrolase activity (GO:0033961)|epoxide hydrolase activity (GO:0004301)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(7)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	28	Breast(184;0.197)					GGCATCCTCCAAGAAGGGTACGG	0.606																																						dbGAP											0																																										-	-	-	SO:0001651	inframe_deletion	0			J03518	CCDS1547.1	1q42.1	2009-07-10			ENSG00000143819	ENSG00000143819	3.3.2.9		3401	protein-coding gene	gene with protein product		132810		EPHX		9925921	Standard	NM_000120		Approved		uc001hpk.3	P07099	OTTHUMG00000037743	ENST00000366837.4:c.586_588delAAG	1.37:g.226026579_226026581delAAG	ENSP00000355802:p.Lys197del	Somatic		WXS	Illumina GAIIx	Phase_IV	B2R8N0|Q5VTJ6|Q9NP75|Q9NPE7|Q9NQU6|Q9NQU7|Q9NQU8|Q9NQU9|Q9NQV0|Q9NQV1|Q9NQV2	In_Frame_Del	DEL	pfam_Epoxide_hydro_N,pfam_AB_hydrolase_1,pirsf_Epoxide_hydrolase,prints_Epox_hydrolase-like	p.K197in_frame_del	ENST00000366837.4	37	c.586_588	CCDS1547.1	1																																																																																			EPHX1	-	pfam_AB_hydrolase_1,pirsf_Epoxide_hydrolase	ENSG00000143819		0.606	EPHX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	EPHX1	HGNC	protein_coding	OTTHUMT00000092064.1	47	0.00	0	AAG	NM_000120		226026576	226026578	+1	no_errors	ENST00000272167	ensembl	human	known	69_37n	in_frame_del	37	35.00	21	DEL	1.000:1.000:1.000	-
ABHD17A	81926	genome.wustl.edu	37	19	1881527	1881527	+	Frame_Shift_Del	DEL	G	G	-	rs377128884		TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr19:1881527delG	ENST00000292577.7	-	2	472	c.39delC	c.(37-39)ttcfs	p.F13fs	ABHD17A_ENST00000590661.1_Frame_Shift_Del_p.F13fs|ABHD17A_ENST00000250974.9_Frame_Shift_Del_p.F13fs	NM_001130111.1	NP_001123583.1	Q96GS6	AB17A_HUMAN	abhydrolase domain containing 17A	13						extracellular region (GO:0005576)|membrane (GO:0016020)	hydrolase activity (GO:0016787)	p.F13delF(1)									GCGGGCAGCAGAAGAGGCAGC	0.756																																						dbGAP											1	Deletion - In frame(1)	upper_aerodigestive_tract(1)											9.0	13.0	11.0					19																	1881527		2041	4133	6174	-	-	-	SO:0001589	frameshift_variant	0			BC020512	CCDS32867.1, CCDS45902.1	19p13.3	2013-03-15	2013-03-15	2013-03-15	ENSG00000129968	ENSG00000129968		"""Abhydrolase domain containing"""	28756	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 27"", ""family with sequence similarity 108, member A1"""	C19orf27, FAM108A1		14702039	Standard	NM_031213		Approved	MGC5244	uc002lug.3	Q96GS6	OTTHUMG00000171872	ENST00000292577.7:c.39delC	19.37:g.1881527delG	ENSP00000292577:p.Phe13fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K0G8|D6W5Z9|Q6PJU2|Q8WUH9|Q9BWL0|Q9H7Q9	Frame_Shift_Del	DEL	pfam_Dienelactn_hydro	p.C14fs	ENST00000292577.7	37	c.39	CCDS45902.1	19																																																																																			FAM108A1	-	NULL	ENSG00000129968		0.756	ABHD17A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FAM108A1	HGNC	protein_coding	OTTHUMT00000415556.2	9	0.00	0	G	NM_031213		1881527	1881527	-1	no_errors	ENST00000250974	ensembl	human	known	69_37n	frame_shift_del	4	42.86	3	DEL	1.000	-
ABHD17A	81926	genome.wustl.edu	37	19	1881529	1881530	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	AG	AG					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr19:1881529_1881530delAG	ENST00000292577.7	-	2	469_470	c.36_37delCT	c.(34-39)ctcttcfs	p.F13fs	ABHD17A_ENST00000590661.1_Frame_Shift_Del_p.F13fs|ABHD17A_ENST00000250974.9_Frame_Shift_Del_p.F13fs	NM_001130111.1	NP_001123583.1	Q96GS6	AB17A_HUMAN	abhydrolase domain containing 17A	13						extracellular region (GO:0005576)|membrane (GO:0016020)	hydrolase activity (GO:0016787)										GGGCAGCAGAAGAGGCAGCAGA	0.762																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			BC020512	CCDS32867.1, CCDS45902.1	19p13.3	2013-03-15	2013-03-15	2013-03-15	ENSG00000129968	ENSG00000129968		"""Abhydrolase domain containing"""	28756	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 27"", ""family with sequence similarity 108, member A1"""	C19orf27, FAM108A1		14702039	Standard	NM_031213		Approved	MGC5244	uc002lug.3	Q96GS6	OTTHUMG00000171872	ENST00000292577.7:c.36_37delCT	19.37:g.1881531_1881532delAG	ENSP00000292577:p.Phe13fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K0G8|D6W5Z9|Q6PJU2|Q8WUH9|Q9BWL0|Q9H7Q9	Frame_Shift_Del	DEL	pfam_Dienelactn_hydro	p.F13fs	ENST00000292577.7	37	c.37_36	CCDS45902.1	19																																																																																			FAM108A1	-	NULL	ENSG00000129968		0.762	ABHD17A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FAM108A1	HGNC	protein_coding	OTTHUMT00000415556.2	10	0.00	0	AG	NM_031213		1881529	1881530	-1	no_errors	ENST00000250974	ensembl	human	known	69_37n	frame_shift_del	4	42.86	3	DEL	1.000:0.997	-
GALNT2	2590	genome.wustl.edu	37	1	230417408	230417408	+	3'UTR	SNP	T	T	C	rs11620	byFrequency	TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr1:230417408T>C	ENST00000366672.4	+	0	3992				GALNT2_ENST00000485438.1_3'UTR|RP5-956O18.3_ENST00000414640.1_RNA	NM_004481.3	NP_004472.1	Q10471	GALT2_HUMAN	polypeptide N-acetylgalactosaminyltransferase 2						cellular protein metabolic process (GO:0044267)|immunoglobulin biosynthetic process (GO:0002378)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|protein O-linked glycosylation via serine (GO:0018242)|protein O-linked glycosylation via threonine (GO:0018243)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|manganese ion binding (GO:0030145)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(5)|skin(2)	32	Breast(184;0.193)|Ovarian(103;0.249)	all_cancers(173;0.156)|Prostate(94;0.179)				GCCCATGCCCTGGGGGCGGCG	0.662													T|||	2508	0.500799	0.5711	0.4452	5008	,	,		12854	0.5109		0.4404	False		,,,				2504	0.4969					dbGAP											0																																										-	-	-	SO:0001624	3_prime_UTR_variant	0			BC041120	CCDS1582.1	1q41-q42	2014-03-13	2014-03-13		ENSG00000143641	ENSG00000143641	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4124	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 2"""	602274	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2 (GalNAc-T2)"""			9592121, 7592619	Standard	NM_004481		Approved	GalNAc-T2	uc010pwa.1	Q10471	OTTHUMG00000037771	ENST00000366672.4:c.*2204T>C	1.37:g.230417408T>C		Somatic		WXS	Illumina GAIIx	Phase_IV	A8K1Y3|B7Z8V8|C5HU00|Q9NPY4	RNA	SNP	-	NULL	ENST00000366672.4	37	NULL	CCDS1582.1	1																																																																																			GALNT2	-	-	ENSG00000143641		0.662	GALNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GALNT2	HGNC	protein_coding	OTTHUMT00000092158.1	39	0.00	0	T	NM_004481		230417408	230417408	+1	no_errors	ENST00000485438	ensembl	human	known	69_37n	rna	47	11.32	6	SNP	0.000	C
GPC2	221914	genome.wustl.edu	37	7	99767587	99767587	+	3'UTR	SNP	A	A	G	rs1918353	byFrequency	TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr7:99767587A>G	ENST00000292377.2	-	0	2173				GAL3ST4_ENST00000423751.1_5'Flank|GAL3ST4_ENST00000482469.1_5'Flank|GAL3ST4_ENST00000360039.4_5'Flank|GAL3ST4_ENST00000426974.2_5'Flank|GAL3ST4_ENST00000411994.1_5'Flank|GAL3ST4_ENST00000413800.1_5'Flank|GPC2_ENST00000471050.1_5'UTR	NM_152742.1	NP_689955.1	Q8N158	GPC2_HUMAN	glypican 2						carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|neuron differentiation (GO:0030182)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|smoothened signaling pathway (GO:0007224)	anchored component of membrane (GO:0031225)|endoplasmic reticulum (GO:0005783)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|pancreas(1)|skin(3)	18	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					TTAGAGGGCTAGAGACTATAC	0.483													G|||	3004	0.59984	0.5015	0.6671	5008	,	,		13897	0.7093		0.5656	False		,,,				2504	0.6074					dbGAP											0																																										-	-	-	SO:0001624	3_prime_UTR_variant	0			BX375153	CCDS5689.1	7q22.1	2007-02-16	2007-02-15		ENSG00000213420	ENSG00000213420		"""Proteoglycans / Cell Surface : Glypicans"""	4450	protein-coding gene	gene with protein product	"""glypican proteoglycan 2, cerebroglycan proteoglycan"""		"""glypican 2 (cerebroglycan)"""			8294498	Standard	NM_152742		Approved	cerebroglycan, FLJ38962, DKFZp547M109	uc003utv.3	Q8N158	OTTHUMG00000154894	ENST00000292377.2:c.*266T>C	7.37:g.99767587A>G		Somatic		WXS	Illumina GAIIx	Phase_IV	A4D2A7	RNA	SNP	-	NULL	ENST00000292377.2	37	NULL	CCDS5689.1	7																																																																																			GPC2	-	-	ENSG00000213420		0.483	GPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GPC2	HGNC	protein_coding	OTTHUMT00000337556.1	32	0.00	0	A	NM_152742		99767587	99767587	-1	no_errors	ENST00000471050	ensembl	human	known	69_37n	rna	43	14.00	7	SNP	0.000	G
