#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_EVS_AA	i_EVS_All	i_EVS_EA	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains_WU	i_amino_acid_change_WU	i_annotation_transcript	i_build	i_c_position_WU	i_ccds_id	i_chromosome_name_WU	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_default_gene_name_WU	i_deletion_substructures_WU	i_domain_WU	i_ensembl_gene_id	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_name_WU	i_gene_name_source_WU	i_gene_type	i_havana_transcript	i_normal_ref_reads	i_normal_vaf	i_normal_var_reads	i_reference_WU	i_refseq_mrna_id	i_secondary_variant_classification	i_start_WU	i_stop_WU	i_strand_WU	i_transcript_error_WU	i_transcript_name_WU	i_transcript_source_WU	i_transcript_species_WU	i_transcript_status_WU	i_transcript_version_WU	i_trv_type_WU	i_tumor_ref_reads	i_tumor_vaf	i_tumors_var_reads	i_type_WU	i_ucsc_cons_WU	i_variant_WU
ASB16	92591	genome.wustl.edu	37	17	42255078	42255078	+	Silent	SNP	A	A	T			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr17:42255078A>T	ENST00000293414.1	+	4	1248	c.1164A>T	c.(1162-1164)ccA>ccT	p.P388P	ASB16-AS1_ENST00000588785.1_RNA|ASB16-AS1_ENST00000585457.1_RNA|ASB16-AS1_ENST00000591166.1_RNA|ASB16-AS1_ENST00000592897.1_RNA	NM_080863.4	NP_543139.4	Q96NS5	ASB16_HUMAN	ankyrin repeat and SOCS box containing 16	388					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|liver(2)|lung(2)|prostate(1)	14		Breast(137;0.00765)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.114)		CGGTGCTCCCAGAGCTGTGGA	0.602																																						dbGAP											0													128.0	101.0	110.0					17																	42255078		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AK054727	CCDS11478.1	17q21.31	2013-01-10	2011-01-25		ENSG00000161664	ENSG00000161664		"""Ankyrin repeat domain containing"""	19768	protein-coding gene	gene with protein product		615056	"""ankyrin repeat and SOCS box-containing 16"""			12076535	Standard	NM_080863		Approved	FLJ30165	uc002ifl.1	Q96NS5	OTTHUMG00000181809	ENST00000293414.1:c.1164A>T	17.37:g.42255078A>T		Somatic		WXS	Illumina GAIIx	Phase_IV	B2RBC0|Q8WXK0	Silent	SNP	pfam_Ankyrin_rpt,pfam_SOCS_C,superfamily_Ankyrin_rpt-contain_dom,smart_Ankyrin_rpt,smart_SOCS_C,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom,pfscan_SOCS_C	p.P388	ENST00000293414.1	37	c.1164	CCDS11478.1	17																																																																																			ASB16	-	NULL	ENSG00000161664		0.602	ASB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ASB16	HGNC	protein_coding	OTTHUMT00000457703.1	118	0.00	0	A			42255078	42255078	+1	no_errors	ENST00000293414	ensembl	human	known	69_37n	silent	133	19.88	33	SNP	0.454	T
ATRX	546	genome.wustl.edu	37	X	76940008	76940008	+	Missense_Mutation	SNP	T	T	C			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chrX:76940008T>C	ENST00000373344.5	-	9	954	c.740A>G	c.(739-741)aAc>aGc	p.N247S	ATRX_ENST00000395603.3_Missense_Mutation_p.N209S|ATRX_ENST00000480283.1_5'UTR	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	247	ADD. {ECO:0000255|PROSITE- ProRule:PRU00865}.				ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						TCGACCAAGGTTGCGTAGAAT	0.403			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome																															dbGAP		Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	1	Unknown(1)	bone(1)											129.0	123.0	125.0					X																	76940008		2203	4295	6498	-	-	-	SO:0001583	missense	0			U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"""RAD54 homolog (S. cerevisiae)"""	300032	"""alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)"", ""Juberg-Marsidi syndrome"""	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.740A>G	X.37:g.76940008T>C	ENSP00000362441:p.Asn247Ser	Somatic		WXS	Illumina GAIIx	Phase_IV	D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Missense_Mutation	SNP	pfam_SNF2_N,pfam_Helicase_C,superfamily_Znf_FYVE_PHD,smart_Helicase_ATP-bd,smart_Helicase_C,pfscan_Helicase_ATP-bd,pfscan_Helicase_C	p.N247S	ENST00000373344.5	37	c.740	CCDS14434.1	X	.	.	.	.	.	.	.	.	.	.	T	12.87	2.066170	0.36470	.	.	ENSG00000085224	ENST00000373344;ENST00000395603;ENST00000400862	D;D	0.98807	-5.15;-5.15	5.42	5.42	0.78866	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	D	0.99086	0.9686	M	0.84082	2.675	0.80722	D	1	D;D;D;D	0.76494	0.989;0.999;0.994;0.992	D;D;D;D	0.83275	0.931;0.996;0.969;0.949	D	0.99632	1.0986	10	0.87932	D	0	-13.7026	14.493	0.67665	0.0:0.0:0.0:1.0	.	247;208;209;247	A4LAA3;P46100-6;P46100-4;P46100	.;.;.;ATRX_HUMAN	S	247;209;203	ENSP00000362441:N247S;ENSP00000378967:N209S	ENSP00000362441:N247S	N	-	2	0	ATRX	76826664	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	7.698000	0.84413	1.803000	0.52742	0.417000	0.27973	AAC	ATRX	-	superfamily_Znf_FYVE_PHD	ENSG00000085224		0.403	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ATRX	HGNC	protein_coding	OTTHUMT00000058860.2	96	0.00	0	T	NM_000489		76940008	76940008	-1	no_errors	ENST00000373344	ensembl	human	known	69_37n	missense	81	40.44	55	SNP	1.000	C
AZU1	566	genome.wustl.edu	37	19	831801	831802	+	In_Frame_Ins	INS	-	-	CTT			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr19:831801_831802insCTT	ENST00000233997.2	+	5	701_702	c.680_681insCTT	c.(679-684)gacttc>gaCTTcttc	p.229_230insF		NM_001700.3	NP_001691.1	P20160	CAP7_HUMAN	azurocidin 1	229	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cellular extravasation (GO:0045123)|defense response to Gram-negative bacterium (GO:0050829)|glial cell migration (GO:0008347)|induction of positive chemotaxis (GO:0050930)|inflammatory response (GO:0006954)|macrophage chemotaxis (GO:0048246)|microglial cell activation (GO:0001774)|monocyte activation (GO:0042117)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell adhesion (GO:0045785)|positive regulation of fractalkine biosynthetic process (GO:0050754)|positive regulation of interleukin-1 beta biosynthetic process (GO:0050725)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of phagocytosis (GO:0050766)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of vascular permeability (GO:0043114)	azurophil granule (GO:0042582)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)|toxic substance binding (GO:0015643)			NS(1)|endometrium(1)|kidney(1)|lung(4)|pancreas(1)|upper_aerodigestive_tract(2)	10		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CGAGGCCCTGACTTCTTCACCC	0.703																																						dbGAP											0																																										-	-	-	SO:0001652	inframe_insertion	0			X58794	CCDS12044.1	19p13.3	2012-03-30	2008-08-01		ENSG00000172232	ENSG00000172232			913	protein-coding gene	gene with protein product	"""cationic antimicrobial protein 37"", ""heparin-binding protein"", ""neutrophil azurocidin"""	162815				1919011	Standard	NM_001700		Approved	AZU, CAP37, AZAMP, HBP, NAZC, HUMAZUR	uc002lpz.1	P20160		ENST00000233997.2:c.684_686dupCTT	19.37:g.831805_831807dupCTT	ENSP00000233997:p.Phe229_Phe229dup	Somatic		WXS	Illumina GAIIx	Phase_IV	P80014|Q52LG4|Q9UCM1|Q9UCT5	In_Frame_Ins	INS	pfam_Peptidase_S1_S6,superfamily_Pept_cys/ser_Trypsin-like,smart_Peptidase_S1_S6,pfscan_Peptidase_S1_S6,prints_Peptidase_S1A	p.230in_frame_insF	ENST00000233997.2	37	c.680_681	CCDS12044.1	19																																																																																			AZU1	-	pfam_Peptidase_S1_S6,superfamily_Pept_cys/ser_Trypsin-like,smart_Peptidase_S1_S6,pfscan_Peptidase_S1_S6	ENSG00000172232		0.703	AZU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	AZU1	HGNC	protein_coding	OTTHUMT00000457472.2	9	0.00	0	-	NM_001700		831801	831802	+1	no_errors	ENST00000233997	ensembl	human	known	69_37n	in_frame_ins	4	33.33	2	INS	0.168:0.216	CTT
CADPS	8618	genome.wustl.edu	37	3	62535703	62535703	+	Missense_Mutation	SNP	A	A	C			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr3:62535703A>C	ENST00000383710.4	-	11	2190	c.1841T>G	c.(1840-1842)cTg>cGg	p.L614R	CADPS_ENST00000357948.3_Missense_Mutation_p.L614R|CADPS_ENST00000283269.9_Missense_Mutation_p.L614R	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator	614	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				catecholamine secretion (GO:0050432)|exocytosis (GO:0006887)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)|vesicle organization (GO:0016050)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|synapse (GO:0045202)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(24)|lung(38)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(2)	92		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		CTGGACCCACAGGATGCGGTC	0.567																																						dbGAP											0													160.0	144.0	149.0					3																	62535703		2203	4300	6503	-	-	-	SO:0001583	missense	0			U36448	CCDS2898.1, CCDS2899.1, CCDS46858.1	3p21.1	2013-01-10	2008-08-28		ENSG00000163618	ENSG00000163618		"""Pleckstrin homology (PH) domain containing"""	1426	protein-coding gene	gene with protein product		604667				1516133	Standard	NM_183393		Approved	CAPS, KIAA1121, CAPS1	uc003dll.2	Q9ULU8	OTTHUMG00000158651	ENST00000383710.4:c.1841T>G	3.37:g.62535703A>C	ENSP00000373215:p.Leu614Arg	Somatic		WXS	Illumina GAIIx	Phase_IV	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	Missense_Mutation	SNP	pfam_Ca-dep_secretion_activator,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_Pleckstrin_homology,pfscan_Pleckstrin_homology	p.L614R	ENST00000383710.4	37	c.1841	CCDS46858.1	3	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	23.9|23.9	4.468037|4.468037	0.84533|0.84533	.|.	.|.	ENSG00000163618|ENSG00000163618	ENST00000478434|ENST00000383709;ENST00000383710;ENST00000357948;ENST00000283269;ENST00000542833	.|T;T;T;T	.|0.73152	.|0.66;0.68;0.65;-0.72	4.71|4.71	4.71|4.71	0.59529|0.59529	.|Pleckstrin homology-type (1);Pleckstrin homology domain (2);	.|0.000000	.|0.64402	.|D	.|0.000007	D|D	0.82582|0.82582	0.5068|0.5068	M|M	0.72118|0.72118	2.19|2.19	0.80722|0.80722	D|D	1|1	.|P;D;D;D	.|0.65815	.|0.942;0.979;0.995;0.967	.|P;D;D;P	.|0.79108	.|0.8;0.988;0.992;0.882	D|D	0.85008|0.85008	0.0904|0.0904	5|10	.|0.87932	.|D	.|0	.|.	14.6319|14.6319	0.68663|0.68663	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|614;614;614;614	.|Q9ULU8-2;Q9ULU8-3;Q9ULU8;Q9ULU8-4	.|.;.;CAPS1_HUMAN;.	G|R	45|614;614;614;614;109	.|ENSP00000373215:L614R;ENSP00000350632:L614R;ENSP00000283269:L614R;ENSP00000439528:L109R	.|ENSP00000283269:L614R	C|L	-|-	1|2	0|0	CADPS|CADPS	62510743|62510743	1.000000|1.000000	0.71417|0.71417	0.803000|0.803000	0.32268|0.32268	0.996000|0.996000	0.88848|0.88848	9.087000|9.087000	0.94110|0.94110	2.111000|2.111000	0.64477|0.64477	0.477000|0.477000	0.44152|0.44152	TGT|CTG	CADPS	-	smart_Pleckstrin_homology,pfscan_Pleckstrin_homology	ENSG00000163618		0.567	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	CADPS	HGNC	protein_coding	OTTHUMT00000351951.5	72	0.00	0	A	NM_003716, NM_183393, NM_183394		62535703	62535703	-1	no_errors	ENST00000383710	ensembl	human	known	69_37n	missense	69	24.18	22	SNP	1.000	C
CEP97	79598	genome.wustl.edu	37	3	101477254	101477254	+	Missense_Mutation	SNP	G	G	A			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr3:101477254G>A	ENST00000341893.3	+	9	2556	c.1804G>A	c.(1804-1806)Gat>Aat	p.D602N	CEP97_ENST00000494050.1_Missense_Mutation_p.D543N|CEP97_ENST00000327230.4_Missense_Mutation_p.D602N			Q8IW35	CEP97_HUMAN	centrosomal protein 97kDa	602	CCP110-binding.				cell projection organization (GO:0030030)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)				cervix(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	29						CTGCTTAACTGATGAAATAAG	0.443																																						dbGAP											0													42.0	45.0	44.0					3																	101477254		2195	4297	6492	-	-	-	SO:0001583	missense	0			AL833269	CCDS2944.1	3q12.3	2014-02-20	2008-01-08	2008-01-08	ENSG00000182504	ENSG00000182504			26244	protein-coding gene	gene with protein product		615864	"""leucine-rich repeats and IQ motif containing 2"""	LRRIQ2		17719545, 18068367	Standard	NM_024548		Approved	FLJ23047	uc003dvk.1	Q8IW35	OTTHUMG00000159162	ENST00000341893.3:c.1804G>A	3.37:g.101477254G>A	ENSP00000342510:p.Asp602Asn	Somatic		WXS	Illumina GAIIx	Phase_IV	B5MDY8|Q8NA71|Q9H5T9	Missense_Mutation	SNP	pfam_IQ_motif_EF-hand-BS,pfscan_IQ_motif_EF-hand-BS	p.D602N	ENST00000341893.3	37	c.1804	CCDS2944.1	3	.	.	.	.	.	.	.	.	.	.	G	16.70	3.196557	0.58126	.	.	ENSG00000182504	ENST00000341893;ENST00000327230;ENST00000494050	T;T;T	0.54479	0.71;0.67;0.57	5.47	5.47	0.80525	.	0.675467	0.16434	N	0.214586	T	0.55970	0.1954	M	0.64997	1.995	0.45216	D	0.998225	B;B;B	0.16166	0.005;0.016;0.005	B;B;B	0.17433	0.004;0.018;0.005	T	0.53422	-0.8441	10	0.56958	D	0.05	-3.3695	19.3166	0.94216	0.0:0.0:1.0:0.0	.	543;602;602	E9PG22;Q8IW35-2;Q8IW35	.;.;CEP97_HUMAN	N	602;602;543	ENSP00000342510:D602N;ENSP00000325881:D602N;ENSP00000418185:D543N	ENSP00000325881:D602N	D	+	1	0	CEP97	102959944	0.988000	0.35896	0.999000	0.59377	0.809000	0.45718	6.121000	0.71602	2.557000	0.86248	0.305000	0.20034	GAT	CEP97	-	NULL	ENSG00000182504		0.443	CEP97-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	CEP97	HGNC	protein_coding	OTTHUMT00000353597.2	36	0.00	0	G	NM_024548		101477254	101477254	+1	no_errors	ENST00000327230	ensembl	human	known	69_37n	missense	23	20.69	6	SNP	0.982	A
