#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
BCR	613	genome.wustl.edu	37	22	23658000	23658000	+	3'UTR	SNP	G	G	A			TCGA-A7-A3IY-01A-21D-A21Q-09	TCGA-A7-A3IY-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48173064-ea1c-4cf2-89a3-f08baae2ea05	d4ab2281-9ee9-45c9-9e97-686602678727	g.chr22:23658000G>A	ENST00000305877.8	+	0	4858				BCR_ENST00000436990.2_3'UTR|BCR_ENST00000359540.3_3'UTR	NM_004327.3	NP_004318.3	P11274	BCR_HUMAN	breakpoint cluster region						actin cytoskeleton organization (GO:0030036)|brain development (GO:0007420)|inner ear morphogenesis (GO:0042472)|negative regulation of cell migration (GO:0030336)|negative regulation of inflammatory response (GO:0050728)|negative regulation of neutrophil degranulation (GO:0043314)|neuromuscular process controlling balance (GO:0050885)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of phagocytosis (GO:0050766)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|kinase activity (GO:0016301)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)|Rac GTPase activator activity (GO:0030675)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)		BCR/JAK2(6)	central_nervous_system(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	35					Bosutinib(DB06616)|Ponatinib(DB08901)	ACAGGGTGAAGGGAGTGGTTT	0.532			T	"""ABL1,  FGFR1, JAK2 """	"""CML, ALL, AML"""																																	dbGAP		Dom	yes		22	22q11.21	613	breakpoint cluster region		L	0																																										-	-	-	SO:0001624	3_prime_UTR_variant	0				CCDS13806.1, CCDS13807.1	22q11	2013-01-10			ENSG00000186716	ENSG00000186716		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	1014	protein-coding gene	gene with protein product		151410		D22S11, BCR1		1657398, 18070886	Standard	NM_004327		Approved	D22S662, CML, PHL, ALL	uc002zww.3	P11274	OTTHUMG00000150655	ENST00000305877.8:c.*291G>A	22.37:g.23658000G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	P78501|Q12842|Q4LE80|Q6NZI3	RNA	SNP	-	NULL	ENST00000305877.8	37	NULL	CCDS13806.1	22																																																																																			BCR	-	-	ENSG00000186716		0.532	BCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	BCR	HGNC	protein_coding	OTTHUMT00000075819.1	36	0.00	0	G	NM_004327		23658000	23658000	+1	no_errors	ENST00000436990	ensembl	human	known	69_37n	rna	42	16.00	8	SNP	0.002	A
BCR	613	genome.wustl.edu	37	22	23658002	23658002	+	3'UTR	SNP	G	G	C			TCGA-A7-A3IY-01A-21D-A21Q-09	TCGA-A7-A3IY-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48173064-ea1c-4cf2-89a3-f08baae2ea05	d4ab2281-9ee9-45c9-9e97-686602678727	g.chr22:23658002G>C	ENST00000305877.8	+	0	4860				BCR_ENST00000436990.2_3'UTR|BCR_ENST00000359540.3_3'UTR	NM_004327.3	NP_004318.3	P11274	BCR_HUMAN	breakpoint cluster region						actin cytoskeleton organization (GO:0030036)|brain development (GO:0007420)|inner ear morphogenesis (GO:0042472)|negative regulation of cell migration (GO:0030336)|negative regulation of inflammatory response (GO:0050728)|negative regulation of neutrophil degranulation (GO:0043314)|neuromuscular process controlling balance (GO:0050885)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of phagocytosis (GO:0050766)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|kinase activity (GO:0016301)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)|Rac GTPase activator activity (GO:0030675)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)		BCR/JAK2(6)	central_nervous_system(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	35					Bosutinib(DB06616)|Ponatinib(DB08901)	AGGGTGAAGGGAGTGGTTTTT	0.532			T	"""ABL1,  FGFR1, JAK2 """	"""CML, ALL, AML"""																																	dbGAP		Dom	yes		22	22q11.21	613	breakpoint cluster region		L	0																																										-	-	-	SO:0001624	3_prime_UTR_variant	0				CCDS13806.1, CCDS13807.1	22q11	2013-01-10			ENSG00000186716	ENSG00000186716		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	1014	protein-coding gene	gene with protein product		151410		D22S11, BCR1		1657398, 18070886	Standard	NM_004327		Approved	D22S662, CML, PHL, ALL	uc002zww.3	P11274	OTTHUMG00000150655	ENST00000305877.8:c.*293G>C	22.37:g.23658002G>C		Somatic		WXS	Illumina GAIIx	Phase_IV	P78501|Q12842|Q4LE80|Q6NZI3	RNA	SNP	-	NULL	ENST00000305877.8	37	NULL	CCDS13806.1	22																																																																																			BCR	-	-	ENSG00000186716		0.532	BCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	BCR	HGNC	protein_coding	OTTHUMT00000075819.1	35	0.00	0	G	NM_004327		23658002	23658002	+1	no_errors	ENST00000436990	ensembl	human	known	69_37n	rna	40	16.67	8	SNP	0.329	C
SMIM7	79086	genome.wustl.edu	37	19	16757702	16757702	+	3'UTR	SNP	T	T	C	rs8106284	byFrequency	TCGA-A7-A3IY-01A-21D-A21Q-09	TCGA-A7-A3IY-10A-01D-A21Q-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48173064-ea1c-4cf2-89a3-f08baae2ea05	d4ab2281-9ee9-45c9-9e97-686602678727	g.chr19:16757702T>C	ENST00000487416.2	-	0	629				SMIM7_ENST00000597711.1_3'UTR|CTC-429P9.4_ENST00000600705.1_Intron|CTC-429P9.1_ENST00000601040.1_RNA|CTC-429P9.4_ENST00000593962.1_Intron|SMIM7_ENST00000397349.2_5'UTR	NM_024104.3	NP_077009.2	Q9BQ49	SMIM7_HUMAN	small integral membrane protein 7							integral component of membrane (GO:0016021)											TGTCCAAAAATACGGCTGTGT	0.463													C|||	518	0.103435	0.2095	0.0692	5008	,	,		17832	0.003		0.0855	False		,,,				2504	0.1063					dbGAP											0																																										-	-	-	SO:0001624	3_prime_UTR_variant	0			AK025602	CCDS12348.2, CCDS74307.1	19p13.11	2012-10-26	2012-10-26	2012-10-26	ENSG00000214046	ENSG00000214046			28419	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 42"""	C19orf42		12477932	Standard	NM_024104		Approved	MGC2747	uc002ner.3	Q9BQ49	OTTHUMG00000149895	ENST00000487416.2:c.*355A>G	19.37:g.16757702T>C		Somatic		WXS	Illumina GAIIx	Phase_IV	A8MX44	RNA	SNP	-	NULL	ENST00000487416.2	37	NULL	CCDS12348.2	19																																																																																			C19orf42	-	-	ENSG00000214046		0.463	SMIM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	C19orf42	HGNC	protein_coding	OTTHUMT00000313801.2	31	0.00	0	T	NM_024104		16757702	16757702	-1	no_errors	ENST00000397349	ensembl	human	known	69_37n	rna	30	11.76	4	SNP	0.000	C
