#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_ENSG_ID	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_Ens_Gene	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GMAF	i_HGNC	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_Normal_Alt_Count	i_Normal_Ref_Count	i_Normal_VAF	i_ORegAnno_bin	i_PurityEst	i_RNA_Tum_Ref_count	i_RNA_Tum_VAF	i_RNA_Tum_Var_count	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_Tier	i_Tumor_Alt_Count	i_Tumor_Ref_Count	i_Tumor_VAF	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_WGS_Norm_Ref_count	i_WGS_Norm_VAF	i_WGS_Norm_Var_count	i_WGS_Tum_Ref_count	i_WGS_Tum_VAF	i_WGS_Tum_Var_count	i_all_domains	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	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_deletion_substructures	i_domain	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	i_gene_type	i_havana_transcript	i_reference	i_refseq_mrna_id	i_rs_id	i_secondary_variant_classification	i_stop	i_strand	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_type	i_ucsc_cons	i_variant
SLC4A5	57835	genome.wustl.edu	37	2	74474299	74474299	+	Silent	SNP	G	G	T			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr2:74474299G>T	ENST00000377634.4	-	19	2322	c.1923C>A	c.(1921-1923)tcC>tcA	p.S641S	SLC4A5_ENST00000423644.1_Silent_p.S641S|SLC4A5_ENST00000346834.4_Silent_p.S641S|SLC4A5_ENST00000357822.5_Silent_p.S641S|SLC4A5_ENST00000359484.4_Silent_p.S577S|RP11-287D1.3_ENST00000451608.2_3'UTR|SLC4A5_ENST00000377632.1_Silent_p.S641S|SLC4A5_ENST00000394019.2_Silent_p.S641S|SLC4A5_ENST00000483195.1_5'UTR|SLC4A5_ENST00000358683.4_Silent_p.S577S					solute carrier family 4 (sodium bicarbonate cotransporter), member 5											breast(5)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(12)|lung(13)|ovary(5)|pancreas(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48						TGATAAGGGTGGAGAAGCCCT	0.473																																																	0								ENSG00000188687						226.0	222.0	223.0					2																	74474299		2203	4300	6503	SLC4A5	SO:0001819	synonymous_variant	0			-	HGNC	AF243499	CCDS1936.1, CCDS1937.1	2p13.1	2013-07-19	2013-07-19		ENSG00000188687	ENSG00000188687		"""Solute carriers"""	18168	protein-coding gene	gene with protein product		606757	"""solute carrier family 4, sodium bicarbonate cotransporter, member 5"""			10978526, 11087115	Standard	NM_133478		Approved	NBC4	uc002sko.1	Q9BY07	OTTHUMG00000090263	ENST00000377634.4:c.1923C>A	2.37:g.74474299G>T		Somatic	0	46	0.00		0.5521987511953187	3	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	42	8.70		Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_HCO3_transpt_C,pfam_Band3_cytoplasmic_dom,superfamily_PTrfase/Anion_transptr,prints_HCO3_transpt_euk,prints_Na/HCO3_transpt,tigrfam_HCO3_transpt_euk	p.S641	ENST00000377634.4	37	c.1923	CCDS1936.1	2																																																																																			-	pfam_HCO3_transpt_C,tigrfam_HCO3_transpt_euk		0.473	SLC4A5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	SLC4A5	protein_coding	OTTHUMT00000206583.3	G		-		74474299	-1	no_errors	ENST00000357822	ensembl	human	known	74_37	silent	SNP	1.000	T
MAN1B1	11253	genome.wustl.edu	37	9	140002840	140002840	+	Splice_Site	SNP	G	G	T			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr9:140002840G>T	ENST00000371589.4	+	13	1970	c.1897G>T	c.(1897-1899)Gtc>Ttc	p.V633F	MAN1B1_ENST00000540391.1_3'UTR|MAN1B1_ENST00000474902.1_Splice_Site_p.V336F	NM_016219.4	NP_057303.2	Q9UKM7	MA1B1_HUMAN	mannosidase, alpha, class 1B, member 1	633					cellular protein metabolic process (GO:0044267)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum quality control compartment (GO:0044322)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			autonomic_ganglia(1)|central_nervous_system(2)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|ovary(2)	14	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;3.08e-05)|Epithelial(140;0.000513)		TGCTGCACAGGTCCCCTCGGG	0.627																																																	0								ENSG00000177239						76.0	73.0	74.0					9																	140002840		2203	4300	6503	MAN1B1	SO:0001630	splice_region_variant	0			-	HGNC	AF145732	CCDS7029.1	9q34.3	2014-05-27			ENSG00000177239	ENSG00000177239			6823	protein-coding gene	gene with protein product	"""endoplasmic reticulum alpha-mannosidase 1"", ""alpha 1,2-mannosidase"", ""endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase 1"", ""ER alpha 1,2-mannosidase"", ""Man9GlcNAc2-specific processing alpha-mannosidase"""	604346				10409699, 10521544	Standard	NM_016219		Approved	MANA-ER, MRT15	uc004cld.3	Q9UKM7	OTTHUMG00000020978	ENST00000371589.4:c.1897-1G>T	9.37:g.140002840G>T		Somatic	0	25	0.00		0.5521987511953187	136	29.90	58	WXS	Illumina HiSeq 2500	Phase_IV	tier1	8	10	44.44	Q5VSG3|Q9BRS9|Q9Y5K7	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Glyco_hydro_47,superfamily_Glyco_hydro_47,prints_Glyco_hydro_47	p.V633F	ENST00000371589.4	37	c.1897	CCDS7029.1	9	.	.	.	.	.	.	.	.	.	.	G	19.96	3.923503	0.73213	.	.	ENSG00000177239	ENST00000371589;ENST00000474902	T;T	0.74526	-0.85;-0.85	5.44	5.44	0.79542	.	.	.	.	.	D	0.92080	0.7490	H	0.98542	4.26	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.87578	0.997;0.998	D	0.94988	0.8132	8	.	.	.	.	18.2271	0.89921	0.0:0.0:1.0:0.0	.	306;633	B3KXZ1;Q9UKM7	.;MA1B1_HUMAN	F	633;336	ENSP00000360645:V633F;ENSP00000447256:V336F	.	V	+	1	0	MAN1B1	139122661	1.000000	0.71417	1.000000	0.80357	0.155000	0.21991	9.147000	0.94646	2.561000	0.86390	0.561000	0.74099	GTC	-	pfam_Glyco_hydro_47,superfamily_Glyco_hydro_47		0.627	MAN1B1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	MAN1B1	protein_coding	OTTHUMT00000055294.2	G	NM_016219	-	Missense_Mutation	140002840	+1	no_errors	ENST00000371589	ensembl	human	known	74_37	missense	SNP	1.000	T
SP110	3431	genome.wustl.edu	37	2	231033804	231033804	+	3'UTR	SNP	C	C	A			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr2:231033804C>A	ENST00000358662.4	-	0	2184				SP110_ENST00000258381.6_3'UTR|AC009950.2_ENST00000595586.2_RNA|AC009950.2_ENST00000609120.1_RNA|AC009950.2_ENST00000445199.1_RNA	NM_004509.3	NP_004500	Q9HB58	SP110_HUMAN	SP110 nuclear body protein						regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			breast(4)|endometrium(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Renal(207;0.0112)|all_lung(227;0.0223)|Lung NSC(271;0.0983)|all_hematologic(139;0.104)|Acute lymphoblastic leukemia(138;0.169)		Epithelial(121;2.61e-12)|all cancers(144;6.39e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.0097)		CAGCTGAATCCTGAGGTGGGG	0.507																																																	0								ENSG00000135899						109.0	115.0	113.0					2																	231033804		2203	4300	6503	SP110	SO:0001624	3_prime_UTR_variant	0			-	HGNC	L22343	CCDS2474.1, CCDS2475.1, CCDS2476.1, CCDS54435.1	2q37.1	2014-09-17	2001-12-19	2001-12-20	ENSG00000135899	ENSG00000135899			5401	protein-coding gene	gene with protein product		604457	"""interferon-induced protein 41, 30kD"""	IFI41, IFI75		7693701, 10388521	Standard	NM_080424		Approved		uc002vqg.3	Q9HB58	OTTHUMG00000133204	ENST00000358662.4:c.*36G>T	2.37:g.231033804C>A		Somatic	0	47	0.00		0.5521987511953187	5	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	35	10.26	B4DVI4|F5H1M1|Q14976|Q14977|Q53TG2|Q8WUZ6|Q9HCT8	RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000358662.4	37	NULL	CCDS2474.1	2																																																																																			-	-		0.507	SP110-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	SP110	protein_coding	OTTHUMT00000332414.1	C	NM_080424	-		231033804	-1	no_errors	ENST00000480916	ensembl	human	known	74_37	rna	SNP	0.663	A
GATA4	2626	genome.wustl.edu	37	8	11615950	11615950	+	Missense_Mutation	SNP	T	T	C			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr8:11615950T>C	ENST00000335135.4	+	7	1853	c.1295T>C	c.(1294-1296)tTg>tCg	p.L432S	GATA4_ENST00000532059.1_Missense_Mutation_p.L433S|GATA4_ENST00000528712.1_Missense_Mutation_p.L226S|C8orf49_ENST00000525043.2_5'Flank	NM_002052.3	NP_002043.2	P43694	GATA4_HUMAN	GATA binding protein 4	432					atrial septum morphogenesis (GO:0060413)|atrial septum primum morphogenesis (GO:0003289)|atrial septum secundum morphogenesis (GO:0003290)|atrioventricular valve morphogenesis (GO:0003181)|blood coagulation (GO:0007596)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac ventricle morphogenesis (GO:0003208)|cell growth involved in cardiac muscle cell development (GO:0061049)|cell-cell signaling (GO:0007267)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to glucose stimulus (GO:0071333)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic foregut morphogenesis (GO:0048617)|embryonic heart tube anterior/posterior pattern specification (GO:0035054)|endocardial cushion development (GO:0003197)|endoderm development (GO:0007492)|endoderm formation (GO:0001706)|epithelial cell fate commitment (GO:0072148)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|intestinal epithelial cell differentiation (GO:0060575)|lung lobe formation (GO:0060464)|male gonad development (GO:0008584)|negative regulation of autophagy (GO:0010507)|positive regulation of angiogenesis (GO:0045766)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to mechanical stimulus (GO:0009612)|seminiferous tubule development (GO:0072520)|Sertoli cell differentiation (GO:0060008)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular cardiac muscle tissue development (GO:0003229)|ventricular septum development (GO:0003281)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|co-SMAD binding (GO:0070410)|DNA binding (GO:0003677)|enhancer sequence-specific DNA binding (GO:0001158)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(10)	13	all_epithelial(15;0.0839)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.199)		AGCCTGGTCTTGGCCGACAGT	0.577																																																	0								ENSG00000136574						117.0	96.0	103.0					8																	11615950		2203	4300	6503	GATA4	SO:0001583	missense	0			-	HGNC	AK097060	CCDS5983.1	8p23.1-p22	2013-01-25	2001-11-28		ENSG00000136574	ENSG00000136574		"""GATA zinc finger domain containing"""	4173	protein-coding gene	gene with protein product		600576	"""GATA-binding protein 4"""			7665171	Standard	NM_002052		Approved		uc003wuc.2	P43694	OTTHUMG00000090800	ENST00000335135.4:c.1295T>C	8.37:g.11615950T>C	ENSP00000334458:p.Leu432Ser	Somatic	0	40	0.00		0.5521987511953187	1	50.00	1	WXS	Illumina HiSeq 2500	Phase_IV	tier1	19	25	43.18	B7ZKX0|B7ZKZ4|Q3MJ45|Q5IFM8	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_GATA_N,pfam_Znf_GATA,smart_Znf_GATA,pirsf_TF_GATA_4/5/6,pfscan_Znf_GATA,prints_Znf_GATA	p.L432S	ENST00000335135.4	37	c.1295	CCDS5983.1	8	.	.	.	.	.	.	.	.	.	.	T	21.8	4.207690	0.79240	.	.	ENSG00000136574	ENST00000528712;ENST00000335135;ENST00000259090;ENST00000532059	D;D;D	0.99282	-5.68;-5.34;-5.35	5.18	5.18	0.71444	.	0.000000	0.51477	D	0.000100	D	0.99302	0.9756	M	0.77103	2.36	0.58432	D	0.999997	D;D	0.71674	0.998;0.998	D;D	0.78314	0.991;0.991	D	0.99056	1.0829	10	0.87932	D	0	-19.2496	14.3663	0.66807	0.0:0.0:0.0:1.0	.	433;432	B7ZKZ4;P43694	.;GATA4_HUMAN	S	226;432;431;433	ENSP00000435043:L226S;ENSP00000334458:L432S;ENSP00000435712:L433S	ENSP00000259090:L431S	L	+	2	0	GATA4	11653359	1.000000	0.71417	0.999000	0.59377	0.928000	0.56348	6.803000	0.75180	2.175000	0.68902	0.460000	0.39030	TTG	-	pirsf_TF_GATA_4/5/6		0.577	GATA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	GATA4	protein_coding	OTTHUMT00000207587.2	T	NM_002052	-		11615950	+1	no_errors	ENST00000335135	ensembl	human	known	74_37	missense	SNP	1.000	C
PCDHB3	56132	genome.wustl.edu	37	5	140482187	140482187	+	Missense_Mutation	SNP	C	C	T			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr5:140482187C>T	ENST00000231130.2	+	1	1954	c.1954C>T	c.(1954-1956)Cgc>Tgc	p.R652C	AC005754.7_ENST00000607216.1_RNA	NM_018937.2	NP_061760.1	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3	652	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	72			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGAGCCTCCGCGCTCGGCCAC	0.711																																																	0								ENSG00000113205						20.0	24.0	23.0					5																	140482187		2031	3972	6003	PCDHB3	SO:0001583	missense	0			-	HGNC	AF152496	CCDS4245.1	5q31	2010-01-26			ENSG00000113205	ENSG00000113205		"""Cadherins / Protocadherins : Clustered"""	8688	other	protocadherin		606329				10380929	Standard	NM_018937		Approved	PCDH-BETA3	uc003lio.3	Q9Y5E6	OTTHUMG00000129622	ENST00000231130.2:c.1954C>T	5.37:g.140482187C>T	ENSP00000231130:p.Arg652Cys	Somatic	0	65	0.00		0.5521987511953187	6	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	23	40	36.51	B2R8P2	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Cadherin,pfam_Cadherin_N,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	p.R652C	ENST00000231130.2	37	c.1954	CCDS4245.1	5	.	.	.	.	.	.	.	.	.	.	C	9.756	1.168849	0.21621	.	.	ENSG00000113205	ENST00000231130	T	0.55234	0.53	4.38	3.47	0.39725	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.56292	0.1975	M	0.78801	2.425	0.44432	D	0.997357	B	0.22800	0.075	B	0.27715	0.082	T	0.59423	-0.7457	9	0.66056	D	0.02	.	13.5398	0.61668	0.1686:0.8314:0.0:0.0	.	652	Q9Y5E6	PCDB3_HUMAN	C	652	ENSP00000231130:R652C	ENSP00000231130:R652C	R	+	1	0	PCDHB3	140462371	0.003000	0.15002	0.227000	0.23927	0.089000	0.18198	2.015000	0.40961	0.875000	0.35847	0.556000	0.70494	CGC	-	pfam_Cadherin,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin		0.711	PCDHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PCDHB3	protein_coding	OTTHUMT00000251817.2	C	NM_018937	-		140482187	+1	no_errors	ENST00000231130	ensembl	human	known	74_37	missense	SNP	0.752	T
NFKB1	4790	genome.wustl.edu	37	4	103531766	103531766	+	Silent	SNP	C	C	A			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr4:103531766C>A	ENST00000505458.1	+	20	2536	c.2259C>A	c.(2257-2259)ctC>ctA	p.L753L	NFKB1_ENST00000394820.4_Silent_p.L753L|NFKB1_ENST00000226574.4_Silent_p.L754L|NFKB1_ENST00000600343.1_Silent_p.L573L			P19838	NFKB1_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 1	753	Interaction with CFLAR.				apoptotic process (GO:0006915)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|cellular response to nicotine (GO:0071316)|cellular response to peptide hormone stimulus (GO:0071375)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|membrane protein intracellular domain proteolysis (GO:0031293)|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 calcidiol 1-monooxygenase activity (GO:0010956)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of cytokine production (GO:0001818)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-12 biosynthetic process (GO:0045083)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vitamin D biosynthetic process (GO:0010957)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|response to copper ion (GO:0046688)|response to oxidative stress (GO:0006979)|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 from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|I-kappaB/NF-kappaB complex (GO:0033256)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleic acid binding transcription factor activity (GO:0001071)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			biliary_tract(1)|breast(4)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	27		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.59e-08)	Acetylsalicylic acid(DB00945)|Pranlukast(DB01411)|Thalidomide(DB01041)|Triflusal(DB08814)	TTGAGCCTCTCTATGACCTGG	0.517																																																	0								ENSG00000109320						136.0	132.0	133.0					4																	103531766		2203	4300	6503	NFKB1	SO:0001819	synonymous_variant	0			-	HGNC	M58603	CCDS3657.1, CCDS54783.1	4q24	2013-01-10	2008-07-28		ENSG00000109320	ENSG00000109320		"""Ankyrin repeat domain containing"""	7794	protein-coding gene	gene with protein product		164011				1992489	Standard	NM_003998		Approved	KBF1, p105, NFKB-p50, p50, NF-kappaB, NFkappaB, NF-kB1	uc011cep.2	P19838	OTTHUMG00000161080	ENST00000505458.1:c.2259C>A	4.37:g.103531766C>A		Somatic	0	34	0.00		0.5521987511953187	104	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	32	11.11	A8K5Y5|B3KVE8|Q68D84|Q86V43|Q8N4X7|Q9NZC0	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_RHD,pfam_Ankyrin_rpt,pfam_Death_domain,superfamily_p53-like_TF_DNA-bd,superfamily_Ankyrin_rpt-contain_dom,superfamily_Ig_E-set,superfamily_DEATH-like_dom,smart_IPT,smart_Ankyrin_rpt,smart_Death_domain,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom,pfscan_RHD,prints_NF_Rel_Dor,prints_Ankyrin_rpt	p.L754	ENST00000505458.1	37	c.2262	CCDS54783.1	4																																																																																			-	superfamily_Ankyrin_rpt-contain_dom		0.517	NFKB1-003	KNOWN	alternative_5_UTR|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	NFKB1	protein_coding	OTTHUMT00000363411.1	C		-		103531766	+1	no_errors	ENST00000226574	ensembl	human	known	74_37	silent	SNP	0.944	A