CHRD	8646	genome.wustl.edu	37	3	184104637	184104637	+	Missense_Mutation	SNP	G	G	A			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr3:184104637G>A	ENST00000204604.1	+	17	2447	c.2201G>A	c.(2200-2202)cGa>cAa	p.R734Q	CHRD_ENST00000450923.1_Missense_Mutation_p.R734Q|CHRD_ENST00000545352.1_Missense_Mutation_p.R276Q|CHRD_ENST00000348986.3_Missense_Mutation_p.R694Q|EIF2B5_ENST00000444495.1_Intron	NM_003741.2	NP_003732.2	Q9H2X0	CHRD_HUMAN	chordin	734	VWFC 2. {ECO:0000255|PROSITE- ProRule:PRU00220}.				BMP signaling pathway involved in spinal cord dorsal/ventral patterning (GO:0021919)|floor plate development (GO:0033504)|forebrain development (GO:0030900)|gastrulation with mouth forming second (GO:0001702)|mesoderm formation (GO:0001707)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell migration (GO:0030336)|negative regulation of osteoblast differentiation (GO:0045668)|osteoblast differentiation (GO:0001649)|positive regulation of cell adhesion (GO:0045785)|positive regulation of mesenchymal cell proliferation (GO:0002053)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)	cytokine binding (GO:0019955)|heparin binding (GO:0008201)			NS(1)|biliary_tract(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(23)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48	all_cancers(143;6.33e-11)|Ovarian(172;0.0339)		Epithelial(37;4.96e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			CTGCAGAGACGAACGGTGATC	0.657																																						dbGAP											0													58.0	45.0	49.0					3																	184104637		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF076612	CCDS3266.1	3q27	2008-07-18			ENSG00000090539	ENSG00000090539			1949	protein-coding gene	gene with protein product		603475				9782094, 11472837	Standard	NM_003741		Approved		uc003fov.3	Q9H2X0	OTTHUMG00000141267	ENST00000204604.1:c.2201G>A	3.37:g.184104637G>A	ENSP00000204604:p.Arg734Gln	Somatic		WXS	Illumina GAIIx	Phase_IV	O95254|Q2M1I8|Q6UW83|Q9H2D3|Q9H2W8|Q9H2W9|Q9P0Z2|Q9P0Z3|Q9P0Z4|Q9P0Z5	Missense_Mutation	SNP	pfam_CHRD,pfam_VWF_C,smart_VWF_C,smart_CHRD,pirsf_Chordin,pfscan_CHRD,pfscan_VWF_C	p.R734Q	ENST00000204604.1	37	c.2201	CCDS3266.1	3	.	.	.	.	.	.	.	.	.	.	G	28.8	4.950877	0.92660	.	.	ENSG00000090539	ENST00000204604;ENST00000450923;ENST00000348986;ENST00000545352;ENST00000342610	T;T;T;T	0.64991	-0.13;-0.13;-0.13;-0.13	4.44	4.44	0.53790	von Willebrand factor, type C (4);	0.069651	0.56097	D	0.000030	T	0.67618	0.2912	L	0.47716	1.5	0.32184	N	0.580028	D;D;P;D	0.71674	0.959;0.998;0.769;0.996	P;P;B;P	0.58970	0.464;0.819;0.418;0.849	T	0.69584	-0.5106	10	0.22706	T	0.39	-16.3589	14.9202	0.70832	0.0:0.0:1.0:0.0	.	276;694;734;734	B7Z6F4;Q9H2X0-5;E7ESX1;Q9H2X0	.;.;.;CHRD_HUMAN	Q	734;734;694;276;447	ENSP00000204604:R734Q;ENSP00000408972:R734Q;ENSP00000334036:R694Q;ENSP00000442948:R276Q	ENSP00000204604:R734Q	R	+	2	0	CHRD	185587331	1.000000	0.71417	0.998000	0.56505	0.913000	0.54294	5.904000	0.69886	2.181000	0.69327	0.462000	0.41574	CGA	CHRD	-	pfam_VWF_C,smart_VWF_C,pirsf_Chordin,pfscan_VWF_C	ENSG00000090539		0.657	CHRD-001	KNOWN	basic|CCDS	protein_coding	CHRD	HGNC	protein_coding	OTTHUMT00000280432.1	14	0.00	0	G	NM_003741		184104637	184104637	+1	no_errors	ENST00000204604	ensembl	human	known	69_37n	missense	8	38.46	5	SNP	1.000	A
CPNE3	8895	genome.wustl.edu	37	8	87568396	87568396	+	Missense_Mutation	SNP	A	A	G			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr8:87568396A>G	ENST00000521271.1	+	16	1483	c.1321A>G	c.(1321-1323)Ata>Gta	p.I441V	CPNE3_ENST00000198765.4_Missense_Mutation_p.I441V	NM_003909.3	NP_003900.1	O75131	CPNE3_HUMAN	copine III	441	VWFA.				lipid metabolic process (GO:0006629)|protein phosphorylation (GO:0006468)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	calcium-dependent phospholipid binding (GO:0005544)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)|transporter activity (GO:0005215)			NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	23						CAGACAAGCTATAGTTAATGC	0.443																																						dbGAP											0													153.0	148.0	149.0					8																	87568396		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB014536	CCDS6243.1	8q21	2008-07-03				ENSG00000085719			2316	protein-coding gene	gene with protein product		604207				9430674	Standard	NM_003909		Approved		uc003ydv.2	O75131		ENST00000521271.1:c.1321A>G	8.37:g.87568396A>G	ENSP00000430934:p.Ile441Val	Somatic		WXS	Illumina GAIIx	Phase_IV	A8KA47|Q8IYA1	Missense_Mutation	SNP	pfam_Copine,pfam_C2_Ca-dep,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_C2_Ca-dep,smart_VWF_A,pfscan_C2_membr_targeting	p.I441V	ENST00000521271.1	37	c.1321	CCDS6243.1	8	.	.	.	.	.	.	.	.	.	.	A	16.40	3.112451	0.56398	.	.	ENSG00000085719	ENST00000198765;ENST00000521271	T;T	0.27890	1.64;1.64	5.72	5.72	0.89469	von Willebrand factor, type A (1);Copine (1);	0.042368	0.85682	D	0.000000	T	0.35248	0.0925	L	0.52364	1.645	0.80722	D	1	B	0.30326	0.276	B	0.37508	0.252	T	0.08617	-1.0713	10	0.33141	T	0.24	-18.05	16.0032	0.80310	1.0:0.0:0.0:0.0	.	441	O75131	CPNE3_HUMAN	V	441	ENSP00000198765:I441V;ENSP00000430934:I441V	ENSP00000198765:I441V	I	+	1	0	CPNE3	87637512	1.000000	0.71417	0.726000	0.30738	0.609000	0.37215	7.576000	0.82467	2.187000	0.69744	0.528000	0.53228	ATA	CPNE3	-	pfam_Copine,smart_VWF_A	ENSG00000085719		0.443	CPNE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CPNE3	HGNC	protein_coding	OTTHUMT00000374994.1	241	0.00	0	A			87568396	87568396	+1	no_errors	ENST00000198765	ensembl	human	known	69_37n	missense	181	42.54	134	SNP	0.998	G
CPNE8	144402	genome.wustl.edu	37	12	39087515	39087515	+	Missense_Mutation	SNP	G	G	C			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr12:39087515G>C	ENST00000331366.5	-	15	1183	c.1087C>G	c.(1087-1089)Cta>Gta	p.L363V	CPNE8_ENST00000360449.3_Missense_Mutation_p.L351V|CPNE8_ENST00000538596.2_Missense_Mutation_p.L32V	NM_153634.2	NP_705898.1	Q86YQ8	CPNE8_HUMAN	copine VIII	363	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.					extracellular vesicular exosome (GO:0070062)				NS(1)|breast(1)|endometrium(1)|large_intestine(6)|lung(6)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)	21	Esophageal squamous(101;0.187)	Lung NSC(34;0.137)|Melanoma(24;0.152)|all_lung(34;0.157)				CCAAATCCTAGAGCTGGAAAC	0.368																																						dbGAP											0													151.0	139.0	143.0					12																	39087515		2203	4300	6503	-	-	-	SO:0001583	missense	0			AY177785	CCDS8733.1	12q12	2008-02-05				ENSG00000139117			23498	protein-coding gene	gene with protein product						12670487	Standard	NM_153634		Approved		uc001rls.1	Q86YQ8	OTTHUMG00000169396	ENST00000331366.5:c.1087C>G	12.37:g.39087515G>C	ENSP00000329748:p.Leu363Val	Somatic		WXS	Illumina GAIIx	Phase_IV	Q2TB41|Q86VY2	Missense_Mutation	SNP	pfam_Copine,pfam_C2_Ca-dep,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_C2_Ca-dep,smart_VWF_A,pfscan_C2_membr_targeting,pfscan_VWF_A	p.L363V	ENST00000331366.5	37	c.1087	CCDS8733.1	12	.	.	.	.	.	.	.	.	.	.	G	18.13	3.555176	0.65425	.	.	ENSG00000139117	ENST00000331366;ENST00000538596;ENST00000360449	T;T;T	0.24538	1.85;1.85;1.85	4.76	1.85	0.25348	von Willebrand factor, type A (2);Copine (1);	0.079753	0.52532	D	0.000070	T	0.45236	0.1332	M	0.78916	2.43	0.53688	D	0.999973	P	0.37101	0.582	P	0.55087	0.768	T	0.36962	-0.9726	10	0.62326	D	0.03	-12.1078	9.4007	0.38431	0.2425:0.0:0.7575:0.0	.	363	Q86YQ8	CPNE8_HUMAN	V	363;32;351	ENSP00000329748:L363V;ENSP00000439237:L32V;ENSP00000353633:L351V	ENSP00000329748:L363V	L	-	1	2	CPNE8	37373782	1.000000	0.71417	0.981000	0.43875	0.994000	0.84299	2.327000	0.43858	0.263000	0.21812	0.585000	0.79938	CTA	CPNE8	-	pfam_Copine,smart_VWF_A,pfscan_VWF_A	ENSG00000139117		0.368	CPNE8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CPNE8	HGNC	protein_coding	OTTHUMT00000403856.1	326	0.00	0	G	NM_153634		39087515	39087515	-1	no_errors	ENST00000331366	ensembl	human	known	69_37n	missense	331	16.20	64	SNP	0.998	C
CYTH1	9267	genome.wustl.edu	37	17	76676295	76676297	+	In_Frame_Del	DEL	CTT	CTT	-	rs147739265		TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	CTT	CTT					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr17:76676295_76676297delCTT	ENST00000446868.3	-	13	1163_1165	c.1093_1095delAAG	c.(1093-1095)aagdel	p.K365del	CYTH1_ENST00000589297.1_In_Frame_Del_p.K306del|CYTH1_ENST00000591455.1_In_Frame_Del_p.K364del|CYTH1_ENST00000586175.1_5'UTR|CYTH1_ENST00000589296.1_Intron|CYTH1_ENST00000585509.1_In_Frame_Del_p.K306del|CYTH1_ENST00000361101.4_In_Frame_Del_p.K365del			Q15438	CYH1_HUMAN	cytohesin 1	365	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				establishment of epithelial cell polarity (GO:0090162)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|regulation of cell adhesion (GO:0030155)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|lipid binding (GO:0008289)			endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	19						TCCACTCCTCCTTCTCCTCGGGC	0.557																																						dbGAP											0																																										-	-	-	SO:0001651	inframe_deletion	0			M85169	CCDS32754.1, CCDS42392.2	17q25	2014-05-02	2008-08-14	2008-08-14	ENSG00000108669	ENSG00000108669		"""Pleckstrin homology (PH) domain containing"""	9501	protein-coding gene	gene with protein product		182115	"""pleckstrin homology, Sec7 and coiled-coil domains 1"""	PSCD1		1511013, 8449036, 21628335, 20018626	Standard	XM_006722180		Approved	B2-1, D17S811E, cytohesin-1	uc002jvw.3	Q15438	OTTHUMG00000150253	ENST00000446868.3:c.1093_1095delAAG	17.37:g.76676295_76676297delCTT	ENSP00000389095:p.Lys365del	Somatic		WXS	Illumina GAIIx	Phase_IV	A6NFW7|B7Z1T4|Q9P123|Q9P124	In_Frame_Del	DEL	pfam_Sec7,pfam_Pleckstrin_homology,superfamily_Sec7,smart_Sec7,smart_Pleckstrin_homology,pfscan_Pleckstrin_homology,pfscan_Sec7	p.K365in_frame_del	ENST00000446868.3	37	c.1095_1093		17																																																																																			CYTH1	-	pfam_Pleckstrin_homology,smart_Pleckstrin_homology,pfscan_Pleckstrin_homology	ENSG00000108669		0.557	CYTH1-001	KNOWN	basic|appris_candidate_longest	protein_coding	CYTH1	HGNC	protein_coding	OTTHUMT00000317099.1	125	0.00	0	CTT	NM_004762		76676295	76676297	-1	no_errors	ENST00000361101	ensembl	human	known	69_37n	in_frame_del	129	17.83	28	DEL	1.000:1.000:1.000	-
EPB41L4A	64097	genome.wustl.edu	37	5	111595650	111595650	+	Frame_Shift_Del	DEL	T	T	-			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr5:111595650delT	ENST00000261486.5	-	8	945	c.669delA	c.(667-669)ttafs	p.L223fs	RP11-526F3.1_ENST00000504004.1_RNA	NM_022140.3	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte membrane protein band 4.1 like 4A	223	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)				breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(2)|skin(1)	34		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)		GAGTTAATCCTAAGAAATACT	0.358																																						dbGAP											0													138.0	132.0	134.0					5																	111595650		1835	4084	5919	-	-	-	SO:0001589	frameshift_variant	0			AB030240	CCDS43350.1	5q21.3	2008-02-05			ENSG00000129595	ENSG00000129595			13278	protein-coding gene	gene with protein product		612141				10874211	Standard	XM_005272043		Approved	NBL4	uc003kpv.1	Q9HCS5	OTTHUMG00000162902	ENST00000261486.5:c.669delA	5.37:g.111595650delT	ENSP00000261486:p.Leu223fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A4FUI6	Frame_Shift_Del	DEL	pfam_FERM_central,pfam_FERM_N,pfam_FERM_PH-like_C,pfam_FERM-adjacent,superfamily_FERM_central,smart_Band_41_domain,pfscan_FERM_domain,prints_Band_41_fam,prints_Ez/rad/moesin	p.G224fs	ENST00000261486.5	37	c.669	CCDS43350.1	5																																																																																			EPB41L4A	-	pfam_FERM_PH-like_C,pfscan_FERM_domain,prints_Ez/rad/moesin	ENSG00000129595		0.358	EPB41L4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	EPB41L4A	HGNC	protein_coding	OTTHUMT00000370969.1	406	0.00	0	T			111595650	111595650	-1	no_errors	ENST00000261486	ensembl	human	known	69_37n	frame_shift_del	456	12.24	65	DEL	0.997	-