CCDC73	493860	genome.wustl.edu	37	11	32635498	32635498	+	Missense_Mutation	SNP	G	G	T			TCGA-A7-A3IY-01A-21D-A21Q-09	TCGA-A7-A3IY-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48173064-ea1c-4cf2-89a3-f08baae2ea05	d4ab2281-9ee9-45c9-9e97-686602678727	g.chr11:32635498G>T	ENST00000335185.5	-	16	2409	c.2366C>A	c.(2365-2367)gCc>gAc	p.A789D	CCDC73_ENST00000534415.1_5'Flank	NM_001008391.2	NP_001008392.2	Q6ZRK6	CCD73_HUMAN	coiled-coil domain containing 73	789										NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	51	Breast(20;0.112)					CACATCTTTGGCTTGTGAAGC	0.343																																						dbGAP											0													97.0	83.0	88.0					11																	32635498		1836	4091	5927	-	-	-	SO:0001583	missense	0			AK128159	CCDS41630.1	11p13	2006-02-11			ENSG00000186714	ENSG00000186714			23261	protein-coding gene	gene with protein product		612328					Standard	NM_001008391		Approved	NY-SAR-79	uc001mtv.4	Q6ZRK6	OTTHUMG00000166279	ENST00000335185.5:c.2366C>A	11.37:g.32635498G>T	ENSP00000335325:p.Ala789Asp	Somatic		WXS	Illumina GAIIx	Phase_IV	Q6P5Q7|Q6ZMW0|Q86WE7	Missense_Mutation	SNP	NULL	p.A789D	ENST00000335185.5	37	c.2366	CCDS41630.1	11	.	.	.	.	.	.	.	.	.	.	G	10.27	1.303878	0.23736	.	.	ENSG00000186714	ENST00000335185	.	.	.	5.43	3.5	0.40072	.	0.429522	0.21904	N	0.067410	T	0.55417	0.1919	L	0.53249	1.67	0.80722	D	1	B	0.11235	0.004	B	0.16722	0.016	T	0.57505	-0.7800	9	0.87932	D	0	.	9.1023	0.36676	0.0753:0.0:0.7813:0.1434	.	789	Q6ZRK6	CCD73_HUMAN	D	789	.	ENSP00000335325:A789D	A	-	2	0	CCDC73	32592074	0.007000	0.16637	0.652000	0.29579	0.327000	0.28475	0.893000	0.28336	1.237000	0.43756	0.650000	0.86243	GCC	CCDC73	-	NULL	ENSG00000186714		0.343	CCDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CCDC73	HGNC	protein_coding	OTTHUMT00000388874.2	34	0.00	0	G	NM_001008391		32635498	32635498	-1	no_errors	ENST00000335185	ensembl	human	known	69_37n	missense	36	10.00	4	SNP	0.829	T
COL6A3	1293	genome.wustl.edu	37	2	238303516	238303516	+	Silent	SNP	T	T	A			TCGA-A7-A3IY-01A-21D-A21Q-09	TCGA-A7-A3IY-10A-01D-A21Q-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48173064-ea1c-4cf2-89a3-f08baae2ea05	d4ab2281-9ee9-45c9-9e97-686602678727	g.chr2:238303516T>A	ENST00000295550.4	-	3	875	c.423A>T	c.(421-423)ggA>ggT	p.G141G	COL6A3_ENST00000392003.2_Intron|COL6A3_ENST00000353578.4_Intron|COL6A3_ENST00000392004.3_Intron|COL6A3_ENST00000346358.4_Silent_p.G141G|COL6A3_ENST00000472056.1_Intron|COL6A3_ENST00000347401.3_Silent_p.G141G|COL6A3_ENST00000409809.1_Intron	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	141	Nonhelical region.|VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		CCTGAGGGACTCCGTCACCGG	0.493																																						dbGAP											0													83.0	84.0	83.0					2																	238303516		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"""Collagens"""	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.423A>T	2.37:g.238303516T>A		Somatic		WXS	Illumina GAIIx	Phase_IV	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	pfam_VWF_A,pfam_Collagen,pfam_Prot_inh_Kunz-m,superfamily_Prot_inh_Kunz-m,superfamily_Fibronectin_type3,smart_VWF_A,smart_Prot_inh_Kunz-m,pfscan_Fibronectin_type3,pfscan_VWF_A,pfscan_Prot_inh_Kunz-m,prints_Prot_inh_Kunz-m	p.G141	ENST00000295550.4	37	c.423	CCDS33412.1	2																																																																																			COL6A3	-	pfam_VWF_A,smart_VWF_A,pfscan_VWF_A	ENSG00000163359		0.493	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	COL6A3	HGNC	protein_coding	OTTHUMT00000315790.2	30	0.00	0	T	NM_004369		238303516	238303516	-1	no_errors	ENST00000295550	ensembl	human	known	69_37n	silent	36	14.29	6	SNP	0.984	A
CROCCP2	84809	genome.wustl.edu	37	1	16946097	16946097	+	lincRNA	SNP	G	G	T	rs144168507		TCGA-A7-A3IY-01A-21D-A21Q-09	TCGA-A7-A3IY-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48173064-ea1c-4cf2-89a3-f08baae2ea05	d4ab2281-9ee9-45c9-9e97-686602678727	g.chr1:16946097G>T	ENST00000412962.1	-	0	1422				RP5-1182A14.5_ENST00000607700.1_lincRNA			Q86T23	CROL1_HUMAN	ciliary rootlet coiled-coil, rootletin pseudogene 2						centrosome organization (GO:0051297)	ciliary rootlet (GO:0035253)											ATATGGAACAGCTTTCCTGGT	0.577																																						dbGAP											0																																										-	-	-			0			AK090414		1p36.13	2010-07-08	2010-07-08	2010-07-08	ENSG00000215908	ENSG00000215908			28170	pseudogene	pseudogene			"""ciliary rootlet coiled-coil, rootletin-like 1"""	CROCCL1		12477932	Standard	NR_026752		Approved	MGC12760	uc001azf.3	Q86T23	OTTHUMG00000037884		1.37:g.16946097G>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q8NF65|Q96FR5|Q9BRE8	RNA	SNP	-	NULL	ENST00000412962.1	37	NULL		1																																																																																			CROCCP2	-	-	ENSG00000215908		0.577	CROCCP2-003	KNOWN	basic	lincRNA	CROCCP2	HGNC	lincRNA	OTTHUMT00000092784.1	8	0.00	0	G	NR_026752.1		16946097	16946097	-1	no_errors	ENST00000412962	ensembl	human	known	69_37n	rna	10	37.50	6	SNP	0.009	T
TAPT1-AS1	202020	genome.wustl.edu	37	4	16258155	16258155	+	RNA	SNP	G	G	A	rs2940	byFrequency	TCGA-A7-A3IY-01A-21D-A21Q-09	TCGA-A7-A3IY-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48173064-ea1c-4cf2-89a3-f08baae2ea05	d4ab2281-9ee9-45c9-9e97-686602678727	g.chr4:16258155G>A	ENST00000570786.1	+	0	510				TAPT1-AS1_ENST00000573950.1_RNA|TAPT1-AS1_ENST00000573308.1_RNA	NR_027696.1				TAPT1 antisense RNA 1 (head to head)																		ACAGGTCCACGAACTCGCCGG	0.597													G|||	695	0.138778	0.233	0.1556	5008	,	,		16949	0.0109		0.1382	False		,,,				2504	0.1319					dbGAP											0																																										-	-	-			0					4p15.32	2012-11-06	2012-11-06		ENSG00000263327	ENSG00000263327		"""Long non-coding RNAs"""	26832	non-coding RNA	RNA, long non-coding							Standard	NR_027696		Approved	FLJ39653			OTTHUMG00000160321		4.37:g.16258155G>A		Somatic		WXS	Illumina GAIIx	Phase_IV		RNA	SNP	-	NULL	ENST00000570786.1	37	NULL		4																																																																																			RP11-783N5.1	-	-	ENSG00000263327		0.597	TAPT1-AS1-002	KNOWN	basic	antisense	FLJ39653	Clone_based_vega_gene	antisense	OTTHUMT00000439459.1	8	0.00	0	G	NR_027696		16258155	16258155	+1	no_errors	ENST00000570786	ensembl	human	known	69_37n	rna	8	38.46	5	SNP	1.000	A
FSIP2	401024	genome.wustl.edu	37	2	186670925	186670925	+	Missense_Mutation	SNP	C	C	A			TCGA-A7-A3IY-01A-21D-A21Q-09	TCGA-A7-A3IY-10A-01D-A21Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48173064-ea1c-4cf2-89a3-f08baae2ea05	d4ab2281-9ee9-45c9-9e97-686602678727	g.chr2:186670925C>A	ENST00000424728.1	+	17	16892	c.16892C>A	c.(16891-16893)tCc>tAc	p.S5631Y	FSIP2_ENST00000343098.5_Missense_Mutation_p.S5720Y			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	5631										NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						CAGTTATCCTCCTTGAAGTCC	0.378																																						dbGAP											0													47.0	46.0	46.0					2																	186670925		1824	4075	5899	-	-	-	SO:0001583	missense	0			AK092099	CCDS54426.1	2q32.1	2010-06-18			ENSG00000188738	ENSG00000188738			21675	protein-coding gene	gene with protein product		615796				14702039	Standard	NM_173651		Approved	FLJ34780	uc002upl.3	Q5CZC0	OTTHUMG00000153874	ENST00000424728.1:c.16892C>A	2.37:g.186670925C>A	ENSP00000401306:p.Ser5631Tyr	Somatic		WXS	Illumina GAIIx	Phase_IV	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Missense_Mutation	SNP	NULL	p.S5720Y	ENST00000424728.1	37	c.17159		2	.	.	.	.	.	.	.	.	.	.	C	8.903	0.956804	0.18507	.	.	ENSG00000188738	ENST00000343098;ENST00000424728	T;T	0.47177	0.85;0.85	4.23	-2.47	0.06442	.	.	.	.	.	T	0.23289	0.0563	N	0.14661	0.345	0.09310	N	1	.	.	.	.	.	.	T	0.18587	-1.0332	7	0.36615	T	0.2	.	0.6896	0.00889	0.2892:0.2379:0.2845:0.1884	.	.	.	.	Y	5720;5631	ENSP00000344403:S5720Y;ENSP00000401306:S5631Y	ENSP00000344403:S5720Y	S	+	2	0	FSIP2	186379170	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.222000	0.17699	-0.396000	0.07703	0.591000	0.81541	TCC	FSIP2	-	NULL	ENSG00000188738		0.378	FSIP2-001	KNOWN	basic	protein_coding	FSIP2	HGNC	protein_coding	OTTHUMT00000332778.3	21	0.00	0	C	NM_173651		186670925	186670925	+1	no_errors	ENST00000343098	ensembl	human	known	69_37n	missense	17	26.09	6	SNP	0.000	A