GCC1	79571	genome.wustl.edu	37	7	127224987	127224987	+	Missense_Mutation	SNP	C	C	A			TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr7:127224987C>A	ENST00000321407.2	-	1	674	c.250G>T	c.(250-252)Gat>Tat	p.D84Y	GCC1_ENST00000497650.1_Intron	NM_024523.5	NP_078799.2	Q96CN9	GCC1_HUMAN	GRIP and coiled-coil domain containing 1	84					protein targeting to Golgi (GO:0000042)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)				breast(2)|endometrium(6)|kidney(4)|large_intestine(6)|lung(13)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						CACCGGTCATCCACAGAGTCA	0.597																																						dbGAP											0													80.0	76.0	78.0					7																	127224987		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF525417	CCDS5796.1	7q22.3	2004-03-05	2003-10-17		ENSG00000179562	ENSG00000179562			19095	protein-coding gene	gene with protein product		607418	"""golgi coiled-coil 1"""			10209125	Standard	NM_024523		Approved	FLJ22035, GCC88, GCC1P, MGC20706	uc003vma.3	Q96CN9	OTTHUMG00000023590	ENST00000321407.2:c.250G>T	7.37:g.127224987C>A	ENSP00000318821:p.Asp84Tyr	Somatic		WXS	Illumina GAIIx	Phase_IV	Q9H6N7	Missense_Mutation	SNP	pfam_GRIP,superfamily_ARM-type_fold,smart_GRIP,pfscan_GRIP	p.D84Y	ENST00000321407.2	37	c.250	CCDS5796.1	7	.	.	.	.	.	.	.	.	.	.	C	24.1	4.496951	0.85069	.	.	ENSG00000179562	ENST00000321407	T	0.17854	2.25	5.78	5.78	0.91487	.	0.050361	0.85682	D	0.000000	T	0.39784	0.1091	L	0.59436	1.845	0.80722	D	1	D	0.89917	1.0	D	0.73380	0.98	T	0.03306	-1.1050	10	0.56958	D	0.05	-21.1469	17.4821	0.87675	0.0:1.0:0.0:0.0	.	84	Q96CN9	GCC1_HUMAN	Y	84	ENSP00000318821:D84Y	ENSP00000318821:D84Y	D	-	1	0	GCC1	127012223	1.000000	0.71417	0.990000	0.47175	0.888000	0.51559	7.391000	0.79828	2.733000	0.93635	0.579000	0.79373	GAT	GCC1	-	NULL	ENSG00000179562		0.597	GCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GCC1	HGNC	protein_coding	OTTHUMT00000059911.3	40	0.00	0	C	NM_024523		127224987	127224987	-1	no_errors	ENST00000321407	ensembl	human	known	69_37n	missense	27	30.77	12	SNP	1.000	A
GPRIN1	114787	genome.wustl.edu	37	5	176025940	176025940	+	Missense_Mutation	SNP	G	G	T			TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr5:176025940G>T	ENST00000303991.4	-	2	1073	c.896C>A	c.(895-897)cCc>cAc	p.P299H		NM_052899.2	NP_443131.2	Q7Z2K8	GRIN1_HUMAN	G protein regulated inducer of neurite outgrowth 1	299					neuron projection development (GO:0031175)	cell projection (GO:0042995)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CAAGGGCATGGGATCTGCCTT	0.542																																						dbGAP											0													99.0	106.0	104.0					5																	176025940		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB067480	CCDS4405.1	5q35.2	2008-02-05			ENSG00000169258	ENSG00000169258			24835	protein-coding gene	gene with protein product		611239				11572484	Standard	NM_052899		Approved	GRIN1, KIAA1893	uc003meo.1	Q7Z2K8	OTTHUMG00000130659	ENST00000303991.4:c.896C>A	5.37:g.176025940G>T	ENSP00000305839:p.Pro299His	Somatic		WXS	Illumina GAIIx	Phase_IV	C9JM70|Q8ND74|Q96PZ4	Missense_Mutation	SNP	NULL	p.P299H	ENST00000303991.4	37	c.896	CCDS4405.1	5	.	.	.	.	.	.	.	.	.	.	G	12.62	1.993602	0.35131	.	.	ENSG00000169258	ENST00000303991;ENST00000335532	T	0.08193	3.12	4.98	4.98	0.66077	.	0.436861	0.17239	N	0.181613	T	0.29914	0.0748	M	0.76328	2.33	0.09310	N	1	D	0.89917	1.0	D	0.76575	0.988	T	0.04294	-1.0962	10	0.66056	D	0.02	-0.3538	15.7407	0.77894	0.0:0.0:1.0:0.0	.	299	Q7Z2K8	GRIN1_HUMAN	H	299	ENSP00000305839:P299H	ENSP00000305839:P299H	P	-	2	0	GPRIN1	175958546	0.062000	0.20869	0.004000	0.12327	0.003000	0.03518	1.691000	0.37721	2.296000	0.77279	0.462000	0.41574	CCC	GPRIN1	-	NULL	ENSG00000169258		0.542	GPRIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GPRIN1	HGNC	protein_coding	OTTHUMT00000253149.1	53	0.00	0	G	NM_052899		176025940	176025940	-1	no_errors	ENST00000303991	ensembl	human	known	69_37n	missense	27	25.00	9	SNP	0.018	T
INPP5J	27124	genome.wustl.edu	37	22	31521404	31521404	+	Missense_Mutation	SNP	G	G	A	rs2240432	byFrequency	TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr22:31521404G>A	ENST00000331075.5	+	2	728	c.679G>A	c.(679-681)Gca>Aca	p.A227T	INPP5J_ENST00000412277.2_Missense_Mutation_p.A160T|INPP5J_ENST00000401755.1_5'Flank|INPP5J_ENST00000405300.1_Intron|INPP5J_ENST00000402238.1_5'Flank|INPP5J_ENST00000404453.1_5'Flank|INPP5J_ENST00000404390.3_Intron|INPP5J_ENST00000400294.2_Intron	NM_001284285.1	NP_001271214.1	Q15735	PI5PA_HUMAN	inositol polyphosphate-5-phosphatase J	227	Pro-rich.				inositol phosphate metabolic process (GO:0043647)|negative regulation of microtubule polymerization (GO:0031115)|negative regulation of neuron projection development (GO:0010977)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity (GO:0052659)|inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|inositol-polyphosphate 5-phosphatase activity (GO:0004445)|phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity (GO:0034485)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|skin(1)	12						GGCATCAGGCGCAGCCTCTGT	0.632													A|||	1895	0.378395	0.2277	0.4697	5008	,	,		16530	0.5387		0.333	False		,,,				2504	0.3988					dbGAP											0																																										-	-	-	SO:0001583	missense	0			U45975	CCDS46687.1, CCDS63453.1, CCDS63454.1, CCDS63455.1, CCDS74847.1	22q12.2	2008-09-09	2008-09-09	2008-09-09	ENSG00000185133	ENSG00000185133			8956	protein-coding gene	gene with protein product		606481	"""phosphatidylinositol (4,5) bisphosphate 5-phosphatase, A"""	PIB5PA		10591208	Standard	NM_001284287		Approved	INPP5	uc003aju.4	Q15735	OTTHUMG00000151206	ENST00000331075.5:c.679G>A	22.37:g.31521404G>A	ENSP00000333262:p.Ala227Thr	Somatic		WXS	Illumina GAIIx	Phase_IV	B3KS54|Q32M61|Q6ZTH6|Q8N902|Q9UDT9	Missense_Mutation	SNP	pfam_Endo/exonuclease/phosphatase,superfamily_Endo/exonuclease/phosphatase,smart_IPPc	p.A227T	ENST00000331075.5	37	c.679		22	839	0.3841575091575092	110	0.22357723577235772	139	0.3839779005524862	322	0.5629370629370629	268	0.35356200527704484	A	6.511	0.462520	0.12342	.	.	ENSG00000185133	ENST00000331075;ENST00000412277	D;D	0.97404	-4.37;-4.36	4.37	2.25	0.28309	.	0.970438	0.08448	N	0.944325	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.26608	-1.0098	8	0.72032	D	0.01	.	3.5973	0.08010	0.1725:0.5689:0.1647:0.0939	rs2240432;rs17220138;rs57414940;rs2240432	227	Q15735	PI5PA_HUMAN	T	227;160	ENSP00000333262:A227T;ENSP00000392924:A160T	ENSP00000333262:A227T	A	+	1	0	INPP5J	29851404	0.000000	0.05858	0.005000	0.12908	0.059000	0.15707	-0.682000	0.05185	0.116000	0.18110	-2.303000	0.00259	GCA	INPP5J	-	NULL	ENSG00000185133		0.632	INPP5J-002	KNOWN	basic|appris_candidate_longest	protein_coding	INPP5J	HGNC	protein_coding	OTTHUMT00000321784.1	25	0.00	0	G	NM_001002837		31521404	31521404	+1	no_errors	ENST00000331075	ensembl	human	known	69_37n	missense	26	13.33	4	SNP	0.011	A
KATNAL2	83473	genome.wustl.edu	37	18	44610718	44610718	+	Silent	SNP	T	T	C	rs16954999	byFrequency	TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr18:44610718T>C	ENST00000592005.1	+	6	943	c.270T>C	c.(268-270)ttT>ttC	p.F90F	KATNAL2_ENST00000245121.5_Intron|RP11-49K24.4_ENST00000592747.1_RNA|KATNAL2_ENST00000356157.7_Intron					katanin p60 subunit A-like 2											central_nervous_system(2)|endometrium(3)|large_intestine(8)|lung(8)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	27						ACATGCATTTTTGGGCTCCAG	0.463													C|||	2393	0.477835	0.5098	0.4914	5008	,	,		20385	0.3502		0.6083	False		,,,				2504	0.4223					dbGAP											0																																										-	-	-	SO:0001819	synonymous_variant	0			BC034999	CCDS32828.1	18q21.1	2010-04-21			ENSG00000167216	ENSG00000167216		"""ATPases / AAA-type"""	25387	protein-coding gene	gene with protein product		614697				12477932	Standard	NM_031303		Approved	MGC33211, DKFZP667C165	uc002lco.3	Q8IYT4		ENST00000592005.1:c.270T>C	18.37:g.44610718T>C		Somatic		WXS	Illumina GAIIx	Phase_IV		Silent	SNP	pfam_ATPase_AAA_core	p.F90	ENST00000592005.1	37	c.270		18																																																																																			KATNAL2	-	NULL	ENSG00000167216		0.463	KATNAL2-008	PUTATIVE	basic|exp_conf	protein_coding	KATNAL2	HGNC	protein_coding	OTTHUMT00000446324.2	35	0.00	0	T	NM_031303		44610718	44610718	+1	no_errors	ENST00000592005	ensembl	human	putative	69_37n	silent	35	10.26	4	SNP	0.000	C