TTC39A	22996	genome.wustl.edu	37	1	51753754	51753754	+	3'UTR	DEL	A	A	-			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr1:51753754delA	ENST00000447632.2	-	0	1965				TTC39A_ENST00000262675.7_3'UTR|TTC39A_ENST00000413473.2_3'UTR|TTC39A_ENST00000371750.5_3'UTR|TTC39A_ENST00000451380.1_3'UTR|TTC39A_ENST00000530004.1_3'UTR|TTC39A_ENST00000534098.1_5'UTR			Q5SRH9	TT39A_HUMAN	tetratricopeptide repeat domain 39A									p.0?(2)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(2)|prostate(2)|skin(3)|urinary_tract(1)	17						GGGCAGGGGGAGGGGGTATTT	0.552																																																	2	Whole gene deletion(2)	thyroid(1)|central_nervous_system(1)						ENSG00000085831																																			TTC39A	SO:0001624	3_prime_UTR_variant	0				HGNC	AB007921	CCDS44143.1, CCDS44144.1, CCDS72789.1, CCDS72790.1	1p32.3	2013-01-11	2008-06-23	2008-06-23	ENSG00000085831	ENSG00000085831		"""Tetratricopeptide (TTC) repeat domain containing"""	18657	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 34"""	C1orf34		9455484, 9461476	Standard	XM_005270643		Approved	KIAA0452, DEME-6	uc010onf.2	Q5SRH9	OTTHUMG00000008193	ENST00000447632.2:c.*75T>-	1.37:g.51753754delA		Somatic	0	35	0.00		0.5521987511953187	1	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	27	10.00	B7Z782|E7EQY9|G3XAF8|O43417|O75040|Q5SRH5|Q5SRH6|Q5SRH7|Q5SRH8|Q5SRI0|Q5SRI1|Q5SRI2|Q5T7S1|Q6PIU8|Q9BT24	RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000447632.2	37	NULL		1																																																																																			-	-		0.552	TTC39A-004	KNOWN	basic	protein_coding	TTC39A	protein_coding	OTTHUMT00000022434.2	A				51753754	-1	no_errors	ENST00000534098	ensembl	human	known	74_37	rna	DEL	0.000	-
CTTNBP2NL	55917	genome.wustl.edu	37	1	112991755	112991755	+	Missense_Mutation	SNP	G	G	T			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr1:112991755G>T	ENST00000271277.6	+	4	516	c.291G>T	c.(289-291)atG>atT	p.M97I		NM_018704.2	NP_061174.1	Q9P2B4	CT2NL_HUMAN	CTTNBP2 N-terminal like	97					negative regulation of transmembrane transport (GO:0034763)|negative regulation of transporter activity (GO:0032410)|protein dephosphorylation (GO:0006470)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	protein phosphatase 2A binding (GO:0051721)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	29		all_cancers(81;0.00064)|all_epithelial(167;0.000415)|all_lung(203;0.00045)|Lung NSC(69;0.000705)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		AGGAGCGCATGCTGTCCCAGC	0.458																																																	0								ENSG00000143079						59.0	57.0	58.0					1																	112991755		2203	4300	6503	CTTNBP2NL	SO:0001583	missense	0			-	HGNC	AB037854	CCDS845.1	1p13.2	2008-02-05			ENSG00000143079	ENSG00000143079			25330	protein-coding gene	gene with protein product		615100				10718198	Standard	NM_018704		Approved	DKFZp547A023	uc001ebx.3	Q9P2B4	OTTHUMG00000011154	ENST00000271277.6:c.291G>T	1.37:g.112991755G>T	ENSP00000271277:p.Met97Ile	Somatic	0	35	0.00		0.5521987511953187	7	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	17	15.00	B3KMS5|Q96B40	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Cortactin-binding_p2_N	p.M97I	ENST00000271277.6	37	c.291	CCDS845.1	1	.	.	.	.	.	.	.	.	.	.	G	33	5.201860	0.94997	.	.	ENSG00000143079	ENST00000271277;ENST00000441739	T;T	0.46063	0.88;0.88	5.65	5.65	0.86999	Cortactin-binding protein-2, N-terminal (1);	0.035822	0.85682	D	0.000000	T	0.54565	0.1866	L	0.59436	1.845	0.80722	D	1	D	0.69078	0.997	D	0.79108	0.992	T	0.43798	-0.9369	10	0.34782	T	0.22	-23.3098	19.3262	0.94262	0.0:0.0:1.0:0.0	.	97	Q9P2B4	CT2NL_HUMAN	I	97	ENSP00000271277:M97I;ENSP00000390976:M97I	ENSP00000271277:M97I	M	+	3	0	CTTNBP2NL	112793278	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.476000	0.97823	2.677000	0.91161	0.561000	0.74099	ATG	-	pfam_Cortactin-binding_p2_N		0.458	CTTNBP2NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CTTNBP2NL	protein_coding	OTTHUMT00000030686.1	G	NM_018704	-		112991755	+1	no_errors	ENST00000271277	ensembl	human	known	74_37	missense	SNP	1.000	T
DENND4B	9909	genome.wustl.edu	37	1	153914353	153914353	+	Silent	SNP	G	G	T			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr1:153914353G>T	ENST00000361217.4	-	6	1465	c.1047C>A	c.(1045-1047)ccC>ccA	p.P349P		NM_014856.2	NP_055671.2	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	349	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab protein signal transduction (GO:0032483)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	36	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			ACGCTTCCAAGGGTAGGCGGT	0.632																																																	0								ENSG00000198837						41.0	47.0	45.0					1																	153914353		2112	4218	6330	DENND4B	SO:0001819	synonymous_variant	0			-	HGNC	AB007945	CCDS44228.1	1q21.3	2012-10-03	2006-01-27	2006-01-27	ENSG00000198837	ENSG00000198837		"""DENN/MADD domain containing"""	29044	protein-coding gene	gene with protein product			"""KIAA0476"""	KIAA0476		9455484, 12906859	Standard	NM_014856		Approved		uc001fdd.1	O75064	OTTHUMG00000037157	ENST00000361217.4:c.1047C>A	1.37:g.153914353G>T		Somatic	0	41	0.00		0.5521987511953187	35	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	45	8.16	Q5T4K0	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_DENN_dom,pfam_dDENN_dom,pfam_uDENN_dom,smart_uDENN_dom,smart_DENN_dom,smart_dDENN_dom,pfscan_DENN_dom,pfscan_uDENN_dom,pfscan_dDENN_dom	p.P349	ENST00000361217.4	37	c.1047	CCDS44228.1	1																																																																																			-	pfam_DENN_dom,smart_DENN_dom,pfscan_DENN_dom		0.632	DENND4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DENND4B	protein_coding	OTTHUMT00000090278.2	G	XM_375806	-		153914353	-1	no_errors	ENST00000361217	ensembl	human	known	74_37	silent	SNP	1.000	T
COQ9	57017	genome.wustl.edu	37	16	57486822	57486822	+	Missense_Mutation	SNP	G	G	T			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr16:57486822G>T	ENST00000262507.6	+	3	421	c.352G>T	c.(352-354)Gca>Tca	p.A118S	COQ9_ENST00000567933.1_Missense_Mutation_p.A118S|COQ9_ENST00000567072.1_Missense_Mutation_p.A118S	NM_020312.3	NP_064708.1	O75208	COQ9_HUMAN	coenzyme Q9	118					mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|ubiquinone biosynthetic process (GO:0006744)	mitochondrion (GO:0005739)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|prostate(1)	16						CGGGTGGACAGCAGAGGCGAT	0.632																																																	0								ENSG00000088682						94.0	83.0	87.0					16																	57486822		2198	4300	6498	COQ9	SO:0001583	missense	0			-	HGNC	BC064946	CCDS32459.1	16q13	2013-10-18	2013-10-18	2006-01-13	ENSG00000088682	ENSG00000088682			25302	protein-coding gene	gene with protein product		612837	"""chromosome 16 open reading frame 49"", ""coenzyme Q9 homolog (yeast)"", ""coenzyme Q9 homolog (S. cerevisiae)"""	C16orf49		19375058	Standard	NM_020312		Approved	DKFZP434K046	uc002elq.3	O75208		ENST00000262507.6:c.352G>T	16.37:g.57486822G>T	ENSP00000262507:p.Ala118Ser	Somatic	0	44	0.00		0.5521987511953187	373	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	46	8.00	A8K3L2|Q7L5V7|Q7Z5T6|Q8NBL4|Q9NTJ2|Q9P056	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_COQ9,superfamily_Homeodomain-like,tigrfam_Ubiq_biosynth_COQ9	p.A118S	ENST00000262507.6	37	c.352	CCDS32459.1	16	.	.	.	.	.	.	.	.	.	.	G	14.23	2.472001	0.43942	.	.	ENSG00000088682	ENST00000262507	.	.	.	5.01	2.93	0.34026	.	0.286626	0.38605	N	0.001632	T	0.28200	0.0696	L	0.37897	1.145	0.26825	N	0.96871	B;P;P;B;B	0.35628	0.041;0.499;0.513;0.036;0.091	B;B;B;B;B	0.34873	0.018;0.102;0.191;0.017;0.039	T	0.12451	-1.0547	9	0.09590	T	0.72	-7.9282	11.7967	0.52104	0.0:0.1301:0.736:0.1339	.	118;118;118;118;118	B4E0U3;B4DIV2;B4DEE3;O75208;O75208-2	.;.;.;COQ9_HUMAN;.	S	118	.	ENSP00000262507:A118S	A	+	1	0	COQ9	56044323	1.000000	0.71417	0.966000	0.40874	0.980000	0.70556	3.044000	0.49830	2.325000	0.78763	0.650000	0.86243	GCA	-	superfamily_Homeodomain-like,tigrfam_Ubiq_biosynth_COQ9		0.632	COQ9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	COQ9	protein_coding	OTTHUMT00000432598.3	G	NM_020312	-		57486822	+1	no_errors	ENST00000262507	ensembl	human	known	74_37	missense	SNP	0.602	T
LDLRAP1	26119	genome.wustl.edu	37	1	25880262	25880262	+	Intron	DEL	A	A	-	rs34367689		TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr1:25880262delA	ENST00000374338.4	+	2	207				LDLRAP1_ENST00000488127.1_3'UTR	NM_015627.2	NP_056442.2	Q5SW96	ARH_HUMAN	low density lipoprotein receptor adaptor protein 1						amyloid precursor protein metabolic process (GO:0042982)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|positive regulation of cholesterol metabolic process (GO:0090205)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of signal transduction (GO:0009967)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|regulation of protein binding (GO:0043393)|transport (GO:0006810)	axon (GO:0030424)|basal plasma membrane (GO:0009925)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|early endosome (GO:0005769)|neurofilament (GO:0005883)|recycling endosome (GO:0055037)	AP-2 adaptor complex binding (GO:0035612)|beta-amyloid binding (GO:0001540)|clathrin adaptor activity (GO:0035615)|clathrin binding (GO:0030276)|low-density lipoprotein particle receptor binding (GO:0050750)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphotyrosine binding (GO:0001784)|receptor signaling complex scaffold activity (GO:0030159)|signaling adaptor activity (GO:0035591)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)|urinary_tract(1)	9		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.63e-26)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000728)|STAD - Stomach adenocarcinoma(196;0.000766)|BRCA - Breast invasive adenocarcinoma(304;0.000969)|GBM - Glioblastoma multiforme(114;0.00914)|READ - Rectum adenocarcinoma(331;0.0649)		actcagtctcaaaaaaaaaaa	0.527																																																	0								ENSG00000157978																																			LDLRAP1	SO:0001627	intron_variant	0				HGNC	BC029770	CCDS30639.1	1p36-p35	2014-09-17			ENSG00000157978	ENSG00000157978			18640	protein-coding gene	gene with protein product		605747					Standard	NM_015627		Approved	ARH, ARH2, FHCB1, FHCB2, MGC34705, DKFZp586D0624	uc001bkl.4	Q5SW96	OTTHUMG00000007386	ENST00000374338.4:c.89-151A>-	1.37:g.25880262delA		Somatic	0	10	0.00		0.5521987511953187	0	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	11	31.25	A2BHI5|Q6TQS9|Q8N2Y0|Q9UFI9	RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000374338.4	37	NULL	CCDS30639.1	1																																																																																			-	-		0.527	LDLRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LDLRAP1	protein_coding	OTTHUMT00000019350.3	A	NM_015627			25880262	+1	no_errors	ENST00000488127	ensembl	human	known	74_37	rna	DEL	0.007	-
LRP1	4035	genome.wustl.edu	37	12	57561246	57561246	+	Silent	SNP	C	C	A	rs149857225	byFrequency	TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr12:57561246C>A	ENST00000243077.3	+	19	3400	c.2934C>A	c.(2932-2934)ccC>ccA	p.P978P	LRP1_ENST00000553446.1_3'UTR	NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	978	LDL-receptor class A 6. {ECO:0000255|PROSITE-ProRule:PRU00124}.				aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	CCTGCTTCCCCCTGACTCAGT	0.517																																																	0								ENSG00000123384						198.0	165.0	177.0					12																	57561246		2203	4300	6503	LRP1	SO:0001819	synonymous_variant	0			-	HGNC	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.2934C>A	12.37:g.57561246C>A		Somatic	0	48	0.00		0.5521987511953187	33	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	45	8.16	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_LDrepeatLR_classA_rpt,pfam_LDLR_classB_rpt,superfamily_Growth_fac_rcpt_N_dom,superfamily_LDrepeatLR_classA_rpt,smart_LDrepeatLR_classA_rpt,smart_EGF-like_Ca-bd_dom,smart_EG-like_dom,smart_LDLR_classB_rpt,pfscan_EG-like_dom,pfscan_LDrepeatLR_classA_rpt,pfscan_LDLR_classB_rpt,prints_LDrepeatLR_classA_rpt	p.P978	ENST00000243077.3	37	c.2934	CCDS8932.1	12																																																																																			-	pfam_LDrepeatLR_classA_rpt,superfamily_LDrepeatLR_classA_rpt,smart_LDrepeatLR_classA_rpt,pfscan_LDrepeatLR_classA_rpt		0.517	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LRP1	protein_coding	OTTHUMT00000412772.2	C	NM_002332	-		57561246	+1	no_errors	ENST00000243077	ensembl	human	known	74_37	silent	SNP	1.000	A
LRBA	987	genome.wustl.edu	37	4	151502697	151502698	+	Intron	INS	-	-	A	rs57457692|rs35940180|rs558262000	byFrequency	TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr4:151502697_151502698insA	ENST00000357115.3	-	41	6607				LRBA_ENST00000535741.1_Intron|LRBA_ENST00000507224.1_Intron|RP11-1336O20.2_ENST00000507934.1_RNA|MAB21L2_ENST00000317605.4_5'Flank|LRBA_ENST00000510413.1_Intron|LRBA_ENST00000503716.1_5'UTR	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing							cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					TAGAATCATTTAAAAAAAAAAA	0.391																																																	0								ENSG00000198589																																			LRBA	SO:0001627	intron_variant	0				HGNC	AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589		"""WD repeat domain containing"""	1742	protein-coding gene	gene with protein product		606453		CDC4L		1505956, 11254716	Standard	NM_006726		Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000357115.3:c.6363+6501->T	4.37:g.151502708_151502708dupA		Somatic	0	12	0.00		0.5521987511953187	1	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	2	12	14.29	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	RNA	INS	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000357115.3	37	NULL	CCDS3773.1	4																																																																																			-	-		0.391	LRBA-002	KNOWN	basic|CCDS	protein_coding	LRBA	protein_coding	OTTHUMT00000364939.1	-				151502698	-1	no_errors	ENST00000503716	ensembl	human	known	74_37	rna	INS	0.000:0.000	A
CAPN11	11131	genome.wustl.edu	37	6	44137083	44137083	+	Missense_Mutation	SNP	G	G	A	rs555946152		TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr6:44137083G>A	ENST00000398776.1	+	3	192	c.154G>A	c.(154-156)Gtg>Atg	p.V52M	CAPN11_ENST00000542245.1_Missense_Mutation_p.V52M	NM_007058.3	NP_008989.2	Q9UMQ6	CAN11_HUMAN	calpain 11	52					proteolysis (GO:0006508)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|peptidase activity (GO:0008233)			breast(3)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)	36	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			GGCCAAGGGCGTGGGCCAGCA	0.507													G|||	1	0.000199681	0.0	0.0	5008	,	,		18377	0.001		0.0	False		,,,				2504	0.0																0								ENSG00000137225						40.0	42.0	41.0					6																	44137083		1930	4140	6070	CAPN11	SO:0001583	missense	0			-	HGNC	AJ242832	CCDS47436.1	6p12	2013-01-10			ENSG00000137225	ENSG00000137225		"""EF-hand domain containing"""	1478	protein-coding gene	gene with protein product		604822				10409436	Standard	NM_007058		Approved		uc003owt.1	Q9UMQ6	OTTHUMG00000014758	ENST00000398776.1:c.154G>A	6.37:g.44137083G>A	ENSP00000381758:p.Val52Met	Somatic	0	46	0.00		0.5521987511953187	0	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	38	9.52	B2RA64|Q5T3G1|Q8N4R5	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Peptidase_C2_calpain_cat,pfam_Calpain_domain_III,superfamily_Calpain_domain_III,smart_Peptidase_C2_calpain_cat,smart_Calpain_III,smart_EF_hand_dom,pfscan_EF_hand_dom,pfscan_Peptidase_C2_calpain_cat,prints_Calpain_cysteine_protease	p.V52M	ENST00000398776.1	37	c.154	CCDS47436.1	6	.	.	.	.	.	.	.	.	.	.	G	6.331	0.429249	0.11987	.	.	ENSG00000137225	ENST00000398776;ENST00000542245;ENST00000532171	D;D;T	0.97505	-4.41;-4.41;0.81	4.1	-4.32	0.03688	.	1.343570	0.05096	N	0.486237	D	0.84183	0.5416	N	0.19112	0.55	0.09310	N	0.999996	B	0.30709	0.291	B	0.13407	0.009	T	0.81611	-0.0854	10	0.52906	T	0.07	.	7.0583	0.25111	0.1302:0.4717:0.3146:0.0835	.	52	Q9UMQ6	CAN11_HUMAN	M	52;52;82	ENSP00000381758:V52M;ENSP00000441078:V52M;ENSP00000432420:V82M	ENSP00000381758:V52M	V	+	1	0	CAPN11	44245061	0.000000	0.05858	0.311000	0.25182	0.025000	0.11179	-2.444000	0.01012	-0.993000	0.03467	0.650000	0.86243	GTG	-	NULL		0.507	CAPN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	CAPN11	protein_coding	OTTHUMT00000040714.3	G		-		44137083	+1	no_errors	ENST00000398776	ensembl	human	known	74_37	missense	SNP	0.252	A
SAMD3	154075	genome.wustl.edu	37	6	130505678	130505678	+	Nonsense_Mutation	SNP	G	G	T			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr6:130505678G>T	ENST00000368134.2	-	8	1082	c.474C>A	c.(472-474)tgC>tgA	p.C158*	SAMD3_ENST00000439090.2_Nonsense_Mutation_p.C158*|SAMD3_ENST00000437477.2_Nonsense_Mutation_p.C158*|SAMD3_ENST00000533296.1_5'UTR|SAMD3_ENST00000324172.6_Nonsense_Mutation_p.C158*|SAMD3_ENST00000457563.2_Nonsense_Mutation_p.C182*|SAMD3_ENST00000532763.1_Nonsense_Mutation_p.C156*	NM_001258275.1	NP_001245204.1	Q8N6K7	SAMD3_HUMAN	sterile alpha motif domain containing 3	158										breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(3)|lung(15)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	29				GBM - Glioblastoma multiforme(226;0.00594)|OV - Ovarian serous cystadenocarcinoma(155;0.128)		CTGCTAACATGCATTTGACAT	0.428																																																	0								ENSG00000164483						130.0	114.0	119.0					6																	130505678		2203	4300	6503	SAMD3	SO:0001587	stop_gained	0			-	HGNC	AK091351	CCDS34539.1, CCDS64525.1	6q23.1	2013-01-10			ENSG00000164483	ENSG00000164483		"""Sterile alpha motif (SAM) domain containing"""	21574	protein-coding gene	gene with protein product							Standard	NM_001017373		Approved	bA73O6.2, FLJ34032	uc031spp.1	Q8N6K7	OTTHUMG00000015556	ENST00000368134.2:c.474C>A	6.37:g.130505678G>T	ENSP00000357116:p.Cys158*	Somatic	0	34	0.00		0.5521987511953187	1	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	19	13.64	B4DY20|E1P576|J3KQK4|Q4VXD8|Q8NAY1|Q8NB96	Nonsense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_SAM_type1,pfam_SAM_2,superfamily_SAM/pointed,smart_SAM,pfscan_SAM	p.C158*	ENST00000368134.2	37	c.474	CCDS34539.1	6	.	.	.	.	.	.	.	.	.	.	G	26.5	4.740079	0.89573	.	.	ENSG00000164483	ENST00000368134;ENST00000457563;ENST00000439090;ENST00000437477;ENST00000532763;ENST00000324172;ENST00000532309;ENST00000531544;ENST00000529723	.	.	.	5.67	4.8	0.61643	.	0.222293	0.40908	D	0.000987	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.9399	0.41574	0.0742:0.138:0.7878:0.0	.	.	.	.	X	158;182;158;158;156;158;157;158;155	.	ENSP00000324874:C158X	C	-	3	2	SAMD3	130547371	1.000000	0.71417	0.999000	0.59377	0.928000	0.56348	1.701000	0.37825	1.392000	0.46585	0.655000	0.94253	TGC	-	NULL		0.428	SAMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SAMD3	protein_coding	OTTHUMT00000042197.3	G	NM_152552	-		130505678	-1	no_errors	ENST00000368134	ensembl	human	known	74_37	nonsense	SNP	1.000	T