HOXB3	3213	genome.wustl.edu	37	17	46627865	46627865	+	Missense_Mutation	SNP	A	A	G			TCGA-A7-A3IY-01A-21D-A21Q-09	TCGA-A7-A3IY-10A-01D-A21Q-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48173064-ea1c-4cf2-89a3-f08baae2ea05	d4ab2281-9ee9-45c9-9e97-686602678727	g.chr17:46627865A>G	ENST00000470495.1	-	2	2574	c.1127T>C	c.(1126-1128)cTt>cCt	p.L376P	HOXB3_ENST00000485909.2_Missense_Mutation_p.L244P|HOXB-AS1_ENST00000502764.2_RNA|HOXB3_ENST00000490677.1_Missense_Mutation_p.L242P|HOXB3_ENST00000498678.1_Missense_Mutation_p.L376P|HOXB-AS3_ENST00000465846.2_RNA|HOXB-AS1_ENST00000508688.1_RNA|HOXB3_ENST00000311626.4_Missense_Mutation_p.L376P|HOXB3_ENST00000489475.1_Missense_Mutation_p.L303P|HOXB3_ENST00000472863.1_Missense_Mutation_p.L303P|HOXB-AS1_ENST00000435312.1_RNA|HOXB3_ENST00000460160.1_Missense_Mutation_p.L244P|HOXB3_ENST00000476342.1_Missense_Mutation_p.L376P			P14651	HXB3_HUMAN	homeobox B3	376					angiogenesis (GO:0001525)|anterior/posterior pattern specification (GO:0009952)|cartilage development (GO:0051216)|definitive hemopoiesis (GO:0060216)|embryonic skeletal system morphogenesis (GO:0048704)|face development (GO:0060324)|glossopharyngeal nerve morphogenesis (GO:0021615)|hematopoietic progenitor cell differentiation (GO:0002244)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of neurogenesis (GO:0050767)|rhombomere development (GO:0021546)|thyroid gland development (GO:0030878)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|kidney(2)|large_intestine(2)|lung(16)|prostate(4)|upper_aerodigestive_tract(1)	30						GTGATGGGAAAGGTGGTTGAG	0.701											OREG0024516	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										dbGAP											0													31.0	40.0	37.0					17																	46627865		2185	4280	6465	-	-	-	SO:0001583	missense	0				CCDS11528.1	17q21.32	2011-06-20	2005-12-22		ENSG00000120093	ENSG00000120093		"""Homeoboxes / ANTP class : HOXL subclass"""	5114	protein-coding gene	gene with protein product		142966	"""homeo box B3"""	HOX2, HOX2G		1973146, 1358459	Standard	XM_006721854		Approved		uc002ino.3	P14651	OTTHUMG00000159922	ENST00000470495.1:c.1127T>C	17.37:g.46627865A>G	ENSP00000417207:p.Leu376Pro	Somatic	940	WXS	Illumina GAIIx	Phase_IV	A8K567|B7Z5N8|B7Z5P8|B7ZAD0|D3DTV3|O95615|P17484	Missense_Mutation	SNP	pfam_Homeodomain,superfamily_Homeodomain-like,smart_Homeodomain,pfscan_Homeodomain,prints_Homeobox_metazoa	p.L376P	ENST00000470495.1	37	c.1127	CCDS11528.1	17	.	.	.	.	.	.	.	.	.	.	A	19.31	3.802333	0.70682	.	.	ENSG00000120093	ENST00000470495;ENST00000472863;ENST00000311626;ENST00000498678;ENST00000490677;ENST00000460160;ENST00000485909;ENST00000489475;ENST00000476342	D;D;D;D;D;D;D;D;D	0.92149	-2.89;-2.9;-2.89;-2.89;-2.98;-2.97;-2.97;-2.9;-2.89	4.35	4.35	0.52113	.	0.000000	0.85682	D	0.000000	D	0.95746	0.8616	M	0.80982	2.52	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96300	0.9220	10	0.87932	D	0	.	13.9757	0.64271	1.0:0.0:0.0:0.0	.	376	P14651	HXB3_HUMAN	P	376;303;376;376;242;244;244;303;376	ENSP00000417207:L376P;ENSP00000419676:L303P;ENSP00000308252:L376P;ENSP00000420595:L376P;ENSP00000449977:L242P;ENSP00000418035:L244P;ENSP00000438747:L244P;ENSP00000418729:L303P;ENSP00000418892:L376P	ENSP00000308252:L376P	L	-	2	0	HOXB3	43982864	1.000000	0.71417	0.999000	0.59377	0.952000	0.60782	8.989000	0.93506	1.958000	0.56883	0.379000	0.24179	CTT	HOXB3	-	NULL	ENSG00000120093		0.701	HOXB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HOXB3	HGNC	protein_coding	OTTHUMT00000358261.1	62	0.00	0	A			46627865	46627865	-1	no_errors	ENST00000311626	ensembl	human	known	69_37n	missense	77	23.76	24	SNP	1.000	G
IGHJ6	28475	genome.wustl.edu	37	14	106329445	106329445	+	RNA	SNP	G	G	A			TCGA-A7-A3IY-01A-21D-A21Q-09	TCGA-A7-A3IY-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48173064-ea1c-4cf2-89a3-f08baae2ea05	d4ab2281-9ee9-45c9-9e97-686602678727	g.chr14:106329445G>A	ENST00000390560.2	-	0	23				IGHD7-27_ENST00000439842.1_RNA|IGHJ3_ENST00000463911.1_RNA|IGHJ4_ENST00000461719.1_RNA|IGHJ1_ENST00000390565.1_RNA|IGHJ2_ENST00000390564.2_RNA|IGHJ5_ENST00000488476.1_RNA					immunoglobulin heavy joining 6																		TGCCCCAGACGTCCATGTAGT	0.532																																						dbGAP											0													136.0	130.0	132.0					14																	106329445		1992	4148	6140	-	-	-			0			J00256		14q32.33	2012-02-08			ENSG00000211900	ENSG00000211900		"""Immunoglobulins / IGH locus"""	5540	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000152455		14.37:g.106329445G>A		Somatic		WXS	Illumina GAIIx	Phase_IV		Silent	SNP	NULL	p.D8	ENST00000390560.2	37	c.24		14																																																																																			IGHJ6	-	NULL	ENSG00000211900		0.532	IGHJ6-001	KNOWN	mRNA_start_NF|mRNA_end_NF|cds_start_NF|cds_end_NF|basic|appris_principal	IG_J_gene	IGHJ6	HGNC	IG_J_gene	OTTHUMT00000326277.1	26	0.00	0	G	NG_001019		106329445	106329445	-1	no_start_codon:no_stop_codon:bad_bp_length_for_coding_region	ENST00000390560	ensembl	human	known	69_37n	silent	26	25.71	9	SNP	0.000	A
KIAA0430	9665	genome.wustl.edu	37	16	15696497	15696498	+	Intron	INS	-	-	C	rs370453498|rs546564067|rs528582430	byFrequency	TCGA-A7-A3IY-01A-21D-A21Q-09	TCGA-A7-A3IY-10A-01D-A21Q-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48173064-ea1c-4cf2-89a3-f08baae2ea05	d4ab2281-9ee9-45c9-9e97-686602678727	g.chr16:15696497_15696498insC	ENST00000396368.3	-	23	4620				KIAA0430_ENST00000548025.1_Intron|KIAA0430_ENST00000540441.2_Intron|KIAA0430_ENST00000602337.1_Intron|KIAA0430_ENST00000551742.1_Intron|KIAA0430_ENST00000344181.3_Frame_Shift_Ins_p.P1108fs|KIAA0430_ENST00000547936.1_Intron	NM_001184998.1|NM_001184999.1|NM_014647.3	NP_001171927.1|NP_001171928.1|NP_055462.2	Q9Y4F3	MARF1_HUMAN	KIAA0430						double-strand break repair (GO:0006302)|female meiotic division (GO:0007143)|negative regulation of phosphatase activity (GO:0010923)|oogenesis (GO:0048477)|regulation of gene expression (GO:0010468)	membrane (GO:0016020)|peroxisome (GO:0005777)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(4)|endometrium(8)|kidney(4)|large_intestine(2)|lung(13)|ovary(3)|prostate(5)|skin(1)	40						gaaggaagaggagaaagaaAAG	0.431																																						dbGAP											0																																										-	-	-	SO:0001627	intron_variant	0			AB007890	CCDS10562.2, CCDS53990.1, CCDS55991.1	16p13.11	2013-01-11			ENSG00000166783	ENSG00000166783		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	29562	protein-coding gene	gene with protein product	"""limkain b1"", ""protein phosphatase 1, regulatory subunit 34"", ""meiosis arrest female 1"""	614593				9455477, 10493829, 15932519, 22442484, 23090997	Standard	NM_014647		Approved	LKAP, PPP1R34, Marf1	uc010uzw.2	Q9Y4F3	OTTHUMG00000129884	ENST00000396368.3:c.4414-437->G	16.37:g.15696497_15696498insC		Somatic		WXS	Illumina GAIIx	Phase_IV	A8MSK2|B2RNX2|B4DYY9|B7ZMG1|B7ZMG2|F8VV09|Q6P1R6|Q8WYR2|Q9Y4J9	Frame_Shift_Ins	INS	pfam_Limkain_b1_cons_dom,pfam_NYN_limkain-b1,smart_RRM_dom,pfscan_RRM_dom	p.P1107fs	ENST00000396368.3	37	c.3322_3321	CCDS10562.2	16																																																																																			KIAA0430	-	NULL	ENSG00000166783		0.431	KIAA0430-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	KIAA0430	HGNC	protein_coding	OTTHUMT00000252131.2	19	0.00	0	-	NM_014647		15696497	15696498	-1	no_errors	ENST00000344181	ensembl	human	known	69_37n	frame_shift_ins	14	30.00	6	INS	0.001:0.000	C
