#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
ABCA12	26154	genome.wustl.edu	37	2	215813332	215813332	+	Missense_Mutation	SNP	C	C	G	rs572494384		TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr2:215813332C>G	ENST00000272895.7	-	47	7311	c.7092G>C	c.(7090-7092)aaG>aaC	p.K2364N	AC072062.1_ENST00000607412.1_RNA|ABCA12_ENST00000389661.4_Missense_Mutation_p.K2046N	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	2364	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		CTTTAATATCCTTTTCTGGAA	0.418																																					Ovarian(66;664 1488 5121 34295)	dbGAP											0													84.0	80.0	81.0					2																	215813332		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"""ATP binding cassette transporters / subfamily A"""	14637	protein-coding gene	gene with protein product		607800	"""ichthyosis congenita II, lamellar ichthyosis B"""	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.7092G>C	2.37:g.215813332C>G	ENSP00000272895:p.Lys2364Asn	Somatic		WXS	Illumina GAIIx	Phase_IV	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	pfam_ABC_transporter-like,smart_AAA+_ATPase,pfscan_ABC_transporter-like	p.K2364N	ENST00000272895.7	37	c.7092	CCDS33372.1	2	.	.	.	.	.	.	.	.	.	.	C	12.73	2.024704	0.35701	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	T;T	0.80566	-1.39;-1.39	5.48	-3.55	0.04639	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.368768	0.26207	N	0.025703	T	0.64483	0.2602	N	0.25890	0.77	0.58432	D	0.999999	B;B	0.09022	0.001;0.002	B;B	0.15870	0.014;0.008	T	0.30031	-0.9992	10	0.56958	D	0.05	.	9.684	0.40087	0.1116:0.545:0.0:0.3435	.	2364;2046	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	N	2364;2046	ENSP00000272895:K2364N;ENSP00000374312:K2046N	ENSP00000272895:K2364N	K	-	3	2	ABCA12	215521577	0.958000	0.32768	0.951000	0.38953	0.993000	0.82548	0.021000	0.13489	-0.985000	0.03503	-0.345000	0.07892	AAG	ABCA12	-	pfam_ABC_transporter-like,smart_AAA+_ATPase,pfscan_ABC_transporter-like	ENSG00000144452		0.418	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ABCA12	HGNC	protein_coding	OTTHUMT00000337111.1	233	0.00	0	C	NM_173076		215813332	215813332	-1	no_errors	ENST00000272895	ensembl	human	known	69_37n	missense	108	18.80	25	SNP	0.823	G
ABCA7	10347	genome.wustl.edu	37	19	1043354	1043356	+	In_Frame_Del	DEL	TTG	TTG	-			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	TTG	TTG					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr19:1043354_1043356delTTG	ENST00000263094.6	+	9	1043_1045	c.812_814delTTG	c.(811-816)attgga>aga	p.271_272IG>R	ABCA7_ENST00000433129.1_In_Frame_Del_p.271_272IG>R|ABCA7_ENST00000435683.2_In_Frame_Del_p.133_134IG>R	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	271					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		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)		TCGGAGCTGATTGGAGCCCTGGA	0.635																																						dbGAP											0																																										-	-	-	SO:0001651	inframe_deletion	0			AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"""ATP binding cassette transporters / subfamily A"""	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.812_814delTTG	19.37:g.1043354_1043356delTTG	ENSP00000263094:p.Ile271_Gly272delinsArg	Somatic		WXS	Illumina GAIIx	Phase_IV	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	In_Frame_Del	DEL	pfam_ABC_transporter-like,superfamily_GroES-like,smart_AAA+_ATPase,pfscan_ABC_transporter-like	p.IG271in_frame_delR	ENST00000263094.6	37	c.812_814	CCDS12055.1	19																																																																																			ABCA7	-	NULL	ENSG00000064687		0.635	ABCA7-001	KNOWN	basic|CCDS	protein_coding	ABCA7	HGNC	protein_coding	OTTHUMT00000394993.1	30	0.00	0	TTG	NM_019112		1043354	1043356	+1	no_errors	ENST00000263094	ensembl	human	known	69_37n	in_frame_del	15	59.46	22	DEL	0.338:0.041:0.030	-
ART5	116969	genome.wustl.edu	37	11	3661041	3661043	+	In_Frame_Del	DEL	AAA	AAA	-			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	AAA	AAA					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr11:3661041_3661043delAAA	ENST00000397068.3	-	2	1008_1010	c.616_618delTTT	c.(616-618)tttdel	p.F206del	ART5_ENST00000359918.4_In_Frame_Del_p.F206del|ART5_ENST00000397067.3_Intron|TRPC2_ENST00000526541.1_RNA	NM_053017.3	NP_443750.2	Q96L15	NAR5_HUMAN	ADP-ribosyltransferase 5	206					protein ADP-ribosylation (GO:0006471)	extracellular region (GO:0005576)|membrane (GO:0016020)	NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|NAD+ nucleosidase activity (GO:0003953)			breast(1)|central_nervous_system(1)|large_intestine(2)|lung(6)|ovary(1)	11		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0336)|LUSC - Lung squamous cell carcinoma(625;0.19)		TAGGGGCCCCAAAGCAAGTTGTT	0.547																																						dbGAP											0																																										-	-	-	SO:0001651	inframe_deletion	0			Y16835	CCDS7743.1, CCDS73242.1	11p15.4	2008-02-05			ENSG00000167311	ENSG00000167311			24049	protein-coding gene	gene with protein product		610625				11587854, 10448534	Standard	NM_001079536		Approved		uc001lyb.1	Q96L15	OTTHUMG00000011842	ENST00000397068.3:c.616_618delTTT	11.37:g.3661041_3661043delAAA	ENSP00000380258:p.Phe206del	Somatic		WXS	Illumina GAIIx	Phase_IV	C9IYG7|Q6UX84|Q86W02	In_Frame_Del	DEL	pfam_ART,prints_ART	p.F206in_frame_del	ENST00000397068.3	37	c.618_616	CCDS7743.1	11																																																																																			ART5	-	pfam_ART,prints_ART	ENSG00000167311		0.547	ART5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ART5	HGNC	protein_coding	OTTHUMT00000032760.2	161	0.00	0	AAA	NM_053017		3661041	3661043	-1	no_errors	ENST00000359918	ensembl	human	known	69_37n	in_frame_del	81	34.15	42	DEL	1.000:1.000:1.000	-
ARHGEF17	9828	genome.wustl.edu	37	11	73064010	73064010	+	Nonsense_Mutation	SNP	C	C	T			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr11:73064010C>T	ENST00000263674.3	+	3	3756	c.3406C>T	c.(3406-3408)Cag>Tag	p.Q1136*	ARHGEF17_ENST00000536170.1_3'UTR	NM_014786.3	NP_055601.2	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	1136	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(2)	32						GCACTGCATGCAGACCTGGCA	0.632																																						dbGAP											0													71.0	66.0	68.0					11																	73064010		2200	4293	6493	-	-	-	SO:0001587	stop_gained	0			AF378754	CCDS8221.1	11q13.3	2011-11-16			ENSG00000110237	ENSG00000110237		"""Rho guanine nucleotide exchange factors"""	21726	protein-coding gene	gene with protein product	"""Rho-specific guanine-nucleotide exchange factor 164 kDa"", ""tumor endothelial marker 4"""					11559528, 12071859	Standard	NM_014786		Approved	TEM4, KIAA0337, p164-RhoGEF	uc001otu.3	Q96PE2	OTTHUMG00000167971	ENST00000263674.3:c.3406C>T	11.37:g.73064010C>T	ENSP00000263674:p.Gln1136*	Somatic		WXS	Illumina GAIIx	Phase_IV	B2RP20|Q86XU2|Q8N2S0|Q9Y4G3	Nonsense_Mutation	SNP	pfam_DH-domain,superfamily_DH-domain,superfamily_WD40_repeat_dom,superfamily_Vinculin/catenin,smart_DH-domain,pfscan_DH-domain	p.Q1136*	ENST00000263674.3	37	c.3406	CCDS8221.1	11	.	.	.	.	.	.	.	.	.	.	C	44	10.708233	0.99454	.	.	ENSG00000110237	ENST00000263674	.	.	.	5.29	5.29	0.74685	.	0.524057	0.22145	N	0.063984	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	-10.768	17.8862	0.88855	0.0:1.0:0.0:0.0	.	.	.	.	X	1136	.	ENSP00000263674:Q1136X	Q	+	1	0	ARHGEF17	72741658	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	2.223000	0.42936	2.625000	0.88918	0.655000	0.94253	CAG	ARHGEF17	-	pfam_DH-domain,superfamily_DH-domain,smart_DH-domain,pfscan_DH-domain	ENSG00000110237		0.632	ARHGEF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ARHGEF17	HGNC	protein_coding	OTTHUMT00000397365.1	43	0.00	0	C	NM_014786		73064010	73064010	+1	no_errors	ENST00000263674	ensembl	human	known	69_37n	nonsense	21	19.23	5	SNP	1.000	T