ERVMER34-1	100288413	genome.wustl.edu	37	4	53610409	53610409	+	Missense_Mutation	SNP	C	C	G			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr4:53610409C>G	ENST00000443173.1	-	3	2139	c.1279G>C	c.(1279-1281)Gat>Cat	p.D427H	ERVMER34-1_ENST00000440542.1_Missense_Mutation_p.D427H|ERVMER34-1_ENST00000540758.1_Missense_Mutation_p.D427H|ERVMER34-1_ENST00000454756.2_Intron	NM_001242690.1	NP_001229619.1	Q9H9K5	MER34_HUMAN	endogenous retrovirus group MER34, member 1	427						integral component of membrane (GO:0016021)|viral envelope (GO:0019031)				endometrium(3)|kidney(1)	4						gtcggtatatccaagacatga	0.433																																						dbGAP											0													230.0	179.0	194.0					4																	53610409		692	1591	2283	-	-	-	SO:0001583	missense	0					4q12	2011-10-20			ENSG00000226887	ENSG00000226887			42970	other	endogenous retrovirus							Standard	NM_024534		Approved		uc003gzs.3	Q9H9K5	OTTHUMG00000150366	ENST00000443173.1:c.1279G>C	4.37:g.53610409C>G	ENSP00000460602:p.Asp427His	Somatic		WXS	Illumina GAIIx	Phase_IV	B3KTB4|Q0P5R3|Q6NWN0	Missense_Mutation	SNP	pfam_TLV/ENV_coat_polyprotein	p.D427H	ENST00000443173.1	37	c.1279		4																																																																																			ERVMER34-1	-	pfam_TLV/ENV_coat_polyprotein	ENSG00000226887		0.433	ERVMER34-1-002	KNOWN	alternative_5_UTR|basic|appris_principal	protein_coding	ERVMER34-1	HGNC	protein_coding	OTTHUMT00000317860.2	332	0.00	0	C	NM_024534		53610409	53610409	-1	no_errors	ENST00000440542	ensembl	human	known	69_37n	missense	320	14.21	53	SNP	0.000	G
FAM208A	23272	genome.wustl.edu	37	3	56716828	56716828	+	Silent	SNP	G	G	A			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr3:56716828G>A	ENST00000493960.2	-	1	217	c.207C>T	c.(205-207)ctC>ctT	p.L69L	FAM208A_ENST00000355628.5_Silent_p.L69L	NM_001112736.1	NP_001106207.1	Q9UK61	F208A_HUMAN	family with sequence similarity 208, member A	69							poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(11)|prostate(3)|skin(1)	32						GCTCGTGGCTGAGGCTCTGGG	0.706																																						dbGAP											0													33.0	31.0	32.0					3																	56716828		692	1591	2283	-	-	-	SO:0001819	synonymous_variant	0			AF180425	CCDS2877.1, CCDS46853.1	3p14.3	2011-09-14	2011-09-14	2011-09-14	ENSG00000163946	ENSG00000163946			30314	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 63"""	C3orf63		10470851, 11149944	Standard	NM_015224		Approved	se89-1, RAP140, KIAA1105	uc003die.4	Q9UK61	OTTHUMG00000158827	ENST00000493960.2:c.207C>T	3.37:g.56716828G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	A1L3A4|B5ME28|Q9H2F7|Q9UPP7	Silent	SNP	pfam_DUF3715	p.L69	ENST00000493960.2	37	c.207	CCDS46853.1	3																																																																																			FAM208A	-	NULL	ENSG00000163946		0.706	FAM208A-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	FAM208A	HGNC	protein_coding	OTTHUMT00000352352.2	49	0.00	0	G	NM_015224		56716828	56716828	-1	no_errors	ENST00000355628	ensembl	human	known	69_37n	silent	44	22.81	13	SNP	0.389	A
BRINP2	57795	genome.wustl.edu	37	1	177199036	177199037	+	Frame_Shift_Ins	INS	-	-	T			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr1:177199036_177199037insT	ENST00000361539.4	+	2	336_337	c.24_25insT	c.(25-27)tttfs	p.F9fs		NM_021165.2	NP_066988.1	Q9C0B6	BRNP2_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 2	9					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	extracellular region (GO:0005576)											GTGGCACTCGGTTTAGAGGGCT	0.668																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0				CCDS1320.1	1q24	2013-08-06	2013-08-06	2013-07-31	ENSG00000198797	ENSG00000198797			13746	protein-coding gene	gene with protein product			"""family with sequence similarity 5, member B"""	FAM5B		15193423	Standard	NM_021165		Approved	DBCCR1L2	uc001glf.3	Q9C0B6	OTTHUMG00000034953	ENST00000361539.4:c.27dupT	1.37:g.177199039_177199039dupT	ENSP00000354481:p.Phe9fs	Somatic		WXS	Illumina GAIIx	Phase_IV	O95560|Q6ZWC1|Q7LCZ9|Q8N360	Frame_Shift_Ins	INS	pfam_MACPF,smart_MACPF	p.R9fs	ENST00000361539.4	37	c.24_25	CCDS1320.1	1																																																																																			FAM5B	-	NULL	ENSG00000198797		0.668	BRINP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FAM5B	HGNC	protein_coding	OTTHUMT00000084599.1	22	0.00	0	-	NM_021165		177199036	177199037	+1	no_errors	ENST00000361539	ensembl	human	known	69_37n	frame_shift_ins	38	11.63	5	INS	0.497:0.446	T
FGFR1	2260	genome.wustl.edu	37	8	38271457	38271457	+	Silent	SNP	G	G	A	rs369782405		TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr8:38271457G>A	ENST00000447712.2	-	17	3212	c.2271C>T	c.(2269-2271)atC>atT	p.I757I	FGFR1_ENST00000397091.5_Silent_p.I755I|FGFR1_ENST00000341462.5_Silent_p.I757I|FGFR1_ENST00000397113.2_Silent_p.I755I|FGFR1_ENST00000397103.1_Silent_p.I668I|FGFR1_ENST00000356207.5_Silent_p.I668I|FGFR1_ENST00000397108.4_Silent_p.I755I|FGFR1_ENST00000532791.1_Silent_p.I755I|FGFR1_ENST00000425967.3_Silent_p.I788I|FGFR1_ENST00000326324.6_Silent_p.I666I|FGFR1_ENST00000335922.5_Silent_p.I747I	NM_001174063.1|NM_015850.3|NM_023110.2	NP_001167534.1|NP_056934.2|NP_075598.2	P11362	FGFR1_HUMAN	fibroblast growth factor receptor 1	757	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|auditory receptor cell development (GO:0060117)|axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell maturation (GO:0048469)|cell migration (GO:0016477)|chondrocyte differentiation (GO:0002062)|chordate embryonic development (GO:0043009)|embryonic limb morphogenesis (GO:0030326)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lung-associated mesenchyme development (GO:0060484)|MAPK cascade (GO:0000165)|mesenchymal cell differentiation (GO:0048762)|midbrain development (GO:0030901)|middle ear morphogenesis (GO:0042474)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|outer ear morphogenesis (GO:0042473)|paraxial mesoderm development (GO:0048339)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)|regulation of cell differentiation (GO:0045595)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of lateral mesodermal cell fate specification (GO:0048378)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ventricular zone neuroblast division (GO:0021847)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)		FGFR1/ZNF703(2)	breast(2)|central_nervous_system(7)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(18)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	50	all_cancers(2;9.05e-47)|all_epithelial(2;2.64e-50)|all_lung(3;1.71e-23)|Lung NSC(2;3.61e-23)|Colorectal(12;0.000442)	Breast(189;1.48e-05)|all_lung(54;0.00354)|Lung NSC(58;0.0138)|Hepatocellular(245;0.065)	Epithelial(3;3.96e-34)|all cancers(3;3.06e-30)|BRCA - Breast invasive adenocarcinoma(5;2.28e-21)|COAD - Colon adenocarcinoma(9;0.24)		Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	TCAAGGCCACGATGCGGTCCA	0.642		1	T	"""BCR, FOP, ZNF198, CEP1"""	"""MPD, NHL"""		"""Pfeiffer syndrome, Kallman syndrome"""																														Melanoma(146;1153 1840 21453 21841 43625)	dbGAP		Dom	yes		8	8p11.2-p11.1	2260	fibroblast growth factor receptor 1	yes	L	0													51.0	58.0	56.0					8																	38271457		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			M34185	CCDS6107.2, CCDS43730.1, CCDS43731.1, CCDS43732.1, CCDS55221.1, CCDS55222.1, CCDS55223.1	8p11.23-p11.22	2014-04-03	2008-08-01		ENSG00000077782	ENSG00000077782	2.7.10.1	"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3688	protein-coding gene	gene with protein product	"""Pfeiffer syndrome"""	136350	"""fms-related tyrosine kinase 2"""	FLT2, KAL2		2162671	Standard	NM_015850		Approved	H2, H3, H4, H5, CEK, FLG, BFGFR, N-SAM, CD331	uc011lbu.2	P11362	OTTHUMG00000147366	ENST00000447712.2:c.2271C>T	8.37:g.38271457G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	A8K6T9|A8K8V5|C1KBH8|P17049|Q02063|Q02065|Q14306|Q14307|Q53H63|Q59H40|Q5BJG2|Q8N685|Q9UD50|Q9UDF0|Q9UDF1|Q9UDF2	Silent	SNP	pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_cat_dom,pfam_Ig_I-set,pfam_Immunoglobulin,superfamily_Kinase-like_dom,smart_Ig_sub,smart_Ig_sub2,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pirsf_Tyr_kinase_fibroblast_GF_rcpt,pfscan_Prot_kinase_cat_dom,pfscan_Ig-like,prints_Ser-Thr/Tyr_kinase_cat_dom	p.I788	ENST00000447712.2	37	c.2364	CCDS6107.2	8																																																																																			FGFR1	-	superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,pirsf_Tyr_kinase_fibroblast_GF_rcpt,pfscan_Prot_kinase_cat_dom	ENSG00000077782		0.642	FGFR1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	FGFR1	HGNC	protein_coding		43	0.00	0	G			38271457	38271457	-1	no_errors	ENST00000425967	ensembl	human	known	69_37n	silent	16	42.86	12	SNP	0.027	A
GGNBP2	79893	genome.wustl.edu	37	17	34937779	34937779	+	Silent	SNP	C	C	T			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr17:34937779C>T	ENST00000304718.4	+	9	1342	c.1026C>T	c.(1024-1026)acC>acT	p.T342T		NM_024835.3	NP_079111.1	Q9H3C7	GGNB2_HUMAN	gametogenetin binding protein 2	342					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)	38		Breast(25;0.00957)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)		AATAGATGACCGTGGAAAAAG	0.388																																						dbGAP											0													74.0	78.0	76.0					17																	34937779		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF126964	CCDS11314.1	17q21.1	2014-05-06	2007-08-20	2007-08-20	ENSG00000005955	ENSG00000278311			19357	protein-coding gene	gene with protein product		612275	"""zinc finger protein 403"""	ZNF403		11728448	Standard	NM_024835		Approved	ZFP403, LZK1, FLJ22561, FLJ21230, DIF-3, DIF3	uc002hnb.3	Q9H3C7	OTTHUMG00000188440	ENST00000304718.4:c.1026C>T	17.37:g.34937779C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	B2RPK7|Q96T90|Q9GZR8|Q9H767	Silent	SNP	NULL	p.T342	ENST00000304718.4	37	c.1026	CCDS11314.1	17																																																																																			GGNBP2	-	NULL	ENSG00000005955		0.388	GGNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GGNBP2	HGNC	protein_coding	OTTHUMT00000256684.2	232	0.43	1	C	NM_024835		34937779	34937779	+1	no_errors	ENST00000304718	ensembl	human	known	69_37n	silent	182	23.53	56	SNP	1.000	T
GOLGA4	2803	genome.wustl.edu	37	3	37356982	37356982	+	Missense_Mutation	SNP	G	G	A			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr3:37356982G>A	ENST00000361924.2	+	11	1680	c.1306G>A	c.(1306-1308)Gaa>Aaa	p.E436K	GOLGA4_ENST00000435830.2_3'UTR|GOLGA4_ENST00000356847.4_Missense_Mutation_p.E458K|GOLGA4_ENST00000444882.1_Intron	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	436	Glu-rich.				Golgi to plasma membrane protein transport (GO:0043001)|protein targeting to Golgi (GO:0000042)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	GTPase binding (GO:0051020)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						ACTGAAGGCAGAAATGGATGA	0.378																																						dbGAP											0													99.0	99.0	99.0					3																	37356982		2203	4300	6503	-	-	-	SO:0001583	missense	0			U31906	CCDS2666.1, CCDS54564.1	3p22-p21.3	2010-02-12	2010-02-12		ENSG00000144674	ENSG00000144674			4427	protein-coding gene	gene with protein product	"""golgin 245"""	602509	"""golgi autoantigen, golgin subfamily a, 4"""			8626529	Standard	NM_002078		Approved	GOLG, GCP2, p230, golgin-240	uc003cgw.3	Q13439	OTTHUMG00000130799	ENST00000361924.2:c.1306G>A	3.37:g.37356982G>A	ENSP00000354486:p.Glu436Lys	Somatic		WXS	Illumina GAIIx	Phase_IV	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Missense_Mutation	SNP	pfam_GRIP,superfamily_GRIP,superfamily_tRNA-bd_arm,superfamily_t-SNARE,superfamily_Prefoldin,smart_GRIP,pfscan_GRIP	p.E436K	ENST00000361924.2	37	c.1306	CCDS2666.1	3	.	.	.	.	.	.	.	.	.	.	G	33	5.261043	0.95368	.	.	ENSG00000144674	ENST00000361924;ENST00000356847;ENST00000450863;ENST00000437131	T;T;T	0.26067	1.77;1.76;1.81	5.82	5.82	0.92795	.	0.000000	0.35936	N	0.002889	T	0.52058	0.1711	M	0.72479	2.2	0.47819	D	0.999521	D;D;D	0.89917	0.998;0.995;1.0	D;D;D	0.83275	0.994;0.922;0.996	T	0.40440	-0.9563	10	0.40728	T	0.16	.	18.2948	0.90141	0.0:0.0:1.0:0.0	.	436;458;436	Q13439-4;F8W8Q7;Q13439	.;.;GOGA4_HUMAN	K	436;458;441;307	ENSP00000354486:E436K;ENSP00000349305:E458K;ENSP00000405842:E307K	ENSP00000349305:E458K	E	+	1	0	GOLGA4	37331986	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.112000	0.64634	2.765000	0.95021	0.650000	0.86243	GAA	GOLGA4	-	NULL	ENSG00000144674		0.378	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	GOLGA4	HGNC	protein_coding	OTTHUMT00000253339.2	336	0.00	0	G	NM_002078		37356982	37356982	+1	no_errors	ENST00000361924	ensembl	human	known	69_37n	missense	295	16.67	59	SNP	1.000	A
