#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
ADAM21P1	145241	genome.wustl.edu	37	14	70714144	70714144	+	RNA	SNP	A	A	G	rs111296958		TCGA-E2-A3DX-01A-21D-A20S-09	TCGA-E2-A3DX-10A-01D-A20S-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7a89a261-0177-4378-b89a-b1ead9e093bf	1ab484a1-6e7d-485f-938a-6d1d2f74cf40	g.chr14:70714144A>G	ENST00000530196.1	-	0	374					NR_003951.1				ADAM metallopeptidase domain 21 pseudogene 1																		AGAGCTTCTTAACCCTCATAT	0.502																																						dbGAP											0																																										-	-	-			0					14q24.2	2014-03-25	2010-01-12	2010-01-12	ENSG00000235812	ENSG00000235812			19822	pseudogene	pseudogene			"""a disintegrin and metalloproteinase domain 21 pseudogene"", ""ADAM metallopeptidase domain 21 pseudogene"""	ADAM21P			Standard	NR_003951		Approved		uc010ttg.2		OTTHUMG00000166565		14.37:g.70714144A>G		Somatic		WXS	Illumina GAIIx	Phase_IV		RNA	SNP	-	NULL	ENST00000530196.1	37	NULL		14																																																																																			ADAM21P1	-	-	ENSG00000235812		0.502	ADAM21P1-002	KNOWN	basic	processed_transcript	ADAM21P1	HGNC	pseudogene	OTTHUMT00000390451.1	18	0.00	0	A	NG_002467		70714144	70714144	-1	no_errors	ENST00000530196	ensembl	human	known	69_37n	rna	15	28.57	6	SNP	0.121	G
CNTN1	1272	genome.wustl.edu	37	12	41330620	41330620	+	Missense_Mutation	SNP	G	G	T			TCGA-E2-A3DX-01A-21D-A20S-09	TCGA-E2-A3DX-10A-01D-A20S-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7a89a261-0177-4378-b89a-b1ead9e093bf	1ab484a1-6e7d-485f-938a-6d1d2f74cf40	g.chr12:41330620G>T	ENST00000551295.2	+	10	1140	c.1023G>T	c.(1021-1023)gaG>gaT	p.E341D	CNTN1_ENST00000547849.1_Missense_Mutation_p.E341D|CNTN1_ENST00000360099.3_Missense_Mutation_p.E341D|CNTN1_ENST00000347616.1_Missense_Mutation_p.E341D|CNTN1_ENST00000348761.2_Missense_Mutation_p.E330D|CNTN1_ENST00000547702.1_Missense_Mutation_p.E341D	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1	341	Ig-like C2-type 4.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transport (GO:0010765)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(21)|lung(49)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	90	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				ATGACACAGAGGTGGACATAG	0.433																																						dbGAP											0													196.0	158.0	171.0					12																	41330620		2203	4300	6503	-	-	-	SO:0001583	missense	0			Z21488	CCDS8737.1, CCDS8738.1, CCDS58225.1	12q11-q12	2014-01-30				ENSG00000018236		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"", ""Endogenous ligands"""	2171	protein-coding gene	gene with protein product	"""glycoprotein gP135"""	600016				7959734, 8586965	Standard	NM_001843		Approved	F3, GP135	uc031qgz.1	Q12860		ENST00000551295.2:c.1023G>T	12.37:g.41330620G>T	ENSP00000447006:p.Glu341Asp	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K0H9|A8K0Y3|Q12861|Q14030|Q7M4P0|Q8N466	Missense_Mutation	SNP	pfam_Ig_I-set,pfam_Fibronectin_type3,pfam_Ig_V-set,pfam_Immunoglobulin,superfamily_Fibronectin_type3,smart_Ig_sub,smart_Ig_sub2,smart_Fibronectin_type3,pfscan_Fibronectin_type3,pfscan_Ig-like	p.E341D	ENST00000551295.2	37	c.1023	CCDS8737.1	12	.	.	.	.	.	.	.	.	.	.	G	15.37	2.813532	0.50527	.	.	ENSG00000018236	ENST00000547702;ENST00000551295;ENST00000547849;ENST00000347616;ENST00000360099;ENST00000348761	T;T;T;T;T;T	0.69040	-0.37;-0.37;-0.37;-0.37;-0.37;-0.37	5.37	-0.929	0.10444	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.051333	0.85682	D	0.000000	T	0.62720	0.2451	L	0.41079	1.255	0.40239	D	0.977931	P;P;P	0.45044	0.815;0.819;0.849	B;P;P	0.50860	0.37;0.52;0.652	T	0.60342	-0.7282	10	0.36615	T	0.2	.	12.3002	0.54870	0.507:0.0:0.493:0.0	.	341;330;341	Q12860-3;Q12860-2;Q12860	.;.;CNTN1_HUMAN	D	341;341;341;341;341;330	ENSP00000448004:E341D;ENSP00000447006:E341D;ENSP00000448653:E341D;ENSP00000325660:E341D;ENSP00000353213:E341D;ENSP00000261160:E330D	ENSP00000325660:E341D	E	+	3	2	CNTN1	39616887	0.996000	0.38824	0.995000	0.50966	0.996000	0.88848	0.314000	0.19432	-0.132000	0.11557	-0.157000	0.13467	GAG	CNTN1	-	pfam_Ig_I-set,smart_Ig_sub,pfscan_Ig-like	ENSG00000018236		0.433	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CNTN1	HGNC	protein_coding	OTTHUMT00000403692.2	29	0.00	0	G	NM_001843		41330620	41330620	+1	no_errors	ENST00000347616	ensembl	human	known	69_37n	missense	21	12.50	3	SNP	0.997	T
FAM182B	728882	genome.wustl.edu	37	20	25848629	25848629	+	5'UTR	SNP	C	C	T			TCGA-E2-A3DX-01A-21D-A20S-09	TCGA-E2-A3DX-10A-01D-A20S-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7a89a261-0177-4378-b89a-b1ead9e093bf	1ab484a1-6e7d-485f-938a-6d1d2f74cf40	g.chr20:25848629C>T	ENST00000478164.1	-	0	157				FAM182B_ENST00000376404.2_5'UTR			Q5T319	F182B_HUMAN	family with sequence similarity 182, member B											lung(1)	1						gctgggatgccgtgctgcttc	0.667																																						dbGAP											0																																										-	-	-	SO:0001623	5_prime_UTR_variant	0					20p11.1	2010-07-14			ENSG00000175170	ENSG00000175170			34503	pseudogene	pseudogene							Standard	NR_027061		Approved			Q5T319	OTTHUMG00000032136	ENST00000478164.1:c.-835G>A	20.37:g.25848629C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q4G0Q1	RNA	SNP	-	NULL	ENST00000478164.1	37	NULL		20																																																																																			FAM182B	-	-	ENSG00000175170		0.667	FAM182B-005	KNOWN	basic	processed_transcript	FAM182B	HGNC	protein_coding	OTTHUMT00000316665.1	31	0.00	0	C	NR_026714		25848629	25848629	-1	no_errors	ENST00000478164	ensembl	human	known	69_37n	rna	15	21.05	4	SNP	0.002	T
FAM86B2	653333	genome.wustl.edu	37	8	12285146	12285146	+	Intron	DEL	G	G	-			TCGA-E2-A3DX-01A-21D-A20S-09	TCGA-E2-A3DX-10A-01D-A20S-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7a89a261-0177-4378-b89a-b1ead9e093bf	1ab484a1-6e7d-485f-938a-6d1d2f74cf40	g.chr8:12285146delG	ENST00000262365.4	-	7	892				FAM86B2_ENST00000393715.3_Frame_Shift_Del_p.P76fs|FAM86B2_ENST00000351291.4_Intron|FAM86B2_ENST00000309608.5_Intron	NM_001137610.1	NP_001131082.1	P0C5J1	F86B2_HUMAN	family with sequence similarity 86, member B2											endometrium(1)|kidney(2)	3						ATGTAGGCCCGGGTGGGCGTG	0.612																																						dbGAP											0																																										-	-	-	SO:0001627	intron_variant	0				CCDS59092.1	8p23.1	2011-07-01			ENSG00000145002	ENSG00000145002			32222	protein-coding gene	gene with protein product							Standard	NM_001137610		Approved		uc003wvt.4	P0C5J1	OTTHUMG00000165462	ENST00000262365.4:c.892+19C>-	8.37:g.12285146delG		Somatic		WXS	Illumina GAIIx	Phase_IV		Frame_Shift_Del	DEL	NULL	p.P78fs	ENST00000262365.4	37	c.228	CCDS59092.1	8																																																																																			FAM86B2	-	NULL	ENSG00000145002		0.612	FAM86B2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	FAM86B2	HGNC	protein_coding		8	0.00	0	G	XM_928336		12285146	12285146	-1	no_errors	ENST00000393715	ensembl	human	known	69_37n	frame_shift_del	4	42.86	3	DEL	0.002	-