ABCD3	5825	genome.wustl.edu	37	1	94948795	94948795	+	Splice_Site	SNP	G	G	T			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr1:94948795G>T	ENST00000370214.4	+	10	921	c.897G>T	c.(895-897)ctG>ctT	p.L299L	ABCD3_ENST00000454898.2_Splice_Site_p.L323L|ABCD3_ENST00000394233.2_Intron|ABCD3_ENST00000484213.1_3'UTR|ABCD3_ENST00000536817.1_Splice_Site_p.L226L	NM_002858.3	NP_002849.1	P28288	ABCD3_HUMAN	ATP-binding cassette, sub-family D (ALD), member 3	299	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				ATP catabolic process (GO:0006200)|fatty acid beta-oxidation (GO:0006635)|peroxisome organization (GO:0007031)|transmembrane transport (GO:0055085)|very long-chain fatty acid catabolic process (GO:0042760)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|liver(2)|lung(10)|ovary(1)|pancreas(1)|skin(2)	26		all_lung(203;0.000434)|Lung NSC(277;0.0019)		all cancers(265;0.0261)|Epithelial(280;0.165)		TCCGAAAACTGGTAAGATAAC	0.343																																																	0								ENSG00000117528						73.0	76.0	75.0					1																	94948795		2203	4300	6503	ABCD3	SO:0001630	splice_region_variant	0			-	HGNC	M81182	CCDS749.1, CCDS44175.1	1p21.3	2012-05-16			ENSG00000117528	ENSG00000117528		"""ATP binding cassette transporters / subfamily D"""	67	protein-coding gene	gene with protein product		170995		PXMP1		1301993, 8449508	Standard	NM_002858		Approved	PMP70, ZWS2	uc001dqn.4	P28288	OTTHUMG00000010717	ENST00000370214.4:c.897+1G>T	1.37:g.94948795G>T		Somatic	0	83	0.00		0.5521987511953187	18	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	38	9.30	D3DT46|Q15271|Q6NUN5|Q96DA3|Q9H529	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_ABC_Peroxi_TM,pfam_ABC_transporter-like,superfamily_P-loop_NTPase,superfamily_ABC1_TM_dom,smart_AAA+_ATPase,pfscan_ABC_transporter-like,pfscan_ABC1_TM_dom,tigrfam_FA_transporter	p.L323	ENST00000370214.4	37	c.969	CCDS749.1	1																																																																																			-	pfam_ABC_Peroxi_TM,superfamily_ABC1_TM_dom,pfscan_ABC1_TM_dom,tigrfam_FA_transporter		0.343	ABCD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ABCD3	protein_coding	OTTHUMT00000029597.1	G	NM_002858	-	Silent	94948795	+1	no_errors	ENST00000454898	ensembl	human	known	74_37	silent	SNP	1.000	T
STRADB	55437	genome.wustl.edu	37	2	202319526	202319526	+	5'UTR	SNP	G	G	T			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr2:202319526G>T	ENST00000194530.3	+	0	328				STRADB_ENST00000488196.1_3'UTR|STRADB_ENST00000392249.2_5'UTR	NM_001206864.1|NM_018571.5	NP_001193793.1|NP_061041.2	Q9C0K7	STRAB_HUMAN	STE20-related kinase adaptor beta						activation of protein kinase activity (GO:0032147)|cell cycle arrest (GO:0007050)|cell morphogenesis (GO:0000902)|insulin receptor signaling pathway (GO:0008286)|JNK cascade (GO:0007254)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|transferase activity, transferring phosphorus-containing groups (GO:0016772)			breast(1)|large_intestine(2)|lung(5)|prostate(1)|skin(3)|stomach(1)	13						TGGAATAGATGGATTTTTGTC	0.289																																																	0								ENSG00000082146						141.0	139.0	140.0					2																	202319526		2203	4295	6498	STRADB	SO:0001623	5_prime_UTR_variant	0			-	HGNC	AB038950	CCDS2348.1, CCDS56161.1	2q33.1	2010-09-30	2008-09-15	2008-09-15	ENSG00000082146	ENSG00000082146			13205	protein-coding gene	gene with protein product		607333	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 2"""	ALS2CR2		11161814, 14511394	Standard	NM_018571		Approved	CALS-21, PAPK, ILPIPA, ILPIP	uc002uyd.4	Q9C0K7	OTTHUMG00000132831	ENST00000194530.3:c.-38G>T	2.37:g.202319526G>T		Somatic	0	35	0.00		0.5521987511953187	5	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	36	10.00	Q5BKY7|Q9P1L0	RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000194530.3	37	NULL	CCDS2348.1	2																																																																																			-	-		0.289	STRADB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	STRADB	protein_coding	OTTHUMT00000256297.1	G	NM_018571	-		202319526	+1	no_errors	ENST00000488196	ensembl	human	known	74_37	rna	SNP	1.000	T
PSMA8	143471	genome.wustl.edu	37	18	23731924	23731924	+	Missense_Mutation	SNP	G	G	A	rs371854509		TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr18:23731924G>A	ENST00000308268.6	+	3	439	c.350G>A	c.(349-351)cGc>cAc	p.R117H	PSMA8_ENST00000415576.2_Missense_Mutation_p.R111H|PSMA8_ENST00000343848.6_Missense_Mutation_p.R73H	NM_001025096.1|NM_144662.2	NP_001020267.1|NP_653263.2	Q8TAA3	PSA7L_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 8	117					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)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|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 cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|proteasome core complex, alpha-subunit complex (GO:0019773)|spermatoproteasome complex (GO:1990111)	threonine-type endopeptidase activity (GO:0004298)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|skin(2)	16	all_cancers(21;0.000585)|Lung NSC(5;0.00148)|all_lung(6;0.0038)|Ovarian(20;0.124)		OV - Ovarian serous cystadenocarcinoma(3;0.000324)|all cancers(3;0.000954)|LUSC - Lung squamous cell carcinoma(2;0.181)			TACATAACTCGCTTCATAGCA	0.393													G|||	1	0.000199681	0.0008	0.0	5008	,	,		15159	0.0		0.0	False		,,,				2504	0.0																0								ENSG00000154611	G	HIS/ARG,HIS/ARG,HIS/ARG	0,4406		0,0,2203	96.0	86.0	89.0		332,218,350	5.3	1.0	18		89	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	PSMA8	NM_001025096.1,NM_001025097.1,NM_144662.2	29,29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	111/251,73/213,117/257	23731924	1,13005	2203	4300	6503	PSMA8	SO:0001583	missense	0			-	HGNC	BC047355	CCDS32808.1, CCDS45842.1, CCDS45843.1	18q11.2	2006-12-18				ENSG00000154611		"""Proteasome (prosome, macropain) subunits"""	22985	protein-coding gene	gene with protein product							Standard	XM_005258199		Approved	MGC26605, PSMA7L	uc002kvq.3	Q8TAA3		ENST00000308268.6:c.350G>A	18.37:g.23731924G>A	ENSP00000311121:p.Arg117His	Somatic	0	59	0.00		0.5521987511953187	0	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	38	44	46.34	B0YJ75|Q8IVP4|Q8TA98|Q8TAA2	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Proteasome_sua/b,pfam_Proteasome_asu_N,smart_Proteasome_asu_N	p.R117H	ENST00000308268.6	37	c.350	CCDS32808.1	18	.	.	.	.	.	.	.	.	.	.	G	22.1	4.237688	0.79800	0.0	1.16E-4	ENSG00000154611	ENST00000308268;ENST00000415576;ENST00000343848;ENST00000538664;ENST00000536423	T;T;T	0.45668	0.89;0.89;0.89	5.34	5.34	0.76211	.	0.109676	0.64402	N	0.000005	T	0.55970	0.1954	M	0.78456	2.415	0.80722	D	1	P;D;P;B	0.53745	0.651;0.962;0.953;0.227	B;P;P;B	0.49665	0.081;0.618;0.483;0.119	T	0.62562	-0.6828	10	0.87932	D	0	-5.3374	16.5892	0.84760	0.0:0.0:1.0:0.0	.	85;117;111;73	F5GY34;Q8TAA3;Q8TAA3-5;Q8TAA3-2	.;PSA7L_HUMAN;.;.	H	117;111;73;85;73	ENSP00000311121:R117H;ENSP00000409284:R111H;ENSP00000345584:R73H	ENSP00000311121:R117H	R	+	2	0	PSMA8	21985922	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.640000	0.61368	2.785000	0.95823	0.655000	0.94253	CGC	-	pfam_Proteasome_sua/b		0.393	PSMA8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PSMA8	protein_coding	OTTHUMT00000446255.1	G	NM_144662	-		23731924	+1	no_errors	ENST00000308268	ensembl	human	known	74_37	missense	SNP	1.000	A
BTBD11	121551	genome.wustl.edu	37	12	108013765	108013765	+	Missense_Mutation	SNP	G	G	A	rs201620480		TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr12:108013765G>A	ENST00000280758.5	+	11	2983	c.2455G>A	c.(2455-2457)Gtc>Atc	p.V819I	BTBD11_ENST00000420571.2_Missense_Mutation_p.V700I|BTBD11_ENST00000490090.2_Missense_Mutation_p.V819I|BTBD11_ENST00000357167.4_Missense_Mutation_p.V356I|RP11-128P10.1_ENST00000548473.1_RNA	NM_001018072.1	NP_001018082.1	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11	819						integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(18)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						CGCTCCAGGCGTCCCGTGGAC	0.587																																																	0								ENSG00000151136	G	ILE/VAL,ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	25.0	24.0	24.0		1066,2455	5.2	1.0	12		24	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	BTBD11	NM_001017523.1,NM_001018072.1	29,29	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	possibly-damaging,possibly-damaging	356/642,819/1105	108013765	2,13004	2203	4300	6503	BTBD11	SO:0001583	missense	0			-	HGNC	AK091276	CCDS31893.1, CCDS41827.1	12q24.11	2013-10-02			ENSG00000151136	ENSG00000151136		"""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	23844	protein-coding gene	gene with protein product							Standard	XM_005268645		Approved	FLJ33957, ABTB2B	uc001tmk.1	A6QL63	OTTHUMG00000150413	ENST00000280758.5:c.2455G>A	12.37:g.108013765G>A	ENSP00000280758:p.Val819Ile	Somatic	0	20	0.00		0.5521987511953187	1	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	14	22	38.89	A4FU41|B3KXG3|C9J019|C9JK80|E9PHS4|Q3ZTQ4|Q52M89|Q6ZV99|Q8N245	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Ankyrin_rpt,pfam_BTB_POZ,superfamily_BTB/POZ_fold,superfamily_Ankyrin_rpt-contain_dom,superfamily_Histone-fold,smart_Ankyrin_rpt,smart_BTB/POZ-like,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom,pfscan_BTB/POZ-like	p.V819I	ENST00000280758.5	37	c.2455	CCDS31893.1	12	.	.	.	.	.	.	.	.	.	.	G	27.8	4.868192	0.91587	2.27E-4	1.16E-4	ENSG00000151136	ENST00000280758;ENST00000420571;ENST00000490090;ENST00000357167	T;T;T;T	0.55052	0.65;0.65;0.67;0.54	5.15	5.15	0.70609	.	0.117935	0.56097	D	0.000021	T	0.72495	0.3467	M	0.70275	2.135	0.80722	D	1	D;P;D;D	0.71674	0.998;0.508;0.987;0.99	D;B;B;P	0.73708	0.981;0.073;0.403;0.496	T	0.75560	-0.3275	10	0.66056	D	0.02	.	18.6524	0.91435	0.0:0.0:1.0:0.0	.	700;356;819;819	A6QL63-2;E9PHS4;A6QL63;A6QL63-3	.;.;BTBDB_HUMAN;.	I	819;700;819;356	ENSP00000280758:V819I;ENSP00000413889:V700I;ENSP00000447319:V819I;ENSP00000349690:V356I	ENSP00000280758:V819I	V	+	1	0	BTBD11	106537895	1.000000	0.71417	1.000000	0.80357	0.727000	0.41649	7.975000	0.88055	2.398000	0.81561	0.650000	0.86243	GTC	-	NULL		0.587	BTBD11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	BTBD11	protein_coding	OTTHUMT00000318003.1	G	NM_152322	rs201620480		108013765	+1	no_errors	ENST00000280758	ensembl	human	known	74_37	missense	SNP	1.000	A
AGAP1	116987	genome.wustl.edu	37	2	236877199	236877199	+	Missense_Mutation	SNP	G	G	A	rs3207205		TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr2:236877199G>A	ENST00000304032.8	+	13	2157	c.1577G>A	c.(1576-1578)aGa>aAa	p.R526K	AGAP1_ENST00000409538.1_Missense_Mutation_p.R738K|AGAP1_ENST00000428334.2_Missense_Mutation_p.R365K|AGAP1_ENST00000336665.5_Missense_Mutation_p.R473K	NM_001037131.2	NP_001032208.1	Q9UPQ3	AGAP1_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	526	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|phospholipid binding (GO:0005543)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						CACGCCAACAGAAAGAAGCAC	0.622																																																	0								ENSG00000157985						45.0	55.0	52.0					2																	236877199		2203	4300	6503	AGAP1	SO:0001583	missense	0			-	HGNC	AF413078	CCDS2514.1, CCDS33408.1, CCDS58756.1	2q37	2013-01-10	2008-09-22	2008-09-22	ENSG00000157985	ENSG00000157985		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16922	protein-coding gene	gene with protein product		608651	"""centaurin, gamma 2"""	CENTG2			Standard	NM_001037131		Approved	KIAA1099, GGAP1	uc002vvs.3	Q9UPQ3	OTTHUMG00000133293	ENST00000304032.8:c.1577G>A	2.37:g.236877199G>A	ENSP00000307634:p.Arg526Lys	Somatic	0	66	0.00		0.5521987511953187	9	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	30	58	33.71	B2RTX7|Q541S5|Q6P9D7|Q9NV93	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_ArfGAP,pfam_MIRO-like,pfam_Small_GTPase,pfam_Ankyrin_rpt,pfam_Pleckstrin_homology,superfamily_P-loop_NTPase,superfamily_Ankyrin_rpt-contain_dom,smart_Small_GTPase_Ras,smart_Small_GTPase_Rab_type,smart_Pleckstrin_homology,smart_ArfGAP,smart_Ankyrin_rpt,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom,pfscan_Pleckstrin_homology,pfscan_ArfGAP,prints_ArfGAP,prints_Small_GTPase	p.R526K	ENST00000304032.8	37	c.1577	CCDS33408.1	2	.	.	.	.	.	.	.	.	.	.	G	17.43	3.388720	0.61956	.	.	ENSG00000157985	ENST00000304032;ENST00000336665;ENST00000409538;ENST00000428334	T;T;T;T	0.75821	-0.32;-0.97;-0.97;0.74	5.09	5.09	0.68999	Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	T	0.75766	0.3894	N	0.25825	0.765	0.80722	D	1	D;B	0.56035	0.974;0.005	D;B	0.70487	0.969;0.021	T	0.68614	-0.5362	10	0.02654	T	1	.	18.5143	0.90930	0.0:0.0:1.0:0.0	rs3207205	473;526	Q9UPQ3-2;Q9UPQ3	.;AGAP1_HUMAN	K	526;473;738;365	ENSP00000307634:R526K;ENSP00000338378:R473K;ENSP00000386897:R738K;ENSP00000411824:R365K	ENSP00000307634:R526K	R	+	2	0	AGAP1	236541938	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.744000	0.98853	2.359000	0.80004	0.650000	0.86243	AGA	-	pfam_Pleckstrin_homology,smart_Pleckstrin_homology,pfscan_Pleckstrin_homology		0.622	AGAP1-001	KNOWN	basic|CCDS	protein_coding	AGAP1	protein_coding	OTTHUMT00000257076.2	G	NM_014914	rs3207205		236877199	+1	no_errors	ENST00000304032	ensembl	human	known	74_37	missense	SNP	1.000	A
FIP1L1	81608	genome.wustl.edu	37	4	54319248	54319249	+	Frame_Shift_Del	DEL	AG	AG	-	rs143671659		TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	AG	AG					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr4:54319248_54319249delAG	ENST00000337488.6	+	16	1641_1642	c.1447_1448delAG	c.(1447-1449)agafs	p.R483fs	FIP1L1_ENST00000306932.6_Frame_Shift_Del_p.R409fs|FIP1L1_ENST00000507166.1_Intron|FIP1L1_ENST00000358575.5_Frame_Shift_Del_p.R477fs	NM_030917.3	NP_112179.2	Q6UN15	FIP1_HUMAN	factor interacting with PAPOLA and CPSF1	483	Arg-rich.|Glu-rich.|Sufficient for interaction with CPSF1 and CSTF3.				mRNA processing (GO:0006397)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.R487fs*3(2)		large_intestine(3)|liver(1)|ovary(1)|skin(1)	6			GBM - Glioblastoma multiforme(3;3.31e-36)|LUSC - Lung squamous cell carcinoma(32;0.0134)			agaACGCACCAGAGAGAGAGAG	0.47			T	PDGFRA	idiopathic hypereosinophilic syndrome																																			Dom	yes		4	4q12	81608	FIP1 like 1 (S. cerevisiae)		L	2	Deletion - Frameshift(2)	large_intestine(1)|kidney(1)						ENSG00000145216																																			FIP1L1	SO:0001589	frameshift_variant	0				HGNC	AF161429	CCDS3491.1, CCDS47055.1, CCDS47056.1	4q12	2013-06-18	2013-06-18		ENSG00000145216	ENSG00000145216			19124	protein-coding gene	gene with protein product		607686	"""FIP1 like 1 (S. cerevisiae)"", ""FIP1L1 cleavage and polyadenylation specific factor subunit"""			11230166, 14749727	Standard	NM_030917		Approved	DKFZp586K0717, FIP1	uc003hae.3	Q6UN15	OTTHUMG00000128701	ENST00000337488.6:c.1447_1448delAG	4.37:g.54319258_54319259delAG	ENSP00000336752:p.Arg483fs	Somatic	0	22	0.00		0.5521987511953187	230	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	18	14.29	B4DIR3|G3XAD6|Q0VGE0|Q499Y4|Q49AU3|Q7Z608|Q8WVN3|Q96F80|Q9H077	Frame_Shift_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_Fip1	p.E486fs	ENST00000337488.6	37	c.1447_1448	CCDS3491.1	4																																																																																			-	NULL		0.470	FIP1L1-001	KNOWN	basic|CCDS	protein_coding	FIP1L1	protein_coding	OTTHUMT00000250602.1	AG	NM_030917			54319249	+1	no_errors	ENST00000337488	ensembl	human	known	74_37	frame_shift_del	DEL	0.975:0.991	-