HFE	3077	genome.wustl.edu	37	6	26092916	26092916	+	Missense_Mutation	SNP	C	C	T			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr6:26092916C>T	ENST00000357618.5	+	4	742	c.620C>T	c.(619-621)cCt>cTt	p.P207L	HFE_ENST00000353147.5_Missense_Mutation_p.P27L|HFE_ENST00000397022.3_Missense_Mutation_p.P184L|HFE_ENST00000470149.1_Intron|HFE_ENST00000352392.4_Intron|HFE_ENST00000461397.1_Intron|HFE_ENST00000349999.4_Missense_Mutation_p.P119L|HFE_ENST00000336625.8_Intron|HFE_ENST00000317896.7_Missense_Mutation_p.P115L|HFE_ENST00000488199.1_Intron|HFE_ENST00000309234.6_Missense_Mutation_p.P207L	NM_000410.3|NM_139006.2	NP_000401.1|NP_620575.1	Q30201	HFE_HUMAN	hemochromatosis	207	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular iron ion homeostasis (GO:0006879)|cellular response to iron ion starvation (GO:0010106)|female pregnancy (GO:0007565)|hormone biosynthetic process (GO:0042446)|immune response (GO:0006955)|iron ion import into cell (GO:0097459)|multicellular organismal iron ion homeostasis (GO:0060586)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protein complex assembly (GO:0006461)	apical part of cell (GO:0045177)|basal part of cell (GO:0045178)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|integral component of plasma membrane (GO:0005887)|MHC class I protein complex (GO:0042612)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	peptide antigen binding (GO:0042605)|receptor binding (GO:0005102)			endometrium(3)|large_intestine(3)|liver(2)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						TGTCAAGTGCCTCCTTTGGTG	0.502									Hemochromatosis																													dbGAP											0													166.0	155.0	159.0					6																	26092916		2203	4300	6503	-	-	-	SO:0001583	missense	0	Familial Cancer Database			CCDS4578.1, CCDS4579.1, CCDS4580.1, CCDS4581.1, CCDS4582.1, CCDS47386.1, CCDS47387.1, CCDS54974.1, CCDS54975.1, CCDS75412.1	6p21.3	2014-09-17			ENSG00000010704	ENSG00000010704		"""Immunoglobulin superfamily / C1-set domain containing"""	4886	protein-coding gene	gene with protein product	"""high Fe"""	613609				3460331	Standard	XR_241893		Approved	HLA-H	uc003nfx.1	Q30201	OTTHUMG00000016348	ENST00000357618.5:c.620C>T	6.37:g.26092916C>T	ENSP00000417404:p.Pro207Leu	Somatic		WXS	Illumina GAIIx	Phase_IV	B2CKL0|O75929|O75930|O75931|Q17RT0|Q96KU5|Q96KU6|Q96KU7|Q96KU8|Q9HC64|Q9HC68|Q9HC70|Q9HC83	Missense_Mutation	SNP	pfam_MHC_I_a_a1/a2,pfam_Ig_C1-set,superfamily_MHC_I/II-like_Ag-recog,smart_Ig_C1-set,prints_MHC_I_a_a1/a2,pfscan_Ig-like	p.P207L	ENST00000357618.5	37	c.620	CCDS4578.1	6	.	.	.	.	.	.	.	.	.	.	C	13.63	2.293228	0.40594	.	.	ENSG00000010704	ENST00000349999;ENST00000397022;ENST00000317896;ENST00000353147;ENST00000539147;ENST00000357618;ENST00000309234	T;T;T;T;T;T	0.04275	5.63;5.6;4.5;3.66;5.69;5.69	5.14	2.41	0.29592	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.329273	0.26421	N	0.024479	T	0.03520	0.0101	M	0.85373	2.75	0.27922	N	0.938197	B;B;P;B;P	0.52842	0.014;0.449;0.956;0.259;0.736	B;B;B;B;B	0.43251	0.012;0.154;0.413;0.089;0.141	T	0.24799	-1.0150	10	0.72032	D	0.01	.	5.6834	0.17788	0.0:0.6672:0.1597:0.1732	.	27;115;119;184;207	Q30201-6;Q30201-7;Q30201-2;Q30201-5;Q30201	.;.;.;.;HFE_HUMAN	L	119;184;115;27;102;207;207	ENSP00000259699:P119L;ENSP00000380217:P184L;ENSP00000313776:P115L;ENSP00000312342:P27L;ENSP00000417404:P207L;ENSP00000311698:P207L	ENSP00000311698:P207L	P	+	2	0	HFE	26200895	0.002000	0.14202	0.094000	0.20943	0.313000	0.28021	0.238000	0.18004	0.435000	0.26365	-0.834000	0.03071	CCT	HFE	-	pfscan_Ig-like	ENSG00000010704		0.502	HFE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	HFE	HGNC	protein_coding	OTTHUMT00000356133.1	213	0.47	1	C			26092916	26092916	+1	no_errors	ENST00000357618	ensembl	human	known	69_37n	missense	177	37.46	106	SNP	0.395	T
HP1BP3	50809	genome.wustl.edu	37	1	21097424	21097424	+	Splice_Site	SNP	T	T	A			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr1:21097424T>A	ENST00000312239.5	-	6	792	c.653A>T	c.(652-654)cAg>cTg	p.Q218L	HP1BP3_ENST00000375003.2_Splice_Site_p.Q66L	NM_016287.3	NP_057371.2	Q5SSJ5	HP1B3_HUMAN	heterochromatin protein 1, binding protein 3	218	H15 1. {ECO:0000255|PROSITE- ProRule:PRU00837}.				nucleosome assembly (GO:0006334)	nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(5)|prostate(2)|skin(2)|urinary_tract(1)	16		all_lung(284;6.55e-06)|Lung NSC(340;6.59e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.26e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00015)|GBM - Glioblastoma multiforme(114;0.000521)|Kidney(64;0.000529)|STAD - Stomach adenocarcinoma(196;0.00311)|KIRC - Kidney renal clear cell carcinoma(64;0.00687)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.201)		GTGTAATACCTGTTTGATGAC	0.328																																						dbGAP											0													152.0	144.0	147.0					1																	21097424		2203	4300	6503	-	-	-	SO:0001630	splice_region_variant	0			BC053327	CCDS30621.1	1p36.12	2008-02-05			ENSG00000127483	ENSG00000127483			24973	protein-coding gene	gene with protein product						12477932	Standard	NM_016287		Approved	HP1-BP74	uc001bdw.1	Q5SSJ5	OTTHUMG00000002622	ENST00000312239.5:c.654+1A>T	1.37:g.21097424T>A		Somatic		WXS	Illumina GAIIx	Phase_IV	A6NI71|A8K5D7|B3KMZ8|B4E210|Q05BI0|Q5SSJ6|Q5SWC6|Q6PIM9|Q8NDF0|Q9UHY0	Missense_Mutation	SNP	pfam_Histone_H1/H5,smart_Histone_H1/H5	p.Q218L	ENST00000312239.5	37	c.653	CCDS30621.1	1	.	.	.	.	.	.	.	.	.	.	T	24.4	4.526267	0.85600	.	.	ENSG00000127483	ENST00000312239;ENST00000375004;ENST00000375003;ENST00000419948;ENST00000438032;ENST00000424732	T;T;T;T;T	0.26810	1.71;1.71;1.71;1.71;1.71	6.16	6.16	0.99307	Histone H1/H5 (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.50171	0.1600	M	0.62209	1.925	0.80722	D	1	D;D	0.69078	0.997;0.969	D;D	0.79784	0.993;0.968	T	0.48937	-0.8990	10	0.72032	D	0.01	-12.4415	16.8061	0.85666	0.0:0.0:0.0:1.0	.	180;218	Q5SSJ5-2;Q5SSJ5	.;HP1B3_HUMAN	L	218;180;66;104;218;180	ENSP00000312625:Q218L;ENSP00000364142:Q66L;ENSP00000391721:Q104L;ENSP00000403039:Q218L;ENSP00000402754:Q180L	ENSP00000312625:Q218L	Q	-	2	0	HP1BP3	20970011	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	6.078000	0.71282	2.367000	0.80283	0.528000	0.53228	CAG	HP1BP3	-	pfam_Histone_H1/H5,smart_Histone_H1/H5	ENSG00000127483		0.328	HP1BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HP1BP3	HGNC	protein_coding	OTTHUMT00000007457.2	434	0.00	0	T	NM_016287	Missense_Mutation	21097424	21097424	-1	no_errors	ENST00000312239	ensembl	human	known	69_37n	missense	260	31.22	118	SNP	1.000	A
ITGA10	8515	genome.wustl.edu	37	1	145539030	145539030	+	Silent	SNP	C	C	T			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr1:145539030C>T	ENST00000369304.3	+	25	3145	c.2970C>T	c.(2968-2970)ctC>ctT	p.L990L	RP11-315I20.3_ENST00000415065.2_RNA|ITGA10_ENST00000538811.1_Silent_p.L859L|ITGA10_ENST00000539363.1_Silent_p.L847L	NM_003637.3	NP_003628.2	O75578	ITA10_HUMAN	integrin, alpha 10	990					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	integrin alpha10-beta1 complex (GO:0034680)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					TCTCAGCCCTCCTTCCAGCTG	0.522																																						dbGAP											0													115.0	107.0	110.0					1																	145539030		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF074015	CCDS72869.1	1q21.1	2010-03-23			ENSG00000143127	ENSG00000143127		"""Integrins"""	6135	protein-coding gene	gene with protein product		604042				9685391, 10702680	Standard	NM_003637		Approved		uc001eoa.3	O75578	OTTHUMG00000013751	ENST00000369304.3:c.2970C>T	1.37:g.145539030C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	B2RAM4|B2RTV5|Q6UXJ6|Q9UHZ8	Silent	SNP	pfam_Integrin_alpha-2,pfam_VWF_A,pfam_FG-GAP,smart_Int_alpha_beta-p,smart_VWF_A,pfscan_VWF_A,prints_Integrin_alpha	p.L990	ENST00000369304.3	37	c.2970	CCDS918.1	1																																																																																			ITGA10	-	pfam_Integrin_alpha-2	ENSG00000143127		0.522	ITGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ITGA10	HGNC	protein_coding	OTTHUMT00000038537.2	150	0.00	0	C	NM_003637		145539030	145539030	+1	no_errors	ENST00000369304	ensembl	human	known	69_37n	silent	190	28.84	77	SNP	0.992	T
LRP4	4038	genome.wustl.edu	37	11	46896381	46896381	+	Missense_Mutation	SNP	T	T	C			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr11:46896381T>C	ENST00000378623.1	-	28	4441	c.4199A>G	c.(4198-4200)tAt>tGt	p.Y1400C	LRP4-AS1_ENST00000502049.2_RNA|LRP4-AS1_ENST00000531719.1_RNA	NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	1400					dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)			breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		ATCTGTGTAATAGACCTTTCC	0.493																																						dbGAP											0													138.0	115.0	123.0					11																	46896381		2201	4299	6500	-	-	-	SO:0001583	missense	0			AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"""Low density lipoprotein receptors"""	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.4199A>G	11.37:g.46896381T>C	ENSP00000367888:p.Tyr1400Cys	Somatic		WXS	Illumina GAIIx	Phase_IV	B2RN39|Q4AC85|Q5KTZ5	Missense_Mutation	SNP	pfam_LDLR_classB_rpt,pfam_LDrepeatLR_classA_rpt,pfam_EGF-like_Ca-bd,superfamily_Growth_fac_rcpt,superfamily_LDrepeatLR_classA_rpt,smart_LDrepeatLR_classA_rpt,smart_EGF-like,smart_EGF-like_Ca-bd,smart_LDLR_classB_rpt,pfscan_LDrepeatLR_classA_rpt,pfscan_LDLR_classB_rpt	p.Y1400C	ENST00000378623.1	37	c.4199	CCDS31478.1	11	.	.	.	.	.	.	.	.	.	.	T	21.6	4.179909	0.78564	.	.	ENSG00000134569	ENST00000378623	D	0.99304	-5.72	5.67	5.67	0.87782	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	D	0.99324	0.9763	M	0.73598	2.24	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.99250	1.0887	10	0.87932	D	0	.	15.924	0.79597	0.0:0.0:0.0:1.0	.	1400	O75096	LRP4_HUMAN	C	1400	ENSP00000367888:Y1400C	ENSP00000367888:Y1400C	Y	-	2	0	LRP4	46852957	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.026000	0.88783	2.163000	0.67991	0.459000	0.35465	TAT	LRP4	-	pfam_LDLR_classB_rpt,smart_LDLR_classB_rpt,pfscan_LDLR_classB_rpt	ENSG00000134569		0.493	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LRP4	HGNC	protein_coding	OTTHUMT00000391133.1	98	0.00	0	T	NM_002334		46896381	46896381	-1	no_errors	ENST00000378623	ensembl	human	known	69_37n	missense	62	47.01	55	SNP	1.000	C
MYO15A	51168	genome.wustl.edu	37	17	18065989	18065989	+	Missense_Mutation	SNP	T	T	C			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr17:18065989T>C	ENST00000205890.5	+	58	9946	c.9608T>C	c.(9607-9609)aTg>aCg	p.M3203T	MYO15A_ENST00000451725.2_Missense_Mutation_p.M95T|MYO15A_ENST00000418233.3_Missense_Mutation_p.M467T	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	3203	MyTH4 2. {ECO:0000255|PROSITE- ProRule:PRU00359}.|Tail.				inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					CTTCGGGCCATGTTGGTGAGC	0.602																																						dbGAP											0													35.0	36.0	35.0					17																	18065989		1947	4143	6090	-	-	-	SO:0001583	missense	0			AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"""Myosins / Myosin superfamily : Class XV"""	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.9608T>C	17.37:g.18065989T>C	ENSP00000205890:p.Met3203Thr	Somatic		WXS	Illumina GAIIx	Phase_IV	B4DFC7	Missense_Mutation	SNP	pfam_Myosin_head_motor_dom,pfam_MyTH4_dom,pfam_SH3_2,pfam_FERM_central,pfam_IQ_motif_EF-hand-BS,superfamily_FERM_central,superfamily_SH3_domain,smart_Myosin_head_motor_dom,smart_IQ_motif_EF-hand-BS,smart_MyTH4_dom,smart_SH3_domain,smart_Band_41_domain,pfscan_FERM_domain,pfscan_IQ_motif_EF-hand-BS,pfscan_MyTH4_dom,prints_Myosin_head_motor_dom	p.M3203T	ENST00000205890.5	37	c.9608	CCDS42271.1	17	.	.	.	.	.	.	.	.	.	.	T	16.09	3.024060	0.54683	.	.	ENSG00000091536	ENST00000205890;ENST00000418233;ENST00000557190;ENST00000451725	D;D	0.91068	-2.78;-2.78	4.94	4.94	0.65067	MyTH4 domain (3);	.	.	.	.	D	0.87394	0.6166	N	0.11560	0.145	0.54753	D	0.999987	B;P;P;D;D;D	0.58620	0.168;0.833;0.741;0.959;0.967;0.983	B;P;B;B;P;P	0.54270	0.18;0.601;0.348;0.412;0.634;0.747	D	0.89846	0.4006	9	0.62326	D	0.03	.	14.5933	0.68386	0.0:0.0:0.0:1.0	.	95;192;467;3203;125;210	B4DQJ3;B4DLV9;B4DFC7;Q9UKN7;Q7Z382;Q8TCK0	.;.;.;MYO15_HUMAN;.;.	T	3203;192;95;95	ENSP00000205890:M3203T;ENSP00000409098:M95T	ENSP00000205890:M3203T	M	+	2	0	MYO15A	18006714	1.000000	0.71417	1.000000	0.80357	0.737000	0.42083	7.851000	0.86920	1.854000	0.53819	0.374000	0.22700	ATG	MYO15A	-	pfam_MyTH4_dom,smart_MyTH4_dom,pfscan_MyTH4_dom	ENSG00000091536		0.602	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MYO15A	HGNC	protein_coding	OTTHUMT00000132048.1	41	0.00	0	T	NM_016239		18065989	18065989	+1	no_errors	ENST00000205890	ensembl	human	known	69_37n	missense	34	27.66	13	SNP	1.000	C