FBXO42	54455	genome.wustl.edu	37	1	16641842	16641842	+	Silent	SNP	C	C	T			TCGA-E2-A3DX-01A-21D-A20S-09	TCGA-E2-A3DX-10A-01D-A20S-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7a89a261-0177-4378-b89a-b1ead9e093bf	1ab484a1-6e7d-485f-938a-6d1d2f74cf40	g.chr1:16641842C>T	ENST00000375592.3	-	2	288	c.72G>A	c.(70-72)ggG>ggA	p.G24G	FBXO42_ENST00000478089.1_5'UTR	NM_018994.1	NP_061867.1	Q6P3S6	FBX42_HUMAN	F-box protein 42	24										autonomic_ganglia(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	26		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00475)|all_lung(284;0.00671)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0193)|Colorectal(212;3.16e-07)|COAD - Colon adenocarcinoma(227;1.46e-05)|BRCA - Breast invasive adenocarcinoma(304;4.37e-05)|Kidney(64;0.000246)|KIRC - Kidney renal clear cell carcinoma(64;0.00336)|STAD - Stomach adenocarcinoma(313;0.0139)|READ - Rectum adenocarcinoma(331;0.0693)		GATCCATTGTCCCTTCCAGCA	0.498																																						dbGAP											0													111.0	93.0	99.0					1																	16641842		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			BC063864	CCDS30613.1	1p36.23-p36.11	2008-02-05			ENSG00000037637	ENSG00000037637		"""F-boxes /  ""other"""""	29249	protein-coding gene	gene with protein product		609109				10718198	Standard	XM_006710698		Approved	KIAA1332, Fbx42	uc001ayg.3	Q6P3S6	OTTHUMG00000002218	ENST00000375592.3:c.72G>A	1.37:g.16641842C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	B3KP30|Q5TEU8|Q86XI0|Q8N3N4|Q8N5F8|Q9BRM0|Q9P2L4	Silent	SNP	pfam_Kelch_2,pfam_Kelch_1,pfam_F-box_dom_cyclin-like,superfamily_F-box_dom_cyclin-like,smart_F-box_dom_cyclin-like,pfscan_F-box_dom_cyclin-like	p.G24	ENST00000375592.3	37	c.72	CCDS30613.1	1																																																																																			FBXO42	-	NULL	ENSG00000037637		0.498	FBXO42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FBXO42	HGNC	protein_coding	OTTHUMT00000006285.1	25	0.00	0	C			16641842	16641842	-1	no_errors	ENST00000375592	ensembl	human	known	69_37n	silent	31	11.43	4	SNP	1.000	T
GGH	8836	genome.wustl.edu	37	8	63927746	63927746	+	3'UTR	SNP	T	T	C	rs17279558	byFrequency	TCGA-E2-A3DX-01A-21D-A20S-09	TCGA-E2-A3DX-10A-01D-A20S-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7a89a261-0177-4378-b89a-b1ead9e093bf	1ab484a1-6e7d-485f-938a-6d1d2f74cf40	g.chr8:63927746T>C	ENST00000260118.6	-	0	1504				RP11-659E9.2_ENST00000524309.1_RNA	NM_003878.2	NP_003869.1	Q92820	GGH_HUMAN	gamma-glutamyl hydrolase (conjugase, folylpolygammaglutamyl hydrolase)						glutamine metabolic process (GO:0006541)|proteolysis (GO:0006508)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to insulin (GO:0032868)|response to zinc ion (GO:0010043)	cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	exopeptidase activity (GO:0008238)|gamma-glutamyl-peptidase activity (GO:0034722)|omega peptidase activity (GO:0008242)			breast(1)|kidney(1)|large_intestine(1)|liver(1)|lung(6)|stomach(1)	11	Breast(64;0.0716)	all_cancers(86;0.189)|Lung NSC(129;0.0324)|all_lung(136;0.0593)|all_epithelial(80;0.131)			Folic Acid(DB00158)|Methotrexate(DB00563)	GTTATATAAATAGTCACATAC	0.289													T|||	376	0.0750799	0.0189	0.0375	5008	,	,		15426	0.0873		0.0934	False		,,,				2504	0.1462					dbGAP											0																																										-	-	-	SO:0001624	3_prime_UTR_variant	0			U55206	CCDS6177.1	8q12.3	2008-02-05			ENSG00000137563	ENSG00000137563	3.4.19.9		4248	protein-coding gene	gene with protein product		601509				8816764, 10570974	Standard	NM_003878		Approved		uc003xuw.3	Q92820	OTTHUMG00000164365	ENST00000260118.6:c.*145A>G	8.37:g.63927746T>C		Somatic		WXS	Illumina GAIIx	Phase_IV		RNA	SNP	-	NULL	ENST00000260118.6	37	NULL	CCDS6177.1	8																																																																																			GGH	-	-	ENSG00000137563		0.289	GGH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GGH	HGNC	protein_coding	OTTHUMT00000378453.1	10	0.00	0	T			63927746	63927746	-1	no_errors	ENST00000518466	ensembl	human	known	69_37n	rna	11	50.00	11	SNP	0.000	C
GOLGA8G	283768	genome.wustl.edu	37	15	28776254	28776254	+	Silent	SNP	T	T	C	rs201822908		TCGA-E2-A3DX-01A-21D-A20S-09	TCGA-E2-A3DX-10A-01D-A20S-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7a89a261-0177-4378-b89a-b1ead9e093bf	1ab484a1-6e7d-485f-938a-6d1d2f74cf40	g.chr15:28776254T>C	ENST00000525590.2	-	2	166	c.105A>G	c.(103-105)agA>agG	p.R35R	GOLGA8G_ENST00000329523.6_5'UTR			Q08AF8	GOG8F_HUMAN	golgin A8 family, member G	0						Golgi apparatus (GO:0005794)				lung(1)	1		all_lung(180;1.98e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;4.69e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0201)|GBM - Glioblastoma multiforme(186;0.0503)|Lung(196;0.171)		CAGGGCTGTTTCTCTGCCAAT	0.453																																						dbGAP											0																																										-	-	-	SO:0001819	synonymous_variant	0					15q13.1	2013-01-17	2010-02-12		ENSG00000183629	ENSG00000183629			25328	other	unknown			"""golgi autoantigen, golgin subfamily a, 8G"""			12477932	Standard	NR_033353		Approved	DKFZp434K052		Q08AF8	OTTHUMG00000167134	ENST00000525590.2:c.105A>G	15.37:g.28776254T>C		Somatic		WXS	Illumina GAIIx	Phase_IV	A4FTY1|Q1A5X9|Q8NDK0	Silent	SNP	NULL	p.R35	ENST00000525590.2	37	c.105		15																																																																																			GOLGA8G	-	NULL	ENSG00000183629		0.453	GOLGA8G-001	NOVEL	basic|appris_candidate_longest	protein_coding	GOLGA8G	HGNC	protein_coding	OTTHUMT00000393332.2	12	0.00	0	T	NR_033353.1		28776254	28776254	-1	no_errors	ENST00000416855	ensembl	human	known	69_37n	silent	0	100.00	3	SNP	0.041	C