LRP2	4036	genome.wustl.edu	37	2	170100025	170100025	+	Silent	SNP	T	T	C			TCGA-A7-A3IY-01A-21D-A21Q-09	TCGA-A7-A3IY-10A-01D-A21Q-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48173064-ea1c-4cf2-89a3-f08baae2ea05	d4ab2281-9ee9-45c9-9e97-686602678727	g.chr2:170100025T>C	ENST00000263816.3	-	23	3723	c.3438A>G	c.(3436-3438)acA>acG	p.T1146T	LRP2_ENST00000443831.1_Silent_p.T1009T	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	1146					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""""""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"""	GGCATGTCTCTGTCGAATCTA	0.393																																						dbGAP											0													247.0	214.0	225.0					2																	170100025		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0				CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"""Low density lipoprotein receptors"""	6694	protein-coding gene	gene with protein product	"""megalin"""	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.3438A>G	2.37:g.170100025T>C		Somatic		WXS	Illumina GAIIx	Phase_IV	O00711|Q16215	Silent	SNP	pfam_LDrepeatLR_classA_rpt,pfam_LDLR_classB_rpt,superfamily_Growth_fac_rcpt,superfamily_LDrepeatLR_classA_rpt,superfamily_TIL_dom,smart_LDrepeatLR_classA_rpt,smart_EGF-like,smart_EGF-like_Ca-bd,smart_LDLR_classB_rpt,pfscan_EG-like_dom,pfscan_LDrepeatLR_classA_rpt,pfscan_LDLR_classB_rpt	p.T1146	ENST00000263816.3	37	c.3438	CCDS2232.1	2																																																																																			LRP2	-	superfamily_LDrepeatLR_classA_rpt	ENSG00000081479		0.393	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LRP2	HGNC	protein_coding	OTTHUMT00000255231.2	60	0.00	0	T	NM_004525		170100025	170100025	-1	no_errors	ENST00000263816	ensembl	human	known	69_37n	silent	51	19.05	12	SNP	0.001	C
LRP2BP	55805	genome.wustl.edu	37	4	186299270	186299270	+	Missense_Mutation	SNP	T	T	G			TCGA-A7-A3IY-01A-21D-A21Q-09	TCGA-A7-A3IY-10A-01D-A21Q-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48173064-ea1c-4cf2-89a3-f08baae2ea05	d4ab2281-9ee9-45c9-9e97-686602678727	g.chr4:186299270T>G	ENST00000328559.7	-	1	882	c.71A>C	c.(70-72)aAc>aCc	p.N24T	LRP2BP_ENST00000505916.1_Missense_Mutation_p.N24T|RP11-714G18.1_ENST00000514884.1_RNA|LRP2BP_ENST00000362004.3_Missense_Mutation_p.N24T|LRP2BP_ENST00000510776.1_5'UTR	NM_018409.3	NP_060879.2	Q9P2M1	LR2BP_HUMAN	LRP2 binding protein	24						cytoplasm (GO:0005737)				breast(1)|endometrium(2)|large_intestine(6)|lung(3)|prostate(1)|skin(2)	15		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;0.00109)|Colorectal(36;0.0215)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;2.14e-25)|Epithelial(43;1.55e-22)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-11)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.000132)|STAD - Stomach adenocarcinoma(60;0.000766)|Colorectal(24;0.00116)|LUSC - Lung squamous cell carcinoma(40;0.00904)|COAD - Colon adenocarcinoma(29;0.0101)|READ - Rectum adenocarcinoma(43;0.161)		AAATTTTTGGTTTTTAGCAGC	0.368																																						dbGAP											0													144.0	146.0	146.0					4																	186299270		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB037746	CCDS3840.1	4q35.1	2011-05-03			ENSG00000109771	ENSG00000109771			25434	protein-coding gene	gene with protein product						10718198, 12508107	Standard	NM_018409		Approved	DKFZp761O0113	uc003ixj.2	Q9P2M1	OTTHUMG00000160460	ENST00000328559.7:c.71A>C	4.37:g.186299270T>G	ENSP00000332681:p.Asn24Thr	Somatic		WXS	Illumina GAIIx	Phase_IV	A6NJR7|A7E219|B3KX83|Q9NSN6	Missense_Mutation	SNP	pfam_Sel1-like,pfam_TPR_2,smart_Sel1-like,pfscan_TPR_repeat,pfscan_TPR-contain_dom	p.N24T	ENST00000328559.7	37	c.71	CCDS3840.1	4	.	.	.	.	.	.	.	.	.	.	T	2.210	-0.381011	0.05000	.	.	ENSG00000109771	ENST00000362004;ENST00000328559;ENST00000505916;ENST00000511404	T;T;T	0.46819	0.91;0.86;0.86	4.99	2.56	0.30785	.	0.937434	0.09025	N	0.859641	T	0.25457	0.0619	N	0.12182	0.205	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.23940	-1.0174	10	0.17369	T	0.5	-3.8955	4.6571	0.12622	0.0:0.1015:0.2117:0.6867	.	24	Q9P2M1	LR2BP_HUMAN	T	24	ENSP00000354846:N24T;ENSP00000332681:N24T;ENSP00000426203:N24T	ENSP00000332681:N24T	N	-	2	0	LRP2BP	186536264	0.001000	0.12720	0.026000	0.17262	0.010000	0.07245	0.298000	0.19120	0.938000	0.37419	0.533000	0.62120	AAC	LRP2BP	-	NULL	ENSG00000109771		0.368	LRP2BP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	LRP2BP	HGNC	protein_coding	OTTHUMT00000360679.2	45	0.00	0	T	NM_018409		186299270	186299270	-1	no_errors	ENST00000362004	ensembl	human	known	69_37n	missense	38	17.39	8	SNP	0.003	G
MYT1L	23040	genome.wustl.edu	37	2	1819997	1819997	+	Intron	SNP	C	C	T			TCGA-A7-A3IY-01A-21D-A21Q-09	TCGA-A7-A3IY-10A-01D-A21Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48173064-ea1c-4cf2-89a3-f08baae2ea05	d4ab2281-9ee9-45c9-9e97-686602678727	g.chr2:1819997C>T	ENST00000399161.2	-	22	3828				MYT1L_ENST00000428368.2_Intron|MYT1L_ENST00000407844.1_Intron|MYT1L_ENST00000471668.1_5'UTR	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like						cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(16)|lung(50)|ovary(5)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	97	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		ACACATCACACAAGCACTTTC	0.393																																						dbGAP											0																																										-	-	-	SO:0001627	intron_variant	0			AF036943	CCDS46222.1	2p25.3	2013-01-10			ENSG00000186487	ENSG00000186487		"""Zinc fingers, C2HC-type containing"""	7623	protein-coding gene	gene with protein product	"""neural zinc finger transcription factor 1"""	613084				9373037	Standard	XM_006711862		Approved	KIAA1106, NZF1, ZC2HC4B	uc002qxd.3	Q9UL68	OTTHUMG00000151407	ENST00000399161.2:c.3081-7058G>A	2.37:g.1819997C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	RNA	SNP	-	NULL	ENST00000399161.2	37	NULL		2																																																																																			MYT1L	-	-	ENSG00000186487		0.393	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	MYT1L	HGNC	protein_coding	OTTHUMT00000322493.1	56	0.00	0	C	NM_015025		1819997	1819997	-1	no_errors	ENST00000471668	ensembl	human	known	69_37n	rna	63	21.25	17	SNP	0.006	T