PIK3R1	5295	genome.wustl.edu	37	5	67591111	67591112	+	In_Frame_Ins	INS	-	-	GAC			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr5:67591111_67591112insGAC	ENST00000521381.1	+	13	2320_2321	c.1704_1705insGAC	c.(1705-1707)gac>GACgac	p.569_569D>DD	PIK3R1_ENST00000523872.1_In_Frame_Ins_p.206_206D>DD|PIK3R1_ENST00000274335.5_In_Frame_Ins_p.569_569D>DD|PIK3R1_ENST00000336483.5_In_Frame_Ins_p.299_299D>DD|PIK3R1_ENST00000396611.1_In_Frame_Ins_p.569_569D>DD|PIK3R1_ENST00000320694.8_In_Frame_Ins_p.269_269D>DD|PIK3R1_ENST00000521657.1_In_Frame_Ins_p.569_569D>DD	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	569					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.K567_L570delKPDL(1)|p.K267_L270delKPDL(1)|p.0?(1)|p.?(1)|p.K297_L300delKPDL(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	GCATTAAACCAGACCTTATCCA	0.371			"""Mis, F, O"""		"""gliobastoma, ovarian, colorectal"""					TCGA GBM(4;<1E-08)																												dbGAP		Rec	yes		5	5q13.1	5295	"""phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"""		"""E, O"""	5	Deletion - In frame(3)|Whole gene deletion(1)|Unknown(1)	breast(3)|large_intestine(1)|lung(1)																																								-	-	-	SO:0001652	inframe_insertion	0			M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"""SH2 domain containing"""	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.1705_1707dupGAC	5.37:g.67591112_67591114dupGAC	ENSP00000428056:p.Asp569dup	Somatic		WXS	Illumina GAIIx	Phase_IV	B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	In_Frame_Ins	INS	pfam_SH2,pfam_RhoGAP_dom,pfam_SH3_2,superfamily_Rho_GTPase_activation_prot,superfamily_SH3_domain,superfamily_Guanylate-bd_C,smart_SH3_domain,smart_RhoGAP_dom,smart_SH2,pfscan_SH2,pfscan_SH3_domain,pfscan_RhoGAP_dom,prints_PI3kinase_P85,prints_SH2	p.569in_frame_insD	ENST00000521381.1	37	c.1704_1705	CCDS3993.1	5																																																																																			PIK3R1	-	prints_PI3kinase_P85	ENSG00000145675		0.371	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PIK3R1	HGNC	protein_coding	OTTHUMT00000254013.2	316	0.00	0	-	NM_181504		67591111	67591112	+1	no_errors	ENST00000396611	ensembl	human	known	69_37n	in_frame_ins	274	30.98	123	INS	0.152:1.000	GAC
PCDHA2	56146	genome.wustl.edu	37	5	140176351	140176351	+	Missense_Mutation	SNP	C	C	T			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr5:140176351C>T	ENST00000526136.1	+	1	1802	c.1802C>T	c.(1801-1803)tCa>tTa	p.S601L	PCDHA2_ENST00000520672.2_Missense_Mutation_p.S601L|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000378132.1_Missense_Mutation_p.S601L|PCDHA1_ENST00000394633.3_Intron	NM_018905.2	NP_061728.1	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2	601	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(16)|lung(26)|ovary(4)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GACGCTGACTCAGGCTACAAC	0.657																																						dbGAP											0													159.0	143.0	148.0					5																	140176351		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF152480	CCDS54914.1, CCDS64269.1	5q31	2010-11-26				ENSG00000204969		"""Cadherins / Protocadherins : Clustered"""	8668	other	complex locus constituent	"""KIAA0345-like 12"""	606308				10380929	Standard	NM_018905		Approved			Q9Y5H9		ENST00000526136.1:c.1802C>T	5.37:g.140176351C>T	ENSP00000431748:p.Ser601Leu	Somatic		WXS	Illumina GAIIx	Phase_IV	O75287|Q9BTV3	Missense_Mutation	SNP	pfam_Cadherin,pfam_Cadherin_N,superfamily_Cadherin-like,smart_Cadherin,prints_Cadherin,pfscan_Cadherin	p.S601L	ENST00000526136.1	37	c.1802	CCDS54914.1	5	.	.	.	.	.	.	.	.	.	.	c	14.12	2.441995	0.43326	.	.	ENSG00000204969	ENST00000520672;ENST00000378132;ENST00000526136	T;T;T	0.49432	0.78;0.78;0.78	3.91	3.91	0.45181	Cadherin (4);Cadherin-like (1);	0.205133	0.24061	U	0.041912	T	0.71134	0.3304	M	0.84433	2.695	0.09310	N	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.74023	0.969;0.982;0.969	T	0.66594	-0.5884	10	0.87932	D	0	.	15.9633	0.79948	0.0:1.0:0.0:0.0	.	601;601;601	Q9Y5H9-3;Q9Y5H9;Q9Y5H9-2	.;PCDA2_HUMAN;.	L	601	ENSP00000430584:S601L;ENSP00000367372:S601L;ENSP00000431748:S601L	ENSP00000367372:S601L	S	+	2	0	PCDHA2	140156535	0.070000	0.21116	0.604000	0.28916	0.447000	0.32167	3.617000	0.54181	1.917000	0.55516	0.549000	0.68633	TCA	PCDHA2	-	pfam_Cadherin,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin	ENSG00000204969		0.657	PCDHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PCDHA2	HGNC	protein_coding	OTTHUMT00000372877.3	88	0.00	0	C	NM_018905		140176351	140176351	+1	no_errors	ENST00000526136	ensembl	human	known	69_37n	missense	121	13.57	19	SNP	0.121	T
PLCD4	84812	genome.wustl.edu	37	2	219492900	219492900	+	Silent	SNP	C	C	T			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr2:219492900C>T	ENST00000450993.2	+	7	1260	c.921C>T	c.(919-921)acC>acT	p.T307T	PLCD4_ENST00000417849.1_Silent_p.T307T|PLCD4_ENST00000432688.1_Silent_p.T307T	NM_032726.3	NP_116115.1	Q9BRC7	PLCD4_HUMAN	phospholipase C, delta 4	307	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				acrosome reaction (GO:0007340)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phosphatidylinositol metabolic process (GO:0046488)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(3)|prostate(1)|urinary_tract(3)	23		Renal(207;0.0915)		Epithelial(149;5.11e-07)|all cancers(144;0.000104)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		CTCATAACACCTACCTAGTGG	0.527																																						dbGAP											0													166.0	161.0	162.0					2																	219492900		2024	4185	6209	-	-	-	SO:0001819	synonymous_variant	0			AI366170	CCDS46516.1	2q35	2013-01-10			ENSG00000115556	ENSG00000115556	3.1.4.11	"""EF-hand domain containing"""	9062	protein-coding gene	gene with protein product		605939				10702683, 9056492	Standard	NM_032726		Approved		uc021vwx.1	Q9BRC7	OTTHUMG00000154743	ENST00000450993.2:c.921C>T	2.37:g.219492900C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q53FS8	Silent	SNP	pfam_PLipase_C_PInositol-sp_X_dom,pfam_PLipase_C_Pinositol-sp_Y,pfam_PLipase_C_EF-hand-like,pfam_C2_Ca-dep,superfamily_PLC-like_Pdiesterase_TIM-brl,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_Pleckstrin_homology,smart_EF_hand_Ca-bd,smart_PLipase_C_PInositol-sp_X_dom,smart_PLipase_C_Pinositol-sp_Y,smart_C2_Ca-dep,pfscan_EF_HAND_2,pfscan_C2_membr_targeting,pfscan_Pleckstrin_homology,pfscan_PLipase_C_PInositol-sp_X_dom,pfscan_PLipase_C_Pinositol-sp_Y,prints_Pinositol_PLipase_C	p.T307	ENST00000450993.2	37	c.921	CCDS46516.1	2																																																																																			PLCD4	-	pfam_PLipase_C_PInositol-sp_X_dom,superfamily_PLC-like_Pdiesterase_TIM-brl,smart_PLipase_C_PInositol-sp_X_dom,pfscan_PLipase_C_PInositol-sp_X_dom,prints_Pinositol_PLipase_C	ENSG00000115556		0.527	PLCD4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	PLCD4	HGNC	protein_coding	OTTHUMT00000336876.1	232	0.00	0	C			219492900	219492900	+1	no_errors	ENST00000417849	ensembl	human	known	69_37n	silent	152	30.59	67	SNP	0.990	T
PPP4R2	151987	genome.wustl.edu	37	3	73096423	73096423	+	Missense_Mutation	SNP	G	G	C			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr3:73096423G>C	ENST00000356692.5	+	3	456	c.203G>C	c.(202-204)aGa>aCa	p.R68T	PPP4R2_ENST00000394284.3_Intron|PPP4R2_ENST00000295862.9_Missense_Mutation_p.R12T			Q9NY27	PP4R2_HUMAN	protein phosphatase 4, regulatory subunit 2	68					cellular protein modification process (GO:0006464)|hematopoietic progenitor cell differentiation (GO:0002244)|mRNA processing (GO:0006397)|regulation of catalytic activity (GO:0050790)|regulation of double-strand break repair via homologous recombination (GO:0010569)|RNA splicing (GO:0008380)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein phosphatase 4 complex (GO:0030289)	protein binding, bridging (GO:0030674)|protein phosphatase type 4 regulator activity (GO:0030362)			breast(2)|endometrium(1)|large_intestine(1)|lung(3)|skin(2)|stomach(1)|urinary_tract(2)	12		Prostate(10;0.0187)|Lung SC(41;0.236)		Epithelial(33;1.76e-07)|BRCA - Breast invasive adenocarcinoma(55;9.42e-05)|LUSC - Lung squamous cell carcinoma(21;0.00211)|Lung(16;0.00643)|KIRC - Kidney renal clear cell carcinoma(39;0.0164)|Kidney(39;0.0193)|OV - Ovarian serous cystadenocarcinoma(275;0.031)		CCTGAGCCAAGAGGTCCTCCC	0.363																																						dbGAP											0													43.0	45.0	44.0					3																	73096423		2202	4297	6499	-	-	-	SO:0001583	missense	0			AJ271448	CCDS2917.1	3q29	2010-06-18			ENSG00000163605	ENSG00000163605		"""Serine/threonine phosphatases / Protein phosphatase 4, regulatory subunits"""	18296	protein-coding gene	gene with protein product		613822				10769191	Standard	NM_174907		Approved		uc003dph.1	Q9NY27	OTTHUMG00000158816	ENST00000356692.5:c.203G>C	3.37:g.73096423G>C	ENSP00000349124:p.Arg68Thr	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K1I6|Q2TAJ9|Q498B8|Q8WXX6	Missense_Mutation	SNP	pfam_PPP4R2	p.R68T	ENST00000356692.5	37	c.203	CCDS2917.1	3	.	.	.	.	.	.	.	.	.	.	G	25.3	4.626899	0.87560	.	.	ENSG00000163605	ENST00000356692;ENST00000488810;ENST00000295862;ENST00000476505	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.67211	0.2869	M	0.73962	2.25	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.70230	-0.4929	10	0.87932	D	0	.	19.3579	0.94422	0.0:0.0:1.0:0.0	.	68	Q9NY27	PP4R2_HUMAN	T	68;68;12;30	ENSP00000349124:R68T;ENSP00000418750:R68T;ENSP00000295862:R12T;ENSP00000420098:R30T	ENSP00000295862:R12T	R	+	2	0	PPP4R2	73179113	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.700000	0.98707	2.576000	0.86940	0.557000	0.71058	AGA	PPP4R2	-	pfam_PPP4R2	ENSG00000163605		0.363	PPP4R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PPP4R2	HGNC	protein_coding	OTTHUMT00000352321.1	198	0.00	0	G	NM_174907		73096423	73096423	+1	no_errors	ENST00000356692	ensembl	human	known	69_37n	missense	190	22.13	54	SNP	1.000	C
PROM2	150696	genome.wustl.edu	37	2	95944749	95944749	+	Silent	SNP	G	G	A			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr2:95944749G>A	ENST00000317620.9	+	10	1264	c.1131G>A	c.(1129-1131)gtG>gtA	p.V377V	PROM2_ENST00000542147.1_Silent_p.V377V|PROM2_ENST00000403131.2_Silent_p.V377V|PROM2_ENST00000317668.4_Silent_p.V377V	NM_001165978.1	NP_001159450.1	Q8N271	PROM2_HUMAN	prominin 2	377					negative regulation of caveolin-mediated endocytosis (GO:2001287)|negative regulation of pinocytosis (GO:0048550)|positive regulation of cell projection organization (GO:0031346)|positive regulation of protein phosphorylation (GO:0001934)|regulation of Cdc42 GTPase activity (GO:0043088)	cell projection (GO:0042995)|cell surface (GO:0009986)|cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|microspike (GO:0044393)|microvillus (GO:0005902)|prominosome (GO:0071914)	cholesterol binding (GO:0015485)	p.V377V(1)		breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(12)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	32						AGAAGGCAGTGGCCCAGCAGC	0.642																																						dbGAP											1	Substitution - coding silent(1)	lung(1)											37.0	41.0	39.0					2																	95944749		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF245303	CCDS2012.1	2q11.1	2008-02-05			ENSG00000155066	ENSG00000155066			20685	protein-coding gene	gene with protein product						12514187	Standard	NM_001165978		Approved		uc002sui.3	Q8N271	OTTHUMG00000130393	ENST00000317620.9:c.1131G>A	2.37:g.95944749G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	A8K2V1|Q2HIX6|Q8NB84|Q8TAE2	Silent	SNP	pfam_Prominin	p.V377	ENST00000317620.9	37	c.1131	CCDS2012.1	2																																																																																			PROM2	-	pfam_Prominin	ENSG00000155066		0.642	PROM2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	PROM2	HGNC	protein_coding	OTTHUMT00000252771.1	24	0.00	0	G	NM_144707		95944749	95944749	+1	no_errors	ENST00000317620	ensembl	human	known	69_37n	silent	12	40.00	8	SNP	0.387	A