B4GALNT2	124872	genome.wustl.edu	37	17	47236488	47236488	+	Silent	SNP	C	C	A			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr17:47236488C>A	ENST00000300404.2	+	6	827	c.768C>A	c.(766-768)atC>atA	p.I256I	B4GALNT2_ENST00000393354.2_Silent_p.I196I|B4GALNT2_ENST00000504681.1_Silent_p.I170I	NM_153446.2	NP_703147.2	Q8NHY0	B4GN2_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 2	256					lipid glycosylation (GO:0030259)|negative regulation of cell-cell adhesion (GO:0022408)|protein glycosylation (GO:0006486)|UDP-N-acetylgalactosamine metabolic process (GO:0019276)|UDP-N-acetylglucosamine metabolic process (GO:0006047)	integral component of Golgi membrane (GO:0030173)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)			endometrium(3)|large_intestine(6)|liver(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	24			all cancers(6;0.000316)			AGCAGCTGATCATTTCTACCA	0.552																																					GBM(124;244 1635 8663 18097 33175)	dbGAP											0													226.0	199.0	208.0					17																	47236488		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AJ517770	CCDS11544.1, CCDS54139.1, CCDS54140.1	17q21.33	2013-02-22	2006-01-08	2006-01-08	ENSG00000167080	ENSG00000167080	2.4.1.-	"""Beta 4-glycosyltransferases"", ""Glycosyltransferase family 2 domain containing"""	24136	protein-coding gene	gene with protein product		111730	"""UDP-GalNAc:Neu5Acalpha2-3Galbeta-R beta1,4-N-acetylgalactosaminyltransferase"""	GALGT2		8782649, 12678917	Standard	NM_153446		Approved	Sda, Cad	uc002ion.2	Q8NHY0	OTTHUMG00000161307	ENST00000300404.2:c.768C>A	17.37:g.47236488C>A		Somatic		WXS	Illumina GAIIx	Phase_IV	B4DZE4|Q14CP1|Q86Y40	Silent	SNP	pfam_Glyco_trans_2,pirsf_GM2_synthase	p.I256	ENST00000300404.2	37	c.768	CCDS11544.1	17																																																																																			B4GALNT2	-	pirsf_GM2_synthase	ENSG00000167080		0.552	B4GALNT2-001	KNOWN	basic|CCDS	protein_coding	B4GALNT2	HGNC	protein_coding	OTTHUMT00000364477.1	492	0.20	1	C	NM_153446		47236488	47236488	+1	no_errors	ENST00000300404	ensembl	human	known	69_37n	silent	431	17.08	89	SNP	0.917	A
BAG6	7917	genome.wustl.edu	37	6	31609988	31609989	+	Frame_Shift_Ins	INS	-	-	A			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr6:31609988_31609989insA	ENST00000375964.6	-	15	2458_2459	c.2145_2146insT	c.(2143-2148)tccctgfs	p.L716fs	BAG6_ENST00000439687.2_Frame_Shift_Ins_p.L584fs|BAG6_ENST00000470875.1_5'UTR|BAG6_ENST00000362049.6_Frame_Shift_Ins_p.L710fs|BAG6_ENST00000404765.2_Frame_Shift_Ins_p.L746fs|BAG6_ENST00000211379.5_Frame_Shift_Ins_p.L710fs|BAG6_ENST00000375976.4_Frame_Shift_Ins_p.L710fs	NM_004639.3|NM_080703.2	NP_004630.3|NP_542434.1	P46379	BAG6_HUMAN	BCL2-associated athanogene 6	716					brain development (GO:0007420)|cell differentiation (GO:0030154)|chromatin modification (GO:0016568)|embryo development (GO:0009790)|immune system process (GO:0002376)|internal peptidyl-lysine acetylation (GO:0018393)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|kidney development (GO:0001822)|lung development (GO:0030324)|negative regulation of apoptotic process (GO:0043066)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of proteolysis (GO:0045861)|protein stabilization (GO:0050821)|regulation of cell proliferation (GO:0042127)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)|tail-anchored membrane protein insertion into ER membrane (GO:0071816)|transport (GO:0006810)|ubiquitin-dependent protein catabolic process (GO:0006511)	BAT3 complex (GO:0071818)|cytosol (GO:0005829)|nucleus (GO:0005634)	polyubiquitin binding (GO:0031593)|proteasome binding (GO:0070628)|ribosome binding (GO:0043022)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(2)|pancreas(2)|skin(3)|urinary_tract(2)	36						CGAGCCCCCAGGGAGCCCAGCA	0.609																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			M31294	CCDS4709.1, CCDS47403.1, CCDS56414.1, CCDS56415.1	6p21.3	2011-06-14	2010-12-09	2010-12-09	ENSG00000204463	ENSG00000204463			13919	protein-coding gene	gene with protein product		142590	"""HLA-B associated transcript 3"""	BAT3		2156268	Standard	NM_004639		Approved	G3, D6S52E	uc003nvf.4	P46379	OTTHUMG00000031171	ENST00000375964.6:c.2145_2146insT	6.37:g.31609988_31609989insA	ENSP00000365131:p.Leu716fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A2ADJ7|A3KQ42|A3KQ44|A6NGY6|A6PWF7|B0UX84|B4DZ12|B4E3V4|E7EMZ4|F8VXY4|O95874|Q5HYL9|Q5SQ35|Q5SQ36|Q5SQ37|Q5SQ41|Q5SRP8|Q5SRP9|Q5STC1|Q5STX1|Q5STX3|Q96SA6|Q9BCN4	Frame_Shift_Ins	INS	pfam_DUF3538,pfam_Ubiquitin,smart_Ubiquitin,pfscan_Ubiquitin_supergroup	p.L745fs	ENST00000375964.6	37	c.2236_2235	CCDS47403.1	6																																																																																			BAG6	-	NULL	ENSG00000204463		0.609	BAG6-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	BAG6	HGNC	protein_coding		128	0.00	0	-	NM_080703		31609988	31609989	-1	no_errors	ENST00000404765	ensembl	human	known	69_37n	frame_shift_ins	98	22.22	28	INS	0.929:0.933	A
BCAR1	9564	genome.wustl.edu	37	16	75263772	75263773	+	Frame_Shift_Ins	INS	-	-	T			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr16:75263772_75263773insT	ENST00000162330.5	-	7	2375_2376	c.2249_2250insA	c.(2248-2250)cagfs	p.Q750fs	BCAR1_ENST00000393420.6_Frame_Shift_Ins_p.Q768fs|BCAR1_ENST00000546196.1_Frame_Shift_Ins_p.Q721fs|RP11-331F4.4_ENST00000489723.1_RNA|BCAR1_ENST00000393422.2_Frame_Shift_Ins_p.Q768fs|BCAR1_ENST00000535626.2_Frame_Shift_Ins_p.Q602fs|BCAR1_ENST00000542031.2_Frame_Shift_Ins_p.Q748fs|BCAR1_ENST00000418647.3_Frame_Shift_Ins_p.Q796fs|BCAR1_ENST00000566982.1_5'UTR|BCAR1_ENST00000420641.3_Frame_Shift_Ins_p.Q768fs|BCAR1_ENST00000538440.2_Frame_Shift_Ins_p.Q750fs	NM_001170717.1|NM_014567.3	NP_001164188.1|NP_055382.2	P56945	BCAR1_HUMAN	breast cancer anti-estrogen resistance 1	750	Divergent helix-loop-helix motif.				actin filament organization (GO:0007015)|antigen receptor-mediated signaling pathway (GO:0050851)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell division (GO:0051301)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|epidermal growth factor receptor signaling pathway (GO:0007173)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell migration (GO:0010595)|regulation of apoptotic process (GO:0042981)|regulation of cell growth (GO:0001558)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(2)|central_nervous_system(5)|endometrium(1)|kidney(6)|large_intestine(1)|liver(1)|lung(13)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)	35				BRCA - Breast invasive adenocarcinoma(221;0.169)		TGGCCTCACACTGCTCCAGGTA	0.668																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AJ242987	CCDS10915.1, CCDS54037.1, CCDS54038.1, CCDS54039.1, CCDS54040.1, CCDS54041.1, CCDS54042.1, CCDS54043.1	16q22-q23	2011-04-13			ENSG00000050820	ENSG00000050820		"""Cas scaffolding proteins"""	971	protein-coding gene	gene with protein product	"""Crk-associated substrate"", ""Cas scaffolding protein family member 1"""	602941				8413311, 10639512	Standard	NM_001170714		Approved	P130Cas, Crkas, CAS, CASS1	uc010vnb.2	P56945	OTTHUMG00000137604	ENST00000162330.5:c.2250dupA	16.37:g.75263773_75263773dupT	ENSP00000162330:p.Gln750fs	Somatic		WXS	Illumina GAIIx	Phase_IV	B3KWD7|B4DEV4|B4DGB5|B4DIW5|B7Z7X7|E9PCL5|E9PCV2|F5GXA2|F5GXV6|F5H7Z0|F8WA69|Q6QEF7	Frame_Shift_Ins	INS	pfam_CAS_DUF3513,pfam_Serine_rich,pfam_SH3_domain,pfam_SH3_2,superfamily_SH3_domain,smart_SH3_domain,pfscan_SH3_domain,prints_SH3_domain,prints_Spectrin_alpha_SH3	p.C797fs	ENST00000162330.5	37	c.2388_2387	CCDS10915.1	16																																																																																			BCAR1	-	pfam_CAS_DUF3513	ENSG00000050820		0.668	BCAR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	BCAR1	HGNC	protein_coding	OTTHUMT00000269017.1	27	0.00	0	-	NM_014567		75263772	75263773	-1	no_errors	ENST00000418647	ensembl	human	known	69_37n	frame_shift_ins	4	33.33	2	INS	1.000:1.000	T