YAF2	10138	genome.wustl.edu	37	12	42629562	42629563	+	Intron	INS	-	-	A	rs565109622		TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr12:42629562_42629563insA	ENST00000534854.2	-	2	220				YAF2_ENST00000442791.3_Intron|YAF2_ENST00000541702.2_5'UTR|PPHLN1_ENST00000549190.1_5'Flank|YAF2_ENST00000380790.4_Intron|YAF2_ENST00000327791.4_Intron|YAF2_ENST00000555248.2_3'UTR|YAF2_ENST00000380788.3_Intron	NM_005748.4	NP_005739.2	Q8IY57	YAF2_HUMAN	YY1 associated factor 2						negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(1)|large_intestine(1)|lung(3)|skin(1)	8	all_cancers(12;0.000425)	Lung NSC(34;0.0402)|all_lung(34;0.057)		GBM - Glioblastoma multiforme(48;0.0514)		GATGTACTGGTAAAAAAAAAAA	0.441																																																	0								ENSG00000015153																																			YAF2	SO:0001627	intron_variant	0				HGNC	U72209	CCDS31775.1, CCDS53778.1, CCDS53779.1, CCDS53780.1	12q12	2014-09-04			ENSG00000015153	ENSG00000015153			17363	protein-coding gene	gene with protein product		607534				9016636	Standard	NM_001190977		Approved		uc001rmw.3	Q8IY57	OTTHUMG00000169380	ENST00000534854.2:c.152+1837->T	12.37:g.42629573_42629573dupA		Somatic	0	21	0.00		0.5521987511953187	0	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	18	14.29	A8K5P0|B4DFU3|G3V465|Q99710	RNA	INS	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000534854.2	37	NULL	CCDS31775.1	12																																																																																			-	-		0.441	YAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	YAF2	protein_coding	OTTHUMT00000403781.1	-				42629563	-1	no_errors	ENST00000541702	ensembl	human	known	74_37	rna	INS	0.986:0.986	A
PCDH12	51294	genome.wustl.edu	37	5	141334716	141334716	+	Nonsense_Mutation	SNP	G	G	A	rs142096693		TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr5:141334716G>A	ENST00000231484.3	-	1	3911	c.2701C>T	c.(2701-2703)Cag>Tag	p.Q901*	PCDH12_ENST00000512221.1_5'Flank|AC005740.6_ENST00000607378.1_RNA	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	901					calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGTGGCCTCTGTGGGGCTTCC	0.647																																																	0								ENSG00000113555						32.0	37.0	36.0					5																	141334716		2203	4300	6503	PCDH12	SO:0001587	stop_gained	0			-	HGNC	AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"""Cadherins / Protocadherins : Non-clustered"""	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.2701C>T	5.37:g.141334716G>A	ENSP00000231484:p.Gln901*	Somatic	0	59	0.00		0.5521987511953187	85	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	34	53	39.08	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Nonsense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Cadherin,pfam_Cadherin_N,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	p.Q901*	ENST00000231484.3	37	c.2701	CCDS4269.1	5	.	.	.	.	.	.	.	.	.	.	G	46	12.843345	0.99700	.	.	ENSG00000113555	ENST00000231484	.	.	.	4.9	0.888	0.19206	.	1.379100	0.04361	N	0.357472	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.23891	T	0.37	.	8.1948	0.31389	0.0883:0.4667:0.445:0.0	.	.	.	.	X	901	.	ENSP00000231484:Q901X	Q	-	1	0	PCDH12	141314900	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	0.350000	0.20079	0.047000	0.15862	0.655000	0.94253	CAG	-	NULL		0.647	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PCDH12	protein_coding	OTTHUMT00000251858.1	G	NM_016580	-		141334716	-1	no_errors	ENST00000231484	ensembl	human	known	74_37	nonsense	SNP	0.000	A
BPTF	2186	genome.wustl.edu	37	17	65955758	65955759	+	In_Frame_Ins	INS	-	-	CCTCCAGCC	rs139709271|rs202116659		TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr17:65955758_65955759insCCTCCAGCC	ENST00000321892.4	+	26	8467_8468	c.8406_8407insCCTCCAGCC	c.(8407-8409)cct>CCTCCAGCCcct	p.2803_2803P>PPAP	BPTF_ENST00000335221.5_In_Frame_Ins_p.2660_2660P>PPAP|BPTF_ENST00000424123.3_In_Frame_Ins_p.2521_2521P>PPAP|BPTF_ENST00000306378.6_In_Frame_Ins_p.2677_2677P>PPAP			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	2803	Pro-rich.			AP -> VL (in Ref. 1; BAA89208). {ECO:0000305}.	anterior/posterior pattern specification (GO:0009952)|ATP catabolic process (GO:0006200)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|embryonic placenta development (GO:0001892)|endoderm development (GO:0007492)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NURF complex (GO:0016589)	sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.A2676A(1)|p.A2659A(1)		NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			TGACAccagctcctccagcccc	0.579																																																	2	Substitution - coding silent(2)	large_intestine(2)						ENSG00000171634																																			BPTF	SO:0001652	inframe_insertion	0				HGNC	AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634		"""Zinc fingers, PHD-type"""	3581	protein-coding gene	gene with protein product		601819	"""fetal Alzheimer antigen"""	FALZ		8975731, 10662542, 16728976	Standard	NM_182641		Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000321892.4:c.8416_8424dupCCTCCAGCC	17.37:g.65955759_65955767dupCCTCCAGCC	ENSP00000315454:p.ProAlaPro2809dup	Somatic	NA	NA	NA		0.5521987511953187	64	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	Q6NX67|Q7Z7D6|Q9UIG2	In_Frame_Ins	INS	NA	NA	NA	NA	NA	NA	pfam_Bromodomain,pfam_DDT_dom,pfam_Znf_PHD-finger,superfamily_Bromodomain,superfamily_Znf_FYVE_PHD,superfamily_Adenylate_cyclase-assoc_CAP_N,smart_DDT_dom_subgr,smart_Znf_PHD,smart_Bromodomain,pfscan_Znf_PHD-finger,pfscan_DDT_dom_superfamily,pfscan_Bromodomain,prints_Bromodomain	p.2806in_frame_insPAP	ENST00000321892.4	37	c.8406_8407		17																																																																																			-	superfamily_Bromodomain,superfamily_Adenylate_cyclase-assoc_CAP_N		0.579	BPTF-201	KNOWN	basic	protein_coding	BPTF	protein_coding		-	NM_182641, NM_004459			65955759	+1	no_errors	ENST00000321892	ensembl	human	known	74_37	in_frame_ins	INS	0.001:0.001	CCTCCAGCC
ROS1	6098	genome.wustl.edu	37	6	117709109	117709109	+	Silent	SNP	G	G	T	rs140323539		TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr6:117709109G>T	ENST00000368508.3	-	13	2046	c.1848C>A	c.(1846-1848)acC>acA	p.T616T	ROS1_ENST00000368507.3_Silent_p.T611T|GOPC_ENST00000467125.1_Intron	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	616	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		GAGGGTCTTGGGTGGATACTT	0.438			T	"""GOPC, SDC4, SLC34A2, EZR, LRIG3"""	"""glioblastoma, NSCLC"""																																			Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"""O, E"""	0								ENSG00000047936						147.0	146.0	146.0					6																	117709109		2203	4300	6503	ROS1	SO:0001819	synonymous_variant	0			-	HGNC	M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"""Fibronectin type III domain containing"""	10261	protein-coding gene	gene with protein product		165020	"""v-ros avian UR2 sarcoma virus oncogene homolog 1"", ""v-ros UR2 sarcoma virus oncogene homolog 1 (avian)"", ""c-ros oncogene 1 , receptor tyrosine kinase"""			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.1848C>A	6.37:g.117709109G>T		Somatic	0	55	0.00		0.5521987511953187	0	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	23	11.54	Q15368|Q5TDB5	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Fibronectin_type3,pfam_Prot_kinase_dom,superfamily_Kinase-like_dom,superfamily_Fibronectin_type3,smart_Fibronectin_type3,smart_LDLR_classB_rpt,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Fibronectin_type3,pfscan_Prot_kinase_dom,prints_Ser-Thr/Tyr_kinase_cat_dom	p.T616	ENST00000368508.3	37	c.1848	CCDS5116.1	6																																																																																			-	superfamily_Fibronectin_type3,smart_Fibronectin_type3,pfscan_Fibronectin_type3		0.438	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ROS1	protein_coding	OTTHUMT00000043464.1	G		-		117709109	-1	no_errors	ENST00000368508	ensembl	human	known	74_37	silent	SNP	0.018	T
ADAMTS1	9510	genome.wustl.edu	37	21	28214702	28214702	+	Silent	SNP	G	G	T			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr21:28214702G>T	ENST00000284984.3	-	2	1487	c.1033C>A	c.(1033-1035)Cgg>Agg	p.R345R		NM_006988.3	NP_008919.3	Q9UHI8	ATS1_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 1	345	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				heart trabecula formation (GO:0060347)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|negative regulation of cell proliferation (GO:0008285)|ovulation from ovarian follicle (GO:0001542)	basement membrane (GO:0005604)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)	heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(20)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	42		Breast(209;0.000962)		Lung(58;0.215)		TCTGCATCCCGGTCACTGGGT	0.527																																																	0								ENSG00000154734						95.0	71.0	79.0					21																	28214702		2203	4300	6503	ADAMTS1	SO:0001819	synonymous_variant	0			-	HGNC	AF060152	CCDS33524.1	21q21.3	2008-05-14	2005-08-19		ENSG00000154734	ENSG00000154734		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	217	protein-coding gene	gene with protein product		605174	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 1"""			10438512	Standard	NM_006988		Approved	C3-C5, METH1, KIAA1346	uc002ymf.3	Q9UHI8	OTTHUMG00000078688	ENST00000284984.3:c.1033C>A	21.37:g.28214702G>T		Somatic	0	52	0.00		0.5521987511953187	172	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	46	8.00	D3DSD5|Q9NSJ8|Q9P2K0|Q9UH83|Q9UP80	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_ADAM_spacer1,pfam_Peptidase_M12B_N,pfam_Peptidase_M12B,pfam_Thrombospondin_1_rpt,superfamily_Thrombospondin_1_rpt,smart_ADAM_Cys-rich,smart_Thrombospondin_1_rpt,pfscan_Thrombospondin_1_rpt,pfscan_Peptidase_M12B,prints_Pept_M12B_ADAM-TS1,prints_Peptidase_M12B_ADAM-TS	p.R345	ENST00000284984.3	37	c.1033	CCDS33524.1	21																																																																																			-	pfam_Peptidase_M12B,pfscan_Peptidase_M12B		0.527	ADAMTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ADAMTS1	protein_coding	OTTHUMT00000171650.2	G		-		28214702	-1	no_errors	ENST00000284984	ensembl	human	known	74_37	silent	SNP	0.999	T
CELSR1	9620	genome.wustl.edu	37	22	46931967	46931967	+	Missense_Mutation	SNP	C	C	A			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr22:46931967C>A	ENST00000262738.3	-	1	1100	c.1101G>T	c.(1099-1101)gaG>gaT	p.E367D	CELSR1_ENST00000497509.1_5'Flank|CELSR1_ENST00000395964.1_Missense_Mutation_p.E367D	NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	367	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		CGTAGCCCACCTCCAGGTTCT	0.652																																																	0								ENSG00000075275						39.0	36.0	37.0					22																	46931967		2199	4298	6497	CELSR1	SO:0001583	missense	0			-	HGNC	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	1850	protein-coding gene	gene with protein product	"""flamingo homolog 2 (Drosophila)"""	604523	"""cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"""			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.1101G>T	22.37:g.46931967C>A	ENSP00000262738:p.Glu367Asp	Somatic	0	35	0.00		0.5521987511953187	2	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	34	10.53	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Cadherin,pfam_DUF3497,pfam_Laminin_G,pfam_GPCR_2_secretin-like,pfam_GPS_dom,pfam_EG-like_dom,pfam_EGF_laminin,superfamily_ConA-like_lec_gl_sf,superfamily_Cadherin-like,smart_Cadherin,smart_EG-like_dom,smart_EGF-like_Ca-bd_dom,smart_Laminin_G,smart_EGF_laminin,smart_GPCR_2_extracellular_dom,smart_GPS_dom,pfscan_EG-like_dom,pfscan_EGF_laminin,pfscan_GPS_dom,pfscan_Laminin_G,pfscan_Cadherin,pfscan_GPCR_2_extracellular_dom,pfscan_GPCR_2-like,prints_Cadherin,prints_GPCR_2_secretin-like	p.E367D	ENST00000262738.3	37	c.1101	CCDS14076.1	22	.	.	.	.	.	.	.	.	.	.	C	17.61	3.431358	0.62844	.	.	ENSG00000075275	ENST00000262738;ENST00000395964	T;T	0.01745	4.66;4.66	4.44	2.33	0.28932	Cadherin (3);Cadherin-like (1);	0.000000	0.64402	U	0.000004	T	0.03959	0.0111	L	0.39147	1.195	0.29062	N	0.883851	P	0.49635	0.926	P	0.57620	0.824	T	0.24225	-1.0166	10	0.33141	T	0.24	.	10.168	0.42893	0.0:0.8329:0.0:0.1671	.	367	Q9NYQ6	CELR1_HUMAN	D	367	ENSP00000262738:E367D;ENSP00000379293:E367D	ENSP00000262738:E367D	E	-	3	2	CELSR1	45310631	1.000000	0.71417	0.997000	0.53966	0.945000	0.59286	0.941000	0.29005	0.355000	0.24131	0.456000	0.33151	GAG	-	pfam_Cadherin,superfamily_Cadherin-like,pfscan_Cadherin		0.652	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CELSR1	protein_coding	OTTHUMT00000318037.1	C	NM_014246	-		46931967	-1	no_errors	ENST00000262738	ensembl	human	known	74_37	missense	SNP	1.000	A
RP11-782C8.2	0	genome.wustl.edu	37	1	143210392	143210396	+	lincRNA	DEL	ATAAC	ATAAC	-	rs372710968|rs574899120		TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	ATAAC	ATAAC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr1:143210392_143210396delATAAC	ENST00000412204.2	-	0	674_678				RP11-782C8.1_ENST00000438000.1_lincRNA																							ACTCAATAAAATAACATATCATGAT	0.302																																																	0								ENSG00000232274																																			RP11-782C8.2			0				Clone_based_vega_gene																													1.37:g.143210392_143210396delATAAC		Somatic	NA	NA	NA		0.5521987511953187	0	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA		RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000412204.2	37	NULL		1																																																																																			-	-		0.302	RP11-782C8.2-004	KNOWN	basic	lincRNA	ENSG00000232274	lincRNA	OTTHUMT00000037567.2	ATAAC				143210396	-1	no_errors	ENST00000412204	ensembl	human	known	74_37	rna	DEL	0.841:0.809:0.673:0.586:0.231	-
FYB	2533	genome.wustl.edu	37	5	39153561	39153561	+	Silent	SNP	C	C	T	rs115158663		TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr5:39153561C>T	ENST00000351578.6	-	3	1471	c.1281G>A	c.(1279-1281)ccG>ccA	p.P427P	FYB_ENST00000512982.1_Silent_p.P427P|FYB_ENST00000505428.1_Silent_p.P427P|FYB_ENST00000515010.1_Silent_p.P427P|FYB_ENST00000540520.1_Silent_p.P437P	NM_199335.3	NP_955367.1	O15117	FYB_HUMAN	FYN binding protein	427	Interaction with SKAP1.				immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|NLS-bearing protein import into nucleus (GO:0006607)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	receptor binding (GO:0005102)			endometrium(2)|kidney(4)|large_intestine(6)|liver(1)|lung(29)|ovary(2)|upper_aerodigestive_tract(1)	45	all_lung(31;0.000343)		Epithelial(62;0.235)			TTAGGTCAAACGGAGGTTTAA	0.483													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18538	0.0		0.0	False		,,,				2504	0.0																0								ENSG00000082074	C	,	3,3995		0,3,1996	295.0	293.0	293.0		1281,1281	-2.4	1.0	5	dbSNP_132	293	0,8320		0,0,4160	no	coding-synonymous,coding-synonymous	FYB	NM_001465.4,NM_199335.3	,	0,3,6156	TT,TC,CC		0.0,0.075,0.0244	,	427/830,427/784	39153561	3,12315	1999	4160	6159	FYB	SO:0001819	synonymous_variant	0			GMAF=0.0005	HGNC	U93049	CCDS47200.1, CCDS54848.1	5p13.1	2012-05-04	2010-05-04		ENSG00000082074	ENSG00000082074			4036	protein-coding gene	gene with protein product		602731	"""FYN-binding protein (FYB-120/130)"""			9115214, 9207119	Standard	NM_001465		Approved	SLAP-130, FYB-120/130	uc011cpl.2	O15117	OTTHUMG00000162071	ENST00000351578.6:c.1281G>A	5.37:g.39153561C>T		Somatic	0	81	0.00		0.5521987511953187	17	22.73	5	WXS	Illumina HiSeq 2500	Phase_IV	tier1	35	54	39.33	A8K2Y8|B4DLN2|E9PBV9|O00359|Q9NZI9	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_SH3_2,superfamily_SH3_domain,smart_SH3_domain	p.P437	ENST00000351578.6	37	c.1311	CCDS47200.1	5																																																																																			-	NULL		0.483	FYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	FYB	protein_coding	OTTHUMT00000367098.1	C	NM_001465	rs115158663		39153561	-1	no_errors	ENST00000540520	ensembl	human	known	74_37	silent	SNP	0.790	T
UCHL3	7347	genome.wustl.edu	37	13	76123902	76123916	+	5'Flank	DEL	GGCGGCGGCGGCGAA	GGCGGCGGCGGCGAA	-	rs149695719|rs8192737		TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	GGCGGCGGCGGCGAA	GGCGGCGGCGGCGAA					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr13:76123902_76123916delGGCGGCGGCGGCGAA	ENST00000377595.3	+	0	0				RP11-29G8.3_ENST00000563635.1_RNA|COMMD6_ENST00000460675.1_5'Flank	NM_001270952.1|NM_006002.4	NP_001257881.1|NP_005993.1	P15374	UCHL3_HUMAN	ubiquitin carboxyl-terminal esterase L3 (ubiquitin thiolesterase)						protein catabolic process (GO:0030163)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			kidney(1)|large_intestine(2)|lung(3)|skin(1)	7				GBM - Glioblastoma multiforme(99;0.0125)		GggcggaagcggcggcggcggcgaaggcggcggcT	0.716											OREG0022446	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					0								ENSG00000261553			1023,1059		430,163,448						2.7	1.0		dbSNP_130	3	614,4334		166,282,2026	no	near-gene-5				596,445,2474	A1A1,A1R,RR		12.4091,49.1354,23.2859				1637,5393				RP11-29G8.3	SO:0001631	upstream_gene_variant	0				Clone_based_vega_gene	M30496	CCDS9453.1, CCDS73586.1	13q21.33	2008-02-05			ENSG00000118939	ENSG00000118939	3.2.1.15		12515	protein-coding gene	gene with protein product		603090				2530630	Standard	NM_001270952		Approved		uc001vjq.4	P15374	OTTHUMG00000017090		13.37:g.76123902_76123916delGGCGGCGGCGGCGAA	Exception_encountered	Somatic	NA	NA	NA	1165	0.5521987511953187	0	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	B2R970|Q5TBK8|Q6IBE9	RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000377595.3	37	NULL	CCDS9453.1	13																																																																																			-	-		0.716	UCHL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ENSG00000261553	protein_coding	OTTHUMT00000045292.2	GGCGGCGGCGGCGAA	NM_006002			76123916	+1	no_errors	ENST00000563635	ensembl	human	known	74_37	rna	DEL	0.972:0.982:0.960:0.622:0.506:0.040:0.014:0.013:0.030:0.026:0.014:0.007:0.004:0.000:0.000	-