LINC00588	26138	genome.wustl.edu	37	8	58192284	58192284	+	lincRNA	SNP	T	T	C	rs61998258	byFrequency	TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr8:58192284T>C	ENST00000521663.1	+	0	183					NR_026772.1		Q9Y4M8	CH071_HUMAN	long intergenic non-protein coding RNA 588																		ATTCAGGCGATTGGCCTGGCA	0.642													T|||	723	0.144369	0.149	0.1441	5008	,	,		18538	0.1399		0.1899	False		,,,				2504	0.0961					dbGAP											0																																										-	-	-			0					8q12.1	2012-10-12	2012-04-17	2012-04-17	ENSG00000215117	ENSG00000215117		"""Long non-coding RNAs"""	24494	non-coding RNA	RNA, long non-coding			"""chromosome 8 open reading frame 71"""	C8orf71		11230166	Standard	NR_026772		Approved	DKFZP434F122	uc003xtg.3	Q9Y4M8	OTTHUMG00000164424		8.37:g.58192284T>C		Somatic		WXS	Illumina GAIIx	Phase_IV		RNA	SNP	-	NULL	ENST00000521663.1	37	NULL		8																																																																																			LINC00588	-	-	ENSG00000215117		0.642	LINC00588-001	KNOWN	basic	lincRNA	LINC00588	HGNC	lincRNA	OTTHUMT00000378704.1	35	0.00	0	T	NR_026772		58192284	58192284	+1	no_errors	ENST00000521663	ensembl	human	known	69_37n	rna	35	10.26	4	SNP	0.016	C
MATN1	4146	genome.wustl.edu	37	1	31192650	31192650	+	Intron	SNP	T	T	G	rs1149042	byFrequency	TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr1:31192650T>G	ENST00000373765.4	-	3	477				MATN1-AS1_ENST00000414532.2_RNA|MATN1-AS1_ENST00000454613.1_RNA|MATN1_ENST00000477320.1_5'Flank|MATN1-AS1_ENST00000414763.1_RNA	NM_002379.3	NP_002370.1	P21941	MATN1_HUMAN	matrilin 1, cartilage matrix protein						extracellular matrix organization (GO:0030198)|growth plate cartilage chondrocyte morphogenesis (GO:0003429)|protein complex assembly (GO:0006461)|regulation of bone mineralization (GO:0030500)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	12		Colorectal(325;0.00792)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)|Ovarian(437;0.0563)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		Colorectal(126;1.29e-05)|COAD - Colon adenocarcinoma(152;0.000726)|STAD - Stomach adenocarcinoma(196;0.0183)|READ - Rectum adenocarcinoma(331;0.0649)		CTGTTTCTGATTCCTGGGTCC	0.582											OREG0013305	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	1331	0.265775	0.4766	0.2334	5008	,	,		18983	0.3353		0.1034	False		,,,				2504	0.0992					dbGAP											0																																										-	-	-	SO:0001627	intron_variant	0			M55675	CCDS336.1	1p35	2008-02-05			ENSG00000162510	ENSG00000162510			6907	protein-coding gene	gene with protein product		115437		CRTM, CMP		2246248, 9083061	Standard	NM_002379		Approved		uc001brz.3	P21941	OTTHUMG00000003705	ENST00000373765.4:c.442-846A>C	1.37:g.31192650T>G		Somatic	822	WXS	Illumina GAIIx	Phase_IV	B2R7E3|Q5TBB9	RNA	SNP	-	NULL	ENST00000373765.4	37	NULL	CCDS336.1	1																																																																																			MATN1-AS1	-	-	ENSG00000186056		0.582	MATN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MATN1-AS1	HGNC	protein_coding	OTTHUMT00000010458.1	54	0.00	0	T	NM_002379		31192650	31192650	+1	no_errors	ENST00000414532	ensembl	human	known	69_37n	rna	38	11.63	5	SNP	0.001	G
MED23	9439	genome.wustl.edu	37	6	131925356	131925356	+	Missense_Mutation	SNP	T	T	C			TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr6:131925356T>C	ENST00000368068.3	-	15	1897	c.1718A>G	c.(1717-1719)tAt>tGt	p.Y573C	MED23_ENST00000368060.3_Missense_Mutation_p.Y573C|MED23_ENST00000368058.1_Missense_Mutation_p.Y579C|MED23_ENST00000368053.4_Missense_Mutation_p.Y579C|MED23_ENST00000539158.1_Intron|MED23_ENST00000540546.1_Missense_Mutation_p.Y579C|MED23_ENST00000545957.1_Missense_Mutation_p.Y214C|MED23_ENST00000354577.4_Missense_Mutation_p.Y579C|MED23_ENST00000403834.3_Missense_Mutation_p.Y579C	NM_004830.3	NP_004821.2	Q9ULK4	MED23_HUMAN	mediator complex subunit 23	573					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(12)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	44	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0115)|OV - Ovarian serous cystadenocarcinoma(155;0.0608)		TATTTCCATATAGACCAATAA	0.393																																						dbGAP											0													107.0	110.0	109.0					6																	131925356		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF104255	CCDS5146.1, CCDS5147.1, CCDS59039.1	6q22.33-q24.1	2008-02-05	2007-08-08	2007-07-30	ENSG00000112282	ENSG00000112282			2372	protein-coding gene	gene with protein product		605042	"""cofactor required for Sp1 transcriptional activation, subunit 3, 130kDa"""	CRSP3		9989412	Standard	NM_004830		Approved	CRSP130, DRIP130, Sur2	uc003qcs.2	Q9ULK4	OTTHUMG00000015565	ENST00000368068.3:c.1718A>G	6.37:g.131925356T>C	ENSP00000357047:p.Tyr573Cys	Somatic		WXS	Illumina GAIIx	Phase_IV	B9TX55|O95403|Q5JWT3|Q5JWT4|Q6P9H6|Q9H0J2|Q9NTT9|Q9NTU0|Q9Y5P7|Q9Y667	Missense_Mutation	SNP	pfam_Mediator_Med23	p.Y579C	ENST00000368068.3	37	c.1736	CCDS5147.1	6	.	.	.	.	.	.	.	.	.	.	T	21.7	4.183940	0.78677	.	.	ENSG00000112282	ENST00000354577;ENST00000368068;ENST00000403834;ENST00000368060;ENST00000368058;ENST00000545957;ENST00000368053;ENST00000540546	T;T;T;T;T;T;T;T	0.81078	-1.45;-1.45;-1.45;-1.45;-1.45;-1.45;-1.45;-1.45	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	D	0.84243	0.5429	L	0.53249	1.67	0.80722	D	1	P;D;D;P	0.76494	0.919;0.999;0.965;0.956	P;D;P;P	0.79784	0.663;0.993;0.663;0.532	D	0.84560	0.0649	10	0.44086	T	0.13	-10.9428	15.8513	0.78934	0.0:0.0:0.0:1.0	.	214;579;573;579	B4E3G4;Q9ULK4-2;Q9ULK4;Q9ULK4-3	.;.;MED23_HUMAN;.	C	579;573;579;573;579;214;579;579	ENSP00000346588:Y579C;ENSP00000357047:Y573C;ENSP00000384536:Y579C;ENSP00000357039:Y573C;ENSP00000357037:Y579C;ENSP00000439977:Y214C;ENSP00000357032:Y579C;ENSP00000437818:Y579C	ENSP00000346588:Y579C	Y	-	2	0	MED23	131967049	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.152000	0.67230	0.533000	0.62120	TAT	MED23	-	pfam_Mediator_Med23	ENSG00000112282		0.393	MED23-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	MED23	HGNC	protein_coding	OTTHUMT00000042215.1	28	0.00	0	T			131925356	131925356	-1	no_errors	ENST00000368058	ensembl	human	known	69_37n	missense	16	27.27	6	SNP	1.000	C
KMT2C	58508	genome.wustl.edu	37	7	151848016	151848019	+	Frame_Shift_Del	DEL	GATG	GATG	-			TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	GATG	GATG					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr7:151848016_151848019delGATG	ENST00000262189.6	-	51	12958_12961	c.12740_12743delCATC	c.(12739-12744)tcatcafs	p.SS4247fs	KMT2C_ENST00000355193.2_Frame_Shift_Del_p.SS4304fs|KMT2C_ENST00000485241.1_5'Flank	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	4247					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										TTGTGCAGTTGATGAATAAAGAAT	0.402																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.12740_12743delCATC	7.37:g.151848016_151848019delGATG	ENSP00000262189:p.Ser4247fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Frame_Shift_Del	DEL	pfam_Znf_PHD-finger,pfam_SET_dom,pfam_FYrich_C,pfam_FYrich_N,superfamily_Znf_FYVE_PHD,superfamily_HMG_superfamily,smart_Znf_PHD,smart_Znf_RING,smart_HMG_superfamily,smart_FYrich_N,smart_FYrich_C,smart_SET_dom,smart_Post-SET_dom,pfscan_SET_dom,pfscan_Post-SET_dom,pfscan_Znf_DHHC_palmitoyltrfase,pfscan_Znf_PHD-finger,pfscan_Znf_RING	p.S4304fs	ENST00000262189.6	37	c.12914_12911	CCDS5931.1	7																																																																																			MLL3	-	NULL	ENSG00000055609		0.402	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	MLL3	HGNC	protein_coding	OTTHUMT00000318887.3	32	0.00	0	GATG			151848016	151848019	-1	no_errors	ENST00000355193	ensembl	human	known	69_37n	frame_shift_del	34	19.05	8	DEL	1.000:0.999:0.998:1.000	-