BCAR1	9564	genome.wustl.edu	37	16	75263776	75263776	+	Frame_Shift_Del	DEL	T	T	-			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr16:75263776delT	ENST00000162330.5	-	7	2372	c.2246delA	c.(2245-2247)gagfs	p.E749fs	BCAR1_ENST00000393420.6_Frame_Shift_Del_p.E767fs|BCAR1_ENST00000546196.1_Frame_Shift_Del_p.E720fs|RP11-331F4.4_ENST00000489723.1_RNA|BCAR1_ENST00000393422.2_Frame_Shift_Del_p.E767fs|BCAR1_ENST00000535626.2_Frame_Shift_Del_p.E601fs|BCAR1_ENST00000542031.2_Frame_Shift_Del_p.E747fs|BCAR1_ENST00000418647.3_Frame_Shift_Del_p.E795fs|BCAR1_ENST00000566982.1_5'UTR|BCAR1_ENST00000420641.3_Frame_Shift_Del_p.E767fs|BCAR1_ENST00000538440.2_Frame_Shift_Del_p.E749fs	NM_001170717.1|NM_014567.3	NP_001164188.1|NP_055382.2	P56945	BCAR1_HUMAN	breast cancer anti-estrogen resistance 1	749	Divergent helix-loop-helix motif.				actin filament organization (GO:0007015)|antigen receptor-mediated signaling pathway (GO:0050851)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell division (GO:0051301)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|epidermal growth factor receptor signaling pathway (GO:0007173)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell migration (GO:0010595)|regulation of apoptotic process (GO:0042981)|regulation of cell growth (GO:0001558)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(2)|central_nervous_system(5)|endometrium(1)|kidney(6)|large_intestine(1)|liver(1)|lung(13)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)	35				BRCA - Breast invasive adenocarcinoma(221;0.169)		CTCACACTGCTCCAGGTAGAA	0.677																																						dbGAP											0													58.0	58.0	58.0					16																	75263776		2198	4300	6498	-	-	-	SO:0001589	frameshift_variant	0			AJ242987	CCDS10915.1, CCDS54037.1, CCDS54038.1, CCDS54039.1, CCDS54040.1, CCDS54041.1, CCDS54042.1, CCDS54043.1	16q22-q23	2011-04-13			ENSG00000050820	ENSG00000050820		"""Cas scaffolding proteins"""	971	protein-coding gene	gene with protein product	"""Crk-associated substrate"", ""Cas scaffolding protein family member 1"""	602941				8413311, 10639512	Standard	NM_001170714		Approved	P130Cas, Crkas, CAS, CASS1	uc010vnb.2	P56945	OTTHUMG00000137604	ENST00000162330.5:c.2246delA	16.37:g.75263776delT	ENSP00000162330:p.Glu749fs	Somatic		WXS	Illumina GAIIx	Phase_IV	B3KWD7|B4DEV4|B4DGB5|B4DIW5|B7Z7X7|E9PCL5|E9PCV2|F5GXA2|F5GXV6|F5H7Z0|F8WA69|Q6QEF7	Frame_Shift_Del	DEL	pfam_CAS_DUF3513,pfam_Serine_rich,pfam_SH3_domain,pfam_SH3_2,superfamily_SH3_domain,smart_SH3_domain,pfscan_SH3_domain,prints_SH3_domain,prints_Spectrin_alpha_SH3	p.E795fs	ENST00000162330.5	37	c.2384	CCDS10915.1	16																																																																																			BCAR1	-	pfam_CAS_DUF3513	ENSG00000050820		0.677	BCAR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	BCAR1	HGNC	protein_coding	OTTHUMT00000269017.1	26	0.00	0	T	NM_014567		75263776	75263776	-1	no_errors	ENST00000418647	ensembl	human	known	69_37n	frame_shift_del	4	33.33	2	DEL	1.000	-
C6orf10	10665	genome.wustl.edu	37	6	32298378	32298378	+	Missense_Mutation	SNP	G	G	T	rs149522773		TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr6:32298378G>T	ENST00000447241.2	-	16	674	c.502C>A	c.(502-504)Cct>Act	p.P168T	C6orf10_ENST00000375015.4_Missense_Mutation_p.P152T|C6orf10_ENST00000375007.4_Missense_Mutation_p.P166T|C6orf10_ENST00000527965.1_Missense_Mutation_p.P145T|C6orf10_ENST00000533191.1_Missense_Mutation_p.P152T|C6orf10_ENST00000442822.2_Missense_Mutation_p.P145T	NM_006781.3	NP_006772.3	Q5SRN2	CF010_HUMAN	chromosome 6 open reading frame 10	168						integral component of membrane (GO:0016021)|nucleus (GO:0005634)		p.P168S(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|skin(1)	25						TTGGATCCAGGATATTGTACT	0.413																																						dbGAP											1	Substitution - Missense(1)	skin(1)											78.0	53.0	62.0					6																	32298378		1511	2709	4220	-	-	-	SO:0001583	missense	0			U60665	CCDS34422.1, CCDS69082.1, CCDS75430.1	6p21.32	2012-11-20			ENSG00000204296	ENSG00000204296			13922	protein-coding gene	gene with protein product	"""testis specific basic protein"""					10803852	Standard	XM_005248810		Approved	TSBP	uc021yvs.1	Q5SRN2	OTTHUMG00000031107	ENST00000447241.2:c.502C>A	6.37:g.32298378G>T	ENSP00000415517:p.Pro168Thr	Somatic		WXS	Illumina GAIIx	Phase_IV	A2BET1|A2BET2|A6NME2|B0S7R2|B0S7R3|E9PMB1|Q5SPI9|Q5SPJ0|Q5SPK9|Q5SPL0|Q5SRN3|Q5TG25|Q5TG26|Q8N4B6	Missense_Mutation	SNP	NULL	p.P168T	ENST00000447241.2	37	c.502	CCDS34422.1	6	.	.	.	.	.	.	.	.	.	.	G	0.007	-2.002600	0.00431	.	.	ENSG00000204296	ENST00000442822;ENST00000447241;ENST00000375015;ENST00000533191;ENST00000527965;ENST00000375007	T;T;T;T;T;T	0.07216	3.21;3.21;3.21;3.21;3.21;3.21	3.14	0.645	0.17782	.	.	.	.	.	T	0.00936	0.0031	N	0.24115	0.695	0.21147	N	0.999774	.	.	.	.	.	.	T	0.47787	-0.9090	7	0.02654	T	1	.	3.4952	0.07653	0.0:0.131:0.2408:0.6282	.	.	.	.	T	145;168;152;152;145;166	ENSP00000411164:P145T;ENSP00000415517:P168T;ENSP00000364155:P152T;ENSP00000431199:P152T;ENSP00000435103:P145T;ENSP00000364146:P166T	ENSP00000364146:P166T	P	-	1	0	C6orf10	32406356	0.088000	0.21588	0.972000	0.41901	0.672000	0.39443	-0.116000	0.10724	0.143000	0.18926	-0.738000	0.03535	CCT	C6orf10	-	NULL	ENSG00000204296		0.413	C6orf10-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	C6orf10	HGNC	protein_coding	OTTHUMT00000076178.4	94	0.00	0	G	NM_006781		32298378	32298378	-1	no_errors	ENST00000447241	ensembl	human	known	69_37n	missense	61	16.44	12	SNP	0.979	T