HMGCR	3156	genome.wustl.edu	37	5	74650339	74650339	+	Missense_Mutation	SNP	A	A	T			TCGA-E2-A3DX-01A-21D-A20S-09	TCGA-E2-A3DX-10A-01D-A20S-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7a89a261-0177-4378-b89a-b1ead9e093bf	1ab484a1-6e7d-485f-938a-6d1d2f74cf40	g.chr5:74650339A>T	ENST00000287936.4	+	12	1536	c.1380A>T	c.(1378-1380)aaA>aaT	p.K460N	HMGCR_ENST00000343975.5_Missense_Mutation_p.K460N|HMGCR_ENST00000511206.1_Missense_Mutation_p.K460N	NM_000859.2	NP_000850.1	P04035	HMDH_HUMAN	3-hydroxy-3-methylglutaryl-CoA reductase	460	Catalytic.				aging (GO:0007568)|cellular lipid metabolic process (GO:0044255)|cholesterol biosynthetic process (GO:0006695)|coenzyme A metabolic process (GO:0015936)|isoprenoid biosynthetic process (GO:0008299)|myoblast differentiation (GO:0045445)|negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of striated muscle cell apoptotic process (GO:0010664)|negative regulation of vasodilation (GO:0045908)|negative regulation of wound healing (GO:0061045)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein tetramerization (GO:0051262)|response to ethanol (GO:0045471)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|ubiquinone metabolic process (GO:0006743)|visual learning (GO:0008542)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|peroxisomal membrane (GO:0005778)	coenzyme binding (GO:0050662)|hydroxymethylglutaryl-CoA reductase (NADPH) activity (GO:0004420)|hydroxymethylglutaryl-CoA reductase activity (GO:0042282)|NADPH binding (GO:0070402)			breast(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	20		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;2.24e-54)	Atorvastatin(DB01076)|Fluvastatin(DB01095)|Lovastatin(DB00227)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rosuvastatin(DB01098)|Simvastatin(DB00641)	AAGGTGCAAAATTCCTTAGTG	0.378																																						dbGAP											0													78.0	70.0	72.0					5																	74650339		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS4027.1, CCDS47234.1	5q13.3-q14	2012-10-02	2010-04-30		ENSG00000113161	ENSG00000113161	1.1.1.88, 1.1.1.34		5006	protein-coding gene	gene with protein product	"""hydroxymethylglutaryl-CoA reductase"", ""3-hydroxy-3-methylglutaryl CoA reductase (NADPH)"""	142910	"""3-hydroxy-3-methylglutaryl-Coenzyme A reductase"""				Standard	NM_000859		Approved		uc003kdp.3	P04035	OTTHUMG00000102069	ENST00000287936.4:c.1380A>T	5.37:g.74650339A>T	ENSP00000287936:p.Lys460Asn	Somatic		WXS	Illumina GAIIx	Phase_IV	B7Z3Y9|Q8N190	Missense_Mutation	SNP	pfam_HMG_CoA_Rdtase,pfam_Patched,superfamily_HMG_CoA_Rdtase_sub-bd,superfamily_HMG_CoA_Rdtase_NAD(P)-bd,pfscan_SSD,pfscan_HMG_CoA_Rdtase,prints_HMG_CoA_Rdtase,tigrfam_HMG_CoA_Rdtase_metazoan,tigrfam_HMG_CoA_Rdtase_eu_arc	p.K460N	ENST00000287936.4	37	c.1380	CCDS4027.1	5	.	.	.	.	.	.	.	.	.	.	A	11.08	1.533356	0.27387	.	.	ENSG00000113161	ENST00000511206;ENST00000544469;ENST00000287936;ENST00000343975	T;T;T	0.43294	0.95;0.95;0.95	5.14	0.469	0.16741	Hydroxymethylglutaryl-CoA reductase, N-terminal (1);Hydroxymethylglutaryl-CoA reductase, class I/II, substrate-binding (1);	0.157982	0.56097	D	0.000033	T	0.24774	0.0601	N	0.21448	0.665	0.40609	D	0.981654	B;B;B	0.14012	0.004;0.009;0.004	B;B;B	0.12837	0.004;0.008;0.004	T	0.07290	-1.0780	10	0.23302	T	0.38	-14.613	9.9072	0.41384	0.5373:0.0:0.4627:0.0	.	460;460;460	B2R649;P04035-2;P04035	.;.;HMDH_HUMAN	N	460;391;460;460	ENSP00000426745:K460N;ENSP00000287936:K460N;ENSP00000340816:K460N	ENSP00000287936:K460N	K	+	3	2	HMGCR	74686095	0.992000	0.36948	0.964000	0.40570	0.957000	0.61999	0.416000	0.21198	-0.071000	0.12886	0.383000	0.25322	AAA	HMGCR	-	superfamily_HMG_CoA_Rdtase_sub-bd,tigrfam_HMG_CoA_Rdtase_metazoan	ENSG00000113161		0.378	HMGCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HMGCR	HGNC	protein_coding	OTTHUMT00000219877.2	26	0.00	0	A			74650339	74650339	+1	no_errors	ENST00000287936	ensembl	human	known	69_37n	missense	35	10.26	4	SNP	0.993	T
HSD17B3	3293	genome.wustl.edu	37	9	99012066	99012066	+	Missense_Mutation	SNP	G	G	T			TCGA-E2-A3DX-01A-21D-A20S-09	TCGA-E2-A3DX-10A-01D-A20S-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7a89a261-0177-4378-b89a-b1ead9e093bf	1ab484a1-6e7d-485f-938a-6d1d2f74cf40	g.chr9:99012066G>T	ENST00000375263.3	-	6	503	c.456C>A	c.(454-456)agC>agA	p.S152R	HSD17B3_ENST00000464104.1_5'UTR|HSD17B3_ENST00000375262.2_Missense_Mutation_p.S152R|RP11-240L7.4_ENST00000448857.1_RNA	NM_000197.1	NP_000188.1	P37058	DHB3_HUMAN	hydroxysteroid (17-beta) dehydrogenase 3	152					androgen biosynthetic process (GO:0006702)|male genitalia development (GO:0030539)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|testosterone biosynthetic process (GO:0061370)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)			breast(1)|endometrium(3)|large_intestine(2)|lung(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	13		Acute lymphoblastic leukemia(62;0.0171)|all_hematologic(171;0.214)				AATGGATGAGGCTCTGTAATA	0.398																																						dbGAP											0													141.0	123.0	129.0					9																	99012066		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS6716.1	9q22	2011-09-20			ENSG00000130948	ENSG00000130948	1.1.1.62	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	5212	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 12C, member 2"""	605573				8075637, 19027726	Standard	NM_000197		Approved	SDR12C2	uc004awa.1	P37058	OTTHUMG00000020292	ENST00000375263.3:c.456C>A	9.37:g.99012066G>T	ENSP00000364412:p.Ser152Arg	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5U0Q6	Missense_Mutation	SNP	pfam_DH_sc/Rdtase_SDR,prints_Glc/ribitol_DH,prints_DH_sc/Rdtase_SDR	p.S152R	ENST00000375263.3	37	c.456	CCDS6716.1	9	.	.	.	.	.	.	.	.	.	.	G	6.805	0.517667	0.13005	.	.	ENSG00000130948	ENST00000375263;ENST00000375262	D;D	0.86497	-2.13;-2.13	4.39	-0.784	0.10954	NAD(P)-binding domain (1);	0.460905	0.25151	N	0.032742	T	0.63200	0.2491	N	0.02192	-0.645	0.09310	N	1	B;B	0.23128	0.005;0.08	B;B	0.23018	0.021;0.043	T	0.55566	-0.8121	10	0.32370	T	0.25	-13.6426	4.2115	0.10514	0.4548:0.0:0.3902:0.155	.	152;152	Q5U0Q6;P37058	.;DHB3_HUMAN	R	152	ENSP00000364412:S152R;ENSP00000364411:S152R	ENSP00000364411:S152R	S	-	3	2	HSD17B3	98051887	0.032000	0.19561	0.498000	0.27564	0.437000	0.31866	-0.541000	0.06099	-0.234000	0.09782	0.563000	0.77884	AGC	HSD17B3	-	pfam_DH_sc/Rdtase_SDR	ENSG00000130948		0.398	HSD17B3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	HSD17B3	HGNC	protein_coding	OTTHUMT00000053259.1	32	0.00	0	G	NM_000197		99012066	99012066	-1	no_errors	ENST00000375263	ensembl	human	known	69_37n	missense	25	13.79	4	SNP	0.066	T