RAP1GAP	5909	genome.wustl.edu	37	1	21928254	21928254	+	Silent	SNP	G	G	A			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr1:21928254G>A	ENST00000374765.4	-	20	1775	c.1575C>T	c.(1573-1575)agC>agT	p.S525S	RAP1GAP_ENST00000542643.2_Silent_p.S551S|RAP1GAP_ENST00000374761.2_Silent_p.S556S|RAP1GAP_ENST00000290101.4_Silent_p.S589S|RAP1GAP_ENST00000374763.2_Silent_p.S610S	NM_002885.2	NP_002876.2	P47736	RPGP1_HUMAN	RAP1 GTPase activating protein	525					GTP catabolic process (GO:0006184)|positive regulation of Rap GTPase activity (GO:0032854)|regulation of Ras GTPase activity (GO:0032318)|signal transduction (GO:0007165)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|protein homodimerization activity (GO:0042803)|Rap GTPase activator activity (GO:0046582)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	17		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.000861)|all_lung(284;0.000901)|Breast(348;0.012)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;2.3e-26)|COAD - Colon adenocarcinoma(152;1.59e-05)|GBM - Glioblastoma multiforme(114;2.7e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000354)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00862)|READ - Rectum adenocarcinoma(331;0.0625)|Lung(427;0.146)		AGACGTGCCCGCTGTCTGGGG	0.667																																						dbGAP											0													70.0	65.0	67.0					1																	21928254		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			BC054490	CCDS218.1, CCDS53276.1, CCDS53277.1	1p36.1-p35	2009-09-14	2006-04-12	2006-04-12	ENSG00000076864	ENSG00000076864			9858	protein-coding gene	gene with protein product		600278	"""RAP1, GTPase activating protein 1"""	RAP1GA1		1904317	Standard	NM_001145657		Approved	KIAA0474, RAP1GAP1, RAP1GAPII	uc001bew.3	P47736	OTTHUMG00000007513	ENST00000374765.4:c.1575C>T	1.37:g.21928254G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	J3QSS6|O75062|Q5T3S9|Q5T3T4|Q7Z5S8|Q9UQ51	Silent	SNP	pfam_Rap_GAP,pfam_GoLoco_motif,smart_GoLoco_motif,pfscan_GoLoco_motif,pfscan_Rap_GAP	p.S589	ENST00000374765.4	37	c.1767	CCDS218.1	1																																																																																			RAP1GAP	-	NULL	ENSG00000076864		0.667	RAP1GAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	RAP1GAP	HGNC	protein_coding	OTTHUMT00000019759.2	60	0.00	0	G	NM_002885		21928254	21928254	-1	no_errors	ENST00000290101	ensembl	human	known	69_37n	silent	57	26.58	21	SNP	0.998	A
ROS1	6098	genome.wustl.edu	37	6	117710620	117710620	+	Missense_Mutation	SNP	G	G	A			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr6:117710620G>A	ENST00000368508.3	-	12	1850	c.1652C>T	c.(1651-1653)tCc>tTc	p.S551F	ROS1_ENST00000368507.3_Missense_Mutation_p.S560F|GOPC_ENST00000467125.1_Intron	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	551					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)		CAGCTGGGAGGATGAGCCAAA	0.512			T	"""GOPC, SDC4, SLC34A2, EZR, LRIG3"""	"""glioblastoma, NSCLC"""																																	dbGAP		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"""O, E"""	0													102.0	106.0	104.0					6																	117710620		2203	4300	6503	-	-	-	SO:0001583	missense	0			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.1652C>T	6.37:g.117710620G>A	ENSP00000357494:p.Ser551Phe	Somatic		WXS	Illumina GAIIx	Phase_IV	Q15368|Q5TDB5	Missense_Mutation	SNP	pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Fibronectin_type3,pfam_Prot_kinase_cat_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,prints_Ser-Thr/Tyr_kinase_cat_dom,pfscan_Fibronectin_type3,pfscan_Prot_kinase_cat_dom	p.S551F	ENST00000368508.3	37	c.1652	CCDS5116.1	6	.	.	.	.	.	.	.	.	.	.	G	9.435	1.086550	0.20390	.	.	ENSG00000047936	ENST00000368508;ENST00000368507	T;T	0.74421	-0.84;-0.77	5.27	2.27	0.28462	.	0.916467	0.09254	N	0.827444	T	0.41351	0.1155	N	0.24115	0.695	0.21802	N	0.999534	B	0.13145	0.007	B	0.11329	0.006	T	0.45220	-0.9276	10	0.72032	D	0.01	.	8.3263	0.32158	0.0858:0.0:0.7178:0.1964	.	551	P08922	ROS1_HUMAN	F	551;560	ENSP00000357494:S551F;ENSP00000357493:S560F	ENSP00000357493:S560F	S	-	2	0	ROS1	117817313	0.267000	0.24122	0.001000	0.08648	0.529000	0.34654	2.600000	0.46240	0.493000	0.27837	0.561000	0.74099	TCC	ROS1	-	NULL	ENSG00000047936		0.512	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ROS1	HGNC	protein_coding	OTTHUMT00000043464.1	153	0.65	1	G			117710620	117710620	-1	no_errors	ENST00000368508	ensembl	human	known	69_37n	missense	133	12.50	19	SNP	0.014	A
SEMA6A	57556	genome.wustl.edu	37	5	115823840	115823842	+	In_Frame_Del	DEL	GAA	GAA	-			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	GAA	GAA					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr5:115823840_115823842delGAA	ENST00000343348.6	-	9	1493_1495	c.706_708delTTC	c.(706-708)ttcdel	p.F236del	SEMA6A_ENST00000510263.1_In_Frame_Del_p.F236del|SEMA6A_ENST00000257414.8_In_Frame_Del_p.F236del|CTB-118N6.3_ENST00000508640.1_RNA|SEMA6A_ENST00000503962.1_5'Flank|CTB-118N6.3_ENST00000510682.1_RNA|CTB-118N6.3_ENST00000514214.1_RNA	NM_020796.3	NP_065847	Q9H2E6	SEM6A_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	236	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|centrosome localization (GO:0051642)|cytoskeleton organization (GO:0007010)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|organ morphogenesis (GO:0009887)|positive regulation of neuron migration (GO:2001224)|semaphorin-plexin signaling pathway (GO:0071526)	axon (GO:0030424)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31		all_cancers(142;0.00316)|all_epithelial(76;5.71e-05)|Prostate(80;0.00845)|Ovarian(225;0.0796)|Lung NSC(810;0.171)|all_lung(232;0.203)		OV - Ovarian serous cystadenocarcinoma(64;1.59e-08)|Epithelial(69;2e-08)|all cancers(49;5.7e-08)|COAD - Colon adenocarcinoma(49;0.151)		CTATTTCCCTGAAGAAGAAGTAG	0.414																																						dbGAP											0																																										-	-	-	SO:0001651	inframe_deletion	0			AB037789	CCDS47256.1, CCDS75288.1	5q23.1	2014-07-29			ENSG00000092421			"""Semaphorins"""	10738	protein-coding gene	gene with protein product	"""sema VIa"""	605885		SEMAQ		9204478, 10993894	Standard	XM_006714663		Approved	KIAA1368, SEMA6A1, SEMA, HT018	uc010jck.3	Q9H2E6	OTTHUMG00000162987	ENST00000343348.6:c.706_708delTTC	5.37:g.115823846_115823848delGAA	ENSP00000345512:p.Phe236del	Somatic		WXS	Illumina GAIIx	Phase_IV	Q9P2H9	In_Frame_Del	DEL	pfam_Semaphorin/CD100_Ag,pfam_Plexin_repeat,superfamily_Semaphorin/CD100_Ag,superfamily_Plexin-like_fold,smart_Semaphorin/CD100_Ag,smart_Plexin-like,pfscan_Semaphorin/CD100_Ag	p.F236in_frame_del	ENST00000343348.6	37	c.708_706	CCDS47256.1	5																																																																																			SEMA6A	-	pfam_Semaphorin/CD100_Ag,superfamily_Semaphorin/CD100_Ag,smart_Semaphorin/CD100_Ag,pfscan_Semaphorin/CD100_Ag	ENSG00000092421		0.414	SEMA6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SEMA6A	HGNC	protein_coding	OTTHUMT00000371270.1	250	0.00	0	GAA	NM_020796		115823840	115823842	-1	no_errors	ENST00000257414	ensembl	human	known	69_37n	in_frame_del	261	29.66	113	DEL	1.000:1.000:1.000	-
SETD1A	9739	genome.wustl.edu	37	16	30977152	30977152	+	Silent	SNP	T	T	A			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr16:30977152T>A	ENST00000262519.8	+	8	2636	c.1950T>A	c.(1948-1950)ccT>ccA	p.P650P		NM_014712.1	NP_055527.1	O15047	SET1A_HUMAN	SET domain containing 1A	650	Pro-rich. {ECO:0000255}.				histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(21)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	59						CCCCACCTCCTCCACCACCCC	0.622																																						dbGAP											0													41.0	40.0	41.0					16																	30977152		2197	4300	6497	-	-	-	SO:0001819	synonymous_variant	0			AB002337	CCDS32435.1	16p11.2	2013-02-12			ENSG00000099381	ENSG00000099381		"""Chromatin-modifying enzymes / K-methyltransferases"", ""RNA binding motif (RRM) containing"""	29010	protein-coding gene	gene with protein product		611052				9205841, 12670868	Standard	XM_005255723		Approved	KIAA0339, Set1, KMT2F	uc002ead.1	O15047	OTTHUMG00000150474	ENST00000262519.8:c.1950T>A	16.37:g.30977152T>A		Somatic		WXS	Illumina GAIIx	Phase_IV	A6NP62|Q6PIF3|Q8TAJ6	Silent	SNP	pfam_COMPASS_Set1_N-SET,pfam_SET_dom,pfam_RRM_dom,smart_RRM_dom,smart_SET_dom,smart_Post-SET_dom,pfscan_SET_dom,pfscan_Post-SET_dom,pfscan_RRM_dom	p.P650	ENST00000262519.8	37	c.1950	CCDS32435.1	16																																																																																			SETD1A	-	NULL	ENSG00000099381		0.622	SETD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SETD1A	HGNC	protein_coding	OTTHUMT00000318244.2	98	0.00	0	T	NM_014712		30977152	30977152	+1	no_errors	ENST00000262519	ensembl	human	known	69_37n	silent	96	25.00	32	SNP	1.000	A
SLC22A25	387601	genome.wustl.edu	37	11	62996780	62996780	+	Silent	SNP	G	G	A			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr11:62996780G>A	ENST00000306494.6	-	1	344	c.345C>T	c.(343-345)ccC>ccT	p.P115P	SLC22A10_ENST00000535888.1_Intron|SLC22A25_ENST00000403374.2_5'Flank|SLC22A10_ENST00000525620.1_Intron	NM_199352.3	NP_955384.3			solute carrier family 22, member 25											NS(2)|breast(2)|endometrium(4)|kidney(2)|large_intestine(7)|lung(7)|ovary(3)|skin(7)	34						CATCCACACAGGGCTCTGTAT	0.517																																						dbGAP											0													139.0	122.0	128.0					11																	62996780		2201	4298	6499	-	-	-	SO:0001819	synonymous_variant	0			AY437532	CCDS31592.1	11q12.3	2014-05-20			ENSG00000196600	ENSG00000196600		"""Solute carriers"""	32935	protein-coding gene	gene with protein product		610792	"""MGI:2442751, MGI:2385316, MGI:3042283, MGI:3645714, MGI:3605624, MGI:2442750"""			17714910	Standard	NM_199352		Approved	UST6, HIMTP, MGC120420	uc001nwr.1	Q6T423	OTTHUMG00000165340	ENST00000306494.6:c.345C>T	11.37:g.62996780G>A		Somatic		WXS	Illumina GAIIx	Phase_IV		Silent	SNP	pfam_MFS,pfam_Sub_transporter,superfamily_MFS_dom_general_subst_transpt,pfscan_MFS_dom	p.P115	ENST00000306494.6	37	c.345	CCDS31592.1	11																																																																																			SLC22A25	-	pfscan_MFS_dom	ENSG00000196600		0.517	SLC22A25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC22A25	HGNC	protein_coding	OTTHUMT00000383519.3	187	0.00	0	G	NM_199352		62996780	62996780	-1	no_errors	ENST00000306494	ensembl	human	known	69_37n	silent	134	48.06	124	SNP	1.000	A
SLC27A3	11000	genome.wustl.edu	37	1	153747796	153747796	+	5'UTR	SNP	T	T	C			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr1:153747796T>C	ENST00000368661.3	+	0	29				SLC27A3_ENST00000484014.1_3'UTR|SLC27A3_ENST00000271857.2_Silent_p.A69A	NM_024330.1	NP_077306.1	Q5K4L6	S27A3_HUMAN	solute carrier family 27 (fatty acid transporter), member 3						fatty acid metabolic process (GO:0006631)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)	fatty-acyl-CoA synthase activity (GO:0004321)|ligase activity (GO:0016874)|nucleotide binding (GO:0000166)			NS(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	14	all_lung(78;6.47e-32)|Lung NSC(65;2.52e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			GGGTTTCTGCTCTCCGCCCGT	0.726																																						dbGAP											0													18.0	23.0	21.0					1																	153747796		2182	4280	6462	-	-	-	SO:0001623	5_prime_UTR_variant	0			BC009916	CCDS1053.1	1q21.1	2013-05-22			ENSG00000143554	ENSG00000143554		"""Acyl-CoA synthetase family"", ""Solute carriers"""	10997	protein-coding gene	gene with protein product		604193				9671728	Standard	NM_024330		Approved	FATP3, MGC4365, ACSVL3	uc001fcz.3	Q5K4L6	OTTHUMG00000037155	ENST00000368661.3:c.-37T>C	1.37:g.153747796T>C		Somatic		WXS	Illumina GAIIx	Phase_IV	Q5VUQ7|Q5VUQ8|Q5VUR3|Q6ZV16|Q8N2X7|Q8TEJ0|Q96SW5|Q9BTJ5|Q9BTY5	Silent	SNP	pfam_AMP-dep_Synth/Lig	p.A69	ENST00000368661.3	37	c.207	CCDS1053.1	1																																																																																			SLC27A3	-	NULL	ENSG00000143554		0.726	SLC27A3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC27A3	HGNC	protein_coding		19	0.00	0	T	NM_024330		153747796	153747796	+1	no_errors	ENST00000271857	ensembl	human	novel	69_37n	silent	12	58.62	17	SNP	0.478	C