NCAPH2	29781	genome.wustl.edu	37	22	50961469	50961469	+	Silent	SNP	C	C	A			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr22:50961469C>A	ENST00000420993.2	+	19	1673	c.1551C>A	c.(1549-1551)atC>atA	p.I517I	NCAPH2_ENST00000395701.3_Silent_p.I517I|CTA-384D8.36_ENST00000608319.1_RNA|NCAPH2_ENST00000299821.11_Silent_p.I518I	NM_001185011.1|NM_152299.3	NP_001171940.1|NP_689512.2	Q6IBW4	CNDH2_HUMAN	non-SMC condensin II complex, subunit H2	517					chromosome condensation (GO:0030261)|mitotic cell cycle (GO:0000278)	chromosome (GO:0005694)|membrane (GO:0016020)|nucleoplasm (GO:0005654)				breast(1)|cervix(1)|endometrium(2)|kidney(3)|lung(10)|ovary(1)|prostate(2)|skin(3)|stomach(1)	24		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.212)		CCTTTGACATCCACACCTATG	0.637																																																	0								ENSG00000025770						58.0	41.0	46.0					22																	50961469		2203	4300	6503	NCAPH2	SO:0001819	synonymous_variant	0			-	HGNC	BC001937	CCDS14094.2, CCDS43038.1, CCDS54546.1	22q13.33	2008-02-04			ENSG00000025770	ENSG00000025770			25071	protein-coding gene	gene with protein product	"""kleisin beta"", ""CAP-H2 subunit of the condensin II complex"""	611230				10493829	Standard	NM_014551		Approved	384D8-2, hCAP-H2, CAP-H2	uc003blx.4	Q6IBW4	OTTHUMG00000150205	ENST00000420993.2:c.1551C>A	22.37:g.50961469C>A		Somatic	0	38	0.00		0.5521987511953187	174	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	40	9.09	B7WPH1|O43788|Q13391|Q96C14|Q96GJ0|Q9BQ71|Q9BUT3|Q9BVD1	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_Condensin_II_H2-like	p.I518	ENST00000420993.2	37	c.1554	CCDS14094.2	22																																																																																			-	pfam_Condensin_II_H2-like		0.637	NCAPH2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NCAPH2	protein_coding	OTTHUMT00000317012.1	C	NM_152299	-		50961469	+1	no_errors	ENST00000299821	ensembl	human	known	74_37	silent	SNP	1.000	A
MAGEA1	4100	genome.wustl.edu	37	X	152482246	152482246	+	Silent	SNP	C	C	T			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chrX:152482246C>T	ENST00000356661.5	-	3	983	c.765G>A	c.(763-765)ccG>ccA	p.P255P		NM_004988.4	NP_004979.3	P43355	MAGA1_HUMAN	melanoma antigen family A, 1 (directs expression of antigen MZ2-E)	255	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone deacetylase binding (GO:0042826)			breast(1)|central_nervous_system(7)|kidney(2)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GATCACTGTCCGGCACCTGCC	0.557																																																	0								ENSG00000198681						95.0	91.0	92.0					X																	152482246		2203	4300	6503	MAGEA1	SO:0001819	synonymous_variant	0			-	HGNC		CCDS76051.1	Xq28	2010-05-26			ENSG00000198681	ENSG00000198681			6796	protein-coding gene	gene with protein product	"""melanoma-associated antigen 1"", ""melanoma-associated antigen MZ2-E"", ""melanoma antigen MAGE-1"", ""melanoma antigen family A 1"", ""cancer/testis antigen family 1, member 1"""	300016		MAGE1		1840703	Standard	NM_004988		Approved	MGC9326, CT1.1	uc004fhf.2	P43355	OTTHUMG00000024192	ENST00000356661.5:c.765G>A	X.37:g.152482246C>T		Somatic	0	93	0.00		0.5521987511953187	0	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	47	76	38.21	B2RC81|O00346	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_MAGE,pfam_Melanoma_ass_antigen_N,pfscan_MAGE	p.P255	ENST00000356661.5	37	c.765	CCDS14720.1	X																																																																																			-	pfam_MAGE,pfscan_MAGE		0.557	MAGEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MAGEA1	protein_coding	OTTHUMT00000060940.1	C	NM_004988	-		152482246	-1	no_errors	ENST00000356661	ensembl	human	known	74_37	silent	SNP	0.000	T
AGAP1	116987	genome.wustl.edu	37	2	236877223	236877223	+	Missense_Mutation	SNP	G	G	C			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr2:236877223G>C	ENST00000304032.8	+	13	2181	c.1601G>C	c.(1600-1602)aGc>aCc	p.S534T	AGAP1_ENST00000409538.1_Missense_Mutation_p.S746T|AGAP1_ENST00000428334.2_Missense_Mutation_p.S373T|AGAP1_ENST00000336665.5_Missense_Mutation_p.S481T	NM_001037131.2	NP_001032208.1	Q9UPQ3	AGAP1_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	534	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|phospholipid binding (GO:0005543)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						AGGAAGAAAAGCACTAGCAAC	0.597																																																	0								ENSG00000157985						48.0	60.0	56.0					2																	236877223		2203	4300	6503	AGAP1	SO:0001583	missense	0			-	HGNC	AF413078	CCDS2514.1, CCDS33408.1, CCDS58756.1	2q37	2013-01-10	2008-09-22	2008-09-22	ENSG00000157985	ENSG00000157985		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16922	protein-coding gene	gene with protein product		608651	"""centaurin, gamma 2"""	CENTG2			Standard	NM_001037131		Approved	KIAA1099, GGAP1	uc002vvs.3	Q9UPQ3	OTTHUMG00000133293	ENST00000304032.8:c.1601G>C	2.37:g.236877223G>C	ENSP00000307634:p.Ser534Thr	Somatic	0	55	0.00		0.5521987511953187	9	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	26	50	34.21	B2RTX7|Q541S5|Q6P9D7|Q9NV93	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_ArfGAP,pfam_MIRO-like,pfam_Small_GTPase,pfam_Ankyrin_rpt,pfam_Pleckstrin_homology,superfamily_P-loop_NTPase,superfamily_Ankyrin_rpt-contain_dom,smart_Small_GTPase_Ras,smart_Small_GTPase_Rab_type,smart_Pleckstrin_homology,smart_ArfGAP,smart_Ankyrin_rpt,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom,pfscan_Pleckstrin_homology,pfscan_ArfGAP,prints_ArfGAP,prints_Small_GTPase	p.S534T	ENST00000304032.8	37	c.1601	CCDS33408.1	2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.41|11.41	1.631222|1.631222	0.28978|0.28978	.|.	.|.	ENSG00000157985|ENSG00000157985	ENST00000448025;ENST00000418654|ENST00000304032;ENST00000336665;ENST00000409538;ENST00000428334	T;T|T;T;T;T	0.60171|0.78816	0.21;2.01|-0.63;-1.21;-1.21;0.43	5.09|5.09	4.21|4.21	0.49690|0.49690	.|Pleckstrin homology domain (3);	.|0.191754	.|0.53938	.|D	.|0.000055	T|T	0.78419|0.78419	0.4280|0.4280	L|L	0.60455|0.60455	1.87|1.87	0.80722|0.80722	D|D	1|1	.|B;P	.|0.40578	.|0.447;0.722	.|B;P	.|0.45913	.|0.125;0.497	T|T	0.77070|0.77070	-0.2724|-0.2724	7|10	0.34782|0.39692	T|T	0.22|0.17	.|.	13.5513|13.5513	0.61734|0.61734	0.0752:0.0:0.9248:0.0|0.0752:0.0:0.9248:0.0	.|.	.|481;534	.|Q9UPQ3-2;Q9UPQ3	.|.;AGAP1_HUMAN	N|T	167;61|534;481;746;373	ENSP00000403482:K167N;ENSP00000393838:K61N|ENSP00000307634:S534T;ENSP00000338378:S481T;ENSP00000386897:S746T;ENSP00000411824:S373T	ENSP00000393838:K61N|ENSP00000307634:S534T	K|S	+|+	3|2	2|0	AGAP1|AGAP1	236541962|236541962	1.000000|1.000000	0.71417|0.71417	0.910000|0.910000	0.35882|0.35882	0.336000|0.336000	0.28762|0.28762	9.751000|9.751000	0.98889|0.98889	1.140000|1.140000	0.42260|0.42260	-0.145000|-0.145000	0.13849|0.13849	AAG|AGC	-	pfam_Pleckstrin_homology,smart_Pleckstrin_homology,pfscan_Pleckstrin_homology		0.597	AGAP1-001	KNOWN	basic|CCDS	protein_coding	AGAP1	protein_coding	OTTHUMT00000257076.2	G	NM_014914	-		236877223	+1	no_errors	ENST00000304032	ensembl	human	known	74_37	missense	SNP	1.000	C
TREH	11181	genome.wustl.edu	37	11	118534048	118534048	+	Splice_Site	SNP	C	C	A			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr11:118534048C>A	ENST00000529101.1	-	2	235	c.190G>T	c.(190-192)Gaa>Taa	p.E64*	TREH_ENST00000264029.4_Splice_Site_p.E64*|TREH_ENST00000525958.1_Splice_Site_p.E64*|TREH_ENST00000397925.1_Splice_Site_p.E64*|TREH_ENST00000530256.1_Intron			O43280	TREA_HUMAN	trehalase (brush-border membrane glycoprotein)	64					carbohydrate metabolic process (GO:0005975)|organ morphogenesis (GO:0009887)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|trehalose catabolic process (GO:0005993)|trehalose metabolic process (GO:0005991)	anchored component of plasma membrane (GO:0046658)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	alpha,alpha-trehalase activity (GO:0004555)			NS(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(3)|ovary(1)|pancreas(1)|urinary_tract(1)	13	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.0564)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;3.16e-05)		GGTGCTTCACCTGGAGCTATA	0.532																																																	0								ENSG00000118094						100.0	99.0	99.0					11																	118534048		2067	4192	6259	TREH	SO:0001630	splice_region_variant	0			-	HGNC	AB000824	CCDS73401.1, CCDS73402.1	11q23.3	2008-07-21				ENSG00000118094	3.2.1.28		12266	protein-coding gene	gene with protein product	"""alpha,alpha-trehalase"", ""alpha,alpha-trehalose glucohydrolase"""	275360				9427547	Standard	NM_007180		Approved	TRE, TREA, MGC129621	uc001pty.1	O43280		ENST00000529101.1:c.190+1G>T	11.37:g.118534048C>A		Somatic	0	58	0.00		0.5521987511953187	0	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	41	8.89	Q32MB9|Q53FY8	Nonsense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Glyco_hydro_37,superfamily_6-hairpin_glycosidase-like,prints_Glyco_hydro_37	p.E64*	ENST00000529101.1	37	c.190		11	.	.	.	.	.	.	.	.	.	.	C	13.21	2.169311	0.38315	.	.	ENSG00000118094	ENST00000529101;ENST00000264029;ENST00000525958;ENST00000397925	.	.	.	5.31	4.39	0.52855	.	0.313406	0.33309	N	0.005052	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-18.6018	10.5699	0.45194	0.0:0.9092:0.0:0.0908	.	.	.	.	X	64	.	.	E	-	1	0	TREH	118039258	1.000000	0.71417	1.000000	0.80357	0.147000	0.21601	2.911000	0.48774	2.512000	0.84698	0.585000	0.79938	GAA	-	pfam_Glyco_hydro_37		0.532	TREH-001	KNOWN	basic|appris_candidate	protein_coding	TREH	protein_coding	OTTHUMT00000389639.1	C	NM_007180	-	Nonsense_Mutation	118534048	-1	no_errors	ENST00000264029	ensembl	human	known	74_37	nonsense	SNP	1.000	A
COL4A1	1282	genome.wustl.edu	37	13	110831646	110831646	+	Silent	SNP	G	G	A	rs377593990		TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr13:110831646G>A	ENST00000375820.4	-	30	2437	c.2316C>T	c.(2314-2316)atC>atT	p.I772I		NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	772	Triple-helical region.				axon guidance (GO:0007411)|basement membrane organization (GO:0071711)|blood vessel morphogenesis (GO:0048514)|brain development (GO:0007420)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)|patterning of blood vessels (GO:0001569)|renal tubule morphogenesis (GO:0061333)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)|platelet-derived growth factor binding (GO:0048407)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	105	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			CAGGGGGTCCGATCGCTCCAT	0.577																																																	0								ENSG00000187498	G		2,4404	4.2+/-10.8	0,2,2201	88.0	93.0	91.0		2316	-7.8	0.0	13		91	0,8600		0,0,4300	no	coding-synonymous	COL4A1	NM_001845.4		0,2,6501	AA,AG,GG		0.0,0.0454,0.0154		772/1670	110831646	2,13004	2203	4300	6503	COL4A1	SO:0001819	synonymous_variant	0			-	HGNC	J04217	CCDS9511.1	13q34	2013-09-05			ENSG00000187498	ENSG00000187498		"""Collagens"""	2202	protein-coding gene	gene with protein product		120130				3691802	Standard	NM_001845		Approved		uc001vqw.4	P02462	OTTHUMG00000017342	ENST00000375820.4:c.2316C>T	13.37:g.110831646G>A		Somatic	0	41	0.00		0.5521987511953187	1615	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	12	75	13.79	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_Collagen,pfam_Collagen_VI_NC,superfamily_C-type_lectin_fold,smart_Collagen_VI_NC	p.I772	ENST00000375820.4	37	c.2316	CCDS9511.1	13																																																																																			-	pfam_Collagen		0.577	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	COL4A1	protein_coding	OTTHUMT00000045759.3	G		-		110831646	-1	no_errors	ENST00000375820	ensembl	human	known	74_37	silent	SNP	0.000	A
DNAJC1	64215	genome.wustl.edu	37	10	22045671	22045671	+	Missense_Mutation	SNP	G	G	T			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr10:22045671G>T	ENST00000376980.3	-	12	1900	c.1610C>A	c.(1609-1611)gCt>gAt	p.A537D	DNAJC1_ENST00000483085.1_5'Flank	NM_022365.3	NP_071760.2	Q96KC8	DNJC1_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 1	537	SANT 2. {ECO:0000255|PROSITE- ProRule:PRU00624}.				negative regulation of proteolysis (GO:0045861)|positive regulation of ATPase activity (GO:0032781)|protein folding (GO:0006457)|regulation of protein secretion (GO:0050708)|regulation of translation (GO:0006417)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ATPase activator activity (GO:0001671)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)			cervix(1)|endometrium(1)|large_intestine(2)|lung(13)|skin(2)|upper_aerodigestive_tract(2)	21		Breast(68;0.00869)|Prostate(175;0.0181)|Lung SC(717;0.0262)				CTTGTACCTAGCGATACAGTC	0.423																																																	0								ENSG00000136770						126.0	117.0	120.0					10																	22045671		2203	4300	6503	DNAJC1	SO:0001583	missense	0			-	HGNC	AK026062	CCDS7136.1	10p11.23	2011-09-02			ENSG00000136770	ENSG00000136770		"""Heat shock proteins / DNAJ (HSP40)"""	20090	protein-coding gene	gene with protein product		611207					Standard	NM_022365		Approved	DNAJL1, ERdj1, MTJ1	uc001irc.3	Q96KC8	OTTHUMG00000017800	ENST00000376980.3:c.1610C>A	10.37:g.22045671G>T	ENSP00000366179:p.Ala537Asp	Somatic	0	28	0.00		0.5521987511953187	103	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	10	23.08	B0YIZ8|Q5VX89|Q9H6B8	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_DnaJ_domain,pfam_SANT/Myb,superfamily_DnaJ_domain,superfamily_Homeodomain-like,smart_DnaJ_domain,smart_SANT/Myb,pfscan_Myb-like_dom,pfscan_DnaJ_domain,prints_DnaJ_domain	p.A537D	ENST00000376980.3	37	c.1610	CCDS7136.1	10	.	.	.	.	.	.	.	.	.	.	G	20.3	3.966404	0.74131	.	.	ENSG00000136770	ENST00000376980	T	0.39592	1.07	5.44	5.44	0.79542	Myb, DNA-binding (1);SANT domain, DNA binding (1);Homeodomain-related (1);Homeodomain-like (1);SANT, eukarya (1);	0.462170	0.24933	N	0.034460	T	0.47097	0.1427	N	0.25992	0.78	0.80722	D	1	D;D	0.61080	0.989;0.976	P;P	0.61003	0.882;0.812	T	0.21008	-1.0258	10	0.27785	T	0.31	-1.8284	15.1369	0.72576	0.0:0.141:0.859:0.0	.	258;537	Q96NY3;Q96KC8	.;DNJC1_HUMAN	D	537	ENSP00000366179:A537D	ENSP00000366179:A537D	A	-	2	0	DNAJC1	22085677	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.723000	0.54955	2.712000	0.92718	0.561000	0.74099	GCT	-	pfam_SANT/Myb,superfamily_Homeodomain-like,smart_SANT/Myb,pfscan_Myb-like_dom		0.423	DNAJC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DNAJC1	protein_coding	OTTHUMT00000047149.1	G	NM_022365	-		22045671	-1	no_errors	ENST00000376980	ensembl	human	known	74_37	missense	SNP	0.996	T
CAPRIN1	4076	genome.wustl.edu	37	11	34121729	34121730	+	3'UTR	INS	-	-	CTAT	rs151202936|rs113052175|rs71644540|rs373001692|rs552033793	byFrequency	TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr11:34121729_34121730insCTAT	ENST00000341394.4	+	0	3134_3135				CAPRIN1_ENST00000532820.1_3'UTR|CAPRIN1_ENST00000533657.1_3'UTR	NM_005898.4	NP_005889.3	Q14444	CAPR1_HUMAN	cell cycle associated protein 1						negative regulation of translation (GO:0017148)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of dendritic spine morphogenesis (GO:0061003)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)	18		Acute lymphoblastic leukemia(5;0.00045)|all_hematologic(20;0.0016)				AAGGATTGGTACTATCTATCAT	0.351																																																	0								ENSG00000135387																																			CAPRIN1	SO:0001624	3_prime_UTR_variant	0				HGNC	BC001731	CCDS31453.1, CCDS31454.1	11p13	2010-08-03	2007-03-27	2007-03-27	ENSG00000135387	ENSG00000135387			6743	protein-coding gene	gene with protein product	"""cytoplasmic activation/proliferation-associated protein-1"""	601178	"""membrane component, chromosome 11, surface marker 1"", ""GPI-anchored membrane protein 1"""	M11S1, GPIAP1		7657653, 16177067, 17210633, 14764709, 15471883	Standard	NM_005898		Approved	caprin-1, RNG105	uc001mvh.1	Q14444	OTTHUMG00000166248	ENST00000341394.4:c.*816->CTAT	11.37:g.34121734_34121737dupCTAT		Somatic	0	8	0.00		0.5521987511953187	230	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	6	40.00	A6NMY7|D3DR06|Q15074|Q6IMN4|Q6IMN7|Q9BV09	RNA	INS	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000341394.4	37	NULL	CCDS31453.1	11																																																																																			-	-		0.351	CAPRIN1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	CAPRIN1	protein_coding	OTTHUMT00000388680.2	-	NM_005898			34121730	+1	no_errors	ENST00000533657	ensembl	human	known	74_37	rna	INS	0.640:0.016	CTAT