CPT1B	1375	genome.wustl.edu	37	22	51014673	51014674	+	Frame_Shift_Ins	INS	-	-	T			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr22:51014673_51014674insT	ENST00000360719.2	-	6	789_790	c.652_653insA	c.(652-654)aggfs	p.R218fs	CPT1B_ENST00000434492.2_Frame_Shift_Ins_p.R15fs|CPT1B_ENST00000457250.1_Frame_Shift_Ins_p.R184fs|CHKB-CPT1B_ENST00000453634.1_3'UTR|CHKB-CPT1B_ENST00000452668.1_5'Flank|CPT1B_ENST00000440709.1_Frame_Shift_Ins_p.R218fs|CPT1B_ENST00000312108.7_Frame_Shift_Ins_p.R218fs|CPT1B_ENST00000405237.3_Frame_Shift_Ins_p.R218fs|CPT1B_ENST00000395650.2_Frame_Shift_Ins_p.R218fs	NM_001145135.1|NM_152245.2	NP_001138607.1|NP_689451.1	Q92523	CPT1B_HUMAN	carnitine palmitoyltransferase 1B (muscle)	218					carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	carnitine O-palmitoyltransferase activity (GO:0004095)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		all cancers(3;3.56e-77)|OV - Ovarian serous cystadenocarcinoma(4;5.39e-74)|Epithelial(4;5.58e-70)|GBM - Glioblastoma multiforme(4;5.59e-08)|LUAD - Lung adenocarcinoma(64;0.0016)|Lung(4;0.00942)|BRCA - Breast invasive adenocarcinoma(115;0.207)		TTTCTGCAGCCTGGGGGCAGTC	0.55											OREG0026685	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									Esophageal Squamous(170;988 1933 25577 30295 48163)	dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			U62733	CCDS14098.1, CCDS46734.1	22q13.33	2007-07-26			ENSG00000205560	ENSG00000205560			2329	protein-coding gene	gene with protein product		601987				9070950	Standard	NM_152245		Approved	M-CPT1, CPT1-M	uc003bmm.3	Q92523	OTTHUMG00000137390	ENST00000360719.2:c.653dupA	22.37:g.51014674_51014674dupT	ENSP00000353945:p.Arg218fs	Somatic	974	WXS	Illumina GAIIx	Phase_IV	B7Z4U4|B7Z5T8|E9PCP2|Q13389|Q99655|Q9BY90	Frame_Shift_Ins	INS	pfam_Carn_acyl_trans	p.R218fs	ENST00000360719.2	37	c.653_652	CCDS14098.1	22																																																																																			CPT1B	-	pfam_Carn_acyl_trans	ENSG00000205560		0.550	CPT1B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	CPT1B	HGNC	protein_coding	OTTHUMT00000317264.5	46	0.00	0	-	NM_152246		51014673	51014674	-1	no_errors	ENST00000312108	ensembl	human	known	69_37n	frame_shift_ins	7	50.00	7	INS	0.989:0.743	T
CPT1B	1375	genome.wustl.edu	37	22	51014680	51014681	+	Frame_Shift_Ins	INS	-	-	T			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr22:51014680_51014681insT	ENST00000360719.2	-	6	782_783	c.645_646insA	c.(643-648)actgccfs	p.A216fs	CPT1B_ENST00000434492.2_Frame_Shift_Ins_p.A13fs|CPT1B_ENST00000457250.1_Frame_Shift_Ins_p.A182fs|CHKB-CPT1B_ENST00000453634.1_3'UTR|CHKB-CPT1B_ENST00000452668.1_5'Flank|CPT1B_ENST00000440709.1_Frame_Shift_Ins_p.A216fs|CPT1B_ENST00000312108.7_Frame_Shift_Ins_p.A216fs|CPT1B_ENST00000405237.3_Frame_Shift_Ins_p.A216fs|CPT1B_ENST00000395650.2_Frame_Shift_Ins_p.A216fs	NM_001145135.1|NM_152245.2	NP_001138607.1|NP_689451.1	Q92523	CPT1B_HUMAN	carnitine palmitoyltransferase 1B (muscle)	216					carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	carnitine O-palmitoyltransferase activity (GO:0004095)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		all cancers(3;3.56e-77)|OV - Ovarian serous cystadenocarcinoma(4;5.39e-74)|Epithelial(4;5.58e-70)|GBM - Glioblastoma multiforme(4;5.59e-08)|LUAD - Lung adenocarcinoma(64;0.0016)|Lung(4;0.00942)|BRCA - Breast invasive adenocarcinoma(115;0.207)		AGCCTGGGGGCAGTCTTGTCCT	0.535											OREG0026685	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									Esophageal Squamous(170;988 1933 25577 30295 48163)	dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			U62733	CCDS14098.1, CCDS46734.1	22q13.33	2007-07-26			ENSG00000205560	ENSG00000205560			2329	protein-coding gene	gene with protein product		601987				9070950	Standard	NM_152245		Approved	M-CPT1, CPT1-M	uc003bmm.3	Q92523	OTTHUMG00000137390	ENST00000360719.2:c.645_646insA	22.37:g.51014680_51014681insT	ENSP00000353945:p.Ala216fs	Somatic	974	WXS	Illumina GAIIx	Phase_IV	B7Z4U4|B7Z5T8|E9PCP2|Q13389|Q99655|Q9BY90	Frame_Shift_Ins	INS	pfam_Carn_acyl_trans	p.A215fs	ENST00000360719.2	37	c.646_645	CCDS14098.1	22																																																																																			CPT1B	-	pfam_Carn_acyl_trans	ENSG00000205560		0.535	CPT1B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	CPT1B	HGNC	protein_coding	OTTHUMT00000317264.5	47	0.00	0	-	NM_152246		51014680	51014681	-1	no_errors	ENST00000312108	ensembl	human	known	69_37n	frame_shift_ins	8	46.67	7	INS	1.000:0.970	T
DENND3	22898	genome.wustl.edu	37	8	142161880	142161880	+	Missense_Mutation	SNP	G	G	A			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr8:142161880G>A	ENST00000262585.2	+	7	1056	c.778G>A	c.(778-780)Gcc>Acc	p.A260T	DENND3_ENST00000424248.1_Missense_Mutation_p.A260T|DENND3_ENST00000519811.1_Missense_Mutation_p.A340T	NM_014957.2	NP_055772.2	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	260	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				cellular protein catabolic process (GO:0044257)|endosome to lysosome transport (GO:0008333)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(4)|stomach(2)|urinary_tract(1)	55	all_cancers(97;7.36e-15)|all_epithelial(106;2.33e-13)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.105)			TTTCGTCATGGCCCCCACGTC	0.557																																						dbGAP											0													147.0	124.0	132.0					8																	142161880		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB020677	CCDS34947.1	8q24.3	2013-01-10				ENSG00000105339		"""DENN/MADD domain containing"", ""WD repeat domain containing"""	29134	protein-coding gene	gene with protein product						10048485	Standard	NM_014957		Approved	KIAA0870	uc003yvy.3	A2RUS2		ENST00000262585.2:c.778G>A	8.37:g.142161880G>A	ENSP00000262585:p.Ala260Thr	Somatic		WXS	Illumina GAIIx	Phase_IV	B7ZM28|O94947|Q2TAM7|Q6ZMS6|Q96DK3	Missense_Mutation	SNP	pfam_DENN_dom,pfam_dDENN_dom,pfam_WD40_repeat,pfam_uDENN_dom,superfamily_WD40_repeat_dom,smart_DENN_dom,smart_dDENN_dom,smart_WD40_repeat,pfscan_DENN_dom,pfscan_uDENN_dom,pfscan_dDENN_dom,pfscan_WD40_repeat_dom	p.A260T	ENST00000262585.2	37	c.778	CCDS34947.1	8	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	36|36	5.823602|5.823602	0.96989|0.96989	.|.	.|.	ENSG00000105339|ENSG00000105339	ENST00000262585;ENST00000424248;ENST00000519811;ENST00000520986|ENST00000518668	T;T;T;T|.	0.15603|.	2.41;2.41;2.41;2.41|.	5.71|5.71	5.71|5.71	0.89125|0.89125	DENN (3);|.	0.151304|.	0.64402|.	D|.	0.000017|.	D|D	0.85754|0.85754	0.5770|0.5770	M|M	0.90019|0.90019	3.08|3.08	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.83275|.	0.996;0.994|.	D|D	0.87538|0.87538	0.2457|0.2457	10|5	0.45353|.	T|.	0.12|.	-25.3052|-25.3052	19.8344|19.8344	0.96650|0.96650	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	340;260|.	E9PF32;A2RUS2|.	.;DEND3_HUMAN|.	T|D	260;260;340;262|316	ENSP00000262585:A260T;ENSP00000410594:A260T;ENSP00000428714:A340T;ENSP00000429780:A262T|.	ENSP00000262585:A260T|.	A|G	+|+	1|2	0|0	DENND3|DENND3	142231062|142231062	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.942000|0.942000	0.58702|0.58702	9.353000|9.353000	0.97080|0.97080	2.691000|2.691000	0.91804|0.91804	0.563000|0.563000	0.77884|0.77884	GCC|GGC	DENND3	-	pfam_DENN_dom,smart_DENN_dom,pfscan_DENN_dom	ENSG00000105339		0.557	DENND3-201	KNOWN	basic|CCDS	protein_coding	DENND3	HGNC	protein_coding		198	0.00	0	G	NM_014957		142161880	142161880	+1	no_errors	ENST00000262585	ensembl	human	known	69_37n	missense	214	21.74	60	SNP	1.000	A
FBN3	84467	genome.wustl.edu	37	19	8188382	8188383	+	Frame_Shift_Ins	INS	-	-	C			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr19:8188382_8188383insC	ENST00000600128.1	-	24	3461_3462	c.3047_3048insG	c.(3046-3048)ggcfs	p.G1016fs	FBN3_ENST00000601739.1_Frame_Shift_Ins_p.G1016fs|FBN3_ENST00000270509.2_Frame_Shift_Ins_p.G1016fs			Q75N90	FBN3_HUMAN	fibrillin 3	1016	EGF-like 12; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						CCAGGGCGAAGCCCCCCGCACA	0.589																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0				CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.3048dupG	19.37:g.8188388_8188388dupC	ENSP00000470498:p.Gly1016fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Frame_Shift_Ins	INS	pfam_EGF-like_Ca-bd,pfam_TB_dom,pfam_EGF-like_dom,superfamily_TB_dom,smart_EGF-like,smart_EGF-like_Ca-bd,pirsf_Fibrillin,pfscan_EG-like_dom	p.F1017fs	ENST00000600128.1	37	c.3048_3047	CCDS12196.1	19																																																																																			FBN3	-	pfam_EGF-like_Ca-bd,smart_EGF-like_Ca-bd,smart_EGF-like,pirsf_Fibrillin,pfscan_EG-like_dom	ENSG00000142449		0.589	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FBN3	HGNC	protein_coding	OTTHUMT00000461428.2	42	0.00	0	-	NM_032447		8188382	8188383	-1	no_errors	ENST00000270509	ensembl	human	known	69_37n	frame_shift_ins	16	15.79	3	INS	1.000:1.000	C