SOX9	6662	genome.wustl.edu	37	17	70117908	70117908	+	Nonsense_Mutation	SNP	C	C	T			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr17:70117908C>T	ENST00000245479.2	+	1	748	c.376C>T	c.(376-378)Cag>Tag	p.Q126*		NM_000346.3	NP_000337.1	P48436	SOX9_HUMAN	SRY (sex determining region Y)-box 9	126					astrocyte fate commitment (GO:0060018)|branching involved in ureteric bud morphogenesis (GO:0001658)|cAMP-mediated signaling (GO:0019933)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cell fate specification (GO:0001708)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to heparin (GO:0071504)|cellular response to interleukin-1 (GO:0071347)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|chondrocyte differentiation involved in endochondral bone morphogenesis (GO:0003413)|chondrocyte hypertrophy (GO:0003415)|chromatin remodeling (GO:0006338)|cochlea morphogenesis (GO:0090103)|cytoskeleton organization (GO:0007010)|endocardial cushion morphogenesis (GO:0003203)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation involved in prostatic bud elongation (GO:0060517)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|ERK1 and ERK2 cascade (GO:0070371)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|heart valve development (GO:0003170)|heart valve formation (GO:0003188)|heart valve morphogenesis (GO:0003179)|intestinal epithelial structure maintenance (GO:0060729)|intrahepatic bile duct development (GO:0035622)|limb bud formation (GO:0060174)|lung epithelial cell differentiation (GO:0060487)|male germ-line sex determination (GO:0019100)|male gonad development (GO:0008584)|mammary gland development (GO:0030879)|metanephric nephron tubule formation (GO:0072289)|morphogenesis of a branching epithelium (GO:0061138)|negative regulation of apoptotic process (GO:0043066)|negative regulation of biomineral tissue development (GO:0070168)|negative regulation of bone mineralization (GO:0030502)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of immune system process (GO:0002683)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of ossification (GO:0030279)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell development (GO:0014032)|notochord development (GO:0030903)|nucleosome assembly (GO:0006334)|oligodendrocyte differentiation (GO:0048709)|ossification (GO:0001503)|otic vesicle formation (GO:0030916)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of extracellular matrix assembly (GO:1901203)|positive regulation of kidney development (GO:0090184)|positive regulation of male gonad development (GO:2000020)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein complex assembly (GO:0006461)|protein kinase B signaling (GO:0043491)|regulation of apoptotic process (GO:0042981)|regulation of branching involved in lung morphogenesis (GO:0061046)|regulation of cell adhesion (GO:0030155)|regulation of cell cycle process (GO:0010564)|regulation of cell proliferation (GO:0042127)|regulation of cell proliferation involved in tissue homeostasis (GO:0060784)|regulation of epithelial cell proliferation involved in lung morphogenesis (GO:2000794)|renal vesicle induction (GO:0072034)|retina development in camera-type eye (GO:0060041)|retinal rod cell differentiation (GO:0060221)|Sertoli cell development (GO:0060009)|Sertoli cell differentiation (GO:0060008)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|spermatogenesis (GO:0007283)|tissue homeostasis (GO:0001894)|transcription from RNA polymerase II promoter (GO:0006366)|ureter morphogenesis (GO:0072197)|ureter smooth muscle cell differentiation (GO:0072193)|ureter urothelium development (GO:0072190)	nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|enhancer binding (GO:0035326)|enhancer sequence-specific DNA binding (GO:0001158)|pre-mRNA intronic binding (GO:0097157)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase activity (GO:0004672)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(4)|large_intestine(11)|lung(5)|pancreas(1)|upper_aerodigestive_tract(2)	26		Colorectal(1115;0.245)	STAD - Stomach adenocarcinoma(260;0.119)			GCTCGCGGACCAGTACCCGCA	0.701																																					Pancreas(42;83 1041 2320 35205 39456)	dbGAP											0													22.0	19.0	20.0					17																	70117908		2200	4297	6497	-	-	-	SO:0001587	stop_gained	0			S74506	CCDS11689.1	17q24.3	2013-10-17	2008-07-31		ENSG00000125398	ENSG00000125398		"""SRY (sex determining region Y)-boxes"""	11204	protein-coding gene	gene with protein product		608160	"""campomelic dysplasia, autosomal sex-reversal"""	CMD1, CMPD1		8348155	Standard	NM_000346		Approved	SRA1	uc002jiw.3	P48436	OTTHUMG00000166300	ENST00000245479.2:c.376C>T	17.37:g.70117908C>T	ENSP00000245479:p.Gln126*	Somatic		WXS	Illumina GAIIx	Phase_IV	Q53Y80	Nonsense_Mutation	SNP	pfam_Sox_N,pfam_HMG_superfamily,superfamily_HMG_superfamily,smart_HMG_superfamily,pfscan_HMG_superfamily	p.Q126*	ENST00000245479.2	37	c.376	CCDS11689.1	17	.	.	.	.	.	.	.	.	.	.	C	40	8.486597	0.98832	.	.	ENSG00000125398	ENST00000245479;ENST00000455872	.	.	.	3.97	2.97	0.34412	.	0.000000	0.85682	U	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	12.5717	0.56341	0.168:0.832:0.0:0.0	.	.	.	.	X	126	.	ENSP00000245479:Q126X	Q	+	1	0	SOX9	67629503	1.000000	0.71417	0.979000	0.43373	0.995000	0.86356	5.863000	0.69568	0.623000	0.30267	0.436000	0.28706	CAG	SOX9	-	pfam_HMG_superfamily,superfamily_HMG_superfamily,smart_HMG_superfamily,pfscan_HMG_superfamily	ENSG00000125398		0.701	SOX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SOX9	HGNC	protein_coding	OTTHUMT00000389032.1	17	0.00	0	C	NM_000346		70117908	70117908	+1	no_errors	ENST00000245479	ensembl	human	known	69_37n	nonsense	6	50.00	6	SNP	1.000	T
SPTA1	6708	genome.wustl.edu	37	1	158644209	158644209	+	Silent	SNP	G	G	A			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr1:158644209G>A	ENST00000368147.4	-	10	1440	c.1260C>T	c.(1258-1260)gaC>gaT	p.D420D		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	420					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					CATCGTAAGAGTCAATCTCAT	0.458																																						dbGAP											0													180.0	173.0	175.0					1																	158644209		1947	4147	6094	-	-	-	SO:0001819	synonymous_variant	0			M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.1260C>T	1.37:g.158644209G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Silent	SNP	pfam_Spectrin_repeat,pfam_EF-hand_Ca_insen,pfam_SH3_domain,pfam_SH3_2,superfamily_SH3_domain,smart_Spectrin/alpha-actinin,smart_SH3_domain,pfscan_EF_HAND_2,pfscan_SH3_domain,prints_Spectrin_alpha_SH3	p.D420	ENST00000368147.4	37	c.1260	CCDS41423.1	1																																																																																			SPTA1	-	pfam_Spectrin_repeat,smart_Spectrin/alpha-actinin	ENSG00000163554		0.458	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SPTA1	HGNC	protein_coding	OTTHUMT00000051851.3	198	0.00	0	G	NM_003126		158644209	158644209	-1	no_errors	ENST00000368148	ensembl	human	known	69_37n	silent	270	14.56	46	SNP	0.999	A
SYS1	90196	genome.wustl.edu	37	20	43992225	43992225	+	Missense_Mutation	SNP	G	G	T			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr20:43992225G>T	ENST00000243918.5	+	2	345	c.54G>T	c.(52-54)caG>caT	p.Q18H	SYS1-DBNDD2_ENST00000452133.1_Missense_Mutation_p.Q18H|SYS1-DBNDD2_ENST00000475242.1_Intron|SYS1_ENST00000414310.1_5'UTR|SYS1_ENST00000426004.1_Missense_Mutation_p.Q18H|SYS1_ENST00000372727.1_Missense_Mutation_p.Q18H	NM_033542.3	NP_291020.1	Q8N2H4	SYS1_HUMAN	Sys1 golgi trafficking protein	18					protein transport (GO:0015031)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(2)|large_intestine(2)|prostate(1)|skin(1)	7		Myeloproliferative disorder(115;0.0122)				TCCTGTCGCAGATCGTCCTCA	0.662																																						dbGAP											0													47.0	30.0	36.0					20																	43992225		2203	4300	6503	-	-	-	SO:0001583	missense	0			AL021578	CCDS13351.1, CCDS56192.1	20q13.12	2014-05-07	2014-05-07	2006-11-06	ENSG00000204070	ENSG00000204070			16162	protein-coding gene	gene with protein product		612979	"""chromosome 20 open reading frame 169"", ""SYS1 Golgi-localized integral membrane protein homolog (S. cerevisiae)"""	C20orf169		15077113	Standard	NM_001197129		Approved	dJ453C12.4	uc002xnv.3	Q8N2H4	OTTHUMG00000032579	ENST00000243918.5:c.54G>T	20.37:g.43992225G>T	ENSP00000243918:p.Gln18His	Somatic		WXS	Illumina GAIIx	Phase_IV	C9JFB3|E1P620|Q5QPU7|Q96SD8|Q9BQZ2|Q9BQZ4|Q9H1F7	Missense_Mutation	SNP	pfam_Integral_membrane_SYS1-rel,pirsf_Integral_membrane_SYS1	p.Q18H	ENST00000243918.5	37	c.54	CCDS13351.1	20	.	.	.	.	.	.	.	.	.	.	G	34	5.381237	0.95945	.	.	ENSG00000204070	ENST00000372727;ENST00000243918;ENST00000426004;ENST00000453003	.	.	.	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	D	0.85588	0.5731	M	0.90019	3.08	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88267	0.2927	9	0.87932	D	0	.	18.0842	0.89452	0.0:0.0:1.0:0.0	.	18	Q8N2H4	SYS1_HUMAN	H	18	.	ENSP00000392522:Q18H	Q	+	3	2	SYS1	43425639	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.056000	0.76662	2.598000	0.87819	0.655000	0.94253	CAG	SYS1	-	pfam_Integral_membrane_SYS1-rel,pirsf_Integral_membrane_SYS1	ENSG00000204070		0.662	SYS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SYS1	HGNC	protein_coding	OTTHUMT00000079453.2	19	0.00	0	G	NM_033542		43992225	43992225	+1	no_errors	ENST00000243918	ensembl	human	known	69_37n	missense	24	22.58	7	SNP	1.000	T
TIMM17A	10440	genome.wustl.edu	37	1	201924671	201924671	+	Missense_Mutation	SNP	G	G	C			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr1:201924671G>C	ENST00000367287.4	+	1	53	c.17G>C	c.(16-18)cGa>cCa	p.R6P		NM_006335.2	NP_006326.1	Q99595	TI17A_HUMAN	translocase of inner mitochondrial membrane 17 homolog A (yeast)	6					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	integral component of mitochondrial inner membrane (GO:0031305)|mitochondrial inner membrane presequence translocase complex (GO:0005744)	P-P-bond-hydrolysis-driven protein transmembrane transporter activity (GO:0015450)	p.R6P(1)		kidney(1)|lung(3)|stomach(1)	5						GAGTACGCGCGAGAGCCTTGG	0.632																																						dbGAP											1	Substitution - Missense(1)	lung(1)											189.0	171.0	177.0					1																	201924671		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF106622	CCDS1417.1	1q32.1	2008-05-23			ENSG00000134375	ENSG00000134375			17315	protein-coding gene	gene with protein product		605057				8893850, 10339406	Standard	NM_006335		Approved	TIM17, TIM17A	uc001gxc.3	Q99595	OTTHUMG00000035806	ENST00000367287.4:c.17G>C	1.37:g.201924671G>C	ENSP00000356256:p.Arg6Pro	Somatic		WXS	Illumina GAIIx	Phase_IV	B2RDM5|Q9BWF5	Missense_Mutation	SNP	pfam_Tim17/Tim22/Tim23/PMP24,tigrfam_Tim17	p.R6P	ENST00000367287.4	37	c.17	CCDS1417.1	1	.	.	.	.	.	.	.	.	.	.	G	35	5.567630	0.96540	.	.	ENSG00000134375	ENST00000367287	T	0.52526	0.66	5.01	5.01	0.66863	.	0.000000	0.85682	D	0.000000	T	0.71913	0.3396	H	0.94771	3.58	0.45567	D	0.998514	D	0.55385	0.971	P	0.54270	0.747	T	0.80935	-0.1160	10	0.87932	D	0	-0.9967	16.1957	0.82024	0.0:0.0:1.0:0.0	.	6	Q99595	TI17A_HUMAN	P	6	ENSP00000356256:R6P	ENSP00000356256:R6P	R	+	2	0	TIMM17A	200191294	0.998000	0.40836	0.021000	0.16686	0.698000	0.40448	8.322000	0.90000	2.770000	0.95276	0.655000	0.94253	CGA	TIMM17A	-	pfam_Tim17/Tim22/Tim23/PMP24,tigrfam_Tim17	ENSG00000134375		0.632	TIMM17A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TIMM17A	HGNC	protein_coding	OTTHUMT00000087092.1	233	0.00	0	G	NM_006335		201924671	201924671	+1	no_errors	ENST00000367287	ensembl	human	known	69_37n	missense	377	27.53	144	SNP	0.223	C
TOPBP1	11073	genome.wustl.edu	37	3	133337228	133337228	+	Missense_Mutation	SNP	C	C	G			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr3:133337228C>G	ENST00000260810.5	-	21	3552	c.3421G>C	c.(3421-3423)Gaa>Caa	p.E1141Q		NM_007027.3	NP_008958.2	Q92547	TOPB1_HUMAN	topoisomerase (DNA) II binding protein 1	1141					cellular response to DNA damage stimulus (GO:0006974)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|response to ionizing radiation (GO:0010212)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(14)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	40						ATGATCTGTTCATTTTGGGAA	0.448								Other conserved DNA damage response genes																													Ovarian(21;193 658 4424 15423 17362)	dbGAP											0													160.0	153.0	155.0					3																	133337228		1946	4153	6099	-	-	-	SO:0001583	missense	0			AB019397	CCDS46919.1	3q22.1	2004-06-21			ENSG00000163781	ENSG00000163781			17008	protein-coding gene	gene with protein product		607760				9461304, 9039502	Standard	NM_007027		Approved	KIAA0259, TOP2BP1	uc003eps.3	Q92547	OTTHUMG00000159773	ENST00000260810.5:c.3421G>C	3.37:g.133337228C>G	ENSP00000260810:p.Glu1141Gln	Somatic		WXS	Illumina GAIIx	Phase_IV	B7Z7W8|Q7LGC1|Q9UEB9	Missense_Mutation	SNP	pfam_BRCT_dom,superfamily_BRCT_dom,superfamily_Secretoglobin,smart_BRCT_dom,pfscan_BRCT_dom	p.E1141Q	ENST00000260810.5	37	c.3421	CCDS46919.1	3	.	.	.	.	.	.	.	.	.	.	C	33	5.277950	0.95459	.	.	ENSG00000163781	ENST00000260810	T	0.13196	2.61	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.36936	0.0985	M	0.71581	2.175	0.80722	D	1	D;D	0.71674	0.998;0.998	P;P	0.62089	0.898;0.898	T	0.00294	-1.1840	10	0.33141	T	0.24	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	1054;1141	A0AV47;Q92547	.;TOPB1_HUMAN	Q	1141	ENSP00000260810:E1141Q	ENSP00000260810:E1141Q	E	-	1	0	TOPBP1	134819918	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	7.778000	0.85637	2.941000	0.99782	0.655000	0.94253	GAA	TOPBP1	-	NULL	ENSG00000163781		0.448	TOPBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TOPBP1	HGNC	protein_coding	OTTHUMT00000357254.1	137	0.00	0	C	NM_007027		133337228	133337228	-1	no_errors	ENST00000260810	ensembl	human	known	69_37n	missense	130	20.73	34	SNP	1.000	G