TENM1	10178	genome.wustl.edu	37	X	123519751	123519751	+	Missense_Mutation	SNP	G	G	T			TCGA-A7-A3IY-01A-21D-A21Q-09	TCGA-A7-A3IY-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48173064-ea1c-4cf2-89a3-f08baae2ea05	d4ab2281-9ee9-45c9-9e97-686602678727	g.chrX:123519751G>T	ENST00000371130.3	-	28	5894	c.5831C>A	c.(5830-5832)aCt>aAt	p.T1944N	STAG2_ENST00000469481.1_Intron|TENM1_ENST00000422452.2_Missense_Mutation_p.T1951N	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	1944					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										GATAAAAGAAGTGCTACTGTC	0.517																																						dbGAP											0													163.0	137.0	146.0					X																	123519751		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"""tenascin M"", ""odz, odd Oz/ten-m homolog 1 (Drosophila)"""	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.5831C>A	X.37:g.123519751G>T	ENSP00000360171:p.Thr1944Asn	Somatic		WXS	Illumina GAIIx	Phase_IV	B2RTR5|Q5JZ17	Missense_Mutation	SNP	pfam_Ten_N,pfam_EGF_extracell,superfamily_CarboxyPept-like_regulatory,smart_EGF-like,pfscan_EG-like_dom,tigrfam_YD	p.T1951N	ENST00000371130.3	37	c.5852	CCDS14609.1	X	.	.	.	.	.	.	.	.	.	.	G	15.69	2.908200	0.52333	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	D;D	0.85556	-2.0;-1.97	5.67	5.67	0.87782	.	0.189077	0.47455	D	0.000223	T	0.74306	0.3699	L	0.29908	0.895	0.43814	D	0.996379	B;B;B	0.28552	0.023;0.09;0.215	B;B;B	0.23574	0.014;0.034;0.047	T	0.69672	-0.5082	10	0.25106	T	0.35	.	8.8358	0.35111	0.08:0.1474:0.7726:0.0	.	1950;1951;1944	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	N	1944;1951	ENSP00000360171:T1944N;ENSP00000403954:T1951N	ENSP00000360171:T1944N	T	-	2	0	ODZ1	123347432	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	6.666000	0.74446	2.400000	0.81607	0.591000	0.81541	ACT	ODZ1	-	NULL	ENSG00000009694		0.517	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ODZ1	HGNC	protein_coding	OTTHUMT00000058985.1	77	0.00	0	G	NM_014253		123519751	123519751	-1	no_errors	ENST00000422452	ensembl	human	known	69_37n	missense	83	11.70	11	SNP	0.996	T
CCND1	595	genome.wustl.edu	37	11	69471746	69471746	+	IGR	SNP	C	C	T	rs75245613	byFrequency	TCGA-A7-A3IY-01A-21D-A21Q-09	TCGA-A7-A3IY-10A-01D-A21Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48173064-ea1c-4cf2-89a3-f08baae2ea05	d4ab2281-9ee9-45c9-9e97-686602678727	g.chr11:69471746C>T	ENST00000227507.2	+	0	4307				ORAOV1_ENST00000542515.1_5'UTR	NM_053056.2	NP_444284.1	P24385	CCND1_HUMAN	cyclin D1						canonical Wnt signaling pathway (GO:0060070)|cell division (GO:0051301)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|fat cell differentiation (GO:0045444)|G1/S transition of mitotic cell cycle (GO:0000082)|lactation (GO:0007595)|Leydig cell differentiation (GO:0033327)|liver development (GO:0001889)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell proliferation (GO:0033598)|mitotic cell cycle (GO:0000278)|mitotic G1 DNA damage checkpoint (GO:0031571)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway (GO:0030178)|Notch signaling pathway (GO:0007219)|organ regeneration (GO:0031100)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|positive regulation of protein phosphorylation (GO:0001934)|re-entry into mitotic cell cycle (GO:0000320)|response to calcium ion (GO:0051592)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to iron ion (GO:0010039)|response to magnesium ion (GO:0032026)|response to organonitrogen compound (GO:0010243)|response to UV-A (GO:0070141)|response to vitamin E (GO:0033197)|response to X-ray (GO:0010165)|transcription, DNA-templated (GO:0006351)	cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytosol (GO:0005829)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|tight junction (GO:0005923)|transcriptional repressor complex (GO:0017053)	cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|proline-rich region binding (GO:0070064)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			NS(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|lung(7)|ovary(1)|urinary_tract(1)	23	all_cancers(3;2.01e-114)|all_epithelial(3;3.59e-122)|Breast(3;5.4e-34)|all_lung(4;1.99e-21)|Lung NSC(4;4.65e-21)|Hepatocellular(3;8.22e-16)|Melanoma(5;1.89e-05)|Ovarian(3;0.0348)		Epithelial(3;7.2e-57)|all cancers(3;7.75e-51)|BRCA - Breast invasive adenocarcinoma(2;4.9e-48)|Lung(3;1.13e-16)|LUSC - Lung squamous cell carcinoma(11;3.74e-15)|STAD - Stomach adenocarcinoma(18;0.0278)|LUAD - Lung adenocarcinoma(13;0.0537)		Arsenic trioxide(DB01169)	GAGACCTCGTCCCTTGTTGGA	0.552			T	"""IGH@, FSTL3"""	"""CLL, B-ALL, breast"""					Multiple Myeloma(6;0.086)			C|||	29	0.00579073	0.0008	0.0058	5008	,	,		20487	0.0		0.0179	False		,,,				2504	0.0061				Pancreas(65;393 884 2788 21700 24360 27795 36895)	dbGAP		Dom	yes		11	11q13	595	cyclin D1		"""L, E"""	0																																										-	-	-	SO:0001628	intergenic_variant	0			Z23022	CCDS8191.1	11q13	2008-07-18	2005-09-12		ENSG00000110092	ENSG00000110092			1582	protein-coding gene	gene with protein product	"""parathyroid adenomatosis 1"", ""B-cell CLL/lymphoma 1"", ""G1/S-specific cyclin D1"""	168461	"""cyclin D1 (PRAD1: parathyroid adenomatosis 1)"""	BCL1, D11S287E, PRAD1		1826542, 1833066	Standard	XM_006718653		Approved	U21B31	uc001opa.3	P24385	OTTHUMG00000167877		11.37:g.69471746C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q6LEF0	RNA	SNP	-	NULL	ENST00000227507.2	37	NULL	CCDS8191.1	11																																																																																			ORAOV1	-	-	ENSG00000149716		0.552	CCND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ORAOV1	HGNC	protein_coding	OTTHUMT00000396775.2	10	0.00	0	C	NM_053056		69471746	69471746	-1	no_errors	ENST00000542515	ensembl	human	known	69_37n	rna	8	38.46	5	SNP	0.001	T
PCDHGB1	56104	genome.wustl.edu	37	5	140731009	140731009	+	Silent	SNP	G	G	A			TCGA-A7-A3IY-01A-21D-A21Q-09	TCGA-A7-A3IY-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48173064-ea1c-4cf2-89a3-f08baae2ea05	d4ab2281-9ee9-45c9-9e97-686602678727	g.chr5:140731009G>A	ENST00000523390.1	+	1	1182	c.1182G>A	c.(1180-1182)tcG>tcA	p.S394S	PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018922.2|NM_032095.1	NP_061745.1|NP_115266.1	Q9Y5G3	PCDGD_HUMAN	protocadherin gamma subfamily B, 1	394	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|prostate(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AATCCACCTCGAAGAATTATT	0.468																																						dbGAP											0													54.0	55.0	55.0					5																	140731009		1931	4137	6068	-	-	-	SO:0001819	synonymous_variant	0			AF152517	CCDS54923.1, CCDS75330.1	5q31	2010-01-26				ENSG00000254221		"""Cadherins / Protocadherins : Clustered"""	8708	other	protocadherin	"""protocadherin gamma subfamily B, 1, isoform 2"""	606299				10380929	Standard	NM_018922		Approved	PCDH-GAMMA-B1		Q9Y5G3		ENST00000523390.1:c.1182G>A	5.37:g.140731009G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	Q3SY75|Q9Y5C8	Silent	SNP	pfam_Cadherin,pfam_Cadherin_N,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	p.S394	ENST00000523390.1	37	c.1182	CCDS54923.1	5																																																																																			PCDHGB1	-	pfam_Cadherin,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin	ENSG00000254221		0.468	PCDHGB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PCDHGB1	HGNC	protein_coding	OTTHUMT00000374740.1	21	0.00	0	G	NM_018922		140731009	140731009	+1	no_errors	ENST00000523390	ensembl	human	known	69_37n	silent	23	23.33	7	SNP	0.001	A