FIP1L1	81608	genome.wustl.edu	37	4	54319224	54319224	+	Silent	SNP	C	C	A			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr4:54319224C>A	ENST00000337488.6	+	16	1617	c.1423C>A	c.(1423-1425)Cgg>Agg	p.R475R	FIP1L1_ENST00000306932.6_Silent_p.R401R|FIP1L1_ENST00000358575.5_Silent_p.R469R|FIP1L1_ENST00000507166.1_Intron	NM_030917.3	NP_112179.2	Q6UN15	FIP1_HUMAN	factor interacting with PAPOLA and CPSF1	475	Arg-rich.|Sufficient for interaction with CPSF1 and CSTF3.				mRNA processing (GO:0006397)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.R475W(1)		large_intestine(3)|liver(1)|ovary(1)|skin(1)	6			GBM - Glioblastoma multiforme(3;3.31e-36)|LUSC - Lung squamous cell carcinoma(32;0.0134)			agaccgtgatcgggacagaga	0.507			T	PDGFRA	idiopathic hypereosinophilic syndrome																																	dbGAP		Dom	yes		4	4q12	81608	FIP1 like 1 (S. cerevisiae)		L	1	Substitution - Missense(1)	large_intestine(1)											79.0	70.0	73.0					4																	54319224		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF161429	CCDS3491.1, CCDS47055.1, CCDS47056.1	4q12	2013-06-18	2013-06-18		ENSG00000145216	ENSG00000145216			19124	protein-coding gene	gene with protein product		607686	"""FIP1 like 1 (S. cerevisiae)"", ""FIP1L1 cleavage and polyadenylation specific factor subunit"""			11230166, 14749727	Standard	NM_030917		Approved	DKFZp586K0717, FIP1	uc003hae.3	Q6UN15	OTTHUMG00000128701	ENST00000337488.6:c.1423C>A	4.37:g.54319224C>A		Somatic		WXS	Illumina GAIIx	Phase_IV	B4DIR3|G3XAD6|Q0VGE0|Q499Y4|Q49AU3|Q7Z608|Q8WVN3|Q96F80|Q9H077	Silent	SNP	pfam_Fip1	p.R475	ENST00000337488.6	37	c.1423	CCDS3491.1	4																																																																																			FIP1L1	-	NULL	ENSG00000145216		0.507	FIP1L1-001	KNOWN	basic|CCDS	protein_coding	FIP1L1	HGNC	protein_coding	OTTHUMT00000250602.1	202	0.00	0	C	NM_030917		54319224	54319224	+1	no_errors	ENST00000337488	ensembl	human	known	69_37n	silent	99	29.79	42	SNP	0.990	A
GABRA1	2554	genome.wustl.edu	37	5	161281210	161281210	+	Missense_Mutation	SNP	G	G	A			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr5:161281210G>A	ENST00000428797.2	+	4	476	c.121G>A	c.(121-123)Gtc>Atc	p.V41I	GABRA1_ENST00000444819.1_Missense_Mutation_p.V41I|GABRA1_ENST00000437025.2_Missense_Mutation_p.V41I|GABRA1_ENST00000023897.6_Missense_Mutation_p.V41I|GABRA1_ENST00000420560.1_Missense_Mutation_p.V41I|GABRA1_ENST00000393943.4_Missense_Mutation_p.V41I	NM_001127643.1	NP_001121115.1	P14867	GBRA1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 1	41					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|drug binding (GO:0008144)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|endometrium(2)|kidney(3)|large_intestine(4)|liver(1)|lung(22)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(1)	42	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.228)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethanol(DB00898)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methohexital(DB00474)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Prazepam(DB01588)|Primidone(DB00794)|Progabide(DB00837)|Propofol(DB00818)|Quazepam(DB01589)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiamylal(DB01154)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zaleplon(DB00962)|Zolpidem(DB00425)|Zopiclone(DB01198)	CAATACCACTGTCTTCACCAG	0.363																																						dbGAP											0													110.0	113.0	112.0					5																	161281210		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS4357.1	5q34	2012-06-22			ENSG00000022355	ENSG00000022355		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4075	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 1"""	137160				1330891	Standard	NM_000806		Approved	EJM5	uc003lyx.4	P14867	OTTHUMG00000163586	ENST00000428797.2:c.121G>A	5.37:g.161281210G>A	ENSP00000393097:p.Val41Ile	Somatic		WXS	Illumina GAIIx	Phase_IV	D3DQK6|Q8N629	Missense_Mutation	SNP	pfam_Neur_chan_lig-bd,pfam_Neurotrans-gated_channel_TM,superfamily_Neur_chan_lig-bd,superfamily_Neurotrans-gated_channel_TM,prints_GABAAa_rcpt,prints_GABAA_rcpt,prints_GABBAa1_rcpt,prints_Neur_channel,prints_GABBAg_rcpt,tigrfam_Neur_channel	p.V41I	ENST00000428797.2	37	c.121	CCDS4357.1	5	.	.	.	.	.	.	.	.	.	.	G	8.175	0.792614	0.16258	.	.	ENSG00000022355	ENST00000023897;ENST00000428797;ENST00000393943;ENST00000437025;ENST00000521339;ENST00000420560;ENST00000522651;ENST00000444819;ENST00000519621	T;T;T;T;T;T;T;T;T	0.78126	-1.15;-1.15;-1.15;-1.15;-0.41;-1.15;-0.41;-1.15;-0.4	5.51	5.51	0.81932	Neurotransmitter-gated ion-channel ligand-binding (1);	0.000000	0.85682	D	0.000000	T	0.57417	0.2052	N	0.14661	0.345	0.48236	D	0.999619	B	0.06786	0.001	B	0.04013	0.001	T	0.53208	-0.8471	10	0.07990	T	0.79	.	10.2866	0.43570	0.1466:0.0:0.8534:0.0	.	41	P14867	GBRA1_HUMAN	I	41;41;41;41;47;41;41;41;41	ENSP00000023897:V41I;ENSP00000393097:V41I;ENSP00000377517:V41I;ENSP00000415441:V41I;ENSP00000430895:V47I;ENSP00000408041:V41I;ENSP00000430507:V41I;ENSP00000414232:V41I;ENSP00000430435:V41I	ENSP00000023897:V41I	V	+	1	0	GABRA1	161213788	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.405000	0.59741	2.746000	0.94184	0.591000	0.81541	GTC	GABRA1	-	superfamily_Neur_chan_lig-bd,prints_GABAAa_rcpt,tigrfam_Neur_channel	ENSG00000022355		0.363	GABRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GABRA1	HGNC	protein_coding	OTTHUMT00000252702.2	158	0.00	0	G	NM_000806.5		161281210	161281210	+1	no_errors	ENST00000023897	ensembl	human	known	69_37n	missense	123	11.51	16	SNP	1.000	A
GPR125	166647	genome.wustl.edu	37	4	22390729	22390729	+	Missense_Mutation	SNP	C	C	A			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr4:22390729C>A	ENST00000334304.5	-	18	2974	c.2705G>T	c.(2704-2706)aGt>aTt	p.S902I	GPR125_ENST00000282943.5_5'UTR	NM_145290.3	NP_660333.2	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125	902					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(33)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	56		Breast(46;0.198)				GTTTGGCCGACTGCCGTAATT	0.413																																						dbGAP											0													215.0	225.0	221.0					4																	22390729		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK095866	CCDS33964.1	4p15.31	2014-08-08			ENSG00000152990	ENSG00000152990		"""-"", ""GPCR / Class B : Orphans"", ""Immunoglobulin superfamily / I-set domain containing"""	13839	protein-coding gene	gene with protein product		612303				12565841	Standard	NM_145290		Approved	FLJ38547, PGR21	uc003gqm.2	Q8IWK6	OTTHUMG00000160926	ENST00000334304.5:c.2705G>T	4.37:g.22390729C>A	ENSP00000334952:p.Ser902Ile	Somatic		WXS	Illumina GAIIx	Phase_IV	Q6UXK9|Q86SQ5|Q8TC55	Missense_Mutation	SNP	pfam_GPCR_2_secretin-like,pfam_GPS_dom,pfam_Leu-rich_rpt,pfam_Ig_I-set,pfam_GPCR_2_extracellular_dom,smart_Leu-rich_rpt_typical-subtyp,smart_Cys-rich_flank_reg_C,smart_Ig_sub,smart_GPS_dom,pfscan_GPS_dom,pfscan_GPCR_2_extracellular_dom,pfscan_GPCR_2-like,pfscan_Ig-like	p.S902I	ENST00000334304.5	37	c.2705	CCDS33964.1	4	.	.	.	.	.	.	.	.	.	.	C	22.1	4.248758	0.80024	.	.	ENSG00000152990	ENST00000334304	T	0.44482	0.92	5.85	5.85	0.93711	GPCR, family 2-like (1);	0.000000	0.85682	D	0.000000	T	0.59059	0.2166	L	0.49350	1.555	0.80722	D	1	P;D	0.76494	0.544;0.999	B;D	0.71184	0.316;0.972	T	0.45585	-0.9251	10	0.19590	T	0.45	-2.7607	20.1496	0.98084	0.0:1.0:0.0:0.0	.	759;902	Q8IWK6-3;Q8IWK6	.;GP125_HUMAN	I	902	ENSP00000334952:S902I	ENSP00000334952:S902I	S	-	2	0	GPR125	21999827	1.000000	0.71417	0.999000	0.59377	0.973000	0.67179	7.484000	0.81180	2.755000	0.94549	0.655000	0.94253	AGT	GPR125	-	pfam_GPCR_2_secretin-like,pfscan_GPCR_2-like	ENSG00000152990		0.413	GPR125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GPR125	HGNC	protein_coding	OTTHUMT00000362960.3	829	0.00	0	C			22390729	22390729	-1	no_errors	ENST00000334304	ensembl	human	known	69_37n	missense	417	17.39	88	SNP	1.000	A