INPP4B	8821	genome.wustl.edu	37	4	143181718	143181718	+	Splice_Site	SNP	C	C	T			TCGA-E2-A3DX-01A-21D-A20S-09	TCGA-E2-A3DX-10A-01D-A20S-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7a89a261-0177-4378-b89a-b1ead9e093bf	1ab484a1-6e7d-485f-938a-6d1d2f74cf40	g.chr4:143181718C>T	ENST00000513000.1	-	12	1049		c.e12-1		INPP4B_ENST00000308502.4_Splice_Site|INPP4B_ENST00000508116.1_Splice_Site|INPP4B_ENST00000509777.1_Splice_Site|INPP4B_ENST00000262992.4_Splice_Site	NM_003866.2	NP_003857.2	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II, 105kDa						cellular calcium ion homeostasis (GO:0006874)|inositol phosphate metabolic process (GO:0043647)|negative regulation of osteoclast differentiation (GO:0045671)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|regulation of bone remodeling (GO:0046850)|regulation of nucleocytoplasmic transport (GO:0046822)|regulation of protein kinase B signaling (GO:0051896)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	lipid binding (GO:0008289)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(29)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58	all_hematologic(180;0.158)					CCAGGGCACACTAGGaaaaaa	0.303																																						dbGAP											0													37.0	37.0	37.0					4																	143181718		2203	4298	6501	-	-	-	SO:0001630	splice_region_variant	0			U96922	CCDS3757.1	4q31.1	2008-02-05	2002-08-29			ENSG00000109452			6075	protein-coding gene	gene with protein product		607494	"""inositol polyphosphate-4-phosphatase, type II, 105kD"""			9295334	Standard	NM_003866		Approved		uc003iiw.4	O15327		ENST00000513000.1:c.616-1G>A	4.37:g.143181718C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q2TAI2|Q5XLE7|Q6IN59|Q6PJB4	Splice_Site	SNP	-	e8-1	ENST00000513000.1	37	c.616-1	CCDS3757.1	4	.	.	.	.	.	.	.	.	.	.	C	20.5	4.008941	0.75046	.	.	ENSG00000109452	ENST00000513000;ENST00000262992;ENST00000308502;ENST00000543161;ENST00000508116;ENST00000509777;ENST00000511838;ENST00000542702;ENST00000510812;ENST00000514525	.	.	.	5.41	5.41	0.78517	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.9633	0.86278	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	INPP4B	143401168	1.000000	0.71417	0.998000	0.56505	0.980000	0.70556	4.746000	0.62133	2.526000	0.85167	0.655000	0.94253	.	INPP4B	-	-	ENSG00000109452		0.303	INPP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	INPP4B	HGNC	protein_coding	OTTHUMT00000364587.1	36	0.00	0	C	NM_003866	Intron	143181718	143181718	-1	no_errors	ENST00000509777	ensembl	human	known	69_37n	splice_site	35	10.26	4	SNP	1.000	T
ITIH2	3698	genome.wustl.edu	37	10	7745330	7745330	+	5'UTR	SNP	C	C	T			TCGA-E2-A3DX-01A-21D-A20S-09	TCGA-E2-A3DX-10A-01D-A20S-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7a89a261-0177-4378-b89a-b1ead9e093bf	1ab484a1-6e7d-485f-938a-6d1d2f74cf40	g.chr10:7745330C>T	ENST00000358415.4	+	0	99				ITIH2_ENST00000379587.4_5'Flank	NM_002216.2	NP_002207.2	P19823	ITIH2_HUMAN	inter-alpha-trypsin inhibitor heavy chain 2						hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(2)|breast(1)|endometrium(8)|kidney(1)|large_intestine(17)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64						GAACTTGGTTCAGTAGGAAGA	0.398																																						dbGAP											0																																										-	-	-	SO:0001623	5_prime_UTR_variant	0			X07173	CCDS31141.1	10p14	2011-10-26	2011-10-26		ENSG00000151655	ENSG00000151655			6167	protein-coding gene	gene with protein product		146640	"""inter-alpha (globulin) inhibitor, H2 polypeptide"""			1385302, 10100603	Standard	NM_002216		Approved	H2P	uc001ijs.3	P19823	OTTHUMG00000017633	ENST00000358415.4:c.-68C>T	10.37:g.7745330C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q14659|Q15484|Q5T986	RNA	SNP	-	NULL	ENST00000358415.4	37	NULL	CCDS31141.1	10																																																																																			ITIH2	-	-	ENSG00000151655		0.398	ITIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ITIH2	HGNC	protein_coding	OTTHUMT00000046678.2	30	0.00	0	C	NM_002216		7745330	7745330	+1	no_errors	ENST00000476165	ensembl	human	known	69_37n	rna	27	12.90	4	SNP	0.001	T
KRTAP5-5	439915	genome.wustl.edu	37	11	1651241	1651241	+	Silent	SNP	A	A	C			TCGA-E2-A3DX-01A-21D-A20S-09	TCGA-E2-A3DX-10A-01D-A20S-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7a89a261-0177-4378-b89a-b1ead9e093bf	1ab484a1-6e7d-485f-938a-6d1d2f74cf40	g.chr11:1651241A>C	ENST00000399676.2	+	1	209	c.171A>C	c.(169-171)ggA>ggC	p.G57G		NM_001001480.2	NP_001001480.2	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	57						keratin filament (GO:0045095)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|urinary_tract(1)	33		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		gctgtgggggatgtggctccg	0.682																																						dbGAP											0													47.0	59.0	55.0					11																	1651241		2188	4272	6460	-	-	-	SO:0001819	synonymous_variant	0			AB125074	CCDS41592.1	11p15.5	2008-10-30			ENSG00000185940	ENSG00000185940		"""Keratin associated proteins"""	23601	protein-coding gene	gene with protein product						15144888	Standard	NM_001001480		Approved	KRTAP5.5, KRTAP5-11	uc001lty.3	Q701N2	OTTHUMG00000057554	ENST00000399676.2:c.171A>C	11.37:g.1651241A>C		Somatic		WXS	Illumina GAIIx	Phase_IV	A8MWN2	Silent	SNP	NULL	p.G57	ENST00000399676.2	37	c.171	CCDS41592.1	11																																																																																			KRTAP5-5	-	NULL	ENSG00000185940		0.682	KRTAP5-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KRTAP5-5	HGNC	protein_coding	OTTHUMT00000127919.1	51	0.00	0	A			1651241	1651241	+1	no_errors	ENST00000399676	ensembl	human	known	69_37n	silent	42	14.29	7	SNP	0.753	C
LARS	51520	genome.wustl.edu	37	5	145522520	145522520	+	Missense_Mutation	SNP	C	C	T			TCGA-E2-A3DX-01A-21D-A20S-09	TCGA-E2-A3DX-10A-01D-A20S-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7a89a261-0177-4378-b89a-b1ead9e093bf	1ab484a1-6e7d-485f-938a-6d1d2f74cf40	g.chr5:145522520C>T	ENST00000394434.2	-	20	2171	c.2005G>A	c.(2005-2007)Gat>Aat	p.D669N	LARS_ENST00000274562.9_Missense_Mutation_p.D642N|LARS_ENST00000545646.1_Missense_Mutation_p.D623N|LARS_ENST00000510191.1_Missense_Mutation_p.D615N	NM_020117.9	NP_064502.9	Q9P2J5	SYLC_HUMAN	leucyl-tRNA synthetase	669					gene expression (GO:0010467)|leucyl-tRNA aminoacylation (GO:0006429)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|leucine-tRNA ligase activity (GO:0004823)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|prostate(1)|skin(2)|stomach(8)	34			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Leucine(DB00149)	ACGCGAAGATCAACAGGATAC	0.378																																						dbGAP											0													107.0	102.0	104.0					5																	145522520		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF151026	CCDS34265.1	5q32	2012-10-02			ENSG00000133706	ENSG00000133706	6.1.1.4	"""Aminoacyl tRNA synthetases / Class I"""	6512	protein-coding gene	gene with protein product	"""leucine tRNA ligase 1, cytoplasmic"""	151350				6933703	Standard	NM_020117		Approved	HSPC192, FLJ10595, FLJ21788, LARS1, LEUS, RNTLS	uc003lnx.1	Q9P2J5	OTTHUMG00000163429	ENST00000394434.2:c.2005G>A	5.37:g.145522520C>T	ENSP00000377954:p.Asp669Asn	Somatic		WXS	Illumina GAIIx	Phase_IV	A2RRR4|A7E266|B4DJ10|Q2TU79|Q9NSE1	Missense_Mutation	SNP	pfam_aa-tRNA-synth_Ia,pfam_Methionyl/Leucyl_tRNA_Synth,pfam_V/L/I-tRNA-synth_anticodon-bd,pfam_Cys-tRNA/MSH_ligase,tigrfam_Leu-tRNA-synth_Ia_arc/euk	p.D669N	ENST00000394434.2	37	c.2005	CCDS34265.1	5	.	.	.	.	.	.	.	.	.	.	C	36	5.798637	0.96960	.	.	ENSG00000133706	ENST00000394434;ENST00000545646;ENST00000510191;ENST00000274562	T;T;T;T	0.44083	0.93;0.93;0.93;0.93	5.74	5.74	0.90152	Rossmann-like alpha/beta/alpha sandwich fold (1);Aminoacyl-tRNA synthetase, class Ia (1);	0.000000	0.85682	D	0.000000	T	0.71476	0.3344	M	0.87269	2.87	0.80722	D	1	D;D;D	0.76494	0.998;0.998;0.999	D;D;D	0.81914	0.951;0.995;0.962	T	0.74509	-0.3642	10	0.66056	D	0.02	-9.2534	20.3362	0.98740	0.0:1.0:0.0:0.0	.	642;623;669	B4DER1;F5H698;Q9P2J5	.;.;SYLC_HUMAN	N	669;623;615;642	ENSP00000377954:D669N;ENSP00000437791:D623N;ENSP00000426005:D615N;ENSP00000274562:D642N	ENSP00000274562:D642N	D	-	1	0	LARS	145502713	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.776000	0.85560	2.885000	0.99019	0.579000	0.79373	GAT	LARS	-	pfam_aa-tRNA-synth_Ia,pfam_Methionyl/Leucyl_tRNA_Synth,pfam_Cys-tRNA/MSH_ligase,tigrfam_Leu-tRNA-synth_Ia_arc/euk	ENSG00000133706		0.378	LARS-001	KNOWN	basic|CCDS	protein_coding	LARS	HGNC	protein_coding	OTTHUMT00000373367.1	21	0.00	0	C	NM_020117		145522520	145522520	-1	no_errors	ENST00000394434	ensembl	human	known	69_37n	missense	22	15.38	4	SNP	1.000	T