DOCK10	55619	genome.wustl.edu	37	2	225668868	225668868	+	Missense_Mutation	SNP	G	G	T			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr2:225668868G>T	ENST00000258390.7	-	39	4296	c.4229C>A	c.(4228-4230)tCc>tAc	p.S1410Y	DOCK10_ENST00000409592.3_Missense_Mutation_p.S1404Y	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	1410					regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		GGAAGGATTGGATCCTTTGAG	0.373																																																	0								ENSG00000135905						104.0	102.0	103.0					2																	225668868		1872	4102	5974	DOCK10	SO:0001583	missense	0			-	HGNC	AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"""Pleckstrin homology (PH) domain containing"""	23479	protein-coding gene	gene with protein product	"""zizimin3"""	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.4229C>A	2.37:g.225668868G>T	ENSP00000258390:p.Ser1410Tyr	Somatic	0	49	0.00		0.5521987511953187	6	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	57	8.06	B3FL70|O75178|Q9NW06|Q9NXI8	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_DOCK_C,pfam_DOCK_C/D_N,pfam_Pleckstrin_homology,superfamily_ARM-type_fold,smart_Pleckstrin_homology,pfscan_Pleckstrin_homology	p.S1410Y	ENST00000258390.7	37	c.4229	CCDS46528.1	2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.91|19.91	3.914098|3.914098	0.72983|0.72983	.|.	.|.	ENSG00000135905|ENSG00000135905	ENST00000422684|ENST00000409592;ENST00000258390	.|T;T	.|0.02103	.|4.45;4.45	5.68|5.68	5.68|5.68	0.88126|0.88126	.|.	.|0.501136	.|0.22110	.|N	.|0.064487	T|T	0.08313|0.08313	0.0207|0.0207	L|L	0.29908|0.29908	0.895|0.895	0.58432|0.58432	D|D	0.999999|0.999999	.|D;D;P;B	.|0.65815	.|0.976;0.995;0.901;0.294	.|P;D;B;B	.|0.75484	.|0.556;0.986;0.312;0.054	T|T	0.31833|0.31833	-0.9929|-0.9929	5|10	.|0.56958	.|D	.|0.05	.|.	19.8009|19.8009	0.96506|0.96506	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1410;264;1404;72	.|Q96BY6;B4DF07;B3FL70;B4DEY4	.|DOC10_HUMAN;.;.;.	T|Y	292|1404;1410	.|ENSP00000386694:S1404Y;ENSP00000258390:S1410Y	.|ENSP00000258390:S1410Y	P|S	-|-	1|2	0|0	DOCK10|DOCK10	225377112|225377112	1.000000|1.000000	0.71417|0.71417	0.968000|0.968000	0.41197|0.41197	0.986000|0.986000	0.74619|0.74619	9.361000|9.361000	0.97122|0.97122	2.680000|2.680000	0.91292|0.91292	0.585000|0.585000	0.79938|0.79938	CCA|TCC	-	superfamily_ARM-type_fold		0.373	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DOCK10	protein_coding	OTTHUMT00000331246.1	G		-		225668868	-1	no_errors	ENST00000258390	ensembl	human	known	74_37	missense	SNP	1.000	T
KITLG	4254	genome.wustl.edu	37	12	88898935	88898935	+	Splice_Site	SNP	C	C	A			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr12:88898935C>A	ENST00000228280.5	-	9	1042		c.e9+1		KITLG_ENST00000357116.4_Splice_Site|KITLG_ENST00000347404.5_Splice_Site|KITLG_ENST00000378535.4_Splice_Site	NM_000899.4	NP_000890.1	P21583	SCF_HUMAN	KIT ligand						cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|negative regulation of mast cell apoptotic process (GO:0033026)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mast cell proliferation (GO:0070668)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of myeloid leukocyte differentiation (GO:0002763)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Ras protein signal transduction (GO:0046579)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	stem cell factor receptor binding (GO:0005173)			kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)|stomach(1)	9						AAAAAACTTACCAATGTACGA	0.303									Testicular Cancer, Familial Clustering of																																								0								ENSG00000049130						70.0	66.0	67.0					12																	88898935		2203	4299	6502	KITLG	SO:0001630	splice_region_variant	0	Familial Cancer Database		-	HGNC	M59964	CCDS31867.1, CCDS31868.1	12q22	2010-11-23			ENSG00000049130	ENSG00000049130			6343	protein-coding gene	gene with protein product	"""mast cell growth factor"", ""stem cell factor"", ""steel factor"", ""familial progressive hyperpigmentation 2"""	184745		MGF		2208279, 1707188, 19375057	Standard	NM_003994		Approved	SCF, SF, Kitl, KL-1, FPH2	uc001tav.3	P21583	OTTHUMG00000169888	ENST00000228280.5:c.819+1G>T	12.37:g.88898935C>A		Somatic	0	30	0.00		0.5521987511953187	2	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	38	9.52	A0AV09|A8K2Q4|B7ZLM4|Q16487|Q68DZ2|Q7M4N8|Q9UQK7	Splice_Site	SNP	NA	NA	NA	NA	NA	NA	-	e9+1	ENST00000228280.5	37	c.822+1	CCDS31868.1	12																																																																																			-	-		0.303	KITLG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	KITLG	protein_coding	OTTHUMT00000406424.2	C	NM_003994	-	Intron	88898935	-1	no_errors	ENST00000228280	ensembl	human	known	74_37	splice_site	SNP	1.000	A
AL359195.1	0	genome.wustl.edu	37	10	82013311	82013311	+	Missense_Mutation	SNP	G	G	T			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr10:82013311G>T	ENST00000356374.4	+	1	3846	c.829G>T	c.(829-831)Ggt>Tgt	p.G277C																								TGTACTACTTGGTATATTTAT	0.458																																																	0								ENSG00000204038																																			AL359195.1	SO:0001583	missense	0			-	Clone_based_ensembl_gene																												ENST00000356374.4:c.829G>T	10.37:g.82013311G>T	ENSP00000348738:p.Gly277Cys	Somatic	0	51	0.00		0.5521987511953187	0	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	22	15.38		Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	NULL	p.G277C	ENST00000356374.4	37	c.829		10	.	.	.	.	.	.	.	.	.	.	g	7.175	0.588419	0.13812	.	.	ENSG00000204038	ENST00000356374	.	.	.	1.08	1.08	0.20341	.	.	.	.	.	T	0.53818	0.1820	.	.	.	.	.	.	.	.	.	.	.	.	T	0.64630	-0.6362	4	0.87932	D	0	.	8.0829	0.30754	0.0:0.0:1.0:0.0	.	.	.	.	C	277	.	ENSP00000348738:G277C	G	+	1	0	AL359195.1	82003291	0.001000	0.12720	0.112000	0.21494	0.175000	0.22909	-0.121000	0.10643	0.921000	0.36994	0.194000	0.17425	GGT	-	NULL		0.458	AL359195.1-201	KNOWN	basic|appris_principal	protein_coding	ENSG00000204038	protein_coding		G		-		82013311	+1	no_errors	ENST00000356374	ensembl	human	known	74_37	missense	SNP	0.243	T
CRTAC1	55118	genome.wustl.edu	37	10	99664503	99664503	+	Missense_Mutation	SNP	C	C	A			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr10:99664503C>A	ENST00000370597.3	-	7	1274	c.919G>T	c.(919-921)Gac>Tac	p.D307Y	CRTAC1_ENST00000298819.4_Missense_Mutation_p.D307Y|CRTAC1_ENST00000370591.2_Missense_Mutation_p.D307Y	NM_018058.6	NP_060528.3	Q9NQ79	CRAC1_HUMAN	cartilage acidic protein 1	307						extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(7)|lung(6)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	35		Colorectal(252;0.24)		Epithelial(162;2.18e-10)|all cancers(201;3.27e-09)		TAGACGATGTCCACTTTGCCA	0.627																																																	0								ENSG00000095713						122.0	118.0	119.0					10																	99664503		2203	4300	6503	CRTAC1	SO:0001583	missense	0			-	HGNC	AJ276171	CCDS31266.1, CCDS55723.1	10q22	2007-12-03			ENSG00000095713	ENSG00000095713			14882	protein-coding gene	gene with protein product		606276				11139377	Standard	NM_018058		Approved	FLJ10320, CEP-68, ASPIC1	uc001kou.2	Q9NQ79	OTTHUMG00000018871	ENST00000370597.3:c.919G>T	10.37:g.99664503C>A	ENSP00000359629:p.Asp307Tyr	Somatic	0	36	0.00		0.5521987511953187	9	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	15	21.05	B1ALN4|Q5T4F8|Q8N4H6|Q8TE52|Q9NQ78|Q9NQ80|Q9NW46	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_FG-GAP,pfam_UnbV_ASPIC,pfam_EGF-like_Ca-bd_dom,smart_EGF-like_Ca-bd_dom	p.D307Y	ENST00000370597.3	37	c.919	CCDS31266.1	10	.	.	.	.	.	.	.	.	.	.	C	26.6	4.752800	0.89753	.	.	ENSG00000095713	ENST00000413387;ENST00000370597;ENST00000298819;ENST00000309155;ENST00000370591	T;T;T;T;T	0.63580	-0.05;-0.05;-0.05;-0.05;-0.05	4.96	4.96	0.65561	.	0.000000	0.85682	D	0.000000	D	0.84325	0.5447	M	0.92317	3.295	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;1.0;0.999	D	0.88699	0.3214	10	0.87932	D	0	-36.5415	18.2232	0.89907	0.0:1.0:0.0:0.0	.	307;307;203	Q9NQ79-2;Q9NQ79;Q5T4F6	.;CRAC1_HUMAN;.	Y	203;307;307;299;307	ENSP00000408445:D203Y;ENSP00000359629:D307Y;ENSP00000298819:D307Y;ENSP00000310810:D299Y;ENSP00000359623:D307Y	ENSP00000298819:D307Y	D	-	1	0	CRTAC1	99654493	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.709000	0.84645	2.303000	0.77524	0.561000	0.74099	GAC	-	pfam_FG-GAP		0.627	CRTAC1-001	KNOWN	basic|CCDS	protein_coding	CRTAC1	protein_coding	OTTHUMT00000049754.1	C	NM_018058	-		99664503	-1	no_errors	ENST00000370597	ensembl	human	known	74_37	missense	SNP	1.000	A
SCAF11	9169	genome.wustl.edu	37	12	46321265	46321265	+	Missense_Mutation	SNP	T	T	C			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr12:46321265T>C	ENST00000369367.3	-	11	2452	c.2219A>G	c.(2218-2220)gAt>gGt	p.D740G	SCAF11_ENST00000465950.1_Missense_Mutation_p.D425G|SCAF11_ENST00000549162.1_Missense_Mutation_p.D548G|SCAF11_ENST00000550629.1_5'Flank|SCAF11_ENST00000419565.2_Missense_Mutation_p.D740G	NM_004719.2	NP_004710.2	Q99590	SCAFB_HUMAN	SR-related CTD-associated factor 11	740					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|spliceosomal complex assembly (GO:0000245)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(17)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	69						TTGTTTAAGATCAGCATTTAC	0.353																																																	0								ENSG00000139218						133.0	128.0	130.0					12																	46321265		2203	4300	6503	SCAF11	SO:0001583	missense	0			-	HGNC	Y11251	CCDS8748.2	12q13.11	2013-01-09	2011-01-10	2011-01-10	ENSG00000139218	ENSG00000139218		"""RING-type (C3HC4) zinc fingers"""	10784	protein-coding gene	gene with protein product		603668	"""splicing factor, arginine/serine-rich 2, interacting protein"", ""serine/arginine-rich splicing factor 2, interacting protein"""	SFRS2IP, SRSF2IP		9224939, 9447963	Standard	NM_004719		Approved	SIP1, SRRP129, CASP11	uc001rox.3	Q99590	OTTHUMG00000149930	ENST00000369367.3:c.2219A>G	12.37:g.46321265T>C	ENSP00000358374:p.Asp740Gly	Somatic	0	21	0.00		0.5521987511953187	7	58.82	10	WXS	Illumina HiSeq 2500	Phase_IV	tier1	8	8	50.00	A6NEU9|A6NLW5|Q8IW59	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	smart_Znf_RING,pfscan_Znf_RING	p.D740G	ENST00000369367.3	37	c.2219	CCDS8748.2	12	.	.	.	.	.	.	.	.	.	.	T	13.30	2.195956	0.38806	.	.	ENSG00000139218	ENST00000465950;ENST00000369367;ENST00000549162;ENST00000419565;ENST00000547018	T;T;T;T;T	0.49720	1.41;2.14;1.4;2.14;0.77	5.93	4.73	0.59995	.	0.259393	0.33382	N	0.004975	T	0.49762	0.1576	L	0.53249	1.67	0.28938	N	0.891168	D;P	0.56287	0.975;0.851	P;B	0.48815	0.591;0.321	T	0.54132	-0.8339	10	0.62326	D	0.03	-27.2192	11.6394	0.51224	0.0:0.0:0.1479:0.8521	.	548;740	F8VXG7;Q99590	.;SCAFB_HUMAN	G	425;740;548;740;680	ENSP00000449812:D425G;ENSP00000358374:D740G;ENSP00000448864:D548G;ENSP00000413036:D740G;ENSP00000446746:D680G	ENSP00000358374:D740G	D	-	2	0	SCAF11	44607532	0.912000	0.30974	0.897000	0.35233	0.504000	0.33889	1.236000	0.32683	2.281000	0.76405	0.533000	0.62120	GAT	-	NULL		0.353	SCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SCAF11	protein_coding	OTTHUMT00000313992.2	T	NM_004719	-		46321265	-1	no_errors	ENST00000369367	ensembl	human	known	74_37	missense	SNP	0.744	C
HKDC1	80201	genome.wustl.edu	37	10	70992535	70992535	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr10:70992535delT	ENST00000354624.5	+	3	375	c.242delT	c.(241-243)cttfs	p.L81fs	HKDC1_ENST00000395086.2_Frame_Shift_Del_p.L81fs|RP11-227H15.4_ENST00000450995.1_RNA	NM_025130.3	NP_079406	Q2TB90	HKDC1_HUMAN	hexokinase domain containing 1	81	Hexokinase type-1 1.				carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)	cytosol (GO:0005829)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|mannokinase activity (GO:0019158)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(11)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						GGGGAGTTCCTTTCCCTGGAT	0.468																																																	0								ENSG00000156510						98.0	98.0	98.0					10																	70992535		2203	4300	6503	HKDC1	SO:0001589	frameshift_variant	0				HGNC		CCDS7288.1	10q22.1	2006-10-24			ENSG00000156510	ENSG00000156510			23302	protein-coding gene	gene with protein product						12477932	Standard	NM_025130		Approved	FLJ37767, FLJ22761	uc001jpf.4	Q2TB90	OTTHUMG00000018371	ENST00000354624.5:c.242delT	10.37:g.70992535delT	ENSP00000346643:p.Leu81fs	Somatic	0	35	0.00		0.5521987511953187	0	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	2	20	9.09	B5MDN9|Q2TB91|Q5VTC7|Q7Z373|Q8WU37|Q96EH2|Q9H5Y9	Frame_Shift_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_Hexokinase_C,pfam_Hexokinase_N,prints_Hexokinase	p.S82fs	ENST00000354624.5	37	c.242	CCDS7288.1	10																																																																																			-	pfam_Hexokinase_N		0.468	HKDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HKDC1	protein_coding	OTTHUMT00000048389.1	T	NM_025130			70992535	+1	no_errors	ENST00000354624	ensembl	human	known	74_37	frame_shift_del	DEL	1.000	-
ITIH5	80760	genome.wustl.edu	37	10	7601820	7601825	+	In_Frame_Del	DEL	TTTTGT	TTTTGT	-	rs550585550|rs141248725|rs368850950|rs111905334	byFrequency	TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	TTTTGT	TTTTGT					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr10:7601820_7601825delTTTTGT	ENST00000397146.2	-	12	2124_2129	c.2019_2024delACAAAA	c.(2017-2025)aaacaaaac>aac	p.KQ673del	ITIH5_ENST00000256861.6_3'UTR			Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	125					hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|kidney(6)|large_intestine(21)|lung(25)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(3)	75						ttttgttttgttttgtttttttttga	0.5														373	0.0744808	0.1808	0.0173	5008	,	,		24271	0.0387		0.006	False		,,,				2504	0.0787																0								ENSG00000123243																																			ITIH5	SO:0001651	inframe_deletion	0				HGNC			10p14	2011-10-26	2011-10-26		ENSG00000123243	ENSG00000123243			21449	protein-coding gene	gene with protein product		609783	"""inter-alpha (globulin) inhibitor H5"""			14744536	Standard	NM_001001851		Approved	MGC10848	uc021pmv.1	Q86UX2	OTTHUMG00000017635	ENST00000397146.2:c.2019_2024delACAAAA	10.37:g.7601820_7601825delTTTTGT	ENSP00000380333:p.Lys673_Gln674del	Somatic	NA	NA	NA		0.5521987511953187	8	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	In_Frame_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_VIT,pfam_VWF_A,smart_VIT,smart_VWF_A,pfscan_VWF_A	p.KQ673in_frame_del	ENST00000397146.2	37	c.2024_2019		10																																																																																			-	NULL		0.500	ITIH5-202	KNOWN	basic	protein_coding	ITIH5	protein_coding		TTTTGT	NM_030569			7601825	-1	no_errors	ENST00000397146	ensembl	human	known	74_37	in_frame_del	DEL	0.003:0.004:0.004:0.005:0.005:0.008	-
RP11-1036E20.9	0	genome.wustl.edu	37	11	59038010	59038011	+	lincRNA	INS	-	-	A	rs56102919|rs77430335|rs397935653|rs112888385		TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr11:59038010_59038011insA	ENST00000399003.1	-	0	1142_1143																											tagttgtttacaaaaaaaaaac	0.371																																																	0								ENSG00000214797																																			RP11-1036E20.9			0				Clone_based_vega_gene																													11.37:g.59038020_59038020dupA		Somatic	0	63	0.00		0.5521987511953187	0	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	47	9.62		RNA	INS	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000399003.1	37	NULL		11																																																																																			-	-		0.371	RP11-1036E20.9-001	KNOWN	basic	lincRNA	ENSG00000214797	lincRNA	OTTHUMT00000394611.1	-				59038011	-1	no_errors	ENST00000399003	ensembl	human	known	74_37	rna	INS	0.006:0.000	A
TMEM88B	643965	genome.wustl.edu	37	1	1361531	1361533	+	In_Frame_Del	DEL	GGA	GGA	-			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	GGA	GGA					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr1:1361531_1361533delGGA	ENST00000378821.3	+	1	24_26	c.24_26delGGA	c.(22-27)acggag>acg	p.E12del		NM_001146685.1	NP_001140157.1	A6NKF7	TM88B_HUMAN	transmembrane protein 88B	12	Poly-Glu.					integral component of membrane (GO:0016021)											GGAGGGAGACGGAGGAGGAGGAG	0.7																																																	0								ENSG00000205116			16,8,2634		2,0,12,2,4,1309						-1.9	0.0			23	1,9,5546		0,0,1,1,7,2769	no	codingComplex	TMEM88B	NM_001146685.1		2,0,13,3,11,4078	A1A1,A1A2,A1R,A2A2,A2R,RR		0.18,0.9029,0.4139				17,17,8180				TMEM88B	SO:0001651	inframe_deletion	0				HGNC		CCDS57964.1	1p36.33	2013-01-16			ENSG00000205116	ENSG00000205116			37099	protein-coding gene	gene with protein product							Standard	NM_001146685		Approved		uc010nyp.2	A6NKF7	OTTHUMG00000153395	ENST00000378821.3:c.24_26delGGA	1.37:g.1361540_1361542delGGA	ENSP00000455099:p.Glu12del	Somatic	0	11	0.00		0.5521987511953187	0	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	6	33.33		In_Frame_Del	DEL	NA	NA	NA	NA	NA	NA	NULL	p.E12in_frame_del	ENST00000378821.3	37	c.24_26	CCDS57964.1	1																																																																																			-	NULL		0.700	TMEM88B-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	TMEM88B	protein_coding	OTTHUMT00000331012.2	GGA	NM_001146685			1361533	+1	no_errors	ENST00000378821	ensembl	human	novel	74_37	in_frame_del	DEL	0.001:0.809:0.920	-
STPG2	285555	genome.wustl.edu	37	4	98865141	98865141	+	Missense_Mutation	SNP	C	C	A			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr4:98865141C>A	ENST00000295268.3	-	8	1040	c.951G>T	c.(949-951)caG>caT	p.Q317H		NM_174952.2	NP_777612.1	Q8N412	STPG2_HUMAN	sperm-tail PG-rich repeat containing 2	317																	TTCCCACACCCTGTGAATGCC	0.328																																																	0								ENSG00000163116						117.0	113.0	114.0					4																	98865141		2203	4300	6503	STPG2	SO:0001583	missense	0			-	HGNC	BC036870	CCDS3645.1	4q22.3-q23	2013-10-11	2012-07-30	2012-07-30	ENSG00000163116	ENSG00000163116			28712	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 37"""	C4orf37		23031811	Standard	NM_174952		Approved	MGC46496	uc003htt.2	Q8N412	OTTHUMG00000131009	ENST00000295268.3:c.951G>T	4.37:g.98865141C>A	ENSP00000295268:p.Gln317His	Somatic	0	45	0.00		0.5521987511953187	0	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	42	8.70		Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	NULL	p.Q317H	ENST00000295268.3	37	c.951	CCDS3645.1	4	.	.	.	.	.	.	.	.	.	.	C	5.180	0.218713	0.09810	.	.	ENSG00000163116	ENST00000522676;ENST00000295268	T;T	0.49432	0.78;2.65	4.0	3.1	0.35709	.	1.491800	0.04640	N	0.405231	T	0.50343	0.1610	L	0.29908	0.895	0.09310	N	1	D	0.65815	0.995	P	0.56278	0.795	T	0.36962	-0.9726	10	0.41790	T	0.15	-27.9385	6.558	0.22471	0.0:0.8584:0.0:0.1416	.	317	Q8N412	CD037_HUMAN	H	31;317	ENSP00000428346:Q31H;ENSP00000295268:Q317H	ENSP00000295268:Q317H	Q	-	3	2	C4orf37	99084164	0.326000	0.24669	0.043000	0.18650	0.032000	0.12392	1.364000	0.34171	1.188000	0.43014	0.558000	0.71614	CAG	-	NULL		0.328	STPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	STPG2	protein_coding	OTTHUMT00000253642.1	C	NM_174952	-		98865141	-1	no_errors	ENST00000295268	ensembl	human	known	74_37	missense	SNP	0.055	A