PHC3	80012	genome.wustl.edu	37	3	169847202	169847202	+	Frame_Shift_Del	DEL	T	T	-			TCGA-A7-A3IY-01A-21D-A21Q-09	TCGA-A7-A3IY-10A-01D-A21Q-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48173064-ea1c-4cf2-89a3-f08baae2ea05	d4ab2281-9ee9-45c9-9e97-686602678727	g.chr3:169847202delT	ENST00000494943.1	-	8	1090	c.1022delA	c.(1021-1023)aatfs	p.N341fs	PHC3_ENST00000495893.2_Frame_Shift_Del_p.N353fs|PHC3_ENST00000467570.1_Frame_Shift_Del_p.N300fs			Q8NDX5	PHC3_HUMAN	polyhomeotic homolog 3 (Drosophila)	341	Gln-rich.				multicellular organismal development (GO:0007275)	actin cytoskeleton (GO:0015629)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(12)|ovary(1)|upper_aerodigestive_tract(2)	26	all_cancers(22;2.67e-22)|all_epithelial(15;4.73e-27)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)			TTGAGTTGAATTCTGAAGTGT	0.488																																						dbGAP											0													205.0	204.0	205.0					3																	169847202		2018	4171	6189	-	-	-	SO:0001589	frameshift_variant	0				CCDS46952.1	3q26.32	2014-01-28	2006-09-12		ENSG00000173889	ENSG00000173889		"""Sterile alpha motif (SAM) domain containing"""	15682	protein-coding gene	gene with protein product	"""early development regulator 3"", ""polyhomeotic like 3"""		"""polyhomeotic like 3 (Drosophila)"""			12167701, 12384788	Standard	NM_024947		Approved	EDR3, FLJ12967, FLJ12729, HPH3	uc003fgl.2	Q8NDX5	OTTHUMG00000158777	ENST00000494943.1:c.1022delA	3.37:g.169847202delT	ENSP00000420271:p.Asn341fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A2RRP9|Q5HYF0|Q6NSG2|Q8NFT7|Q8NFZ1|Q8TBM2|Q9H971|Q9H9I4	Frame_Shift_Del	DEL	pfam_SAM_type1,pfam_SAM_2,superfamily_SAM/pointed,smart_SAM,pfscan_SAM,pfscan_Znf_FCS	p.N353fs	ENST00000494943.1	37	c.1058		3																																																																																			PHC3	-	NULL	ENSG00000173889		0.488	PHC3-004	KNOWN	basic	protein_coding	PHC3	HGNC	protein_coding	OTTHUMT00000352182.3	85	0.00	0	T	NM_024947		169847202	169847202	-1	no_errors	ENST00000495893	ensembl	human	known	69_37n	frame_shift_del	155	20.10	39	DEL	0.075	-
PTCH2	8643	genome.wustl.edu	37	1	45288193	45288194	+	Frame_Shift_Ins	INS	-	-	G			TCGA-A7-A3IY-01A-21D-A21Q-09	TCGA-A7-A3IY-10A-01D-A21Q-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48173064-ea1c-4cf2-89a3-f08baae2ea05	d4ab2281-9ee9-45c9-9e97-686602678727	g.chr1:45288193_45288194insG	ENST00000372192.3	-	22	3635_3636	c.3505_3506insC	c.(3505-3507)ctgfs	p.L1169fs	PTCH2_ENST00000447098.2_Intron|RNU5E-6P_ENST00000365574.1_RNA	NM_003738.4	NP_003729.3	Q9Y6C5	PTC2_HUMAN	patched 2	1169					epidermis development (GO:0008544)|hair cycle (GO:0042633)|negative regulation of smoothened signaling pathway (GO:0045879)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|smoothened binding (GO:0005119)			NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(19)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	50	Acute lymphoblastic leukemia(166;0.155)					GGCACCAGGCAGGGGGGGTGGG	0.653									Basal Cell Nevus syndrome																													dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0	Familial Cancer Database	Gorlin syndrome, Gorlin-Golz syndrome, Naevoid Basal Cell Carcinoma syndrome, NBCCS	AF091501	CCDS516.1, CCDS53312.1	1p34.1	2010-06-24	2010-06-24		ENSG00000117425	ENSG00000117425			9586	protein-coding gene	gene with protein product		603673	"""patched (Drosophila) homolog 2"", ""patched homolog 2 (Drosophila)"""			9811851, 9931336	Standard	NM_003738		Approved		uc010olf.2	Q9Y6C5	OTTHUMG00000008490	ENST00000372192.3:c.3506dupC	1.37:g.45288200_45288200dupG	ENSP00000361266:p.Leu1169fs	Somatic		WXS	Illumina GAIIx	Phase_IV	O95341|O95856|Q53Z57|Q5QP87|Q6UX14	Frame_Shift_Ins	INS	pfam_Patched,pfscan_SSD,tigrfam_TM_rcpt_patched	p.L1169fs	ENST00000372192.3	37	c.3506_3505	CCDS516.1	1																																																																																			PTCH2	-	NULL	ENSG00000117425		0.653	PTCH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PTCH2	HGNC	protein_coding	OTTHUMT00000023428.4	61	0.00	0	-	NM_003738		45288193	45288194	-1	no_errors	ENST00000372192	ensembl	human	known	69_37n	frame_shift_ins	88	16.19	17	INS	0.924:0.616	G
RTN3	10313	genome.wustl.edu	37	11	63487290	63487290	+	Missense_Mutation	SNP	A	A	G			TCGA-A7-A3IY-01A-21D-A21Q-09	TCGA-A7-A3IY-10A-01D-A21Q-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48173064-ea1c-4cf2-89a3-f08baae2ea05	d4ab2281-9ee9-45c9-9e97-686602678727	g.chr11:63487290A>G	ENST00000377819.5	+	3	1470	c.1316A>G	c.(1315-1317)aAt>aGt	p.N439S	RTN3_ENST00000537981.1_Intron|RTN3_ENST00000339997.4_Missense_Mutation_p.N420S|RTN3_ENST00000341307.2_Intron|RTN3_ENST00000540798.1_Missense_Mutation_p.N327S|RTN3_ENST00000356000.3_Intron|RTN3_ENST00000354497.4_Intron	NM_001265589.1	NP_001252518.1	O95197	RTN3_HUMAN	reticulon 3	439					apoptotic process (GO:0006915)|endoplasmic reticulum tubular network organization (GO:0071786)|response to stress (GO:0006950)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	20						GTGCAAGGCAATATGCAGAAA	0.428																																						dbGAP											0													97.0	94.0	95.0					11																	63487290		2201	4298	6499	-	-	-	SO:0001583	missense	0			AF059524	CCDS8048.1, CCDS8049.1, CCDS8050.1, CCDS41664.1, CCDS58141.1, CCDS58142.1, CCDS58143.1	11q13	2011-01-14			ENSG00000133318	ENSG00000133318			10469	protein-coding gene	gene with protein product	"""neuroendocrine-specific protein-like 2"", ""NSP-like protein II"", ""isoforme III"", ""ASY interacting protein"", ""homolog of ASY protein"""	604249				10331947	Standard	NM_006054		Approved	NSPL2, NSPLII, ASYIP, HAP, RTN3-A1	uc001nxq.3	O95197		ENST00000377819.5:c.1316A>G	11.37:g.63487290A>G	ENSP00000367050:p.Asn439Ser	Somatic		WXS	Illumina GAIIx	Phase_IV	B3KQS2|B7Z308|B7Z4M0|F5H774|Q147U9|Q496K2|Q53GN3|Q59EP0|Q5UEP2|Q6T930|Q7RTM7|Q7RTM8|Q7RTN3	Missense_Mutation	SNP	pfam_Reticulon,pfscan_Reticulon	p.N439S	ENST00000377819.5	37	c.1316	CCDS58141.1	11	.	.	.	.	.	.	.	.	.	.	A	0.001	-2.902696	0.00058	.	.	ENSG00000133318	ENST00000377819;ENST00000339997;ENST00000540798	T;T;T	0.15718	2.4;2.4;2.4	6.07	-12.1	0.00011	.	2.669130	0.00986	N	0.003455	T	0.06371	0.0164	N	0.04203	-0.255	0.09310	N	1	B;B;B	0.12630	0.006;0.003;0.006	B;B;B	0.10450	0.005;0.002;0.005	T	0.34976	-0.9807	10	0.02654	T	1	0.0376	14.8528	0.70309	0.1855:0.0:0.658:0.1565	.	327;439;420	F5H774;O95197;O95197-2	.;RTN3_HUMAN;.	S	439;420;327	ENSP00000367050:N439S;ENSP00000344106:N420S;ENSP00000442733:N327S	ENSP00000344106:N420S	N	+	2	0	RTN3	63243866	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.180000	0.01258	-3.175000	0.00224	-2.377000	0.00234	AAT	RTN3	-	NULL	ENSG00000133318		0.428	RTN3-002	KNOWN	basic|CCDS	protein_coding	RTN3	HGNC	protein_coding	OTTHUMT00000397846.1	36	0.00	0	A	NM_006054		63487290	63487290	+1	no_errors	ENST00000377819	ensembl	human	known	69_37n	missense	41	22.64	12	SNP	0.000	G