MUC16	94025	genome.wustl.edu	37	19	8994489	8994489	+	Silent	SNP	G	G	A			TCGA-E2-A3DX-01A-21D-A20S-09	TCGA-E2-A3DX-10A-01D-A20S-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7a89a261-0177-4378-b89a-b1ead9e093bf	1ab484a1-6e7d-485f-938a-6d1d2f74cf40	g.chr19:8994489G>A	ENST00000397910.4	-	64	41606	c.41403C>T	c.(41401-41403)aaC>aaT	p.N13801N	MUC16_ENST00000380951.5_Silent_p.N442N	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13803	SEA 12. {ECO:0000255|PROSITE- ProRule:PRU00188}.			Missing (in Ref. 3; AAK74120). {ECO:0000305}.	cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CATACCGCAGGTTAGTGATGG	0.507																																						dbGAP											0													204.0	182.0	189.0					19																	8994489		1991	4167	6158	-	-	-	SO:0001819	synonymous_variant	0			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.41403C>T	19.37:g.8994489G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	Q6ZQW5|Q96RK2	Silent	SNP	pfam_SEA,smart_SEA,pfscan_SEA	p.N13801	ENST00000397910.4	37	c.41403	CCDS54212.1	19	.	.	.	.	.	.	.	.	.	.	.	0.021	-1.428635	0.01117	.	.	ENSG00000181143	ENST00000542240	.	.	.	2.69	2.69	0.31865	.	.	.	.	.	T	0.49338	0.1551	.	.	.	.	.	.	.	.	.	.	.	.	T	0.58323	-0.7656	3	.	.	.	.	9.0571	0.36412	0.0:0.0:1.0:0.0	.	.	.	.	I	641	.	.	T	-	2	0	MUC16	8855489	0.949000	0.32298	0.384000	0.26145	0.041000	0.13682	1.788000	0.38714	1.828000	0.53243	0.557000	0.71058	ACC	MUC16	-	pfam_SEA	ENSG00000181143		0.507	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MUC16	HGNC	protein_coding	OTTHUMT00000402806.1	48	0.00	0	G	NM_024690		8994489	8994489	-1	no_errors	ENST00000397910	ensembl	human	known	69_37n	silent	53	20.90	14	SNP	0.429	A
MUC20	200958	genome.wustl.edu	37	3	195452814	195452814	+	Missense_Mutation	SNP	C	C	T	rs199753483		TCGA-E2-A3DX-01A-21D-A20S-09	TCGA-E2-A3DX-10A-01D-A20S-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7a89a261-0177-4378-b89a-b1ead9e093bf	1ab484a1-6e7d-485f-938a-6d1d2f74cf40	g.chr3:195452814C>T	ENST00000447234.2	+	2	1466	c.1340C>T	c.(1339-1341)aCg>aTg	p.T447M	MUC20_ENST00000436408.1_Missense_Mutation_p.T447M|MUC20_ENST00000445522.2_Missense_Mutation_p.T412M|MUC20_ENST00000320736.6_Missense_Mutation_p.T276M	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	447					activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)				NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		CTCATCCCCACGGAAGGGGTG	0.537																																						dbGAP											0													35.0	31.0	32.0					3																	195452814		2053	4183	6236	-	-	-	SO:0001583	missense	0			AB037780	CCDS63877.1	3q29	2008-08-07	2006-03-14		ENSG00000176945	ENSG00000176945		"""Mucins"""	23282	protein-coding gene	gene with protein product		610360				14565953	Standard	NM_001282506		Approved	FLJ14408, KIAA1359	uc010hzo.3	Q8N307	OTTHUMG00000155823	ENST00000447234.2:c.1340C>T	3.37:g.195452814C>T	ENSP00000414350:p.Thr447Met	Somatic		WXS	Illumina GAIIx	Phase_IV	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Missense_Mutation	SNP	NULL	p.T447M	ENST00000447234.2	37	c.1340		3	.	.	.	.	.	.	.	.	.	.	C	14.09	2.432260	0.43122	.	.	ENSG00000176945	ENST00000447234;ENST00000320736;ENST00000436408;ENST00000445522	T;T;T;T	0.18016	2.67;2.72;2.84;2.24	4.38	3.51	0.40186	.	1.054240	0.07475	N	0.902873	T	0.29093	0.0723	L	0.34521	1.04	0.09310	N	1	D	0.89917	1.0	D	0.66196	0.942	T	0.20174	-1.0283	10	0.62326	D	0.03	0.7157	8.4723	0.32993	0.0:0.8925:0.0:0.1075	.	276	E9PH32	.	M	447;276;447;412	ENSP00000414350:T447M;ENSP00000325431:T276M;ENSP00000396774:T447M;ENSP00000405629:T412M	ENSP00000325431:T276M	T	+	2	0	MUC20	196938485	0.000000	0.05858	0.002000	0.10522	0.014000	0.08584	-0.101000	0.10973	1.198000	0.43158	0.514000	0.50259	ACG	MUC20	-	NULL	ENSG00000176945		0.537	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	MUC20	HGNC	protein_coding	OTTHUMT00000341835.1	30	0.00	0	C	NM_152673		195452814	195452814	+1	no_errors	ENST00000447234	ensembl	human	known	69_37n	missense	38	17.39	8	SNP	0.002	T
PIK3CG	5294	genome.wustl.edu	37	7	106523363	106523364	+	Intron	DEL	AA	AA	-	rs552794683	byFrequency	TCGA-E2-A3DX-01A-21D-A20S-09	TCGA-E2-A3DX-10A-01D-A20S-09	AA	AA					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7a89a261-0177-4378-b89a-b1ead9e093bf	1ab484a1-6e7d-485f-938a-6d1d2f74cf40	g.chr7:106523363_106523364delAA	ENST00000359195.3	+	8	2939				PIK3CG_ENST00000496166.1_Intron|PIK3CG_ENST00000440650.2_Intron|PIK3CG_ENST00000466738.1_3'UTR	NM_001282427.1|NM_002649.2	NP_001269356.1|NP_002640.2	P48736	PK3CG_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma						adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cytokine production (GO:0001816)|dendritic cell chemotaxis (GO:0002407)|endocytosis (GO:0006897)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte apoptotic process (GO:0097284)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|natural killer cell chemotaxis (GO:0035747)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of triglyceride catabolic process (GO:0010897)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion mediated by integrin (GO:0033628)|respiratory burst involved in defense response (GO:0002679)|secretory granule localization (GO:0032252)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell proliferation (GO:0042098)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|ephrin receptor binding (GO:0046875)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(9)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(16)|liver(4)|lung(59)|ovary(4)|pancreas(4)|prostate(3)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	132						CTCTCTGGTCaaaaaaaaaaaa	0.416																																						dbGAP											0																																										-	-	-	SO:0001627	intron_variant	0				CCDS5739.1	7q22	2012-07-13	2012-07-13		ENSG00000105851	ENSG00000105851	2.7.1.153		8978	protein-coding gene	gene with protein product		601232	"""phosphoinositide-3-kinase, catalytic, gamma polypeptide"""				Standard	XM_005250443		Approved		uc003vdw.3	P48736	OTTHUMG00000157641	ENST00000359195.3:c.2630-114AA>-	7.37:g.106523373_106523374delAA		Somatic		WXS	Illumina GAIIx	Phase_IV	A4D0Q6|Q8IV23|Q9BZC8	RNA	DEL	-	NULL	ENST00000359195.3	37	NULL	CCDS5739.1	7																																																																																			PIK3CG	-	-	ENSG00000105851		0.416	PIK3CG-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	PIK3CG	HGNC	protein_coding	OTTHUMT00000349294.1	10	0.00	0	AA			106523363	106523364	+1	no_errors	ENST00000466738	ensembl	human	putative	69_37n	rna	9	13.33	2	DEL	0.000:0.001	-