MUC19	283463	genome.wustl.edu	37	12	40918902	40918902	+	3'UTR	SNP	T	T	C	rs2933352	byFrequency	TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr12:40918902T>C	ENST00000474954.1	+	0	1600				MUC19_ENST00000454784.4_Intron			Q7Z5P9	MUC19_HUMAN	mucin 19, oligomeric						cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				lung(2)	2						CACCAGAAAGTAGGACAGGTA	0.403													T|||	1062	0.212061	0.1626	0.3516	5008	,	,		18910	0.245		0.2038	False		,,,				2504	0.1544					dbGAP											0																																										-	-	-	SO:0001624	3_prime_UTR_variant	0			AY236870		12q12	2012-04-20	2006-03-14		ENSG00000205592	ENSG00000205592		"""Mucins"""	14362	protein-coding gene	gene with protein product		612170				12882755	Standard	NM_173600		Approved	FLJ35746	uc021qxa.1	Q7Z5P9	OTTHUMG00000060732	ENST00000474954.1:c.*1597T>C	12.37:g.40918902T>C		Somatic		WXS	Illumina GAIIx	Phase_IV	Q8NA85	RNA	SNP	-	NULL	ENST00000474954.1	37	NULL		12																																																																																			MUC19	-	-	ENSG00000205592		0.403	MUC19-006	KNOWN	basic	processed_transcript	MUC19	HGNC	protein_coding	OTTHUMT00000134360.1	30	0.00	0	T	XM_003403524		40918902	40918902	+1	no_errors	ENST00000474954	ensembl	human	known	69_37n	rna	21	16.00	4	SNP	0.002	C
MUC19	283463	genome.wustl.edu	37	12	40954386	40954386	+	3'UTR	SNP	C	C	T	rs17120784	byFrequency	TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr12:40954386C>T	ENST00000454784.4	+	0	18648							Q7Z5P9	MUC19_HUMAN	mucin 19, oligomeric						cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				lung(2)	2						GGACCTCCTACCACAGGTAAG	0.408													C|||	63	0.0125799	0.0477	0.0	5008	,	,		17496	0.0		0.0	False		,,,				2504	0.0					dbGAP											0																																										-	-	-	SO:0001624	3_prime_UTR_variant	0			AY236870		12q12	2012-04-20	2006-03-14		ENSG00000205592	ENSG00000205592		"""Mucins"""	14362	protein-coding gene	gene with protein product		612170				12882755	Standard	NM_173600		Approved	FLJ35746	uc021qxa.1	Q7Z5P9	OTTHUMG00000060732	ENST00000454784.4:c.*7022C>T	12.37:g.40954386C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q8NA85	Silent	SNP	pfam_Cys_knot,smart_VWF_C,smart_Cys_knot_C,pfscan_Cys_knot_C,pfscan_VWF_C	p.Y414	ENST00000454784.4	37	c.1242		12																																																																																			MUC19	-	NULL	ENSG00000205592		0.408	MUC19-001	NOVEL	non_canonical_conserved|non_canonical_genome_sequence_error|basic|appris_principal	protein_coding	MUC19	HGNC	protein_coding	OTTHUMT00000384257.6	24	0.00	0	C	XM_003403524		40954386	40954386	+1	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000380816	ensembl	human	novel	69_37n	silent	17	15.00	3	SNP	0.336	T
MUC5B	727897	genome.wustl.edu	37	11	1280246	1280246	+	Silent	SNP	G	G	A	rs541456427		TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr11:1280246G>A	ENST00000529681.1	+	44	16726	c.16668G>A	c.(16666-16668)acG>acA	p.T5556T	MUC5B_ENST00000447027.1_Silent_p.T5559T	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	5556	VWFC 3. {ECO:0000255|PROSITE- ProRule:PRU00220}.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		AGGACCCAACGGTGCAATGTC	0.647													G|||	1	0.000199681	0.0	0.0	5008	,	,		16252	0.0		0.0	False		,,,				2504	0.001					dbGAP											0													42.0	49.0	47.0					11																	1280246		1952	4099	6051	-	-	-	SO:0001819	synonymous_variant	0			U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.16668G>A	11.37:g.1280246G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	pfam_VWF_type-D,pfam_Unchr_dom_Cys-rich,pfam_TIL_dom,pfam_VWF_C,superfamily_TIL_dom,smart_VWF_type-D,smart_Unchr_dom_Cys-rich,smart_VWC_out,smart_VWF_C,smart_Cys_knot_C,pfscan_Cys_knot_C,pfscan_VWF_C	p.T5559	ENST00000529681.1	37	c.16677	CCDS44515.2	11																																																																																			MUC5B	-	pfam_VWF_C,smart_VWF_C,pfscan_VWF_C	ENSG00000117983		0.647	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	MUC5B	HGNC	protein_coding	OTTHUMT00000390041.2	35	0.00	0	G	XM_001126093		1280246	1280246	+1	no_errors	ENST00000447027	ensembl	human	known	69_37n	silent	26	35.00	14	SNP	0.000	A
NLRP9	338321	genome.wustl.edu	37	19	56226512	56226512	+	Missense_Mutation	SNP	G	G	T			TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr19:56226512G>T	ENST00000332836.2	-	6	2437	c.2410C>A	c.(2410-2412)Ctc>Atc	p.L804I		NM_176820.2	NP_789790.2	Q7RTR0	NALP9_HUMAN	NLR family, pyrin domain containing 9	804						cytoplasm (GO:0005737)	ATP binding (GO:0005524)			NS(2)|breast(5)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(15)|lung(21)|ovary(2)|prostate(3)|skin(7)|urinary_tract(3)	74		Colorectal(82;0.000133)|Ovarian(87;0.133)		GBM - Glioblastoma multiforme(193;0.123)		CCCAGATCGAGGAGGGACAGG	0.547																																						dbGAP											0													123.0	105.0	111.0					19																	56226512		2202	4298	6500	-	-	-	SO:0001583	missense	0			AY154464	CCDS12934.1	19q13.43	2006-12-08	2006-12-08	2006-12-08				"""Nucleotide-binding domain and leucine rich repeat containing"""	22941	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 9"""	609663	"""NACHT, leucine rich repeat and PYD containing 9"""	NALP9		12563287	Standard	NM_176820		Approved	NOD6, PAN12, CLR19.1	uc002qly.3	Q7RTR0		ENST00000332836.2:c.2410C>A	19.37:g.56226512G>T	ENSP00000331857:p.Leu804Ile	Somatic		WXS	Illumina GAIIx	Phase_IV	B2RN12|Q86W27	Missense_Mutation	SNP	pfam_DAPIN,superfamily_DEATH-like,smart_Leu-rich_rpt_RNase_inh_sub-typ,pfscan_NACHT_NTPase,pfscan_DAPIN	p.L804I	ENST00000332836.2	37	c.2410	CCDS12934.1	19	.	.	.	.	.	.	.	.	.	.	g	14.26	2.481858	0.44147	.	.	ENSG00000185792	ENST00000332836;ENST00000333452	T	0.80304	-1.36	2.54	2.54	0.30619	.	.	.	.	.	D	0.90539	0.7035	M	0.92880	3.355	0.09310	N	1	D	0.89917	1.0	D	0.83275	0.996	T	0.79417	-0.1812	9	0.72032	D	0.01	.	8.9048	0.35517	0.0:0.0:1.0:0.0	.	804	Q7RTR0	NALP9_HUMAN	I	804	ENSP00000331857:L804I	ENSP00000331857:L804I	L	-	1	0	NLRP9	60918324	0.037000	0.19845	0.011000	0.14972	0.007000	0.05969	0.995000	0.29706	1.791000	0.52520	0.633000	0.83428	CTC	NLRP9	-	smart_Leu-rich_rpt_RNase_inh_sub-typ	ENSG00000185792		0.547	NLRP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NLRP9	HGNC	protein_coding	OTTHUMT00000453653.1	16	0.00	0	G	NM_176820		56226512	56226512	-1	no_errors	ENST00000332836	ensembl	human	known	69_37n	missense	16	27.27	6	SNP	0.011	T
NOL6	65083	genome.wustl.edu	37	9	33468140	33468140	+	Nonsense_Mutation	SNP	G	G	A			TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr9:33468140G>A	ENST00000379471.2	-	11	1399	c.1312C>T	c.(1312-1314)Cag>Tag	p.Q438*	NOL6_ENST00000455041.2_Nonsense_Mutation_p.Q386*|NOL6_ENST00000464829.1_Intron			Q9H6R4	NOL6_HUMAN	nucleolar protein 6 (RNA-associated)	438					rRNA processing (GO:0006364)	condensed nuclear chromosome (GO:0000794)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|kidney(4)|large_intestine(5)|lung(8)|ovary(2)|prostate(2)|skin(2)	27			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.152)		GCCTCATGCTGTACCTGGAGC	0.527																																						dbGAP											0													70.0	65.0	66.0					9																	33468140		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0			AF361079	CCDS6543.1, CCDS6544.1	9p12	2013-02-22	2013-02-22		ENSG00000165271	ENSG00000165271			19910	protein-coding gene	gene with protein product		611532	"""nucleolar protein family 6 (RNA-associated)"""			11895476, 15590835	Standard	NM_022917		Approved	bA311H10.1, Nrap, FLJ21959, MGC14896, MGC14921, MGC20838, UTP22	uc003zsz.3	Q9H6R4	OTTHUMG00000000394	ENST00000379471.2:c.1312C>T	9.37:g.33468140G>A	ENSP00000368784:p.Gln438*	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5T5M3|Q5T5M4|Q7L4G6|Q8N6I0|Q8TEY9|Q8TEZ0|Q8TEZ1|Q9H675	Nonsense_Mutation	SNP	pfam_Nrap	p.Q438*	ENST00000379471.2	37	c.1312		9	.	.	.	.	.	.	.	.	.	.	G	21.5	4.158636	0.78226	.	.	ENSG00000165271	ENST00000353159;ENST00000297990;ENST00000379471;ENST00000325914;ENST00000455041	.	.	.	5.46	5.46	0.80206	.	0.052898	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10111	T	0.7	.	17.0911	0.86622	0.0:0.0:1.0:0.0	.	.	.	.	X	438;438;438;438;386	.	ENSP00000297990:Q438X	Q	-	1	0	NOL6	33458140	1.000000	0.71417	0.993000	0.49108	0.030000	0.12068	8.643000	0.91040	2.575000	0.86900	0.561000	0.74099	CAG	NOL6	-	pfam_Nrap	ENSG00000165271		0.527	NOL6-005	NOVEL	non_canonical_TEC|basic	protein_coding	NOL6	HGNC	protein_coding	OTTHUMT00000001019.2	56	0.00	0	G	NM_022917		33468140	33468140	-1	no_errors	ENST00000297990	ensembl	human	known	69_37n	nonsense	31	11.43	4	SNP	0.999	A