GRIN2B	2904	genome.wustl.edu	37	12	13722814	13722814	+	Missense_Mutation	SNP	G	G	A			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr12:13722814G>A	ENST00000609686.1	-	11	2518	c.2309C>T	c.(2308-2310)tCt>tTt	p.S770F		NM_000834.3	NP_000825.2	Q13224	NMDE2_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2B	770					behavioral fear response (GO:0001662)|behavioral response to pain (GO:0048266)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|glutamate receptor signaling pathway (GO:0007215)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning (GO:0007612)|learning or memory (GO:0007611)|memory (GO:0007613)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic plasticity (GO:0048167)|response to ethanol (GO:0045471)|sensory organ development (GO:0007423)|startle response (GO:0001964)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)	p.S770Y(1)		NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(12)|liver(1)|lung(70)|ovary(4)|prostate(6)|skin(10)|upper_aerodigestive_tract(5)|urinary_tract(1)	143					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Haloperidol(DB00502)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CTTCCACCCAGAATCTTTTTG	0.512																																						dbGAP											1	Substitution - Missense(1)	large_intestine(1)											74.0	62.0	66.0					12																	13722814		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS8662.1	12p13.1	2014-07-16			ENSG00000273079			"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4586	protein-coding gene	gene with protein product		138252		NMDAR2B		1350383	Standard	NM_000834		Approved	GluN2B	uc001rbt.2	Q13224	OTTHUMG00000137373	ENST00000609686.1:c.2309C>T	12.37:g.13722814G>A	ENSP00000477455:p.Ser770Phe	Somatic		WXS	Illumina GAIIx	Phase_IV	Q12919|Q13220|Q13225|Q14CU4|Q9UM56	Missense_Mutation	SNP	pfam_NMDAR2_C,pfam_Iontro_glu_rcpt,pfam_SBP_bac_3,pfam_Glu_rcpt_Glu/Gly-bd,pfam_ANF_lig-bd_rcpt,smart_Iontro_glu_rcpt,smart_Glu_rcpt_Glu/Gly-bd,prints_NMDA_rcpt	p.S770F	ENST00000609686.1	37	c.2309	CCDS8662.1	12	.	.	.	.	.	.	.	.	.	.	G	21.6	4.175999	0.78564	.	.	ENSG00000150086	ENST00000279593	T	0.58210	0.35	5.55	5.55	0.83447	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (2);	0.066155	0.64402	D	0.000005	T	0.74374	0.3708	M	0.80847	2.515	0.80722	D	1	D	0.62365	0.991	D	0.65233	0.933	T	0.77694	-0.2492	10	0.87932	D	0	.	19.5042	0.95108	0.0:0.0:1.0:0.0	.	770	Q13224	NMDE2_HUMAN	F	770	ENSP00000279593:S770F	ENSP00000279593:S770F	S	-	2	0	GRIN2B	13614081	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.944000	0.87722	2.590000	0.87494	0.655000	0.94253	TCT	GRIN2B	-	pfam_Iontro_glu_rcpt,pfam_SBP_bac_3,smart_Iontro_glu_rcpt	ENSG00000150086		0.512	GRIN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GRIN2B	HGNC	protein_coding	OTTHUMT00000268014.2	135	0.00	0	G			13722814	13722814	-1	no_errors	ENST00000279593	ensembl	human	known	69_37n	missense	124	17.76	27	SNP	1.000	A
GUCY1A3	2982	genome.wustl.edu	37	4	156618138	156618138	+	Missense_Mutation	SNP	G	G	T	rs531839582		TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr4:156618138G>T	ENST00000296518.7	+	3	328	c.119G>T	c.(118-120)tGc>tTc	p.C40F	GUCY1A3_ENST00000511108.1_Missense_Mutation_p.C40F|GUCY1A3_ENST00000393832.3_5'UTR|GUCY1A3_ENST00000513574.1_Missense_Mutation_p.C40F|GUCY1A3_ENST00000515602.1_3'UTR|GUCY1A3_ENST00000455639.2_Missense_Mutation_p.C40F|GUCY1A3_ENST00000511507.1_Missense_Mutation_p.C40F|GUCY1A3_ENST00000506455.1_Missense_Mutation_p.C40F			Q02108	GCYA3_HUMAN	guanylate cyclase 1, soluble, alpha 3	40					blood circulation (GO:0008015)|blood coagulation (GO:0007596)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of cGMP biosynthetic process (GO:0030828)|regulation of blood pressure (GO:0008217)|relaxation of vascular smooth muscle (GO:0060087)|response to defense-related host nitric oxide production (GO:0052565)	guanylate cyclase complex, soluble (GO:0008074)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)|receptor activity (GO:0004872)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|liver(2)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.17)		TCAGAGAGCTGCAAAGCAACC	0.483																																						dbGAP											0													105.0	98.0	100.0					4																	156618138		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS34085.1, CCDS54812.1	4q31.3-q33	2008-03-18				ENSG00000164116	4.6.1.2		4685	protein-coding gene	gene with protein product		139396		GUC1A3		1352257	Standard	NM_001130687		Approved	GC-SA3	uc003iow.3	Q02108		ENST00000296518.7:c.119G>T	4.37:g.156618138G>T	ENSP00000296518:p.Cys40Phe	Somatic		WXS	Illumina GAIIx	Phase_IV	D3DP19|D6RDW3|O43843|Q8TAH3	Missense_Mutation	SNP	pfam_A/G_cyclase,pfam_Haem_no_assoc-bd,pfam_Heme_NO-bd,superfamily_A/G_cyclase,superfamily_NO_sig/Golgi_transp_ligand-bd,smart_A/G_cyclase,pfscan_A/G_cyclase	p.C40F	ENST00000296518.7	37	c.119	CCDS34085.1	4	.	.	.	.	.	.	.	.	.	.	G	10.08	1.252112	0.22880	.	.	ENSG00000164116	ENST00000506455;ENST00000511108;ENST00000511507;ENST00000455639;ENST00000296518;ENST00000513574	D;D;D;D;D;D	0.84660	-1.88;-1.88;-1.73;-1.88;-1.88;-1.88	5.93	3.06	0.35304	.	0.815843	0.11242	N	0.584559	T	0.76666	0.4019	L	0.29908	0.895	0.09310	N	1	B;B;B	0.13145	0.007;0.007;0.0	B;B;B	0.12837	0.008;0.008;0.0	T	0.66236	-0.5974	10	0.59425	D	0.04	.	8.0484	0.30564	0.0769:0.1613:0.6638:0.098	.	40;40;40	B3KU69;Q02108;D6RDW3	.;GCYA3_HUMAN;.	F	40	ENSP00000424361:C40F;ENSP00000421493:C40F;ENSP00000426968:C40F;ENSP00000412201:C40F;ENSP00000296518:C40F;ENSP00000426040:C40F	ENSP00000296518:C40F	C	+	2	0	GUCY1A3	156837588	0.010000	0.17322	0.001000	0.08648	0.472000	0.32918	1.956000	0.40382	0.823000	0.34589	0.591000	0.81541	TGC	GUCY1A3	-	NULL	ENSG00000164116		0.483	GUCY1A3-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	GUCY1A3	HGNC	protein_coding	OTTHUMT00000365786.2	167	0.00	0	G			156618138	156618138	+1	no_errors	ENST00000296518	ensembl	human	known	69_37n	missense	82	18.00	18	SNP	0.000	T