RTTN	25914	genome.wustl.edu	37	18	67741218	67741218	+	Missense_Mutation	SNP	G	G	A			TCGA-E2-A3DX-01A-21D-A20S-09	TCGA-E2-A3DX-10A-01D-A20S-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7a89a261-0177-4378-b89a-b1ead9e093bf	1ab484a1-6e7d-485f-938a-6d1d2f74cf40	g.chr18:67741218G>A	ENST00000255674.6	-	34	4863	c.4577C>T	c.(4576-4578)tCa>tTa	p.S1526L	RTTN_ENST00000454359.1_3'UTR|RTTN_ENST00000437017.1_Missense_Mutation_p.S1526L	NM_173630.3	NP_775901.3	Q86VV8	RTTN_HUMAN	rotatin	1526					determination of left/right symmetry (GO:0007368)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(35)|ovary(4)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Esophageal squamous(42;0.129)				AAACTTGAATGAGTCATCTAA	0.413																																						dbGAP											0													99.0	88.0	91.0					18																	67741218		1863	4098	5961	-	-	-	SO:0001583	missense	0			AL117635	CCDS42443.1	18q22.1	2008-08-01				ENSG00000176225			18654	protein-coding gene	gene with protein product		610436				11900971	Standard	NM_173630		Approved	DKFZP434G145	uc002lkp.2	Q86VV8		ENST00000255674.6:c.4577C>T	18.37:g.67741218G>A	ENSP00000255674:p.Ser1526Leu	Somatic		WXS	Illumina GAIIx	Phase_IV	Q68CS9|Q6ZRL8|Q6ZTK3|Q86TG4|Q8N8N8|Q8TBQ4|Q96IN9|Q9UFJ4	Missense_Mutation	SNP	superfamily_ARM-type_fold	p.S1526L	ENST00000255674.6	37	c.4577	CCDS42443.1	18	.	.	.	.	.	.	.	.	.	.	G	26.2	4.716234	0.89205	.	.	ENSG00000176225	ENST00000255674;ENST00000437017	T;T	0.74632	-0.2;-0.86	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	D	0.85509	0.5713	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.86125	0.1571	10	0.72032	D	0.01	.	18.0976	0.89496	0.0:0.0:1.0:0.0	.	1526	Q86VV8	RTTN_HUMAN	L	1526	ENSP00000255674:S1526L;ENSP00000399520:S1526L	ENSP00000255674:S1526L	S	-	2	0	RTTN	65892198	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	4.460000	0.60108	2.773000	0.95371	0.591000	0.81541	TCA	RTTN	-	NULL	ENSG00000176225		0.413	RTTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RTTN	HGNC	protein_coding	OTTHUMT00000442988.1	37	0.00	0	G	NM_173630		67741218	67741218	-1	no_errors	ENST00000255674	ensembl	human	known	69_37n	missense	17	19.05	4	SNP	1.000	A
TBC1D3P5	440419	genome.wustl.edu	37	17	25748765	25748765	+	RNA	SNP	C	C	A			TCGA-E2-A3DX-01A-21D-A20S-09	TCGA-E2-A3DX-10A-01D-A20S-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7a89a261-0177-4378-b89a-b1ead9e093bf	1ab484a1-6e7d-485f-938a-6d1d2f74cf40	g.chr17:25748765C>A	ENST00000586223.1	+	0	666					NR_033892.1				TBC1 domain family, member 3 pseudogene 5																		CCCCCAGAACCACTCTCTGCA	0.567																																						dbGAP											0																																										-	-	-			0					17q11.1	2014-03-20			ENSG00000266433	ENSG00000266433			43567	pseudogene	pseudogene							Standard	NR_033892		Approved		uc002gzg.3		OTTHUMG00000179156		17.37:g.25748765C>A		Somatic		WXS	Illumina GAIIx	Phase_IV		RNA	SNP	-	NULL	ENST00000586223.1	37	NULL		17																																																																																			TBC1D3P5	-	-	ENSG00000266433		0.567	TBC1D3P5-003	KNOWN	non_canonical_TEC|basic	processed_transcript	TBC1D3P5	HGNC	pseudogene	OTTHUMT00000451073.1	27	0.00	0	C	NR_033892		25748765	25748765	+1	no_errors	ENST00000586223	ensembl	human	known	69_37n	rna	31	20.51	8	SNP	0.187	A
TBL1XR1	79718	genome.wustl.edu	37	3	176769296	176769297	+	Frame_Shift_Del	DEL	TA	TA	-			TCGA-E2-A3DX-01A-21D-A20S-09	TCGA-E2-A3DX-10A-01D-A20S-09	TA	TA					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7a89a261-0177-4378-b89a-b1ead9e093bf	1ab484a1-6e7d-485f-938a-6d1d2f74cf40	g.chr3:176769296_176769297delTA	ENST00000430069.1	-	5	681_682	c.422_423delTA	c.(421-423)atafs	p.I141fs	TBL1XR1_ENST00000457928.2_Frame_Shift_Del_p.I141fs			Q9BZK7	TBL1R_HUMAN	transducin (beta)-like 1 X-linked receptor 1	141					canonical Wnt signaling pathway (GO:0060070)|cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|histone binding (GO:0042393)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)	p.I141fs*3(1)		breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(7)|liver(1)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	31	all_cancers(143;1.44e-17)|Ovarian(172;0.00163)|Breast(254;0.214)	Acute lymphoblastic leukemia(1;0.00599)|all_hematologic(1;0.0632)|Prostate(884;0.215)	OV - Ovarian serous cystadenocarcinoma(80;9.83e-31)			GCTCACTTGCTATAGTATGTGC	0.396																																						dbGAP											1	Deletion - Frameshift(1)	breast(1)																																								-	-	-	SO:0001589	frameshift_variant	0			AK022956	CCDS46961.1	3q26.33	2013-01-10	2008-01-17		ENSG00000177565	ENSG00000177565		"""WD repeat domain containing"""	29529	protein-coding gene	gene with protein product		608628	"""transducin (beta)-like 1X-linked receptor 1"""			11063877, 11931768	Standard	NM_024665		Approved	IRA1, FLJ12894, TBLR1, C21, DC42	uc003fix.4	Q9BZK7	OTTHUMG00000157140	ENST00000430069.1:c.422_423delTA	3.37:g.176769298_176769299delTA	ENSP00000405574:p.Ile141fs	Somatic		WXS	Illumina GAIIx	Phase_IV	D3DNQ9|Q14DC3|Q9H2I1|Q9H9A1	Frame_Shift_Del	DEL	pfam_WD40_repeat,pfam_LisH_dimerisation_subgr,superfamily_WD40_repeat_dom,smart_LisH_dimerisation,smart_WD40_repeat,prints_G-protein_beta_WD-40_rep,pfscan_LisH_dimerisation,pfscan_WD40_repeat,pfscan_WD40_repeat_dom	p.I141fs	ENST00000430069.1	37	c.423_422	CCDS46961.1	3																																																																																			TBL1XR1	-	NULL	ENSG00000177565		0.396	TBL1XR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TBL1XR1	HGNC	protein_coding	OTTHUMT00000347587.3	13	0.00	0	TA	NM_024665		176769296	176769297	-1	no_errors	ENST00000430069	ensembl	human	known	69_37n	frame_shift_del	18	33.33	9	DEL	1.000:1.000	-