NFIL3	4783	genome.wustl.edu	37	9	94171898	94171898	+	Missense_Mutation	SNP	C	C	A			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr9:94171898C>A	ENST00000297689.3	-	2	1513	c.1119G>T	c.(1117-1119)atG>atT	p.M373I		NM_005384.2	NP_005375.2	Q16649	NFIL3_HUMAN	nuclear factor, interleukin 3 regulated	373					cellular response to interleukin-4 (GO:0071353)|circadian rhythm (GO:0007623)|immune response (GO:0006955)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			endometrium(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)	16						AAGAATGTACCATACTTGGGG	0.403																																					Esophageal Squamous(152;732 1832 10053 26981 51762)												0								ENSG00000165030						170.0	164.0	166.0					9																	94171898		2203	4300	6503	NFIL3	SO:0001583	missense	0			-	HGNC	X64318	CCDS6690.1	9q22	2013-01-10			ENSG00000165030	ENSG00000165030		"""basic leucine zipper proteins"""	7787	protein-coding gene	gene with protein product		605327		IL3BP1		7565758, 1620116	Standard	NM_005384		Approved	E4BP4, NFIL3A, NF-IL3A	uc004arh.3	Q16649	OTTHUMG00000020209	ENST00000297689.3:c.1119G>T	9.37:g.94171898C>A	ENSP00000297689:p.Met373Ile	Somatic	0	31	0.00		0.5521987511953187	70	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	41	8.89	B2R9Y8|Q14211|Q6FGQ8|Q96HS0	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Vert_IL3-reg_TF,pfam_bZIP,smart_bZIP,pirsf_TF_bZIP_E4BP4,pfscan_bZIP	p.M373I	ENST00000297689.3	37	c.1119	CCDS6690.1	9	.	.	.	.	.	.	.	.	.	.	C	11.78	1.741921	0.30865	.	.	ENSG00000165030	ENST00000375724;ENST00000297689	.	.	.	4.97	4.97	0.65823	Vertebrate interleukin-3 regulated transcription factor (1);	1.492290	0.03788	N	0.262447	T	0.53530	0.1802	L	0.36672	1.1	0.09310	N	1	B	0.11235	0.004	B	0.15870	0.014	T	0.50491	-0.8822	9	0.52906	T	0.07	-7.6348	18.4124	0.90557	0.0:1.0:0.0:0.0	.	373	Q16649	NFIL3_HUMAN	I	373	.	ENSP00000297689:M373I	M	-	3	0	NFIL3	93211719	0.861000	0.29849	0.509000	0.27700	0.987000	0.75469	2.350000	0.44063	2.594000	0.87642	0.561000	0.74099	ATG	-	pfam_Vert_IL3-reg_TF,pirsf_TF_bZIP_E4BP4		0.403	NFIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NFIL3	protein_coding	OTTHUMT00000053038.2	C	NM_005384	-		94171898	-1	no_errors	ENST00000297689	ensembl	human	known	74_37	missense	SNP	0.119	A
TENM1	10178	genome.wustl.edu	37	X	123556417	123556417	+	Missense_Mutation	SNP	G	G	T			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chrX:123556417G>T	ENST00000371130.3	-	23	4218	c.4155C>A	c.(4153-4155)aaC>aaA	p.N1385K	TENM1_ENST00000422452.2_Missense_Mutation_p.N1392K|STAG2_ENST00000469481.1_3'UTR	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	1385					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)										GCAGCACAATGTTGTTATCCA	0.473																																																	0								ENSG00000009694						151.0	125.0	134.0					X																	123556417		2203	4300	6503	TENM1	SO:0001583	missense	0			-	HGNC	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.4155C>A	X.37:g.123556417G>T	ENSP00000360171:p.Asn1385Lys	Somatic	0	27	0.00		0.5521987511953187	0	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	24	11.11	B2RTR5|Q5JZ17	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Ten_N,pfam_EGF_extracell,superfamily_CarboxyPept-like_regulatory,smart_EG-like_dom,pfscan_EG-like_dom,tigrfam_YD	p.N1392K	ENST00000371130.3	37	c.4176	CCDS14609.1	X	.	.	.	.	.	.	.	.	.	.	G	19.71	3.877977	0.72294	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	D;D	0.90444	-2.67;-2.67	5.68	2.97	0.34412	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	D	0.95156	0.8430	M	0.90369	3.11	0.58432	D	0.999997	D;D;P	0.69078	0.997;0.993;0.944	D;P;P	0.75484	0.986;0.787;0.554	D	0.93556	0.6891	10	0.87932	D	0	.	8.5659	0.33538	0.3034:0.0:0.6966:0.0	.	1391;1392;1385	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	K	1385;1392	ENSP00000360171:N1385K;ENSP00000403954:N1392K	ENSP00000360171:N1385K	N	-	3	2	ODZ1	123384098	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.972000	0.49256	0.204000	0.20548	0.594000	0.82650	AAC	-	NULL		0.473	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TENM1	protein_coding	OTTHUMT00000058985.1	G	NM_014253	-		123556417	-1	no_errors	ENST00000422452	ensembl	human	known	74_37	missense	SNP	1.000	T
IRF2BP2	359948	genome.wustl.edu	37	1	234742800	234742801	+	3'UTR	DEL	AT	AT	-	rs142351268		TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	AT	AT					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr1:234742800_234742801delAT	ENST00000366609.3	-	0	1876_1877				RP4-781K5.2_ENST00000436039.1_RNA|IRF2BP2_ENST00000491430.1_5'Flank|IRF2BP2_ENST00000366610.3_3'UTR	NM_182972.2	NP_892017.2	Q7Z5L9	I2BP2_HUMAN	interferon regulatory factor 2 binding protein 2						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	11	Ovarian(103;0.0303)	all_cancers(173;0.0236)|Prostate(94;0.0115)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)|Epithelial(3;6.2e-05)			CTTGTCTTGGATATATATATAT	0.287																																																	0								ENSG00000228830																																			RP4-781K5.2	SO:0001624	3_prime_UTR_variant	0				Clone_based_vega_gene	AY278023	CCDS1602.1, CCDS41475.1	1q42.3	2008-02-05			ENSG00000168264	ENSG00000168264			21729	protein-coding gene	gene with protein product		615332				12799427	Standard	NM_182972		Approved	IRF-2BP2	uc001hwg.3	Q7Z5L9	OTTHUMG00000037981	ENST00000366609.3:c.*83AT>-	1.37:g.234742810_234742811delAT		Somatic	0	20	0.00		0.5521987511953187	167	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	20	13.04	B1AM35|B1AM36|Q6P083|Q7Z5L8|Q8N351|Q8WUH8	RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000366609.3	37	NULL	CCDS1602.1	1																																																																																			-	-		0.287	IRF2BP2-002	NOVEL	basic|CCDS	protein_coding	ENSG00000228830	protein_coding	OTTHUMT00000092705.1	AT	NM_182972			234742801	+1	no_errors	ENST00000436039	ensembl	human	known	74_37	rna	DEL	1.000:1.000	-
RASGRF2	5924	genome.wustl.edu	37	5	80375986	80375986	+	Missense_Mutation	SNP	G	G	T			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr5:80375986G>T	ENST00000265080.4	+	6	1001	c.934G>T	c.(934-936)Gca>Tca	p.A312S	RASGRF2_ENST00000502677.1_3'UTR	NM_006909.2	NP_008840.1	O14827	RGRF2_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 2	312	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			biliary_tract(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(28)|ovary(5)|prostate(3)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75		Lung NSC(167;0.00498)|all_lung(232;0.00531)|Ovarian(174;0.0357)		OV - Ovarian serous cystadenocarcinoma(54;4.22e-42)|Epithelial(54;4.04e-35)|all cancers(79;2.52e-29)		AGGACTAAAGGCAAGGATAGC	0.294																																																	0								ENSG00000113319						90.0	99.0	96.0					5																	80375986		2203	4300	6503	RASGRF2	SO:0001583	missense	0			-	HGNC	AF023130	CCDS4052.1	5q13	2013-01-10			ENSG00000113319	ENSG00000113319		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	9876	protein-coding gene	gene with protein product		606614					Standard	NM_006909		Approved	GRF2, Ras-GRF2	uc003kha.2	O14827	OTTHUMG00000119015	ENST00000265080.4:c.934G>T	5.37:g.80375986G>T	ENSP00000265080:p.Ala312Ser	Somatic	0	59	0.00		0.5521987511953187	6	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	45	8.16	B9EG89|Q9UK56	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_RasGRF_CDC25,pfam_Ras-like_Gua-exchang_fac_N,pfam_DH-domain,pfam_Pleckstrin_homology,superfamily_Ras_GEF_dom,superfamily_DH-domain,smart_Pleckstrin_homology,smart_DH-domain,smart_Ras-like_Gua-exchang_fac_N,smart_RasGRF_CDC25,pfscan_IQ_motif_EF-hand-BS,pfscan_Pleckstrin_homology,pfscan_DH-domain,pfscan_RasGRF_CDC25,pfscan_Ras-like_Gua-exchang_fac_N	p.A312S	ENST00000265080.4	37	c.934	CCDS4052.1	5	.	.	.	.	.	.	.	.	.	.	G	20.2	3.956613	0.73902	.	.	ENSG00000113319	ENST00000265080	T	0.62941	-0.01	5.74	5.74	0.90152	Dbl homology (DH) domain (5);	0.000000	0.85682	D	0.000000	T	0.57533	0.2060	N	0.13235	0.315	0.80722	D	1	P;P	0.44946	0.846;0.844	P;P	0.52646	0.68;0.705	T	0.50065	-0.8871	10	0.09338	T	0.73	.	19.919	0.97077	0.0:0.0:1.0:0.0	.	312;312	D6RAS9;O14827	.;RGRF2_HUMAN	S	312	ENSP00000265080:A312S	ENSP00000265080:A312S	A	+	1	0	RASGRF2	80411742	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.751000	0.98889	2.712000	0.92718	0.561000	0.74099	GCA	-	pfam_DH-domain,superfamily_DH-domain,smart_DH-domain,pfscan_DH-domain		0.294	RASGRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RASGRF2	protein_coding	OTTHUMT00000239215.2	G	NM_006909	-		80375986	+1	no_errors	ENST00000265080	ensembl	human	known	74_37	missense	SNP	1.000	T
C10orf62	414157	genome.wustl.edu	37	10	99349965	99349965	+	Nonsense_Mutation	SNP	C	C	A			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr10:99349965C>A	ENST00000370640.3	+	1	516	c.311C>A	c.(310-312)tCa>tAa	p.S104*	HOGA1_ENST00000370647.4_Intron|HOGA1_ENST00000370646.4_Intron|PI4K2A_ENST00000555577.1_Intron|PI4K2A_ENST00000370649.3_Intron	NM_001009997.2	NP_001009997.2	Q5T681	CJ062_HUMAN	chromosome 10 open reading frame 62	104										endometrium(2)|kidney(1)|lung(1)	4		Colorectal(252;0.162)		Epithelial(162;9.58e-11)|all cancers(201;8.62e-09)		TCTGGGCCCTCAGTGATCCAA	0.597																																																	0								ENSG00000203942						57.0	58.0	57.0					10																	99349965		2203	4300	6503	C10orf62	SO:0001587	stop_gained	0			-	HGNC		CCDS31261.1	10q24.2	2012-05-31			ENSG00000203942	ENSG00000203942			23294	protein-coding gene	gene with protein product							Standard	NM_001009997		Approved	bA548K23.1	uc001koa.3	Q5T681	OTTHUMG00000018858	ENST00000370640.3:c.311C>A	10.37:g.99349965C>A	ENSP00000359674:p.Ser104*	Somatic	0	32	0.00		0.5521987511953187	0	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	25	13.79	Q49A70|Q8N3Y6	Nonsense_Mutation	SNP	NA	NA	NA	NA	NA	NA	NULL	p.S104*	ENST00000370640.3	37	c.311	CCDS31261.1	10	.	.	.	.	.	.	.	.	.	.	C	15.05	2.717374	0.48622	.	.	ENSG00000203942	ENST00000370640	.	.	.	4.68	1.43	0.22495	.	0.804253	0.10045	U	0.722992	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.0783	2.4055	0.04412	0.2101:0.5046:0.1784:0.1069	.	.	.	.	X	104	.	ENSP00000359674:S104X	S	+	2	0	C10orf62	99339955	0.000000	0.05858	0.000000	0.03702	0.050000	0.14768	0.126000	0.15769	0.549000	0.28973	0.643000	0.83706	TCA	-	NULL		0.597	C10orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	C10orf62	protein_coding	OTTHUMT00000049723.1	C	NM_001009997	-		99349965	+1	no_errors	ENST00000370640	ensembl	human	known	74_37	nonsense	SNP	0.000	A
SNORA11	677799	genome.wustl.edu	37	14	70270921	70270922	+	RNA	INS	-	-	T	rs566317626|rs200703304		TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr14:70270921_70270922insT	ENST00000408133.1	-	0	126_127									small nucleolar RNA, H/ACA box 11																		CATGGATTCTCTTTTTTTTTTT	0.351																																																	0								ENSG00000221060																																			SNORA11			0				RFAM	AM055729		Xp11.21	2013-09-05			ENSG00000221716	ENSG00000221716		"""ncRNAs / Small nucleolar RNAs : H/ACA box containing"""	32599	non-coding RNA	RNA, small nucleolar	"""small nucleolar RNA, H/ACA box 11A"""	300662				16361266, 16381836	Standard	NR_002953		Approved	U107, SNORA11A	uc021ptl.1				14.37:g.70270932_70270932dupT		Somatic	0	17	0.00		0.5521987511953187	0	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	11	21.43		RNA	INS	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000408133.1	37	NULL		14																																																																																			-	-		0.351	SNORA11.1-201	NOVEL	basic	snoRNA	ENSG00000221060	snoRNA		-	NR_002953			70270922	-1	no_errors	ENST00000408133	ensembl	human	novel	74_37	rna	INS	0.001:0.003	T
SENP6	26054	genome.wustl.edu	37	6	76376441	76376443	+	In_Frame_Del	DEL	TGA	TGA	-			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	TGA	TGA					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr6:76376441_76376443delTGA	ENST00000447266.2	+	10	1486_1488	c.1008_1010delTGA	c.(1006-1011)agtgat>agt	p.D341del	SENP6_ENST00000541192.1_5'Flank|SENP6_ENST00000370010.2_In_Frame_Del_p.D334del|SENP6_ENST00000327284.8_In_Frame_Del_p.D334del|SENP6_ENST00000370014.3_In_Frame_Del_p.D341del	NM_015571.2	NP_056386.2	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6	341					protein desumoylation (GO:0016926)|protein modification by small protein removal (GO:0070646)|protein sumoylation (GO:0016925)|regulation of kinetochore assembly (GO:0090234)|regulation of spindle assembly (GO:0090169)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	SUMO-specific protease activity (GO:0016929)	p.D337N(2)		breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(105;0.189)				TTTTGTCCAGTGATGATGATGAT	0.305																																																	2	Substitution - Missense(2)	lung(2)						ENSG00000112701																																			SENP6	SO:0001651	inframe_deletion	0				HGNC		CCDS43483.1, CCDS47454.1	6q13-q14.3	2008-02-05	2005-08-17		ENSG00000112701	ENSG00000112701			20944	protein-coding gene	gene with protein product		605003	"""SUMO1/sentrin specific protease 6"""				Standard	NM_015571		Approved	SUSP1, KIAA0797	uc003pid.4	Q9GZR1	OTTHUMG00000015060	ENST00000447266.2:c.1008_1010delTGA	6.37:g.76376450_76376452delTGA	ENSP00000402527:p.Asp341del	Somatic	0	27	0.00		0.5521987511953187	40	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	20	13.04	A6NNY9|O94891|Q5VUL3|Q5VUL4|Q8TBY4|Q9UJV5	In_Frame_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_Peptidase_C48,pfscan_Peptidase_C48	p.D340in_frame_del	ENST00000447266.2	37	c.1008_1010	CCDS47454.1	6																																																																																			-	NULL		0.305	SENP6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	SENP6	protein_coding	OTTHUMT00000041272.2	TGA	NM_015571			76376443	+1	no_errors	ENST00000370014	ensembl	human	known	74_37	in_frame_del	DEL	1.000:1.000:1.000	-
MIR143HG	728264	genome.wustl.edu	37	5	148810071	148810072	+	lincRNA	INS	-	-	C			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr5:148810071_148810072insC	ENST00000602964.1	+	0	16796				MIR145_ENST00000384967.1_lincRNA|MIR143_ENST00000385300.1_RNA					MIR143 host gene (non-protein coding)																		CGGTCACTACTCCCCCCCAGAG	0.599											OREG0016915	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					0								ENSG00000269936																																			MIR145			0				HGNC			5q32	2013-02-13			ENSG00000249669	ENSG00000249669		"""Long non-coding RNAs"""	42872	non-coding RNA	RNA, long non-coding							Standard	NR_105059		Approved				OTTHUMG00000163464		5.37:g.148810078_148810078dupC		Somatic	0	8	0.00	1720	0.5521987511953187	38	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	7	41.67		RNA	INS	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000602964.1	37	NULL		5																																																																																			-	-		0.599	MIR143HG-009	KNOWN	basic	lincRNA	MIR145	lincRNA	OTTHUMT00000468028.1	-				148810072	+1	no_errors	ENST00000602315	ensembl	human	known	74_37	rna	INS	0.001:0.002	C
CACNB4	785	genome.wustl.edu	37	2	152830203	152830203	+	Intron	SNP	C	C	A			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr2:152830203C>A	ENST00000539935.1	-	3	215				CACNB4_ENST00000201943.5_Intron|CACNB4_ENST00000397327.2_5'UTR|CACNB4_ENST00000534999.1_Nonsense_Mutation_p.G9*|CACNB4_ENST00000360283.6_Nonsense_Mutation_p.G9*|CACNB4_ENST00000427385.1_Intron|CACNB4_ENST00000475848.1_5'UTR	NM_000726.3|NM_001145798.1	NP_000717.2|NP_001139270.1	O00305	CACB4_HUMAN	calcium channel, voltage-dependent, beta 4 subunit						adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|cAMP metabolic process (GO:0046058)|cellular calcium ion homeostasis (GO:0006874)|detection of light stimulus involved in visual perception (GO:0050908)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|membrane depolarization (GO:0051899)|muscle fiber development (GO:0048747)|neuromuscular junction development (GO:0007528)|neuronal action potential propagation (GO:0019227)|Peyer's patch development (GO:0048541)|regulation of voltage-gated calcium channel activity (GO:1901385)|spleen development (GO:0048536)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)|transport (GO:0006810)	cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|synapse (GO:0045202)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)	11				BRCA - Breast invasive adenocarcinoma(221;0.156)	Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	TCTTCAATTCCATGCAGGTAC	0.463																																																	0								ENSG00000182389						69.0	68.0	68.0					2																	152830203		1865	4113	5978	CACNB4	SO:0001627	intron_variant	0			-	HGNC	AF038852	CCDS46426.1, CCDS46427.1, CCDS46428.1, CCDS54409.1	2q22-q23	2009-09-04			ENSG00000182389	ENSG00000182389		"""Calcium channel subunits"""	1404	protein-coding gene	gene with protein product		601949				9628818	Standard	NM_000726		Approved	EJM4	uc002tya.3	O00305	OTTHUMG00000155091	ENST00000539935.1:c.148-90319G>T	2.37:g.152830203C>A		Somatic	0	40	0.00		0.5521987511953187	0	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	29	12.12	A7BJ74|A8K1Y4|B4DG40|O60515|Q6B000|Q96L40	Nonsense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_GK/Ca_channel_bsu,pfam_VDCC_L_bsu,superfamily_P-loop_NTPase,superfamily_SH3_domain,smart_GK/Ca_channel_bsu,pfscan_SH3_domain,prints_VDCC_L_bsu,prints_VDCC_L_b3su	p.G9*	ENST00000539935.1	37	c.25	CCDS46426.1	2	.	.	.	.	.	.	.	.	.	.	C	39	7.685638	0.98431	.	.	ENSG00000182389	ENST00000360283;ENST00000534999	.	.	.	5.78	4.91	0.64330	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.44086	T	0.13	.	13.8402	0.63435	0.0:0.9255:0.0:0.0745	.	.	.	.	X	9	.	ENSP00000353425:G9X	G	-	1	0	CACNB4	152538449	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.633000	0.74286	1.464000	0.47987	0.313000	0.20887	GGA	-	prints_VDCC_L_b3su		0.463	CACNB4-001	KNOWN	basic|CCDS	protein_coding	CACNB4	protein_coding	OTTHUMT00000338385.4	C	NM_000726.3	-		152830203	-1	no_errors	ENST00000360283	ensembl	human	known	74_37	nonsense	SNP	1.000	A