HEATR2	54919	genome.wustl.edu	37	7	810169	810169	+	Silent	SNP	C	C	T			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr7:810169C>T	ENST00000297440.6	+	9	1865	c.1845C>T	c.(1843-1845)ccC>ccT	p.P615P	HEATR2_ENST00000313147.5_Silent_p.P615P|HEATR2_ENST00000403952.3_Silent_p.P40P	NM_017802.3	NP_060272.3	Q86Y56	HEAT2_HUMAN	HEAT repeat containing 2	615						cytoplasm (GO:0005737)				breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|prostate(4)|skin(1)	22		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0182)|Epithelial(4;5.48e-17)|OV - Ovarian serous cystadenocarcinoma(56;1.95e-16)|all cancers(6;2.98e-14)		GTCTGCAGCCCTCCCAAGACC	0.652																																						dbGAP											0													72.0	58.0	63.0					7																	810169		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AL832914, AK000404, NM_017802, AK056233	CCDS34580.1	7p22.3	2014-05-06	2006-05-19		ENSG00000164818	ENSG00000164818			26013	protein-coding gene	gene with protein product		614864				23040496	Standard	NM_017802		Approved	FLJ20397, FLJ31671, FLJ39381, FLJ25564, CILD18	uc010krz.1	Q86Y56	OTTHUMG00000151416	ENST00000297440.6:c.1845C>T	7.37:g.810169C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q69YL1|Q96FI9|Q9NX75	Missense_Mutation	SNP	pfam_HEAT,superfamily_ARM-type_fold,pfscan_HEAT_type_2	p.L417F	ENST00000297440.6	37	c.1249	CCDS34580.1	7	.	.	.	.	.	.	.	.	.	.	C	0.227	-1.023941	0.02061	.	.	ENSG00000164818	ENST00000440747	.	.	.	4.7	-9.4	0.00616	.	.	.	.	.	T	0.41743	0.1172	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46400	-0.9194	4	.	.	.	-30.0857	4.6187	0.12438	0.6005:0.1103:0.0749:0.2143	.	.	.	.	F	417	.	.	L	+	1	0	HEATR2	776695	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-1.893000	0.01609	-2.059000	0.00894	-0.857000	0.03018	CTC	HEATR2	-	superfamily_ARM-type_fold	ENSG00000164818		0.652	HEATR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HEATR2	HGNC	protein_coding	OTTHUMT00000322542.1	25	0.00	0	C	NM_017802		810169	810169	+1	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000440747	ensembl	human	novel	69_37n	missense	16	40.74	11	SNP	0.000	T
HSPD1	3329	genome.wustl.edu	37	2	198352668	198352668	+	Missense_Mutation	SNP	T	T	G			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr2:198352668T>G	ENST00000388968.3	-	11	1750	c.1483A>C	c.(1483-1485)Atg>Ctg	p.M495L	HSPD1_ENST00000345042.2_Missense_Mutation_p.M495L	NM_002156.4	NP_002147.2	P10809	CH60_HUMAN	heat shock 60kDa protein 1 (chaperonin)	495					'de novo' protein folding (GO:0006458)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|ATP catabolic process (GO:0006200)|B cell activation (GO:0042113)|B cell cytokine production (GO:0002368)|B cell proliferation (GO:0042100)|chaperone-mediated protein complex assembly (GO:0051131)|isotype switching to IgG isotypes (GO:0048291)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of apoptotic process (GO:0043066)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage activation (GO:0043032)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell mediated immune response to tumor cell (GO:0002842)|protein maturation (GO:0051604)|protein refolding (GO:0042026)|protein stabilization (GO:0050821)|response to unfolded protein (GO:0006986)|T cell activation (GO:0042110)|viral process (GO:0016032)	cell surface (GO:0009986)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lipopolysaccharide receptor complex (GO:0046696)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|secretory granule (GO:0030141)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|chaperone binding (GO:0051087)|DNA replication origin binding (GO:0003688)|double-stranded RNA binding (GO:0003725)|lipopolysaccharide binding (GO:0001530)|p53 binding (GO:0002039)|poly(A) RNA binding (GO:0044822)|single-stranded DNA binding (GO:0003697)|unfolded protein binding (GO:0051082)			NS(1)|breast(3)|endometrium(2)|large_intestine(3)|lung(7)|skin(1)	17			Epithelial(96;0.225)			GAACTTTGCATAATTTTCTCA	0.358																																						dbGAP											0													63.0	62.0	62.0					2																	198352668		2203	4299	6502	-	-	-	SO:0001583	missense	0			M34664	CCDS33357.1	2q33.1	2011-09-02	2002-08-29		ENSG00000144381	ENSG00000144381		"""Heat Shock Proteins / Chaperonins"""	5261	protein-coding gene	gene with protein product		118190	"""heat shock 60kD protein 1 (chaperonin)"", ""spastic paraplegia 13 (autosomal dominant)"""	SPG13		1980192, 11898127	Standard	NM_002156		Approved	GROEL, HSP60	uc002uui.3	P10809	OTTHUMG00000154463	ENST00000388968.3:c.1483A>C	2.37:g.198352668T>G	ENSP00000373620:p.Met495Leu	Somatic		WXS	Illumina GAIIx	Phase_IV	B2R5M6|B7Z712|Q38L19|Q9UCR6	Missense_Mutation	SNP	pfam_Cpn60/TCP-1,superfamily_Cpn60/TCP-1,prints_Chaprnin_Cpn60,prints_Chaperone_TCP-1,tigrfam_Chaprnin_Cpn60	p.M495L	ENST00000388968.3	37	c.1483	CCDS33357.1	2	.	.	.	.	.	.	.	.	.	.	T	6.333	0.429494	0.11987	.	.	ENSG00000144381	ENST00000388968;ENST00000345042	T;T	0.75938	-0.98;-0.98	5.26	-10.5	0.00291	.	0.460073	0.23865	N	0.043811	T	0.29491	0.0735	N	0.01631	-0.79	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.0	T	0.49360	-0.8948	10	0.02654	T	1	-3.3774	7.4228	0.27081	0.4107:0.0:0.2845:0.3048	.	486;495;495	B7Z597;B3GQS7;P10809	.;.;CH60_HUMAN	L	495	ENSP00000373620:M495L;ENSP00000340019:M495L	ENSP00000340019:M495L	M	-	1	0	HSPD1	198060913	0.989000	0.36119	0.323000	0.25347	0.982000	0.71751	0.110000	0.15437	-1.864000	0.01148	0.374000	0.22700	ATG	HSPD1	-	pfam_Cpn60/TCP-1,superfamily_Cpn60/TCP-1,tigrfam_Chaprnin_Cpn60	ENSG00000144381		0.358	HSPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HSPD1	HGNC	protein_coding	OTTHUMT00000335324.2	57	0.00	0	T	NM_002156		198352668	198352668	-1	no_errors	ENST00000345042	ensembl	human	known	69_37n	missense	46	17.86	10	SNP	0.632	G
IFNA7	3444	genome.wustl.edu	37	9	21201826	21201826	+	Nonsense_Mutation	SNP	G	G	T			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr9:21201826G>T	ENST00000239347.3	-	1	378	c.339C>A	c.(337-339)taC>taA	p.Y113*		NM_021057.2	NP_066401.2	P01567	IFNA7_HUMAN	interferon, alpha 7	113					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			endometrium(3)|kidney(1)|large_intestine(1)|liver(1)|lung(6)	12				GBM - Glioblastoma multiforme(5;4.75e-197)|Lung(24;1.26e-23)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)		TCAGTTGCTGGTAAAGTTCAG	0.478																																						dbGAP											0													62.0	71.0	68.0					9																	21201826		2202	4279	6481	-	-	-	SO:0001587	stop_gained	0				CCDS34995.1	9p22	2010-12-10			ENSG00000214042	ENSG00000214042		"""Interferons"""	5428	protein-coding gene	gene with protein product		147567				1385305	Standard	NM_021057		Approved	IFNA-J, IFN-alphaJ	uc003zop.1	P01567	OTTHUMG00000019662	ENST00000239347.3:c.339C>A	9.37:g.21201826G>T	ENSP00000239347:p.Tyr113*	Somatic		WXS	Illumina GAIIx	Phase_IV	Q14607|Q5VV14	Nonsense_Mutation	SNP	pfam_Interferon_alpha/beta/delta,superfamily_4_helix_cytokine-like_core,smart_Interferon_alpha/beta/delta,prints_Interferon_alpha/beta/delta	p.Y113*	ENST00000239347.3	37	c.339	CCDS34995.1	9	.	.	.	.	.	.	.	.	.	.	G	11.29	1.594421	0.28445	.	.	ENSG00000214042	ENST00000239347	.	.	.	3.71	-3.93	0.04143	.	1.002610	0.08037	N	0.994495	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.3547	0.16055	0.6803:0.1371:0.1826:0.0	.	.	.	.	X	113	.	ENSP00000239347:Y113X	Y	-	3	2	IFNA7	21191826	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.583000	0.05807	-0.869000	0.04052	-0.225000	0.12378	TAC	IFNA7	-	pfam_Interferon_alpha/beta/delta,superfamily_4_helix_cytokine-like_core,smart_Interferon_alpha/beta/delta	ENSG00000214042		0.478	IFNA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	IFNA7	HGNC	protein_coding	OTTHUMT00000051891.1	718	0.00	0	G	NM_021057		21201826	21201826	-1	no_errors	ENST00000239347	ensembl	human	known	69_37n	nonsense	474	13.66	75	SNP	0.000	T