TTLL7	79739	genome.wustl.edu	37	1	84408343	84408343	+	Missense_Mutation	SNP	C	C	T			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr1:84408343C>T	ENST00000260505.8	-	7	903	c.526G>A	c.(526-528)Ggt>Agt	p.G176S	TTLL7_ENST00000477524.1_5'UTR	NM_024686.4	NP_078962.4	Q6ZT98	TTLL7_HUMAN	tubulin tyrosine ligase-like family, member 7	176	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)|protein polyglutamylation (GO:0018095)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)			kidney(1)|large_intestine(8)|lung(15)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29				all cancers(265;0.0126)|Epithelial(280;0.0372)|OV - Ovarian serous cystadenocarcinoma(397;0.16)		AGTTTGTCACCATTTCTTATC	0.284																																						dbGAP											0													33.0	33.0	33.0					1																	84408343		2202	4299	6501	-	-	-	SO:0001583	missense	0			AY170843	CCDS690.2	1p31.1	2013-02-14			ENSG00000137941	ENSG00000137941		"""Tubulin tyrosine ligase-like family"""	26242	protein-coding gene	gene with protein product						15890843	Standard	XM_005271208		Approved	FLJ23033	uc001djc.3	Q6ZT98	OTTHUMG00000009932	ENST00000260505.8:c.526G>A	1.37:g.84408343C>T	ENSP00000260505:p.Gly176Ser	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5TAX8|Q5TAX9|Q6P990|Q86YS1|Q9H5U4	Missense_Mutation	SNP	pfam_Tub_tyr_ligase	p.G176S	ENST00000260505.8	37	c.526	CCDS690.2	1	.	.	.	.	.	.	.	.	.	.	C	14.13	2.442596	0.43326	.	.	ENSG00000137941	ENST00000260505;ENST00000370703	T	0.05139	3.49	5.62	5.62	0.85841	.	0.098369	0.64402	D	0.000001	T	0.03178	0.0093	N	0.26042	0.785	0.50632	D	0.999886	P	0.35468	0.503	B	0.37239	0.244	T	0.56056	-0.8042	10	0.22109	T	0.4	.	19.6432	0.95764	0.0:1.0:0.0:0.0	.	176	Q6ZT98	TTLL7_HUMAN	S	176	ENSP00000260505:G176S	ENSP00000260505:G176S	G	-	1	0	TTLL7	84180931	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.926000	0.70070	2.641000	0.89580	0.591000	0.81541	GGT	TTLL7	-	pfam_Tub_tyr_ligase	ENSG00000137941		0.284	TTLL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TTLL7	HGNC	protein_coding	OTTHUMT00000027498.1	57	0.00	0	C	NM_024686		84408343	84408343	-1	no_errors	ENST00000260505	ensembl	human	known	69_37n	missense	40	13.04	6	SNP	1.000	T
TYR	7299	genome.wustl.edu	37	11	88911241	88911241	+	Missense_Mutation	SNP	C	C	G	rs373294031		TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr11:88911241C>G	ENST00000263321.5	+	1	622	c.120C>G	c.(118-120)agC>agG	p.S40R	TYR_ENST00000526139.1_3'UTR	NM_000372.4	NP_000363.1	P14679	TYRO_HUMAN	tyrosinase	40					cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process from tyrosine (GO:0006583)|thymus development (GO:0048538)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|Golgi-associated vesicle (GO:0005798)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|melanosome (GO:0042470)|perinuclear region of cytoplasm (GO:0048471)	copper ion binding (GO:0005507)|monophenol monooxygenase activity (GO:0004503)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.0033)			Azelaic Acid(DB00548)|Mimosine(DB01055)|Monobenzone(DB00600)	CACCGTGGAGCGGGGACAGGA	0.562																																						dbGAP											0													64.0	60.0	62.0					11																	88911241		2201	4299	6500	-	-	-	SO:0001583	missense	0			M27160	CCDS8284.1	11q14.3	2013-09-27	2012-09-28		ENSG00000077498	ENSG00000077498	1.14.18.1		12442	protein-coding gene	gene with protein product	"""oculocutaneous albinism IA"""	606933					Standard	NM_000372		Approved	OCAIA, OCA1A, OCA1	uc001pcs.3	P14679	OTTHUMG00000167294	ENST00000263321.5:c.120C>G	11.37:g.88911241C>G	ENSP00000263321:p.Ser40Arg	Somatic		WXS	Illumina GAIIx	Phase_IV	Q15675|Q15676|Q15680|Q8TAK4|Q9BYY0|Q9BZX1	Missense_Mutation	SNP	pfam_Tyrosinase,superfamily_Unchr_di-copper_centre,prints_Tyrosinase	p.S40R	ENST00000263321.5	37	c.120	CCDS8284.1	11	.	.	.	.	.	.	.	.	.	.	C	0.011	-1.719970	0.00700	.	.	ENSG00000077498	ENST00000263321	D	0.99129	-5.46	6.07	-12.1	0.00011	.	1.577130	0.02542	N	0.094707	D	0.95046	0.8396	L	0.32530	0.975	0.21105	N	0.999785	B	0.02656	0.0	B	0.06405	0.002	T	0.82400	-0.0476	9	.	.	.	.	1.8022	0.03073	0.2837:0.1591:0.1218:0.4354	.	40	P14679	TYRO_HUMAN	R	40	ENSP00000263321:S40R	.	S	+	3	2	TYR	88550889	0.000000	0.05858	0.000000	0.03702	0.043000	0.13939	-3.453000	0.00465	-5.276000	0.00017	-2.104000	0.00359	AGC	TYR	-	NULL	ENSG00000077498		0.562	TYR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TYR	HGNC	protein_coding	OTTHUMT00000394045.2	95	0.00	0	C	NM_000372		88911241	88911241	+1	no_errors	ENST00000263321	ensembl	human	known	69_37n	missense	95	13.64	15	SNP	0.000	G
VWDE	221806	genome.wustl.edu	37	7	12401033	12401033	+	Missense_Mutation	SNP	C	C	A			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr7:12401033C>A	ENST00000275358.3	-	14	3201	c.3013G>T	c.(3013-3015)Gat>Tat	p.D1005Y		NM_001135924.1	NP_001129396.1	Q8N2E2	VWDE_HUMAN	von Willebrand factor D and EGF domains	1005						extracellular region (GO:0005576)				breast(4)|endometrium(2)|kidney(1)|skin(1)	8						CCCACCAGATCCATGGTATCA	0.393																																						dbGAP											0													72.0	63.0	65.0					7																	12401033		692	1591	2283	-	-	-	SO:0001583	missense	0				CCDS47544.1	7p21.3	2008-09-23			ENSG00000146530	ENSG00000146530			21897	protein-coding gene	gene with protein product						14702039, 16303743	Standard	NM_001135924		Approved	FLJ14712	uc003ssj.2	Q8N2E2	OTTHUMG00000152315	ENST00000275358.3:c.3013G>T	7.37:g.12401033C>A	ENSP00000275358:p.Asp1005Tyr	Somatic		WXS	Illumina GAIIx	Phase_IV	B7ZM77|Q96SQ3	Missense_Mutation	SNP	pfam_VWF_type-D,superfamily_Cadherin-like,smart_VWF_type-D,smart_EGF-like,smart_EGF-like_Ca-bd,pfscan_EG-like_dom	p.D1005Y	ENST00000275358.3	37	c.3013	CCDS47544.1	7	.	.	.	.	.	.	.	.	.	.	C	9.229	1.035255	0.19590	.	.	ENSG00000146530	ENST00000275358;ENST00000536307	D	0.82893	-1.66	3.95	-0.183	0.13284	.	0.695140	0.13016	N	0.420509	T	0.74741	0.3756	L	0.61218	1.895	0.09310	N	1	B	0.16396	0.017	B	0.11329	0.006	T	0.60229	-0.7304	10	0.35671	T	0.21	.	2.7928	0.05393	0.1348:0.4478:0.2623:0.1551	.	1005	Q8N2E2	VWDE_HUMAN	Y	1005;459	ENSP00000275358:D1005Y	ENSP00000275358:D1005Y	D	-	1	0	VWDE	12367558	0.025000	0.19082	0.003000	0.11579	0.467000	0.32768	0.986000	0.29590	-0.154000	0.11118	0.655000	0.94253	GAT	VWDE	-	NULL	ENSG00000146530		0.393	VWDE-001	NOVEL	basic|appris_principal|CCDS	protein_coding	VWDE	HGNC	protein_coding	OTTHUMT00000325870.3	131	0.00	0	C	XM_371878		12401033	12401033	-1	no_errors	ENST00000452576	ensembl	human	known	69_37n	missense	140	34.88	75	SNP	0.128	A
ZNF90	7643	genome.wustl.edu	37	19	20229605	20229605	+	Missense_Mutation	SNP	A	A	G			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr19:20229605A>G	ENST00000418063.2	+	4	1354	c.1242A>G	c.(1240-1242)atA>atG	p.I414M	ZNF90_ENST00000474284.1_Intron	NM_007138.1	NP_009069.1	Q03938	ZNF90_HUMAN	zinc finger protein 90	414					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|lung(2)|ovary(1)|skin(1)	5						CACTTACTATACATAAGATAA	0.373																																						dbGAP											0													43.0	41.0	42.0					19																	20229605		692	1591	2283	-	-	-	SO:0001583	missense	0			M61870	CCDS46028.1	19p12	2013-01-08	2006-02-01		ENSG00000213988	ENSG00000213988		"""Zinc fingers, C2H2-type"", ""-"""	13165	protein-coding gene	gene with protein product		603973	"""zinc finger protein 90 (HTF9)"""			8467795	Standard	NM_007138		Approved	HTF9	uc002nor.2	Q03938	OTTHUMG00000158057	ENST00000418063.2:c.1242A>G	19.37:g.20229605A>G	ENSP00000410466:p.Ile414Met	Somatic		WXS	Illumina GAIIx	Phase_IV	B9EH87	Missense_Mutation	SNP	pfam_Znf_C2H2,pfam_Krueppel-associated_box,superfamily_Krueppel-associated_box,smart_Krueppel-associated_box,smart_Znf_C2H2-like,pfscan_Znf_C2H2,pfscan_Krueppel-associated_box	p.I414M	ENST00000418063.2	37	c.1242	CCDS46028.1	19	.	.	.	.	.	.	.	.	.	.	A	3.561	-0.089631	0.07053	.	.	ENSG00000213988	ENST00000418063	T	0.07567	3.18	1.12	-2.24	0.06909	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.05686	0.0149	N	0.04669	-0.19	0.09310	N	1	D	0.55800	0.973	P	0.56163	0.793	T	0.16129	-1.0413	8	.	.	.	.	3.1502	0.06485	0.3262:0.4492:0.0:0.2246	.	414	Q03938	ZNF90_HUMAN	M	414	ENSP00000410466:I414M	.	I	+	3	3	ZNF90	20090605	0.000000	0.05858	0.008000	0.14137	0.008000	0.06430	-5.902000	0.00091	-1.528000	0.01756	-1.574000	0.00870	ATA	ZNF90	-	pfam_Znf_C2H2,smart_Znf_C2H2-like,pfscan_Znf_C2H2	ENSG00000213988		0.373	ZNF90-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ZNF90	HGNC	protein_coding	OTTHUMT00000350101.1	115	0.00	0	A	NM_007138		20229605	20229605	+1	no_errors	ENST00000418063	ensembl	human	known	69_37n	missense	107	30.52	47	SNP	0.002	G
ZNF569	148266	genome.wustl.edu	37	19	37904255	37904255	+	Missense_Mutation	SNP	C	C	G			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr19:37904255C>G	ENST00000316950.6	-	6	1862	c.1305G>C	c.(1303-1305)gaG>gaC	p.E435D	ZNF569_ENST00000392149.2_Missense_Mutation_p.E435D|ZNF569_ENST00000392150.2_Missense_Mutation_p.E276D	NM_152484.2	NP_689697.2	Q5MCW4	ZN569_HUMAN	zinc finger protein 569	435					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(5)|endometrium(4)|large_intestine(16)|lung(11)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	40			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CATAAGGTTTCTCTCTAGTAT	0.368																																						dbGAP											0													88.0	84.0	86.0					19																	37904255		2203	4299	6502	-	-	-	SO:0001583	missense	0			AL833408	CCDS12503.1	19q13.12	2013-09-20			ENSG00000196437	ENSG00000196437		"""Zinc fingers, C2H2-type"", ""-"""	24737	protein-coding gene	gene with protein product		613904				12477932	Standard	NM_152484		Approved	FLJ32053, ZAP1	uc002ogi.3	Q5MCW4	OTTHUMG00000048172	ENST00000316950.6:c.1305G>C	19.37:g.37904255C>G	ENSP00000325018:p.Glu435Asp	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K1S2|Q15925|Q17RR6|Q96MQ2	Missense_Mutation	SNP	pfam_Znf_C2H2,pfam_Krueppel-associated_box,superfamily_Krueppel-associated_box,smart_Krueppel-associated_box,smart_Znf_C2H2-like,pfscan_Znf_C2H2,pfscan_Krueppel-associated_box	p.E435D	ENST00000316950.6	37	c.1305	CCDS12503.1	19	.	.	.	.	.	.	.	.	.	.	C	16.56	3.157573	0.57368	.	.	ENSG00000196437	ENST00000316950;ENST00000392149;ENST00000392150	T;T	0.57752	0.38;1.71	4.33	-0.126	0.13515	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.38111	N	0.001816	T	0.54647	0.1871	L	0.41961	1.31	0.39389	D	0.966384	P;P	0.48998	0.918;0.918	P;P	0.58130	0.833;0.833	T	0.56238	-0.8012	10	0.66056	D	0.02	.	9.1014	0.36671	0.0:0.6554:0.0:0.3446	.	276;435	Q17RR6;Q5MCW4	.;ZN569_HUMAN	D	435;91;276	ENSP00000325018:E435D;ENSP00000375993:E276D	ENSP00000325018:E435D	E	-	3	2	ZNF569	42596095	0.994000	0.37717	1.000000	0.80357	0.998000	0.95712	0.406000	0.21032	0.203000	0.20529	0.655000	0.94253	GAG	ZNF569	-	pfscan_Znf_C2H2	ENSG00000196437		0.368	ZNF569-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ZNF569	HGNC	protein_coding	OTTHUMT00000109594.2	318	0.00	0	C	NM_152484		37904255	37904255	-1	no_errors	ENST00000316950	ensembl	human	known	69_37n	missense	328	17.59	70	SNP	1.000	G
ZNF415	55786	genome.wustl.edu	37	19	53611669	53611669	+	Silent	SNP	T	T	C			TCGA-BH-A18K-01A-11D-A12B-09	TCGA-BH-A18K-11A-13D-A12B-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f75de986-bc8a-4ffe-9b35-011eee3a1446	1a1312ef-4a37-445c-80e5-529fdf7827ee	g.chr19:53611669T>C	ENST00000500065.4	-	4	1962	c.1629A>G	c.(1627-1629)caA>caG	p.Q543Q	ZNF415_ENST00000594011.1_3'UTR|ZNF415_ENST00000601493.1_Silent_p.Q313Q|ZNF415_ENST00000440291.1_Silent_p.Q530Q|ZNF415_ENST00000597748.1_3'UTR|ZNF415_ENST00000448501.1_Silent_p.Q591Q|ZNF415_ENST00000595193.1_3'UTR|ZNF415_ENST00000243643.4_Silent_p.Q543Q|ZNF415_ENST00000455735.2_Silent_p.Q591Q|ZNF415_ENST00000421033.1_Silent_p.Q555Q|ZNF415_ENST00000597503.1_3'UTR	NM_001136038.2	NP_001129510.2	Q09FC8	ZN415_HUMAN	zinc finger protein 415	591					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31				GBM - Glioblastoma multiforme(134;0.0191)		TATGGATAATTTGATGTCTGA	0.358																																						dbGAP											0													112.0	111.0	112.0					19																	53611669		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AK002053	CCDS12860.1, CCDS54313.1	19q13.42	2014-03-18			ENSG00000170954	ENSG00000170954		"""Zinc fingers, C2H2-type"", ""-"""	20636	protein-coding gene	gene with protein product						14702039	Standard	NM_001136038		Approved		uc002qaw.3	Q09FC8	OTTHUMG00000182865	ENST00000500065.4:c.1629A>G	19.37:g.53611669T>C		Somatic		WXS	Illumina GAIIx	Phase_IV	F5H287|Q09FC7|Q09FC9|Q09FD0|Q6NSZ2|Q6P3S0|Q9NUR2	Silent	SNP	pfam_Znf_C2H2,smart_Znf_C2H2-like,smart_Znf_BED_prd,pfscan_Znf_C2H2	p.Q591	ENST00000500065.4	37	c.1773	CCDS54313.1	19																																																																																			ZNF415	-	pfam_Znf_C2H2,smart_Znf_C2H2-like,pfscan_Znf_C2H2	ENSG00000170954		0.358	ZNF415-025	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ZNF415	HGNC	protein_coding	OTTHUMT00000464043.1	353	0.28	1	T	NM_018355		53611669	53611669	-1	no_errors	ENST00000448501	ensembl	human	known	69_37n	silent	295	70.41	702	SNP	0.007	C