PCDHB12	56124	genome.wustl.edu	37	5	140589906	140589906	+	Missense_Mutation	SNP	C	C	A			TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr5:140589906C>A	ENST00000239450.2	+	1	1616	c.1427C>A	c.(1426-1428)aCa>aAa	p.T476K	PCDHB12_ENST00000541609.1_Missense_Mutation_p.T139K	NM_018932.3	NP_061755.1	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12	476	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(10)|large_intestine(17)|lung(38)|ovary(3)|pancreas(1)|prostate(2)|skin(7)|stomach(1)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ATCAGCGCCACAGACAGAGAC	0.652																																						dbGAP											0													89.0	87.0	88.0					5																	140589906		2203	4298	6501	-	-	-	SO:0001583	missense	0			AF152491	CCDS4254.1	5q31	2010-01-26			ENSG00000120328	ENSG00000120328		"""Cadherins / Protocadherins : Clustered"""	8683	other	protocadherin		606338				10380929	Standard	NM_018932		Approved	PCDH-BETA12	uc003liz.3	Q9Y5F1	OTTHUMG00000129620	ENST00000239450.2:c.1427C>A	5.37:g.140589906C>A	ENSP00000239450:p.Thr476Lys	Somatic		WXS	Illumina GAIIx	Phase_IV	B4DDU1	Missense_Mutation	SNP	pfam_Cadherin,pfam_Cadherin_N,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	p.T476K	ENST00000239450.2	37	c.1427	CCDS4254.1	5	.	.	.	.	.	.	.	.	.	.	C	12.06	1.824561	0.32237	.	.	ENSG00000120328	ENST00000541609;ENST00000239450;ENST00000507840	T;T	0.02890	4.12;4.12	3.61	-1.2	0.09554	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.09291	0.0229	M	0.64404	1.975	0.09310	N	1	D	0.67145	0.996	D	0.74674	0.984	T	0.18085	-1.0348	9	0.49607	T	0.09	.	7.2524	0.26156	0.0:0.1702:0.6207:0.209	.	476	Q9Y5F1	PCDBC_HUMAN	K	139;476;96	ENSP00000440199:T139K;ENSP00000239450:T476K	ENSP00000239450:T476K	T	+	2	0	PCDHB12	140570090	0.000000	0.05858	0.875000	0.34327	0.989000	0.77384	-1.739000	0.01840	0.106000	0.17784	0.485000	0.47835	ACA	PCDHB12	-	pfam_Cadherin,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin	ENSG00000120328		0.652	PCDHB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PCDHB12	HGNC	protein_coding	OTTHUMT00000251815.2	88	0.00	0	C	NM_018932		140589906	140589906	+1	no_errors	ENST00000239450	ensembl	human	known	69_37n	missense	65	27.78	25	SNP	0.018	A
PIK3CA	5290	genome.wustl.edu	37	3	178952085	178952085	+	Missense_Mutation	SNP	A	A	G	rs121913279		TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr3:178952085A>G	ENST00000263967.3	+	21	3297	c.3140A>G	c.(3139-3141)cAt>cGt	p.H1047R	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1047	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		H -> L (in BC; unknown pathological significance). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16353168}.|H -> R (in CLOVE, KERSEB, CRC, BC and OC; also found in an endometrial carcinoma sample; shows an increase in lipid kinase activity; oncogenic in vivo; requires binding to p85 regulatory subunit to induce cellular transformation but not interaction with RAS; may mimic the conformatitonal change triggered by the interaction with RAS; enhances invadopodia-mediated extracellular matrix degradation and invasion in breast cancer cells; increases lipid kinase activity; may alter the interaction of the PI3K/ PI4K kinase domain with the cell membrane). {ECO:0000269|PubMed:15016963, ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15712344, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16114017, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22658544}.|H -> Y (in MCAP; also found in an endometrial carcinoma sample). {ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.H1047R(1387)|p.H1047L(194)|p.H1047P(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	AATGATGCACATCATGGTGGC	0.378	H1047L(EFM19_BREAST)|H1047R(BT20_BREAST)|H1047R(CAL29_URINARY_TRACT)|H1047R(CAL33_UPPER_AERODIGESTIVE_TRACT)|H1047R(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|H1047R(HCC1954_BREAST)|H1047R(HCT116_LARGE_INTESTINE)|H1047R(HSC2_UPPER_AERODIGESTIVE_TRACT)|H1047R(LS180_LARGE_INTESTINE)|H1047R(MCAS_OVARY)|H1047R(MDAMB453_BREAST)|H1047R(NCIH1048_LUNG)|H1047R(RKO_LARGE_INTESTINE)|H1047R(SKOV3_OVARY)|H1047R(T47D_BREAST)	57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)	dbGAP		Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	1582	Substitution - Missense(1582)	breast(961)|large_intestine(245)|endometrium(114)|ovary(77)|urinary_tract(36)|upper_aerodigestive_tract(26)|lung(19)|central_nervous_system(19)|stomach(19)|haematopoietic_and_lymphoid_tissue(11)|thyroid(10)|NS(9)|liver(7)|kidney(6)|soft_tissue(6)|skin(4)|prostate(4)|pituitary(3)|pancreas(3)|meninges(1)|cervix(1)|bone(1)											99.0	89.0	92.0					3																	178952085		1912	4130	6042	-	-	-	SO:0001583	missense	0				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3140A>G	3.37:g.178952085A>G	ENSP00000263967:p.His1047Arg	Somatic		WXS	Illumina GAIIx	Phase_IV	Q14CW1|Q99762	Missense_Mutation	SNP	pfam_PInositide-3_kin_accessory_dom,pfam_PI3/4_kinase_cat_dom,pfam_PI3K_Ras-bd_dom,pfam_PI3K_C2_dom,pfam_PI3K_adapt-bd_dom,superfamily_Kinase-like_dom,superfamily_ARM-type_fold,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_PI3K_adapt-bd_dom,smart_PI3K_Ras-bd_dom,smart_PI3K_C2_dom,smart_PInositide-3_kin_accessory_dom,smart_PI3/4_kinase_cat_dom,pfscan_PI3/4_kinase_cat_dom	p.H1047R	ENST00000263967.3	37	c.3140	CCDS43171.1	3	.	.	.	.	.	.	.	.	.	.	A	14.34	2.506328	0.44558	.	.	ENSG00000121879	ENST00000263967	T	0.80214	-1.35	6.08	6.08	0.98989	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	T	0.62466	0.2430	N	0.08118	0	0.80722	D	1	P	0.38597	0.639	B	0.28011	0.085	T	0.67526	-0.5648	10	0.40728	T	0.16	-21.2893	16.6512	0.85203	1.0:0.0:0.0:0.0	.	1047	P42336	PK3CA_HUMAN	R	1047	ENSP00000263967:H1047R	ENSP00000263967:H1047R	H	+	2	0	PIK3CA	180434779	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	8.859000	0.92264	2.333000	0.79357	0.482000	0.46254	CAT	PIK3CA	-	superfamily_Kinase-like_dom,smart_PI3/4_kinase_cat_dom,pfscan_PI3/4_kinase_cat_dom	ENSG00000121879		0.378	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	PIK3CA	HGNC	protein_coding	OTTHUMT00000348409.2	12	0.00	0	A			178952085	178952085	+1	no_errors	ENST00000263967	ensembl	human	known	69_37n	missense	12	25.00	4	SNP	1.000	G
PTPRE	5791	genome.wustl.edu	37	10	129883933	129883933	+	3'UTR	SNP	C	C	T	rs6911	byFrequency	TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr10:129883933C>T	ENST00000254667.3	+	0	5145				PTPRE_ENST00000306042.5_3'UTR	NM_006504.4	NP_006495.1	P23469	PTPRE_HUMAN	protein tyrosine phosphatase, receptor type, E						negative regulation of insulin receptor signaling pathway (GO:0046627)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of mast cell activation (GO:0033003)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	22		all_epithelial(44;1.66e-05)|all_lung(145;0.00456)|Lung NSC(174;0.0066)|all_neural(114;0.0936)|Colorectal(57;0.141)|Breast(234;0.166)|Melanoma(40;0.203)			Alendronate(DB00630)	TTGTGTTTAACTTATGTGCAG	0.279													T|||	2730	0.545128	0.5915	0.6585	5008	,	,		16728	0.4802		0.5318	False		,,,				2504	0.4826				Colon(52;977 1184 20575 41685)	dbGAP											0																																										-	-	-	SO:0001624	3_prime_UTR_variant	0			AF406557	CCDS7657.1, CCDS7658.1	10q26	2011-06-09			ENSG00000132334	ENSG00000132334		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9669	protein-coding gene	gene with protein product		600926				8595895	Standard	NM_130435		Approved	PTPE	uc001lkb.3	P23469	OTTHUMG00000019254	ENST00000254667.3:c.*2763C>T	10.37:g.129883933C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q13345|Q5VWH3|Q5VWH4|Q96KQ6	RNA	SNP	-	NULL	ENST00000254667.3	37	NULL	CCDS7657.1	10																																																																																			PTPRE	-	-	ENSG00000132334		0.279	PTPRE-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	PTPRE	HGNC	protein_coding	OTTHUMT00000050990.1	52	0.00	0	C			129883933	129883933	+1	no_errors	ENST00000479896	ensembl	human	known	69_37n	rna	33	13.16	5	SNP	1.000	T