TCAM1P	146771	genome.wustl.edu	37	17	61938248	61938248	+	RNA	SNP	G	G	T	rs2236736	byFrequency	TCGA-E2-A3DX-01A-21D-A20S-09	TCGA-E2-A3DX-10A-01D-A20S-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7a89a261-0177-4378-b89a-b1ead9e093bf	1ab484a1-6e7d-485f-938a-6d1d2f74cf40	g.chr17:61938248G>T	ENST00000478379.1	+	0	1353					NR_002947.2				testicular cell adhesion molecule 1, pseudogene																		TTTCTCCTGCGAGGCCTCTTT	0.532													G|||	3636	0.726038	0.9561	0.6801	5008	,	,		17730	0.5526		0.5994	False		,,,				2504	0.7566					dbGAP											0																																										-	-	-			0			AB026156		17q23.3	2013-09-26	2012-12-07	2010-03-12	ENSG00000240280	ENSG00000240280			30707	pseudogene	pseudogene		612756	"""testicular cell adhesion molecule 1 homolog (mouse)"", ""testicular cell adhesion molecule 1 homolog (mouse), pseudogene"""	TCAM1		11195349, 2744760, 19766163	Standard	NR_002947		Approved		uc031rdl.1		OTTHUMG00000154404		17.37:g.61938248G>T		Somatic		WXS	Illumina GAIIx	Phase_IV		RNA	SNP	-	NULL	ENST00000478379.1	37	NULL		17																																																																																			TCAM1P	-	-	ENSG00000240280		0.532	TCAM1P-002	KNOWN	basic	processed_transcript	TCAM1P	HGNC	pseudogene	OTTHUMT00000335083.1	19	0.00	0	G			61938248	61938248	+1	no_errors	ENST00000478379	ensembl	human	known	69_37n	rna	13	18.75	3	SNP	1.000	T
TPTE	7179	genome.wustl.edu	37	21	11026767	11026767	+	5'UTR	SNP	T	T	C	rs56385395		TCGA-E2-A3DX-01A-21D-A20S-09	TCGA-E2-A3DX-10A-01D-A20S-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7a89a261-0177-4378-b89a-b1ead9e093bf	1ab484a1-6e7d-485f-938a-6d1d2f74cf40	g.chr21:11026767T>C	ENST00000415664.2	-	0	194				BAGE2_ENST00000470054.1_RNA			P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology						peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		AGCTTTGACCTGCCTCGGCCA	0.473																																						dbGAP											0																																										-	-	-	SO:0001623	5_prime_UTR_variant	0			AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	12023	protein-coding gene	gene with protein product	"""PTEN-related tyrosine phosphatase"", ""cancer/testis antigen 44"""	604336				10830953, 14659893	Standard	NM_001290224		Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000415664.2:c.-3142A>G	21.37:g.11026767T>C		Somatic		WXS	Illumina GAIIx	Phase_IV	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	RNA	SNP	-	NULL	ENST00000415664.2	37	NULL		21																																																																																			TPTE	-	-	ENSG00000166157		0.473	TPTE-006	KNOWN	basic	processed_transcript	TPTE	HGNC	protein_coding	OTTHUMT00000340030.1	45	0.00	0	T			11026767	11026767	-1	no_errors	ENST00000415664	ensembl	human	known	69_37n	rna	53	13.11	8	SNP	0.997	C
TPTE2	93492	genome.wustl.edu	37	13	20006620	20006620	+	Silent	SNP	C	C	T	rs147012324	byFrequency	TCGA-E2-A3DX-01A-21D-A20S-09	TCGA-E2-A3DX-10A-01D-A20S-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7a89a261-0177-4378-b89a-b1ead9e093bf	1ab484a1-6e7d-485f-938a-6d1d2f74cf40	g.chr13:20006620C>T	ENST00000400230.2	-	16	1259	c.1215G>A	c.(1213-1215)tcG>tcA	p.S405S	TPTE2_ENST00000390680.2_Silent_p.S328S|TPTE2_ENST00000382975.4_Silent_p.S365S|TPTE2_ENST00000382977.4_Silent_p.S405S|TPTE2_ENST00000457266.2_Silent_p.S294S|TPTE2_ENST00000255310.6_Silent_p.S328S|TPTE2_ENST00000382978.1_Silent_p.S365S|TPTE2_ENST00000400103.2_Silent_p.S294S			Q6XPS3	TPTE2_HUMAN	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2	405	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.S405S(2)|p.S328S(2)		NS(2)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(8)|lung(21)|pancreas(1)|prostate(8)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		TACCACGAATCGAATAAATAA	0.388																																						dbGAP											4	Substitution - coding silent(4)	prostate(2)|lung(2)											32.0	29.0	30.0					13																	20006620		2203	4297	6500	-	-	-	SO:0001819	synonymous_variant	0			AJ421032	CCDS9285.1, CCDS45013.1, CCDS45014.1	13q12.11	2012-12-10			ENSG00000132958	ENSG00000132958		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	17299	protein-coding gene	gene with protein product		606791				11716755, 12717346, 15057823	Standard	NM_130785		Approved	TPIP	uc001umd.3	Q6XPS3	OTTHUMG00000016493	ENST00000400230.2:c.1215G>A	13.37:g.20006620C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	A1A4X0|A1A4X1|A8MX64|B1AQ16|B4DWZ2|Q5VUH2|Q8WWL4|Q8WWL5	Silent	SNP	pfam_Tensin_phosphatase_C2-dom,pfam_Ion_trans_dom,pfam_Dual-sp_phosphatase_cat-dom,superfamily_C2_Ca/lipid-bd_dom_CaLB,pfscan_Tyr/Dual-specificity_Pase,pfscan_Phosphatase_tensin-typ,pfscan_Tensin_phosphatase_C2-dom	p.S405	ENST00000400230.2	37	c.1215	CCDS45014.1	13																																																																																			TPTE2	-	pfam_Tensin_phosphatase_C2-dom,superfamily_C2_Ca/lipid-bd_dom_CaLB,pfscan_Tensin_phosphatase_C2-dom	ENSG00000132958		0.388	TPTE2-205	KNOWN	basic|appris_principal|CCDS	protein_coding	TPTE2	HGNC	protein_coding		43	0.00	0	C	NM_199254		20006620	20006620	-1	no_errors	ENST00000382977	ensembl	human	known	69_37n	silent	75	11.76	10	SNP	0.023	T
TRIM66	9866	genome.wustl.edu	37	11	8662623	8662623	+	Silent	SNP	G	G	T			TCGA-E2-A3DX-01A-21D-A20S-09	TCGA-E2-A3DX-10A-01D-A20S-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7a89a261-0177-4378-b89a-b1ead9e093bf	1ab484a1-6e7d-485f-938a-6d1d2f74cf40	g.chr11:8662623G>T	ENST00000299550.6	-	9	1058	c.864C>A	c.(862-864)ccC>ccA	p.P288P	TRIM66_ENST00000402157.2_Silent_p.P286P	NM_014818.1	NP_055633.1	O15016	TRI66_HUMAN	tripartite motif containing 66	288						aggresome (GO:0016235)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|kidney(1)|lung(1)|skin(2)	9						TTTGATAAAAGGGTGATGACC	0.507																																						dbGAP											0													39.0	42.0	41.0					11																	8662623		692	1591	2283	-	-	-	SO:0001819	synonymous_variant	0			AB002296		11p15.4	2013-01-28	2011-01-25		ENSG00000166436	ENSG00000166436		"""Tripartite motif containing / Tripartite motif containing"", ""Zinc fingers, PHD-type"""	29005	protein-coding gene	gene with protein product		612000	"""chromosome 11 open reading frame 29"", ""tripartite motif-containing 66"""	C11orf29		9205841	Standard	NM_014818		Approved	KIAA0298, TIF1D	uc010rbo.2	O15016	OTTHUMG00000150481	ENST00000299550.6:c.864C>A	11.37:g.8662623G>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q9BQQ4	Silent	SNP	pfam_Bromodomain,pfam_Znf_B-box,pfam_Znf_PHD-finger,superfamily_Bromodomain,superfamily_Znf_FYVE_PHD,smart_Znf_B-box,smart_Znf_PHD,smart_Bbox_C,smart_Bromodomain,pfscan_Znf_B-box,pfscan_Znf_PHD-finger,pfscan_Bromodomain	p.P288	ENST00000299550.6	37	c.864		11																																																																																			TRIM66	-	NULL	ENSG00000166436		0.507	TRIM66-201	KNOWN	basic|appris_candidate	protein_coding	TRIM66	HGNC	protein_coding		33	0.00	0	G	XM_084529		8662623	8662623	-1	no_errors	ENST00000299550	ensembl	human	known	69_37n	silent	27	12.90	4	SNP	0.338	T