INO80	54617	genome.wustl.edu	37	15	41272454	41272454	+	Missense_Mutation	SNP	C	C	A			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr15:41272454C>A	ENST00000361937.3	-	36	5062	c.4638G>T	c.(4636-4638)caG>caT	p.Q1546H	INO80_ENST00000401393.3_Missense_Mutation_p.Q1546H			Q9ULG1	INO80_HUMAN	INO80 complex subunit	1546	Assembles INO80 complex module consisting of conserved components INO80B, INO80C, ACTR5, RVBL1, RVBL2.				ATP catabolic process (GO:0006200)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|mitotic sister chromatid segregation (GO:0000070)|positive regulation of cell growth (GO:0030307)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|spindle assembly (GO:0051225)|UV-damage excision repair (GO:0070914)	Ino80 complex (GO:0031011)|microtubule (GO:0005874)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			NS(1)|breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						TGCCTTTGCCCTGTTTCCGGA	0.557																																																	0								ENSG00000128908						134.0	126.0	129.0					15																	41272454		2203	4300	6503	INO80	SO:0001583	missense	0			-	HGNC	AB033085	CCDS10071.1	15q15.1	2013-08-21	2013-08-21	2008-08-07	ENSG00000128908	ENSG00000128908	3.6.1.3	"""INO80 complex subunits"""	26956	protein-coding gene	gene with protein product	"""INO80 complex subunit A"""	610169	"""INO80 complex homolog 1 (S. cerevisiae)"", ""INO80 homolog (S. cerevisiae)"""	INOC1		16298340, 16230350, 20237820	Standard	NM_017553		Approved	KIAA1259, Ino80, hINO80, INO80A	uc001zni.3	Q9ULG1	OTTHUMG00000130209	ENST00000361937.3:c.4638G>T	15.37:g.41272454C>A	ENSP00000355205:p.Gln1546His	Somatic	0	39	0.00		0.5521987511953187	51	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	43	8.51	A6H8X4|Q9NTG6	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_SNF2_N,pfam_Helicase_C,superfamily_P-loop_NTPase,smart_Helicase_ATP-bd,smart_Helicase_C,pfscan_Helicase_ATP-bd,pfscan_Helicase_C	p.Q1546H	ENST00000361937.3	37	c.4638	CCDS10071.1	15	.	.	.	.	.	.	.	.	.	.	C	8.879	0.951190	0.18431	.	.	ENSG00000128908	ENST00000263793;ENST00000361937;ENST00000401393	D;D	0.90900	-2.75;-2.75	5.4	4.49	0.54785	.	0.153645	0.43747	D	0.000522	T	0.74344	0.3704	N	0.03608	-0.345	0.34361	D	0.691021	B	0.06786	0.001	B	0.04013	0.001	T	0.70142	-0.4953	10	0.30854	T	0.27	.	3.8074	0.08783	0.1893:0.5956:0.0:0.2151	.	1546	Q9ULG1	INO80_HUMAN	H	182;1546;1546	ENSP00000355205:Q1546H;ENSP00000384686:Q1546H	ENSP00000263793:Q182H	Q	-	3	2	INO80	39059746	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	1.573000	0.36472	1.517000	0.48917	0.655000	0.94253	CAG	-	NULL		0.557	INO80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	INO80	protein_coding	OTTHUMT00000252527.2	C	NM_017553	-		41272454	-1	no_errors	ENST00000361937	ensembl	human	known	74_37	missense	SNP	1.000	A
HNF1A	6927	genome.wustl.edu	37	12	121434574	121434574	+	Silent	SNP	G	G	T			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr12:121434574G>T	ENST00000402929.1	+	6	1473	c.1338G>T	c.(1336-1338)ctG>ctT	p.L446L	HNF1A_ENST00000400024.2_Intron|HNF1A_ENST00000543427.1_Silent_p.L329L|HNF1A_ENST00000538626.1_Intron|HNF1A_ENST00000544413.1_Intron|HNF1A_ENST00000257555.6_Intron|HNF1A_ENST00000541395.1_Intron			P20823	HNF1A_HUMAN	HNF1 homeobox A	0					glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|insulin secretion (GO:0030073)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|renal glucose absorption (GO:0035623)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(8)|large_intestine(19)|liver(175)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	221	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					GTGGGCACCTGGGTGGGAGGC	0.582									Hepatic Adenoma, Familial Clustering of																																								0								ENSG00000135100						25.0	22.0	23.0					12																	121434574		2203	4299	6502	HNF1A	SO:0001819	synonymous_variant	0	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	-	HGNC	M57732	CCDS9209.1	12q24.31	2014-09-17	2007-08-24	2007-08-24	ENSG00000135100	ENSG00000135100		"""Homeoboxes / HNF class"""	11621	protein-coding gene	gene with protein product		142410	"""transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1), albumin proximal factor"""	MODY3, TCF1		1535333, 7795649	Standard	NM_000545		Approved	HNF1, LFB1	uc001tzg.3	P20823	OTTHUMG00000151015	ENST00000402929.1:c.1338G>T	12.37:g.121434574G>T		Somatic	0	44	0.00		0.5521987511953187	0	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	46	9.80	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_HNF1b_C,pfam_HNF-1_N,pfam_Homeobox_dom,superfamily_Homeodomain-like,superfamily_Lambda_DNA-bd_dom,smart_Homeobox_dom,pfscan_Homeobox_dom	p.L329	ENST00000402929.1	37	c.987		12																																																																																			-	NULL		0.582	HNF1A-003	PUTATIVE	basic	protein_coding	HNF1A	protein_coding	OTTHUMT00000320959.3	G	NM_000545	-		121434574	+1	no_errors	ENST00000543427	ensembl	human	known	74_37	silent	SNP	0.001	T
COL4A1	1282	genome.wustl.edu	37	13	110831720	110831720	+	Missense_Mutation	SNP	G	G	A			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr13:110831720G>A	ENST00000375820.4	-	30	2363	c.2242C>T	c.(2242-2244)Ccc>Tcc	p.P748S		NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	748	Triple-helical region.				axon guidance (GO:0007411)|basement membrane organization (GO:0071711)|blood vessel morphogenesis (GO:0048514)|brain development (GO:0007420)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)|patterning of blood vessels (GO:0001569)|renal tubule morphogenesis (GO:0061333)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)|platelet-derived growth factor binding (GO:0048407)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	105	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			GGAATGCCGGGAAGACCTGGC	0.557																																																	0								ENSG00000187498						69.0	73.0	72.0					13																	110831720		2203	4300	6503	COL4A1	SO:0001583	missense	0			-	HGNC	J04217	CCDS9511.1	13q34	2013-09-05			ENSG00000187498	ENSG00000187498		"""Collagens"""	2202	protein-coding gene	gene with protein product		120130				3691802	Standard	NM_001845		Approved		uc001vqw.4	P02462	OTTHUMG00000017342	ENST00000375820.4:c.2242C>T	13.37:g.110831720G>A	ENSP00000364979:p.Pro748Ser	Somatic	0	53	0.00		0.5521987511953187	1646	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	20	56	26.32	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Collagen,pfam_Collagen_VI_NC,superfamily_C-type_lectin_fold,smart_Collagen_VI_NC	p.P748S	ENST00000375820.4	37	c.2242	CCDS9511.1	13	.	.	.	.	.	.	.	.	.	.	G	16.10	3.026338	0.54683	.	.	ENSG00000187498	ENST00000375820	D	0.97665	-4.48	4.7	4.7	0.59300	.	0.060648	0.64402	D	0.000003	D	0.97813	0.9282	M	0.65320	2	0.80722	D	1	D	0.76494	0.999	D	0.70716	0.97	D	0.97270	0.9910	10	0.29301	T	0.29	.	18.0343	0.89294	0.0:0.0:1.0:0.0	.	748	P02462	CO4A1_HUMAN	S	748	ENSP00000364979:P748S	ENSP00000364979:P748S	P	-	1	0	COL4A1	109629721	1.000000	0.71417	0.116000	0.21606	0.008000	0.06430	5.714000	0.68422	2.328000	0.79073	0.655000	0.94253	CCC	-	pfam_Collagen		0.557	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	COL4A1	protein_coding	OTTHUMT00000045759.3	G		-		110831720	-1	no_errors	ENST00000375820	ensembl	human	known	74_37	missense	SNP	0.891	A
SET	6418	genome.wustl.edu	37	9	131456028	131456028	+	Missense_Mutation	SNP	G	G	T			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr9:131456028G>T	ENST00000372692.4	+	6	884	c.643G>T	c.(643-645)Gat>Tat	p.D215Y	SET_ENST00000322030.8_Missense_Mutation_p.D202Y|SET_ENST00000409104.3_Missense_Mutation_p.D193Y|SET_ENST00000477806.1_3'UTR|SET_ENST00000372688.4_Missense_Mutation_p.D191Y	NM_001122821.1	NP_001116293.1	Q01105	SET_HUMAN	SET nuclear proto-oncogene	215	Earmuff domain.				DNA replication (GO:0006260)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of catalytic activity (GO:0043086)|negative regulation of histone acetylation (GO:0035067)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleocytoplasmic transport (GO:0006913)|nucleosome assembly (GO:0006334)|nucleosome disassembly (GO:0006337)|regulation of catalytic activity (GO:0050790)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	DNA binding (GO:0003677)|histone binding (GO:0042393)|protein phosphatase inhibitor activity (GO:0004864)|protein phosphatase type 2A regulator activity (GO:0008601)			endometrium(2)|kidney(1)|lung(2)	5		Myeloproliferative disorder(178;0.204)		GBM - Glioblastoma multiforme(294;3.1e-09)		TGCAGGTGCTGATGAGTTAGG	0.438			T	NUP214	AML																																			Dom	yes		9	9q34	6418	SET translocation		L	0								ENSG00000119335						76.0	75.0	75.0					9																	131456028		2203	4299	6502	SET	SO:0001583	missense	0			-	HGNC	M93651	CCDS6907.1, CCDS48037.1, CCDS59149.1, CCDS59150.1	9q34	2014-06-25	2014-06-25		ENSG00000119335	ENSG00000119335			10760	protein-coding gene	gene with protein product	"""protein phosphatase type 2A inhibitor"", ""Template-Activating Factor-I, chromatin remodelling factor"""	600960	"""SET translocation (myeloid leukemia-associated)"""			1630450, 8626647	Standard	NM_003011		Approved	PHAPII, 2PP2A, IPP2A2	uc022bol.1	Q01105	OTTHUMG00000020755	ENST00000372692.4:c.643G>T	9.37:g.131456028G>T	ENSP00000361777:p.Asp215Tyr	Somatic	0	40	0.00		0.5521987511953187	447	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	42	8.70	A5A5H4|A6NGV1|B4DUE2|Q15541|Q5VXV1|Q5VXV2|Q6FHZ5	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_NAP_family	p.D215Y	ENST00000372692.4	37	c.643	CCDS48037.1	9	.	.	.	.	.	.	.	.	.	.	G	23.9	4.472054	0.84533	.	.	ENSG00000119335	ENST00000372692;ENST00000409104;ENST00000322030;ENST00000372688;ENST00000372686	T;T;T;T;T	0.24538	1.85;2.96;1.85;2.96;2.96	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.49745	0.1575	L	0.58101	1.795	0.80722	D	1	D;D;D	0.89917	0.999;0.998;1.0	D;D;D	0.83275	0.985;0.961;0.996	T	0.49244	-0.8960	10	0.87932	D	0	.	18.1692	0.89739	0.0:0.0:1.0:0.0	.	191;202;215	A6NGV1;Q01105-2;Q01105	.;.;SET_HUMAN	Y	215;193;202;191;190	ENSP00000361777:D215Y;ENSP00000387321:D193Y;ENSP00000318012:D202Y;ENSP00000361773:D191Y;ENSP00000361771:D190Y	ENSP00000318012:D202Y	D	+	1	0	SET	130495849	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.849000	0.92178	2.538000	0.85594	0.555000	0.69702	GAT	-	pfam_NAP_family		0.438	SET-001	KNOWN	basic|CCDS	protein_coding	SET	protein_coding	OTTHUMT00000054476.2	G	NM_001122821	-		131456028	+1	no_errors	ENST00000372692	ensembl	human	known	74_37	missense	SNP	1.000	T
CLCN2	1181	genome.wustl.edu	37	3	184069817	184069817	+	Missense_Mutation	SNP	C	C	A	rs147728691		TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chr3:184069817C>A	ENST00000265593.4	-	22	2570	c.2399G>T	c.(2398-2400)cGg>cTg	p.R800L	CLCN2_ENST00000434054.2_Missense_Mutation_p.R756L|CLCN2_ENST00000423355.2_3'UTR|EIF2B5_ENST00000444495.1_Intron|CLCN2_ENST00000457512.1_Missense_Mutation_p.R800L|CLCN2_ENST00000344937.7_Missense_Mutation_p.R783L	NM_004366.5	NP_004357.3	P51788	CLCN2_HUMAN	chloride channel, voltage-sensitive 2	800	CBS 2. {ECO:0000255|PROSITE- ProRule:PRU00703}.				cell differentiation involved in salivary gland development (GO:0060689)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|retina development in camera-type eye (GO:0060041)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)|voltage-gated chloride channel activity (GO:0005247)			breast(2)|central_nervous_system(4)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	27	all_cancers(143;6.66e-11)|Ovarian(172;0.0339)		Epithelial(37;2.22e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		Lubiprostone(DB01046)	CAAAGAGGTCCGCTCCACCAG	0.562																																																	0								ENSG00000114859						135.0	131.0	132.0					3																	184069817		2203	4300	6503	CLCN2	SO:0001583	missense	0			-	HGNC	S77770	CCDS3263.1, CCDS54690.1, CCDS54691.1, CCDS54692.1	3q27.1	2013-09-19	2012-02-23		ENSG00000114859	ENSG00000114859		"""Ion channels / Chloride channels : Voltage-sensitive"""	2020	protein-coding gene	gene with protein product		600570	"""chloride channel 2"""			7795595	Standard	NM_004366		Approved	CLC2, EJM6, ClC-2	uc003foi.4	P51788	OTTHUMG00000156747	ENST00000265593.4:c.2399G>T	3.37:g.184069817C>A	ENSP00000265593:p.Arg800Leu	Somatic	0	28	0.00		0.5521987511953187	17	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	19	17.39	B4DQT9|B4DZ58|E9PBD9|E9PCD2|O14864|Q6IPA9|Q8WU13	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Cl-channel_volt-gated,pfam_CBS_dom,superfamily_Cl-channel_core,prints_Cl-channel_volt-gated,prints_Cl-channel-2	p.R800L	ENST00000265593.4	37	c.2399	CCDS3263.1	3	.	.	.	.	.	.	.	.	.	.	c	21.4	4.139919	0.77775	.	.	ENSG00000114859	ENST00000265593;ENST00000344937;ENST00000434054;ENST00000457512	D;D;D;D	0.93366	-3.21;-3.21;-3.21;-2.35	5.59	5.59	0.84812	Cystathionine beta-synthase, core (3);	0.055712	0.64402	D	0.000001	D	0.95095	0.8411	M	0.79926	2.475	0.80722	D	1	P;P;P;P	0.50369	0.934;0.869;0.932;0.934	P;B;P;P	0.48815	0.591;0.268;0.545;0.495	D	0.95443	0.8527	10	0.66056	D	0.02	-26.0779	18.3639	0.90384	0.0:1.0:0.0:0.0	.	756;800;783;800	E9PBD9;E9PCD2;P51788-3;P51788	.;.;.;CLCN2_HUMAN	L	800;783;756;800	ENSP00000265593:R800L;ENSP00000345056:R783L;ENSP00000400425:R756L;ENSP00000391928:R800L	ENSP00000265593:R800L	R	-	2	0	CLCN2	185552511	0.025000	0.19082	1.000000	0.80357	0.997000	0.91878	1.934000	0.40163	2.640000	0.89533	0.462000	0.41574	CGG	-	pfam_CBS_dom		0.562	CLCN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	CLCN2	protein_coding	OTTHUMT00000345571.1	C		-		184069817	-1	no_errors	ENST00000265593	ensembl	human	known	74_37	missense	SNP	1.000	A
HTATSF1	27336	genome.wustl.edu	37	X	135586547	135586547	+	Missense_Mutation	SNP	G	G	T			TCGA-DX-A6B9-01A-12D-A32I-09	TCGA-DX-A6B9-10A-01D-A32I-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e062c178-feb3-4e3f-8ecb-f8bb99831131	d4f1cdfe-f1dd-496c-9021-403dd1e67786	g.chrX:135586547G>T	ENST00000218364.4	+	6	933	c.759G>T	c.(757-759)agG>agT	p.R253S	HTATSF1_ENST00000535601.1_Missense_Mutation_p.R253S	NM_014500.4	NP_055315.2	O43719	HTSF1_HUMAN	HIV-1 Tat specific factor 1	253					regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(14)|ovary(3)|prostate(1)	30	Acute lymphoblastic leukemia(192;0.000127)					GACCTGAGAGGCGAGCCGGAC	0.448																																																	0								ENSG00000102241						111.0	92.0	99.0					X																	135586547		2203	4300	6503	HTATSF1	SO:0001583	missense	0			-	HGNC	U76992	CCDS14657.1	Xq26.3	2013-02-12	2006-01-09		ENSG00000102241	ENSG00000102241		"""RNA binding motif (RRM) containing"""	5276	protein-coding gene	gene with protein product		300346	"""HIV TAT specific factor 1"""			8849451	Standard	NM_014500		Approved	TAT-SF1	uc004ezx.3	O43719	OTTHUMG00000022510	ENST00000218364.4:c.759G>T	X.37:g.135586547G>T	ENSP00000218364:p.Arg253Ser	Somatic	0	37	0.00		0.5521987511953187	213	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	28	12.50	D3DWG9|Q59G06|Q99730	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_RRM_dom,smart_RRM_dom,pfscan_RRM_dom	p.R253S	ENST00000218364.4	37	c.759	CCDS14657.1	X	.	.	.	.	.	.	.	.	.	.	G	16.93	3.258443	0.59321	.	.	ENSG00000102241	ENST00000535601;ENST00000218364;ENST00000415377	T;T	0.23552	1.9;1.9	5.77	1.7	0.24286	.	0.087322	0.85682	D	0.000000	T	0.27933	0.0688	L	0.43923	1.385	0.34011	D	0.651484	D	0.55605	0.972	P	0.50136	0.632	T	0.38308	-0.9667	10	0.66056	D	0.02	-8.4771	9.9163	0.41436	0.276:0.0:0.724:0.0	.	253	O43719	HTSF1_HUMAN	S	253	ENSP00000442699:R253S;ENSP00000218364:R253S	ENSP00000218364:R253S	R	+	3	2	HTATSF1	135414213	1.000000	0.71417	0.774000	0.31636	0.972000	0.66771	1.230000	0.32612	-0.100000	0.12241	0.538000	0.68166	AGG	-	NULL		0.448	HTATSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HTATSF1	protein_coding	OTTHUMT00000058497.1	G	NM_014500	-		135586547	+1	no_errors	ENST00000218364	ensembl	human	known	74_37	missense	SNP	1.000	T