RABEPK	10244	genome.wustl.edu	37	9	127996096	127996096	+	Missense_Mutation	SNP	T	T	C			TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr9:127996096T>C	ENST00000373538.3	+	8	1266	c.956T>C	c.(955-957)cTg>cCg	p.L319P	RABEPK_ENST00000394125.4_Missense_Mutation_p.L319P|RABEPK_ENST00000259460.8_Missense_Mutation_p.L268P|RABEPK_ENST00000394124.4_3'UTR	NM_005833.3	NP_005824.2	Q7Z6M1	RABEK_HUMAN	Rab9 effector protein with kelch motifs	319					receptor-mediated endocytosis (GO:0006898)|vesicle docking involved in exocytosis (GO:0006904)	endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	15						TCTCTCACTCTGAACCATGAA	0.478																																						dbGAP											0													156.0	136.0	143.0					9																	127996096		2203	4300	6503	-	-	-	SO:0001583	missense	0			BC000503	CCDS6862.1, CCDS55341.1	9q33.1-q33.3	2010-04-19			ENSG00000136933	ENSG00000136933			16896	protein-coding gene	gene with protein product		605962				9230071	Standard	NM_005833		Approved	RAB9P40, bA65N13.1	uc004bpi.3	Q7Z6M1	OTTHUMG00000020674	ENST00000373538.3:c.956T>C	9.37:g.127996096T>C	ENSP00000362639:p.Leu319Pro	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K403|O00568|Q69YR2|Q6FHA4|Q6IBG7|Q6P092|Q86Y76|Q9BWB1	Missense_Mutation	SNP	pfam_Kelch_2,pfam_Kelch_1	p.L319P	ENST00000373538.3	37	c.956	CCDS6862.1	9	.	.	.	.	.	.	.	.	.	.	T	0.569	-0.841772	0.02671	.	.	ENSG00000136933	ENST00000394125;ENST00000259460;ENST00000373538	T;T;T	0.46819	1.58;0.86;1.58	4.76	3.59	0.41128	Kelch-type beta propeller (1);	1.208250	0.06086	N	0.662756	T	0.45577	0.1349	L	0.56769	1.78	0.18873	N	0.999987	P;P	0.43169	0.467;0.8	B;B	0.41860	0.26;0.368	T	0.26503	-1.0101	10	0.25106	T	0.35	-0.077	6.026	0.19656	0.1552:0.0:0.3218:0.523	.	268;319	Q7Z6M1-2;Q7Z6M1	.;RABEK_HUMAN	P	319;268;319	ENSP00000377683:L319P;ENSP00000259460:L268P;ENSP00000362639:L319P	ENSP00000259460:L268P	L	+	2	0	RABEPK	127035917	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	0.147000	0.16202	0.937000	0.37394	-0.321000	0.08615	CTG	RABEPK	-	NULL	ENSG00000136933		0.478	RABEPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RABEPK	HGNC	protein_coding	OTTHUMT00000054064.1	41	0.00	0	T	NM_005833		127996096	127996096	+1	no_errors	ENST00000373538	ensembl	human	known	69_37n	missense	32	36.00	18	SNP	0.000	C
RECQL5	9400	genome.wustl.edu	37	17	73657112	73657112	+	Silent	SNP	G	G	A			TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr17:73657112G>A	ENST00000317905.5	-	6	1068	c.909C>T	c.(907-909)aaC>aaT	p.N303N	RECQL5_ENST00000584999.1_Silent_p.N303N|RECQL5_ENST00000420326.2_Silent_p.N303N|RECQL5_ENST00000423245.2_Silent_p.N276N|RECQL5_ENST00000340830.5_Silent_p.N303N	NM_004259.6	NP_004250.4	O94762	RECQ5_HUMAN	RecQ protein-like 5	303	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				chromosome separation (GO:0051304)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|mitotic nuclear division (GO:0007067)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA helicase activity (GO:0003678)|nucleic acid binding (GO:0003676)|RNA polymerase II core binding (GO:0000993)			breast(1)|cervix(3)|endometrium(3)|kidney(7)|large_intestine(7)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	36	all_cancers(13;2.73e-08)|Breast(9;6.04e-09)|all_epithelial(9;6.79e-09)		all cancers(21;1.15e-06)|Epithelial(20;2.19e-06)|Lung(188;0.101)|LUSC - Lung squamous cell carcinoma(166;0.112)			CCATCCAGTCGTTCTGCACCA	0.507								Other identified genes with known or suspected DNA repair function																														dbGAP											0													171.0	139.0	150.0					17																	73657112		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AB006533	CCDS32735.1, CCDS42380.1, CCDS45777.1	17q25	2014-03-07	2014-03-07	2014-03-07	ENSG00000108469	ENSG00000108469			9950	protein-coding gene	gene with protein product	"""RecQ protein 5"""	603781				9878247	Standard	NM_004259		Approved	RecQ5, FLJ90603	uc010dgl.3	O94762		ENST00000317905.5:c.909C>T	17.37:g.73657112G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	Q9H0B1|Q9P1W7|Q9UNC8	Silent	SNP	pfam_RecQ_helicase-like_5,pfam_DNA/RNA_helicase_DEAD/DEAH_N,pfam_Helicase_C,pfam_Helicase/UvrB_dom,smart_Helicase_ATP-bd,smart_Helicase_C,pfscan_Helicase_ATP-bd,pfscan_Helicase_C,tigrfam_DNA_helicase_ATP-dep_RecQ	p.N303	ENST00000317905.5	37	c.909	CCDS42380.1	17																																																																																			RECQL5	-	pfam_Helicase_C,smart_Helicase_C,pfscan_Helicase_C,tigrfam_DNA_helicase_ATP-dep_RecQ	ENSG00000108469		0.507	RECQL5-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	RECQL5	HGNC	protein_coding	OTTHUMT00000448207.1	29	0.00	0	G	NM_004259		73657112	73657112	-1	no_errors	ENST00000317905	ensembl	human	known	69_37n	silent	23	14.81	4	SNP	0.976	A
RNH1	6050	genome.wustl.edu	37	11	499583	499583	+	Intron	SNP	G	G	A	rs61876346	byFrequency	TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr11:499583G>A	ENST00000534797.1	-	3	1851				RNH1_ENST00000354420.2_Intron|RNH1_ENST00000397615.2_Intron|RNH1_ENST00000356187.5_Intron|RNH1_ENST00000533410.1_Intron|RNH1_ENST00000397604.3_Intron|RNH1_ENST00000397614.1_Intron|RNH1_ENST00000438658.2_Intron|RNH1_ENST00000533592.1_5'Flank			O60930	RNH1_HUMAN	ribonuclease/angiogenin inhibitor 1						mitochondrial DNA replication (GO:0006264)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|nucleic acid binding (GO:0003676)|ribonuclease activity (GO:0004540)|RNA binding (GO:0003723)|RNA-DNA hybrid ribonuclease activity (GO:0004523)			endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	10		all_cancers(49;3.02e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;1.26e-26)|Epithelial(43;1.34e-25)|OV - Ovarian serous cystadenocarcinoma(40;5.31e-20)|BRCA - Breast invasive adenocarcinoma(625;8.01e-05)|Lung(200;0.0378)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TGGGGCAGCTGTGCCTTGCAA	0.632													G|||	1248	0.249201	0.3086	0.1657	5008	,	,		16238	0.1815		0.2594	False		,,,				2504	0.2873					dbGAP											0																																										-	-	-	SO:0001627	intron_variant	0				CCDS7697.1	11p15.5	2008-02-05	2005-06-01	2005-06-01	ENSG00000023191	ENSG00000023191			10074	protein-coding gene	gene with protein product		173320	"""ribonuclease/angiogenin inhibitor"""	RNH			Standard	NM_203386		Approved	RAI	uc001lpo.1	P13489	OTTHUMG00000119086	ENST00000534797.1:c.443+245C>T	11.37:g.499583G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	B3KQU4|O60523|O60857|Q57Z93|Q5U0C1|Q6FHD4	Missense_Mutation	SNP	smart_Leu-rich_rpt_RNase_inh_sub-typ	p.T154I	ENST00000534797.1	37	c.461	CCDS7697.1	11	517	0.2367216117216117	139	0.28252032520325204	74	0.20441988950276244	113	0.19755244755244755	191	0.2519788918205805	G	6.800	0.516695	0.12944	.	.	ENSG00000023191	ENST00000531149	T	0.40756	1.02	1.75	-0.502	0.12004	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.36866	-0.9730	5	0.11794	T	0.64	.	2.7255	0.05212	0.21:0.3104:0.4796:0.0	rs61876346	.	.	.	I	154	ENSP00000435798:T154I	ENSP00000435798:T154I	T	-	2	0	RNH1	489583	0.001000	0.12720	0.000000	0.03702	0.029000	0.11900	-0.192000	0.09587	-0.114000	0.11936	0.491000	0.48974	ACA	RNH1	-	NULL	ENSG00000023191		0.632	RNH1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	RNH1	HGNC	protein_coding	OTTHUMT00000384301.1	9	0.00	0	G	NM_203389		499583	499583	-1	no_stop_codon	ENST00000531149	ensembl	human	putative	69_37n	missense	13	31.58	6	SNP	0.001	A
SRL	6345	genome.wustl.edu	37	16	4257777	4257777	+	Intron	SNP	G	G	A	rs185857035		TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr16:4257777G>A	ENST00000399609.3	-	2	74				SRL_ENST00000537996.1_Intron	NM_001098814.1	NP_001092284.1	Q86TD4	SRCA_HUMAN	sarcalumenin							sarcoplasmic reticulum (GO:0016529)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(8)|ovary(3)|skin(3)	21						GAGGGAGGGCGCTTGCCACTG	0.652													G|||	1	0.000199681	0.0	0.0014	5008	,	,		16038	0.0		0.0	False		,,,				2504	0.0					dbGAP											0																																										-	-	-	SO:0001627	intron_variant	0			AK056588	CCDS42113.1	16p13.3	2008-02-05				ENSG00000185739			11295	protein-coding gene	gene with protein product		604992				2762314	Standard	NM_001098814		Approved		uc002cvz.4	Q86TD4		ENST00000399609.3:c.62-3142C>T	16.37:g.4257777G>A		Somatic		WXS	Illumina GAIIx	Phase_IV		Silent	SNP	NULL	p.S130	ENST00000399609.3	37	c.390	CCDS42113.1	16																																																																																			SRL	-	NULL	ENSG00000185739		0.652	SRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SRL	HGNC	protein_coding	OTTHUMT00000438087.1	97	0.00	0	G	XM_064152		4257777	4257777	-1	no_errors	ENST00000572111	ensembl	human	known	69_37n	silent	89	10.89	11	SNP	0.000	A