SEMA5B	54437	genome.wustl.edu	37	3	122631793	122631793	+	Silent	SNP	G	G	A			TCGA-A7-A3IY-01A-21D-A21Q-09	TCGA-A7-A3IY-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48173064-ea1c-4cf2-89a3-f08baae2ea05	d4ab2281-9ee9-45c9-9e97-686602678727	g.chr3:122631793G>A	ENST00000357599.3	-	18	3008	c.2622C>T	c.(2620-2622)cgC>cgT	p.R874R	SEMA5B_ENST00000195173.4_Silent_p.R873R|SEMA5B_ENST00000451055.2_Silent_p.R928R	NM_001031702.3|NM_001256348.1	NP_001026872.2|NP_001243277.1	Q9P283	SEM5B_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	874	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(13)|lung(26)|ovary(2)|pancreas(3)|skin(2)|upper_aerodigestive_tract(3)	55				GBM - Glioblastoma multiforme(114;0.0367)		TCTTGCGGACGCGGAAGCCCA	0.731																																						dbGAP											0													24.0	30.0	28.0					3																	122631793		2201	4298	6499	-	-	-	SO:0001819	synonymous_variant	0			AB040878	CCDS35491.1, CCDS58848.1, CCDS74995.1	3q21.1	2008-07-18			ENSG00000082684	ENSG00000082684		"""Semaphorins"""	10737	protein-coding gene	gene with protein product		609298		SEMAG		8817451	Standard	NM_001256346		Approved	SemG, KIAA1445, FLJ10372	uc031sbm.1	Q9P283	OTTHUMG00000140392	ENST00000357599.3:c.2622C>T	3.37:g.122631793G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	A8K5U2|B7Z393|F8W9U8|Q6DD89|Q6UY12|Q9NW17	Silent	SNP	pfam_Semaphorin/CD100_Ag,pfam_Thrombospondin_1_rpt,superfamily_Semaphorin/CD100_Ag,superfamily_Thrombospondin_1_rpt,superfamily_Plexin-like_fold,smart_Semaphorin/CD100_Ag,smart_Plexin-like,smart_Thrombospondin_1_rpt,pfscan_Semaphorin/CD100_Ag,pfscan_Thrombospondin_1_rpt	p.R928	ENST00000357599.3	37	c.2784	CCDS35491.1	3																																																																																			SEMA5B	-	pfam_Thrombospondin_1_rpt,superfamily_Thrombospondin_1_rpt,smart_Thrombospondin_1_rpt,pfscan_Thrombospondin_1_rpt	ENSG00000082684		0.731	SEMA5B-001	KNOWN	basic|CCDS	protein_coding	SEMA5B	HGNC	protein_coding	OTTHUMT00000277165.1	26	0.00	0	G	NM_001031702		122631793	122631793	-1	no_errors	ENST00000451055	ensembl	human	known	69_37n	silent	33	36.54	19	SNP	0.976	A
SLC35D2	11046	genome.wustl.edu	37	9	99083270	99083270	+	3'UTR	SNP	C	C	G			TCGA-A7-A3IY-01A-21D-A21Q-09	TCGA-A7-A3IY-10A-01D-A21Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48173064-ea1c-4cf2-89a3-f08baae2ea05	d4ab2281-9ee9-45c9-9e97-686602678727	g.chr9:99083270C>G	ENST00000253270.7	-	0	1330				SLC35D2_ENST00000375259.4_3'UTR	NM_007001.2	NP_008932.2	Q76EJ3	S35D2_HUMAN	solute carrier family 35 (UDP-GlcNAc/UDP-glucose transporter), member D2						carbohydrate derivative transport (GO:1901264)|carbohydrate metabolic process (GO:0005975)|carbohydrate transport (GO:0008643)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|nucleotide transmembrane transport (GO:1901679)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	nucleotide-sugar transmembrane transporter activity (GO:0005338)			endometrium(3)|large_intestine(3)|lung(4)|skin(2)	12		Acute lymphoblastic leukemia(62;0.0167)				GCAGCTGGGGCTCCACCTACC	0.517																																						dbGAP											0																																										-	-	-	SO:0001624	3_prime_UTR_variant	0			AB122077	CCDS6717.1, CCDS69625.1	9q22.33	2013-07-17	2013-07-17		ENSG00000130958	ENSG00000130958		"""Solute carriers"""	20799	protein-coding gene	gene with protein product		609182	"""solute carrier family 35, member D2"""			15607426	Standard	NM_007001		Approved	UGTrel8, SQV7L	uc004awc.3	Q76EJ3	OTTHUMG00000020293	ENST00000253270.7:c.*254G>C	9.37:g.99083270C>G		Somatic		WXS	Illumina GAIIx	Phase_IV	O95454|Q498C1|Q75W21|Q7Z5X5	RNA	SNP	-	NULL	ENST00000253270.7	37	NULL	CCDS6717.1	9																																																																																			SLC35D2	-	-	ENSG00000130958		0.517	SLC35D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC35D2	HGNC	protein_coding	OTTHUMT00000053261.1	25	0.00	0	C			99083270	99083270	-1	no_errors	ENST00000490599	ensembl	human	known	69_37n	rna	13	58.06	18	SNP	0.003	G
SMOC2	64094	genome.wustl.edu	37	6	168928398	168928398	+	Missense_Mutation	SNP	C	C	T			TCGA-A7-A3IY-01A-21D-A21Q-09	TCGA-A7-A3IY-10A-01D-A21Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48173064-ea1c-4cf2-89a3-f08baae2ea05	d4ab2281-9ee9-45c9-9e97-686602678727	g.chr6:168928398C>T	ENST00000356284.2	+	4	674	c.454C>T	c.(454-456)Cgg>Tgg	p.R152W	SMOC2_ENST00000354536.5_Missense_Mutation_p.R152W	NM_001166412.1	NP_001159884.1	Q9H3U7	SMOC2_HUMAN	SPARC related modular calcium binding 2	152	Thyroglobulin type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00500}.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)|signal transduction (GO:0007165)	basement membrane (GO:0005604)|interstitial matrix (GO:0005614)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	32		Breast(66;0.000141)|Esophageal squamous(34;0.222)|Ovarian(120;0.231)		OV - Ovarian serous cystadenocarcinoma(33;1.31e-19)|BRCA - Breast invasive adenocarcinoma(81;3.06e-06)|GBM - Glioblastoma multiforme(31;0.00109)		CAAGACGCCCCGGTGCCCGGG	0.582																																						dbGAP											0													19.0	17.0	18.0					6																	168928398		2122	4133	6255	-	-	-	SO:0001583	missense	0			AB014730	CCDS5307.1, CCDS55076.1	6q27	2013-01-10			ENSG00000112562	ENSG00000112562		"""EF-hand domain containing"""	20323	protein-coding gene	gene with protein product		607223				12031507	Standard	NM_022138		Approved	SMAP2	uc003qwr.2	Q9H3U7	OTTHUMG00000016050	ENST00000356284.2:c.454C>T	6.37:g.168928398C>T	ENSP00000348630:p.Arg152Trp	Somatic		WXS	Illumina GAIIx	Phase_IV	B3KPS7|Q4G169|Q5TAT7|Q5TAT8|Q86VV9|Q96SF3|Q9H1L3|Q9H1L4|Q9H3U0|Q9H4F7|Q9HCV2	Missense_Mutation	SNP	pfam_Thyroglobulin_1,pfam_SPARC/Testican_Ca-bd-dom,pfam_Kazal-type_dom,pfam_Prot_inh_Kazal,superfamily_Thyroglobulin_1,smart_Prot_inh_Kazal,smart_Thyroglobulin_1,pfscan_EF_HAND_2,pfscan_Thyroglobulin_1	p.R152W	ENST00000356284.2	37	c.454	CCDS55076.1	6	.	.	.	.	.	.	.	.	.	.	C	16.53	3.150468	0.57151	.	.	ENSG00000112562	ENST00000356284;ENST00000354536;ENST00000366793	T;T	0.64618	-0.11;-0.11	4.92	-5.67	0.02444	Thyroglobulin type-1 (5);	0.070643	0.56097	D	0.000025	T	0.41143	0.1146	L	0.46819	1.47	0.25584	N	0.986767	D;D	0.59767	0.967;0.986	P;P	0.47827	0.558;0.541	T	0.60954	-0.7160	10	0.56958	D	0.05	-14.6964	16.8414	0.85970	0.5671:0.4329:0.0:0.0	.	152;152	Q9H3U7;Q9H3U7-2	SMOC2_HUMAN;.	W	152	ENSP00000348630:R152W;ENSP00000346537:R152W	ENSP00000346537:R152W	R	+	1	2	SMOC2	168671247	0.004000	0.15560	0.317000	0.25265	0.804000	0.45430	-0.440000	0.06888	-1.653000	0.01500	-0.318000	0.08688	CGG	SMOC2	-	pfam_Thyroglobulin_1,superfamily_Thyroglobulin_1,smart_Thyroglobulin_1,pfscan_Thyroglobulin_1	ENSG00000112562		0.582	SMOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SMOC2	HGNC	protein_coding	OTTHUMT00000043201.1	46	0.00	0	C			168928398	168928398	+1	no_errors	ENST00000354536	ensembl	human	known	69_37n	missense	35	28.57	14	SNP	0.406	T