UBC	7316	genome.wustl.edu	37	12	125396902	125396902	+	Silent	SNP	T	T	C	rs17840840	byFrequency	TCGA-E2-A3DX-01A-21D-A20S-09	TCGA-E2-A3DX-10A-01D-A20S-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7a89a261-0177-4378-b89a-b1ead9e093bf	1ab484a1-6e7d-485f-938a-6d1d2f74cf40	g.chr12:125396902T>C	ENST00000536769.1	-	1	2992	c.1416A>G	c.(1414-1416)gaA>gaG	p.E472E	UBC_ENST00000536661.1_5'Flank|UBC_ENST00000339647.5_Silent_p.E472E|UBC_ENST00000538617.1_Intron|UBC_ENST00000546120.1_Silent_p.E396E			P0CG48	UBC_HUMAN	ubiquitin C	472	Ubiquitin-like 7. {ECO:0000255|PROSITE- ProRule:PRU00214}.				activation of MAPK activity (GO:0000187)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protease binding (GO:0002020)			breast(3)|endometrium(4)|kidney(4)|large_intestine(2)|lung(13)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.17e-05)|Epithelial(86;0.000207)|all cancers(50;0.00308)		TCGGCTCCACTTCGAGAGTGA	0.522																																						dbGAP											0													2.0	2.0	2.0					12																	125396902		844	1943	2787	-	-	-	SO:0001819	synonymous_variant	0				CCDS9260.1	12q24.3	2008-09-08			ENSG00000150991	ENSG00000150991			12468	protein-coding gene	gene with protein product	"""polyubiquitin-C"""	191340				1315303, 11872750	Standard	NM_021009		Approved		uc001ugs.4	P0CG48		ENST00000536769.1:c.1416A>G	12.37:g.125396902T>C		Somatic		WXS	Illumina GAIIx	Phase_IV	P02248|P02249|P02250|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Silent	SNP	pfam_Ubiquitin,pfam_SUMO,smart_Ubiquitin,pfscan_Ubiquitin_supergroup,prints_Ubiquitin_subgr	p.E472	ENST00000536769.1	37	c.1416	CCDS9260.1	12																																																																																			UBC	-	pfam_Ubiquitin,pfam_SUMO,smart_Ubiquitin,pfscan_Ubiquitin_supergroup	ENSG00000150991		0.522	UBC-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	UBC	HGNC	protein_coding	OTTHUMT00000400177.1	14	0.00	0	T	NM_021009		125396902	125396902	-1	no_errors	ENST00000339647	ensembl	human	known	69_37n	silent	5	44.44	4	SNP	1.000	C
WDR19	57728	genome.wustl.edu	37	4	39245931	39245931	+	Silent	SNP	C	C	A			TCGA-E2-A3DX-01A-21D-A20S-09	TCGA-E2-A3DX-10A-01D-A20S-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7a89a261-0177-4378-b89a-b1ead9e093bf	1ab484a1-6e7d-485f-938a-6d1d2f74cf40	g.chr4:39245931C>A	ENST00000399820.3	+	22	2639	c.2485C>A	c.(2485-2487)Cga>Aga	p.R829R	WDR19_ENST00000288634.7_Silent_p.R669R	NM_025132.3	NP_079408.3	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19	829					ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium assembly (GO:0042384)|digestive system development (GO:0055123)|ear morphogenesis (GO:0042471)|embryonic camera-type eye development (GO:0031076)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic limb morphogenesis (GO:0030326)|in utero embryonic development (GO:0001701)|intraciliary retrograde transport (GO:0035721)|myotome development (GO:0061055)|neurological system process (GO:0050877)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intraciliary transport particle A (GO:0030991)|motile cilium (GO:0031514)|nonmotile primary cilium (GO:0031513)|photoreceptor connecting cilium (GO:0032391)				large_intestine(1)	1						AGACATACGTCGAGGGGTTAA	0.463																																						dbGAP											0													147.0	141.0	143.0					4																	39245931		1986	4157	6143	-	-	-	SO:0001819	synonymous_variant	0			AB046858, AY029257	CCDS47042.1	4p14	2014-02-21			ENSG00000157796	ENSG00000157796		"""WD repeat domain containing"", ""Intraflagellar transport homologs"""	18340	protein-coding gene	gene with protein product	"""intraflagellar transport 144 homolog (Chlamydomonas)"""	608151				12906858, 22019273	Standard	XM_005262658		Approved	Pwdmp, KIAA1638, FLJ23127, ORF26, DYF-2, Oseg6, IFT144, NPHP13	uc003gtv.3	Q8NEZ3	OTTHUMG00000160466	ENST00000399820.3:c.2485C>A	4.37:g.39245931C>A		Somatic		WXS	Illumina GAIIx	Phase_IV	B5MEF2|Q8N5B4|Q9H5S0|Q9HCD4	Silent	SNP	pfam_WD40_repeat,superfamily_WD40_repeat_dom,smart_WD40_repeat,pfscan_WD40_repeat_dom	p.R829	ENST00000399820.3	37	c.2485	CCDS47042.1	4																																																																																			WDR19	-	NULL	ENSG00000157796		0.463	WDR19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	WDR19	HGNC	protein_coding	OTTHUMT00000360689.1	22	0.00	0	C			39245931	39245931	+1	no_errors	ENST00000399820	ensembl	human	known	69_37n	silent	31	13.89	5	SNP	0.993	A
ZNF101	94039	genome.wustl.edu	37	19	19790603	19790603	+	Missense_Mutation	SNP	C	C	T	rs144162757		TCGA-E2-A3DX-01A-21D-A20S-09	TCGA-E2-A3DX-10A-01D-A20S-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7a89a261-0177-4378-b89a-b1ead9e093bf	1ab484a1-6e7d-485f-938a-6d1d2f74cf40	g.chr19:19790603C>T	ENST00000592502.1	+	4	915	c.805C>T	c.(805-807)Cgg>Tgg	p.R269W	ZNF101_ENST00000415784.2_Missense_Mutation_p.R149W|ZNF101_ENST00000444249.2_3'UTR			Q8IZC7	ZN101_HUMAN	zinc finger protein 101	269					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(4)|ovary(2)|prostate(1)	17						AGGTTACCTTCGGACACATGA	0.408																																						dbGAP											0													46.0	44.0	45.0					19																	19790603		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK097169	CCDS32971.1	19p13.11	2013-01-08	2004-02-10		ENSG00000181896	ENSG00000181896		"""Zinc fingers, C2H2-type"", ""-"""	12881	protein-coding gene	gene with protein product		603983	"""zinc finger protein 101 (Y2)"""			11441184	Standard	XM_005260165		Approved	HZF12, DKFZp570I0164	uc002nni.2	Q8IZC7	OTTHUMG00000167736	ENST00000592502.1:c.805C>T	19.37:g.19790603C>T	ENSP00000468049:p.Arg269Trp	Somatic		WXS	Illumina GAIIx	Phase_IV	C9JU83|Q0VDG9	Missense_Mutation	SNP	pfam_Znf_C2H2,pfam_Krueppel-associated_box,superfamily_Krueppel-associated_box,smart_Krueppel-associated_box,smart_Znf_C2H2-like,pfscan_Znf_C2H2,pfscan_Krueppel-associated_box	p.R269W	ENST00000592502.1	37	c.805	CCDS32971.1	19	.	.	.	.	.	.	.	.	.	.	C	6.656	0.489611	0.12641	.	.	ENSG00000181896	ENST00000318110;ENST00000415440;ENST00000415784	T;T	0.07800	3.16;3.16	0.235	0.235	0.15431	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07638	0.0192	L	0.52759	1.655	0.09310	N	1	B	0.20164	0.042	B	0.12837	0.008	T	0.36383	-0.9750	8	.	.	.	.	6.2532	0.20859	0.0:0.9997:0.0:3.0E-4	.	269	Q8IZC7	ZN101_HUMAN	W	269;269;149	ENSP00000319716:R269W;ENSP00000400952:R149W	.	R	+	1	2	ZNF101	19651603	0.000000	0.05858	0.006000	0.13384	0.006000	0.05464	-0.566000	0.05922	0.308000	0.22923	0.313000	0.20887	CGG	ZNF101	-	smart_Znf_C2H2-like,pfscan_Znf_C2H2	ENSG00000181896		0.408	ZNF101-004	KNOWN	basic|appris_principal|CCDS	protein_coding	ZNF101	HGNC	protein_coding	OTTHUMT00000460559.1	22	0.00	0	C	NM_033204		19790603	19790603	+1	no_errors	ENST00000318110	ensembl	human	known	69_37n	missense	20	23.08	6	SNP	0.151	T