TBX3	6926	genome.wustl.edu	37	12	115115441	115115443	+	In_Frame_Del	DEL	GTC	GTC	-			TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	GTC	GTC					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr12:115115441_115115443delGTC	ENST00000257566.3	-	5	1272_1274	c.883_885delGAC	c.(883-885)gacdel	p.D295del	TBX3_ENST00000349155.2_In_Frame_Del_p.D275del	NM_016569.3	NP_057653.3	O15119	TBX3_HUMAN	T-box 3	295					anterior/posterior axis specification, embryo (GO:0008595)|atrioventricular bundle cell differentiation (GO:0003167)|blood vessel development (GO:0001568)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cardiac muscle cell fate commitment (GO:0060923)|cell aging (GO:0007569)|cellular senescence (GO:0090398)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|female genitalia development (GO:0030540)|follicle-stimulating hormone secretion (GO:0046884)|forelimb morphogenesis (GO:0035136)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|limbic system development (GO:0021761)|luteinizing hormone secretion (GO:0032275)|male genitalia development (GO:0030539)|mammary gland development (GO:0030879)|mammary placode formation (GO:0060596)|mesoderm morphogenesis (GO:0048332)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sinoatrial node cell development (GO:0060931)|skeletal system development (GO:0001501)|specification of organ position (GO:0010159)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum morphogenesis (GO:0060412)	nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D295H(1)		breast(5)|endometrium(1)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0574)		AAGGGTTGTTGTCTATTTTTAAC	0.36																																						dbGAP											1	Substitution - Missense(1)	urinary_tract(1)																																								-	-	-	SO:0001651	inframe_deletion	0			BC025258	CCDS9175.1, CCDS9176.1	12q24.21	2013-09-05	2008-07-31		ENSG00000135111	ENSG00000135111		"""T-boxes"""	11602	protein-coding gene	gene with protein product		601621	"""ulnar mammary syndrome"""	UMS		8988164	Standard	NM_005996		Approved	TBX3-ISO, XHL	uc001tvt.1	O15119	OTTHUMG00000169586	ENST00000257566.3:c.883_885delGAC	12.37:g.115115441_115115443delGTC	ENSP00000257566:p.Asp295del	Somatic		WXS	Illumina GAIIx	Phase_IV	Q8TB20|Q9UKF8	In_Frame_Del	DEL	pfam_TF_T-box,pfam_TBX,superfamily_p53-like_TF_DNA-bd,smart_TF_T-box,pfscan_TF_T-box,prints_TF_T-box	p.D295in_frame_del	ENST00000257566.3	37	c.885_883	CCDS9176.1	12																																																																																			TBX3	-	pfam_TF_T-box,superfamily_p53-like_TF_DNA-bd,smart_TF_T-box,pfscan_TF_T-box	ENSG00000135111		0.360	TBX3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	TBX3	HGNC	protein_coding	OTTHUMT00000404947.2	42	0.00	0	GTC	NM_016569, NM_005996		115115441	115115443	-1	no_errors	ENST00000257566	ensembl	human	known	69_37n	in_frame_del	31	13.89	5	DEL	1.000:1.000:1.000	-
TNFSF13	8741	genome.wustl.edu	37	17	7463369	7463369	+	Missense_Mutation	SNP	A	A	T			TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr17:7463369A>T	ENST00000338784.4	+	4	832	c.389A>T	c.(388-390)gAc>gTc	p.D130V	TNFSF13_ENST00000349228.4_Missense_Mutation_p.D114V|TNFSF13_ENST00000396545.4_Missense_Mutation_p.D130V|TNFSF13_ENST00000483039.1_5'UTR|SENP3_ENST00000321337.7_5'Flank|TNFSF13_ENST00000396542.1_Missense_Mutation_p.D85V|SENP3_ENST00000429205.2_5'Flank|TNFSF12-TNFSF13_ENST00000293826.4_Missense_Mutation_p.D210V|TNFSF13_ENST00000380535.4_Missense_Mutation_p.D102V|TNFSF12_ENST00000557233.1_Missense_Mutation_p.D210V	NM_003808.3	NP_003799.1	O75888	TNF13_HUMAN	tumor necrosis factor (ligand) superfamily, member 13	130					gene expression (GO:0010467)|immunoglobulin production in mucosal tissue (GO:0002426)|mRNA metabolic process (GO:0016071)|positive regulation of cell proliferation (GO:0008284)|positive regulation of germinal center formation (GO:0002636)|positive regulation of isotype switching to IgA isotypes (GO:0048298)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)	receptor binding (GO:0005102)			large_intestine(2)|lung(2)|skin(1)	5		Prostate(122;0.157)				CCTCCAGATGACTCCGATGTG	0.532											OREG0024138	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										dbGAP											0													91.0	87.0	88.0					17																	7463369		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF046888	CCDS11111.1, CCDS11112.1, CCDS42256.1, CCDS56019.1, CCDS73957.1	17p13.1	2007-07-23			ENSG00000161955	ENSG00000161955		"""Tumor necrosis factor (ligand) superfamily"", ""CD molecules"""	11928	protein-coding gene	gene with protein product		604472				9743536	Standard	NM_172088		Approved	APRIL, CD256		O75888	OTTHUMG00000108145	ENST00000338784.4:c.389A>T	17.37:g.7463369A>T	ENSP00000343505:p.Asp130Val	Somatic	641	WXS	Illumina GAIIx	Phase_IV	A8MYD5|B4DVT2|Q541E1|Q5U0G8|Q96HV6|Q9P1M8|Q9P1M9	Missense_Mutation	SNP	pfam_TNF,superfamily_Tumour_necrosis_fac-like,smart_TNF,pfscan_TNF	p.D210V	ENST00000338784.4	37	c.629	CCDS11111.1	17	.	.	.	.	.	.	.	.	.	.	A	14.29	2.492196	0.44352	.	.	ENSG00000239697;ENSG00000248871;ENSG00000161955;ENSG00000161955;ENSG00000161955;ENSG00000161955;ENSG00000161955;ENSG00000161955;ENSG00000161955	ENST00000557233;ENST00000293826;ENST00000396542;ENST00000438470;ENST00000436057;ENST00000349228;ENST00000338784;ENST00000380535;ENST00000396545	D;D;D;T;T;D;D;D;D	0.97553	-4.41;-4.41;-4.43;1.29;1.23;-3.9;-3.84;-4.43;-3.84	5.24	5.24	0.73138	Tumour necrosis factor (2);Tumour necrosis factor-like (2);	0.326123	0.30085	N	0.010441	D	0.97405	0.9151	M	0.62723	1.935	0.48571	D	0.999678	P;P;P;P;P;D	0.65815	0.912;0.912;0.794;0.83;0.894;0.995	B;B;P;B;P;P	0.61201	0.361;0.361;0.456;0.361;0.484;0.885	D	0.96886	0.9649	10	0.39692	T	0.17	-13.9641	12.6614	0.56815	1.0:0.0:0.0:0.0	.	102;103;114;130;130;210	B4DVT2;Q2QBA2;O75888-2;O75888;O75888-3;Q8IZK7	.;.;.;TNF13_HUMAN;.;.	V	210;210;85;97;113;114;130;102;130	ENSP00000451451:D210V;ENSP00000293826:D210V;ENSP00000379792:D85V;ENSP00000390771:D97V;ENSP00000410094:D113V;ENSP00000314455:D114V;ENSP00000343505:D130V;ENSP00000369908:D102V;ENSP00000379794:D130V	ENSP00000293826:D210V	D	+	2	0	TNFSF13;TNFSF12-TNFSF13;TNFSF12	7404093	1.000000	0.71417	1.000000	0.80357	0.165000	0.22458	3.178000	0.50879	1.976000	0.57569	0.459000	0.35465	GAC	TNFSF12-TNFSF13	-	superfamily_Tumour_necrosis_fac-like,smart_TNF,pfscan_TNF	ENSG00000248871		0.532	TNFSF13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	TNFSF12-TNFSF13	HGNC	protein_coding	OTTHUMT00000226948.2	29	0.00	0	A	NM_003808		7463369	7463369	+1	no_errors	ENST00000293826	ensembl	human	known	69_37n	missense	21	16.00	4	SNP	1.000	T
TRAPPC3	27095	genome.wustl.edu	37	1	36603290	36603290	+	Intron	SNP	C	C	T	rs2231317	byFrequency	TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr1:36603290C>T	ENST00000373166.3	-	4	514				TRAPPC3_ENST00000373163.1_Intron|TRAPPC3_ENST00000373162.1_Intron|TRAPPC3_ENST00000462715.1_5'UTR	NM_001270894.1|NM_014408.4	NP_001257823.1|NP_055223.1	O43617	TPPC3_HUMAN	trafficking protein particle complex 3						ER to Golgi vesicle-mediated transport (GO:0006888)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|TRAPP complex (GO:0030008)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(1)	4		Myeloproliferative disorder(586;0.0393)				GGCAGTAAAGCGCTGGGGTGA	0.478													C|||	2541	0.507388	0.3351	0.5375	5008	,	,		19768	0.4643		0.7336	False		,,,				2504	0.5307					dbGAP											0																																										-	-	-	SO:0001627	intron_variant	0			AF041432	CCDS404.1, CCDS59194.1, CCDS72757.1, CCDS72758.1	1p34.2	2011-10-10			ENSG00000054116	ENSG00000054116		"""Trafficking protein particle complex"""	19942	protein-coding gene	gene with protein product		610955				8619474	Standard	NM_014408		Approved	BET3	uc031pls.1	O43617	OTTHUMG00000007664	ENST00000373166.3:c.423+106G>A	1.37:g.36603290C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	A6NDN0|B2RDN2|D3DPS2	RNA	SNP	-	NULL	ENST00000373166.3	37	NULL	CCDS404.1	1																																																																																			TRAPPC3	-	-	ENSG00000054116		0.478	TRAPPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TRAPPC3	HGNC	protein_coding	OTTHUMT00000020384.1	55	0.00	0	C	NM_014408		36603290	36603290	-1	no_errors	ENST00000462715	ensembl	human	known	69_37n	rna	32	15.79	6	SNP	0.000	T