THBS2	7058	genome.wustl.edu	37	6	169641884	169641884	+	Silent	SNP	G	G	A			TCGA-A7-A3IY-01A-21D-A21Q-09	TCGA-A7-A3IY-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48173064-ea1c-4cf2-89a3-f08baae2ea05	d4ab2281-9ee9-45c9-9e97-686602678727	g.chr6:169641884G>A	ENST00000366787.3	-	6	1113	c.864C>T	c.(862-864)aaC>aaT	p.N288N	XXyac-YX65C7_A.2_ENST00000444188.1_RNA	NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	288					cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	111		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		CGCTGAGCTGGTTCACGAGGA	0.667																																					Esophageal Squamous(91;219 1934 18562 44706)	dbGAP											0													84.0	80.0	81.0					6																	169641884		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0				CCDS34574.1	6q27	2008-07-28			ENSG00000186340	ENSG00000186340			11786	protein-coding gene	gene with protein product		188061				18455130	Standard	NM_003247		Approved	TSP2	uc003qwt.3	P35442	OTTHUMG00000045408	ENST00000366787.3:c.864C>T	6.37:g.169641884G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	A6H8N1|A7E232|Q5RI52	Silent	SNP	pfam_Thrombospondin_C,pfam_Thrombospondin_1_rpt,pfam_VWF_C,pfam_Thrombospondin_3-like_rpt,pfam_EGF-like_Ca-bd,pfam_EGF-like_dom,superfamily_ConA-like_lec_gl,superfamily_Thrombospondin_1_rpt,smart_Laminin_G,smart_VWF_C,smart_Thrombospondin_1_rpt,smart_EGF-like_Ca-bd,smart_EGF-like,pfscan_EG-like_dom,pfscan_Thrombospondin_1_rpt,pfscan_VWF_C	p.N288	ENST00000366787.3	37	c.864	CCDS34574.1	6																																																																																			THBS2	-	NULL	ENSG00000186340		0.667	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	THBS2	HGNC	protein_coding	OTTHUMT00000105439.1	52	0.00	0	G	NM_003247		169641884	169641884	-1	no_errors	ENST00000366787	ensembl	human	known	69_37n	silent	54	18.18	12	SNP	1.000	A
TMX1	81542	genome.wustl.edu	37	14	51707075	51707075	+	Missense_Mutation	SNP	C	C	T			TCGA-A7-A3IY-01A-21D-A21Q-09	TCGA-A7-A3IY-10A-01D-A21Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48173064-ea1c-4cf2-89a3-f08baae2ea05	d4ab2281-9ee9-45c9-9e97-686602678727	g.chr14:51707075C>T	ENST00000457354.2	+	1	190	c.65C>T	c.(64-66)cCc>cTc	p.P22L		NM_030755.4	NP_110382.3	Q9H3N1	TMX1_HUMAN	thioredoxin-related transmembrane protein 1	22					cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleolus (GO:0005730)	disulfide oxidoreductase activity (GO:0015036)|protein disulfide isomerase activity (GO:0003756)			endometrium(2)|large_intestine(2)|urinary_tract(1)	5						TGGGGTGCTCCCTGGACGCAC	0.637																																						dbGAP											0													55.0	62.0	60.0					14																	51707075		2042	4177	6219	-	-	-	SO:0001583	missense	0			AB048246	CCDS41953.1	14q22.1	2011-10-19	2009-02-23	2009-02-23				"""Protein disulfide isomerases"""	15487	protein-coding gene	gene with protein product	"""thioredoxin-related transmembrane protein"", ""protein disulfide isomerase family A, member 11"""	610527	"""thioredoxin domain-containing"", ""thioredoxin domain containing"", ""thioredoxin domain containing 1"""	TXNDC, TXNDC1		11152479	Standard	NM_030755		Approved	TMX, PDIA11	uc001wza.4	Q9H3N1		ENST00000457354.2:c.65C>T	14.37:g.51707075C>T	ENSP00000393316:p.Pro22Leu	Somatic		WXS	Illumina GAIIx	Phase_IV	B2R7A4|Q8N487|Q8NBN5|Q9Y4T6	Missense_Mutation	SNP	pfam_Thioredoxin_domain,superfamily_Thioredoxin-like_fold	p.P22L	ENST00000457354.2	37	c.65	CCDS41953.1	14	.	.	.	.	.	.	.	.	.	.	C	22.1	4.244208	0.79912	.	.	ENSG00000139921	ENST00000457354	T	0.14640	2.49	5.76	5.76	0.90799	Thioredoxin-like fold (1);	0.235866	0.43919	D	0.000510	T	0.14141	0.0342	N	0.02697	-0.525	0.45025	D	0.998044	D;D	0.89917	1.0;0.999	D;D	0.69307	0.963;0.942	T	0.33675	-0.9859	10	0.07813	T	0.8	-12.6344	17.8326	0.88687	0.0:1.0:0.0:0.0	.	22;22	B7Z7R5;Q9H3N1	.;TMX1_HUMAN	L	22	ENSP00000393316:P22L	ENSP00000393316:P22L	P	+	2	0	TMX1	50776825	0.070000	0.21116	0.627000	0.29227	0.727000	0.41649	2.504000	0.45416	2.885000	0.99019	0.655000	0.94253	CCC	TMX1	-	NULL	ENSG00000139921		0.637	TMX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TMX1	HGNC	protein_coding	OTTHUMT00000411206.1	61	0.00	0	C	NM_030755		51707075	51707075	+1	no_errors	ENST00000457354	ensembl	human	known	69_37n	missense	54	26.67	20	SNP	0.924	T
ZFP36	7538	genome.wustl.edu	37	19	39899009	39899009	+	Missense_Mutation	SNP	C	C	G			TCGA-A7-A3IY-01A-21D-A21Q-09	TCGA-A7-A3IY-10A-01D-A21Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48173064-ea1c-4cf2-89a3-f08baae2ea05	d4ab2281-9ee9-45c9-9e97-686602678727	g.chr19:39899009C>G	ENST00000248673.3	+	2	709	c.651C>G	c.(649-651)agC>agG	p.S217R	ZFP36_ENST00000597629.1_Missense_Mutation_p.S223R|MIR4530_ENST00000581459.1_RNA	NM_003407.3	NP_003398.2	P26651	TTP_HUMAN	ZFP36 ring finger protein	217					3'-UTR-mediated mRNA stabilization (GO:0070935)|gene expression (GO:0010467)|intracellular signal transduction (GO:0035556)|mRNA catabolic process (GO:0006402)|mRNA metabolic process (GO:0016071)|negative regulation of inflammatory response (GO:0050728)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of tumor necrosis factor production (GO:0032680)|response to starvation (GO:0042594)|RNA destabilization (GO:0050779)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|AU-rich element binding (GO:0017091)|C-C chemokine binding (GO:0019957)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|single-stranded RNA binding (GO:0003727)			large_intestine(1)|lung(5)|pancreas(1)	7	all_cancers(60;6.54e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;1.53e-06)|Ovarian(47;0.0512)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			CGCCCTCCAGCTCCCCACCAC	0.692																																					NSCLC(67;1164 1324 12056 21056 30097)	dbGAP											0													50.0	59.0	56.0					19																	39899009		2199	4296	6495	-	-	-	SO:0001583	missense	0			M63625	CCDS12534.1, CCDS12534.2	19q13.1	2012-11-27	2012-11-27			ENSG00000128016		"""RING-type (C3HC4) zinc fingers"""	12862	protein-coding gene	gene with protein product		190700	"""zinc finger protein 36, C3H type, homolog (mouse)"""			1699942	Standard	NM_003407		Approved	RNF162A, TIS11, G0S24, TTP, NUP475, tristetraprolin	uc002olh.2	P26651		ENST00000248673.3:c.651C>G	19.37:g.39899009C>G	ENSP00000248673:p.Ser217Arg	Somatic		WXS	Illumina GAIIx	Phase_IV	B2RA54	Missense_Mutation	SNP	pfam_Znf_CCCH,smart_Znf_CCCH	p.S217R	ENST00000248673.3	37	c.651		19	.	.	.	.	.	.	.	.	.	.	C	16.13	3.035993	0.54896	.	.	ENSG00000128016	ENST00000248673	T	0.20881	2.04	4.35	0.912	0.19349	.	0.136432	0.49916	D	0.000135	T	0.12263	0.0298	L	0.44542	1.39	0.31211	N	0.69859	B	0.34290	0.447	B	0.23018	0.043	T	0.13764	-1.0497	10	0.29301	T	0.29	-15.4701	6.7708	0.23593	0.0:0.5976:0.0:0.4024	.	217	P26651	TTP_HUMAN	R	217	ENSP00000248673:S217R	ENSP00000248673:S217R	S	+	3	2	ZFP36	44590849	0.767000	0.28508	1.000000	0.80357	0.877000	0.50540	2.302000	0.43637	0.482000	0.27582	0.442000	0.29010	AGC	ZFP36	-	NULL	ENSG00000128016		0.692	ZFP36-201	KNOWN	basic|appris_candidate	protein_coding	ZFP36	HGNC	protein_coding		126	0.00	0	C			39899009	39899009	+1	no_errors	ENST00000248673	ensembl	human	known	69_37n	missense	145	15.20	26	SNP	0.994	G