TRIM49C	642612	genome.wustl.edu	37	11	89774236	89774236	+	Missense_Mutation	SNP	C	C	G	rs74584169	byFrequency	TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr11:89774236C>G	ENST00000448984.1	+	8	1206	c.877C>G	c.(877-879)Cat>Gat	p.H293D	TRIM49C_ENST00000432771.1_Intron	NM_001195234.1	NP_001182163.1	P0CI26	TR49C_HUMAN	tripartite motif containing 49C	293	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|lung(4)	8						TACTCTGCATCATGAAGAAGC	0.313																																						dbGAP											0																																										-	-	-	SO:0001583	missense	0			BC126470	CCDS53694.1	11q14.3	2014-02-17	2012-05-18	2012-05-18	ENSG00000204449	ENSG00000204449		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	38877	protein-coding gene	gene with protein product			"""tripartite motif containing 49-like 2"""	TRIM49L2			Standard	NM_001195234		Approved		uc010rua.2	P0CI26		ENST00000448984.1:c.877C>G	11.37:g.89774236C>G	ENSP00000388299:p.His293Asp	Somatic		WXS	Illumina GAIIx	Phase_IV	A0AVR7|A0AVR9|Q6DJV1|Q9NS80	Missense_Mutation	SNP	pfam_SPRY_rcpt,pfam_Znf_B-box,superfamily_ConA-like_lec_gl,superfamily_Lambda_DNA-bd_dom,smart_Znf_RING,smart_Znf_B-box,smart_SPla/RYanodine_receptor_subgr,pfscan_B30.2/SPRY,pfscan_Znf_B-box,pfscan_Znf_RING,prints_Butyrophylin	p.H293D	ENST00000448984.1	37	c.877	CCDS53694.1	11	815	0.3731684981684982	211	0.42886178861788615	159	0.43922651933701656	224	0.3916083916083916	221	0.29155672823219	C	1.349	-0.591968	0.03799	.	.	ENSG00000204449	ENST00000448984	T	0.60672	0.17	0.823	0.823	0.18812	Concanavalin A-like lectin/glucanase (1);Butyrophylin-like (1);B30.2/SPRY domain (1);	.	.	.	.	T	0.00012	0.0000	L	0.40543	1.245	0.53005	P	3.399999999997849E-5	B	0.14438	0.01	B	0.13407	0.009	T	0.43442	-0.9391	7	.	.	.	.	4.9575	0.14050	0.0:1.0:0.0:0.0	.	293	P0CI26	T49L2_HUMAN	D	293	ENSP00000388299:H293D	.	H	+	1	0	TRIM49L2	89413884	0.000000	0.05858	0.001000	0.08648	0.015000	0.08874	-1.205000	0.03014	0.742000	0.32697	0.305000	0.20034	CAT	TRIM49C	-	superfamily_ConA-like_lec_gl,pfscan_B30.2/SPRY,prints_Butyrophylin	ENSG00000204449		0.313	TRIM49C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	TRIM49C	HGNC	protein_coding	OTTHUMT00000395455.1	33	0.00	0	C	NM_001195234		89774236	89774236	+1	no_errors	ENST00000448984	ensembl	human	known	69_37n	missense	35	12.50	5	SNP	0.024	G
P2RX6	9127	genome.wustl.edu	37	22	21363744	21363744	+	IGR	SNP	T	T	C	rs2075276	byFrequency	TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr22:21363744T>C	ENST00000591411.1	+	0	0				THAP7-AS1_ENST00000452284.1_RNA|TUBA3FP_ENST00000422086.1_RNA|THAP7-AS1_ENST00000436079.1_RNA			O15547	P2RX6_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 6						cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|muscle contraction (GO:0006936)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|channel activity (GO:0015267)|extracellular ATP-gated cation channel activity (GO:0004931)|identical protein binding (GO:0042802)|purinergic nucleotide receptor activity (GO:0001614)|transmembrane signaling receptor activity (GO:0004888)										CAGATCTGCCTGAGAGAAACC	0.587													T|||	1378	0.27516	0.1452	0.4683	5008	,	,		17292	0.1508		0.4583	False		,,,				2504	0.2536					dbGAP											0																																										-	-	-	SO:0001628	intergenic_variant	0				CCDS13788.2, CCDS54504.1	22q11.21	2012-01-17	2008-03-28	2008-03-28	ENSG00000099957	ENSG00000099957		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	8538	protein-coding gene	gene with protein product		608077	"""purinergic receptor P2X-like 1, orphan receptor"""	P2RXL1		9242461, 10591208, 8786426	Standard	NM_005446		Approved	P2XM, MGC129625, P2X6	uc010gsu.1	O15547	OTTHUMG00000150689		22.37:g.21363744T>C		Somatic		WXS	Illumina GAIIx	Phase_IV	F6V3D7|Q32MB6|Q58F04|Q6IC33|Q9UL50	Splice_Site	SNP	-	NULL	ENST00000591411.1	37	c.NULL		22																																																																																			TUBA3FP	-	-	ENSG00000161149		0.587	P2RX6-009	KNOWN	basic	processed_transcript	TUBA3FP	HGNC	protein_coding	OTTHUMT00000459956.1	34	0.00	0	T	NM_005446		21363744	21363744	-1	no_errors	ENST00000292748	ensembl	human	known	69_37n	splice_site	31	11.43	4	SNP	1.000	C
TXNRD1	7296	genome.wustl.edu	37	12	104703836	104703836	+	Missense_Mutation	SNP	A	A	G	rs7134193	byFrequency	TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr12:104703836A>G	ENST00000526950.1	+	1	208	c.130A>G	c.(130-132)Aca>Gca	p.T44A	TXNRD1_ENST00000354940.6_Intron|TXNRD1_ENST00000524698.1_Intron|TXNRD1_ENST00000525566.1_Intron|TXNRD1_ENST00000429002.2_Intron|TXNRD1_ENST00000540716.1_Intron|TXNRD1_ENST00000526390.1_Intron|TXNRD1_ENST00000542918.1_Intron|TXNRD1_ENST00000378070.4_Intron|TXNRD1_ENST00000388854.3_Intron|TXNRD1_ENST00000503506.2_Intron|TXNRD1_ENST00000427956.1_Missense_Mutation_p.T90A|TXNRD1_ENST00000397736.2_Intron|TXNRD1_ENST00000526691.1_Intron|TXNRD1_ENST00000529546.1_Intron			Q16881	TRXR1_HUMAN	thioredoxin reductase 1	0					cell proliferation (GO:0008283)|cell redox homeostasis (GO:0045454)|cellular lipid metabolic process (GO:0044255)|mesoderm formation (GO:0001707)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|NADP binding (GO:0050661)|protein disulfide oxidoreductase activity (GO:0015035)|thioredoxin-disulfide reductase activity (GO:0004791)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(5)|skin(1)|stomach(1)|urinary_tract(1)	16					Arsenic trioxide(DB01169)|Flavin adenine dinucleotide(DB03147)	TTCACCCCCTACATCTGATAG	0.463													A|||	993	0.198283	0.2723	0.1671	5008	,	,		18394	0.0228		0.2475	False		,,,				2504	0.2505				Ovarian(139;555 1836 9186 9946 10884)	dbGAP											0																																										-	-	-	SO:0001583	missense	0				CCDS53820.1, CCDS53821.1, CCDS53823.1, CCDS58274.1	12q23-q24.1	2012-03-01							12437	protein-coding gene	gene with protein product		601112				7589432	Standard	NM_001093771		Approved	TXNR, GRIM-12, Trxr1	uc021rcx.2	Q16881		ENST00000526950.1:c.130A>G	12.37:g.104703836A>G	ENSP00000432812:p.Thr44Ala	Somatic		WXS	Illumina GAIIx	Phase_IV	B7Z1F4|B7Z3Y8|B7Z904|E9PMY9|F5H780|Q6FI31|Q6VB40|Q6VB41|Q6VB42|Q6VBP2|Q6VBP3|Q6VBP4|Q6VBP5|Q6VBP9|Q6VBQ0|Q6YNQ1|Q76P53|Q7LA96|Q8WVC8|Q99475|Q9UES8|Q9UH79	Missense_Mutation	SNP	pfam_Pyr_nucl-diS_OxRdtase_FAD/NAD,pfam_Pyr_nucl-diS_OxRdtase_dimer,pfam_Pyr_OxRdtase_NAD-bd_dom,pfam_FAD_bind_dom,superfamily_FAD/NAD-linked_Rdtase_dimer,prints_FAD_pyr_nucl-diS_OxRdtase,prints_Hg_reductase,prints_Pyridine_nuc-diS_OxRdtase_2,tigrfam_Thioredoxin/glutathione_Rdtase	p.T90A	ENST00000526950.1	37	c.268		12	415	0.190018315018315	147	0.29878048780487804	62	0.1712707182320442	8	0.013986013986013986	198	0.2612137203166227	A	2.304	-0.359540	0.05138	.	.	ENSG00000198431	ENST00000528079;ENST00000427956;ENST00000526950	T;T	0.68331	-0.24;-0.32	5.68	-11.1	0.00147	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	4.000000000004E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.05767	-1.0865	7	0.34782	T	0.22	.	13.9743	0.64262	0.149:0.2166:0.6344:0.0	rs7134193	90	E7EW10	.	A	44;90;44	ENSP00000393328:T90A;ENSP00000432812:T44A	ENSP00000393328:T90A	T	+	1	0	TXNRD1	103227966	0.000000	0.05858	0.000000	0.03702	0.192000	0.23643	-1.760000	0.01806	-1.702000	0.01411	-1.729000	0.00701	ACA	TXNRD1	-	NULL	ENSG00000198431		0.463	TXNRD1-009	PUTATIVE	basic|seleno	protein_coding	TXNRD1	HGNC	protein_coding	OTTHUMT00000389976.1	40	0.00	0	A	NM_003330		104703836	104703836	+1	no_errors	ENST00000427956	ensembl	human	known	69_37n	missense	26	16.13	5	SNP	0.000	G
ZNF467	168544	genome.wustl.edu	37	7	149461958	149461960	+	In_Frame_Del	DEL	AGG	AGG	-			TCGA-A2-A3KC-01A-11D-A20S-09	TCGA-A2-A3KC-10A-01D-A20S-09	AGG	AGG					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f9f04e42-63a2-4ee1-ade4-9e5bb5c20cdd	abba0fe4-8c3b-4b8d-9b68-36708ba3a4ef	g.chr7:149461958_149461960delAGG	ENST00000302017.3	-	5	2044_2046	c.1631_1633delCCT	c.(1630-1635)tcctgc>tgc	p.S544del	ZNF467_ENST00000484747.1_Intron	NM_207336.1	NP_997219.1	Q7Z7K2	ZN467_HUMAN	zinc finger protein 467	544					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|kidney(1)|large_intestine(2)|liver(1)|lung(7)|urinary_tract(1)	13	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CACTGCGGGCAGGAGAAGGGGCG	0.709																																						dbGAP											0																																										-	-	-	SO:0001651	inframe_deletion	0			BC029296	CCDS5899.1	7q36.1	2013-01-08			ENSG00000181444	ENSG00000181444		"""Zinc fingers, C2H2-type"""	23154	protein-coding gene	gene with protein product		614040				12426389	Standard	NM_207336		Approved	EZI, Zfp467	uc003wgd.2	Q7Z7K2	OTTHUMG00000157883	ENST00000302017.3:c.1631_1633delCCT	7.37:g.149461958_149461960delAGG	ENSP00000304769:p.Ser544del	Somatic		WXS	Illumina GAIIx	Phase_IV		In_Frame_Del	DEL	pfam_Znf_C2H2,smart_Znf_C2H2-like,pfscan_Znf_C2H2	p.S544in_frame_del	ENST00000302017.3	37	c.1633_1631	CCDS5899.1	7																																																																																			ZNF467	-	pfam_Znf_C2H2,smart_Znf_C2H2-like,pfscan_Znf_C2H2	ENSG00000181444		0.709	ZNF467-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ZNF467	HGNC	protein_coding	OTTHUMT00000349833.1	62	0.00	0	AGG	NM_207336		149461958	149461960	-1	no_errors	ENST00000302017	ensembl	human	known	69_37n	in_frame_del	24	33.33	12	DEL	0.991:0.317:0.255	-