ITGA2	3673	genome.wustl.edu	37	5	52382807	52382807	+	Missense_Mutation	SNP	C	C	T			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr5:52382807C>T	ENST00000296585.5	+	28	3427	c.3284C>T	c.(3283-3285)aCg>aTg	p.T1095M	CTD-2366F13.2_ENST00000606157.1_RNA	NM_002203.3	NP_002194.2	P17301	ITA2_HUMAN	integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)	1095					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell proliferation (GO:0008283)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular response to hormone stimulus (GO:0032870)|collagen-activated signaling pathway (GO:0038065)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|hepatocyte differentiation (GO:0070365)|hypotonic response (GO:0006971)|integrin-mediated signaling pathway (GO:0007229)|mammary gland development (GO:0030879)|mesodermal cell differentiation (GO:0048333)|organ morphogenesis (GO:0009887)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell projection organization (GO:0031346)|positive regulation of collagen binding (GO:0033343)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA binding (GO:0043388)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of translation (GO:0045727)|positive regulation of transmission of nerve impulse (GO:0051971)|response to amine (GO:0014075)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to L-ascorbic acid (GO:0033591)|response to muscle activity (GO:0014850)|response to organic cyclic compound (GO:0014070)|skin morphogenesis (GO:0043589)|substrate-dependent cell migration (GO:0006929)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	axon terminus (GO:0043679)|basal part of cell (GO:0045178)|cell outer membrane (GO:0009279)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin alpha2-beta1 complex (GO:0034666)|integrin complex (GO:0008305)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(1)|lung(18)|pancreas(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	47		Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181)				GTACAGCTAACGGCAGCTGCA	0.433																																						dbGAP											0													93.0	80.0	84.0					5																	52382807		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS3957.1	5q11.2	2010-03-23			ENSG00000164171	ENSG00000164171		"""CD molecules"", ""Integrins"""	6137	protein-coding gene	gene with protein product		192974		CD49B			Standard	NM_002203		Approved	CD49b	uc003joy.3	P17301	OTTHUMG00000131165	ENST00000296585.5:c.3284C>T	5.37:g.52382807C>T	ENSP00000296585:p.Thr1095Met	Somatic		WXS	Illumina GAIIx	Phase_IV	Q14595	Missense_Mutation	SNP	pfam_Integrin_alpha-2,pfam_VWF_A,pfam_FG-GAP,smart_Int_alpha_beta-p,smart_VWF_A,prints_Integrin_alpha,pfscan_VWF_A	p.T1095M	ENST00000296585.5	37	c.3284	CCDS3957.1	5	.	.	.	.	.	.	.	.	.	.	C	12.87	2.066801	0.36470	.	.	ENSG00000164171	ENST00000296585	T	0.48522	0.81	6.06	2.84	0.33178	.	0.366754	0.32028	N	0.006689	T	0.43722	0.1260	M	0.66939	2.045	0.21878	N	0.999492	D	0.56746	0.977	P	0.45971	0.499	T	0.35351	-0.9792	10	0.37606	T	0.19	.	4.8468	0.13517	0.1584:0.5838:0.0:0.2578	.	1095	P17301	ITA2_HUMAN	M	1095	ENSP00000296585:T1095M	ENSP00000296585:T1095M	T	+	2	0	ITGA2	52418564	0.100000	0.21855	0.884000	0.34674	0.067000	0.16453	0.366000	0.20365	1.481000	0.48307	-0.355000	0.07637	ACG	ITGA2	-	NULL	ENSG00000164171		0.433	ITGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ITGA2	HGNC	protein_coding	OTTHUMT00000253857.2	88	0.00	0	C	NM_002203		52382807	52382807	+1	no_errors	ENST00000296585	ensembl	human	known	69_37n	missense	39	17.02	8	SNP	0.380	T
ITGB1	3688	genome.wustl.edu	37	10	33217124	33217124	+	Missense_Mutation	SNP	T	T	G			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr10:33217124T>G	ENST00000396033.2	-	5	580	c.445A>C	c.(445-447)Atg>Ctg	p.M149L	ITGB1_ENST00000484088.1_Intron|ITGB1_ENST00000302278.3_Missense_Mutation_p.M149L|ITGB1_ENST00000374956.4_Missense_Mutation_p.M149L|ITGB1_ENST00000423113.1_Missense_Mutation_p.M149L	NM_133376.2	NP_596867.1	P05556	ITB1_HUMAN	integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12)	149	VWFA.				axon extension (GO:0048675)|axon guidance (GO:0007411)|B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cardiac muscle cell differentiation (GO:0055007)|cell fate specification (GO:0001708)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular calcium ion homeostasis (GO:0006874)|cellular defense response (GO:0006968)|cellular response to ionizing radiation (GO:0071479)|cellular response to mechanical stimulus (GO:0071260)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|formation of radial glial scaffolds (GO:0021943)|G1/S transition of mitotic cell cycle (GO:0000082)|germ cell migration (GO:0008354)|heterotypic cell-cell adhesion (GO:0034113)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|maternal process involved in female pregnancy (GO:0060135)|mesodermal cell differentiation (GO:0048333)|negative regulation of anoikis (GO:2000811)|negative regulation of cell projection organization (GO:0031345)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of endocytosis (GO:0045807)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein transport within lipid bilayer (GO:0032594)|regulation of cell cycle (GO:0051726)|regulation of collagen catabolic process (GO:0010710)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of immune response (GO:0050776)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|response to transforming growth factor beta (GO:0071559)|sarcomere organization (GO:0045214)|tight junction assembly (GO:0070830)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	acrosomal vesicle (GO:0001669)|basement membrane (GO:0005604)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integrin alpha1-beta1 complex (GO:0034665)|integrin alpha10-beta1 complex (GO:0034680)|integrin alpha11-beta1 complex (GO:0034681)|integrin alpha2-beta1 complex (GO:0034666)|integrin alpha3-beta1 complex (GO:0034667)|integrin alpha7-beta1 complex (GO:0034677)|integrin alpha8-beta1 complex (GO:0034678)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|intercalated disc (GO:0014704)|invadopodium membrane (GO:0071438)|membrane (GO:0016020)|membrane raft (GO:0045121)|myelin sheath abaxonal region (GO:0035748)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|cell adhesion molecule binding (GO:0050839)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)|peptide binding (GO:0042277)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|virus receptor activity (GO:0001618)	p.M149V(2)		autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Ovarian(717;1.34e-05)|Breast(68;0.0634)			Antithymocyte globulin(DB00098)	GACAGGTCCATAAGGTAGTAG	0.368																																						dbGAP											2	Substitution - Missense(2)	lung(2)											151.0	149.0	150.0					10																	33217124		2203	4300	6503	-	-	-	SO:0001583	missense	0			BC020057	CCDS7174.1	10p11.2	2010-10-13			ENSG00000150093	ENSG00000150093		"""CD molecules"", ""Integrins"""	6153	protein-coding gene	gene with protein product		135630		FNRB, MSK12, MDF2		2524991	Standard	NM_033668		Approved	CD29, GPIIA	uc001iwt.4	P05556	OTTHUMG00000017928	ENST00000396033.2:c.445A>C	10.37:g.33217124T>G	ENSP00000379350:p.Met149Leu	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K6N2|D3DRX9|D3DRY3|D3DRY4|D3DRY5|P78466|P78467|Q13089|Q13090|Q13091|Q13212|Q14622|Q14647|Q29RW2|Q7Z3V1|Q8WUM6	Missense_Mutation	SNP	pirsf_Integrin_bsu,pfam_Integrin_bsu_N,pfam_Integrin_bsu_tail,pfam_Integrin_bsu_cyt,pfam_EGF_extracell,superfamily_Integrin_bsu_tail,superfamily_Plexin-like_fold,smart_Plexin-like,smart_Integrin_bsu_N,prints_Integrin_bsu	p.M149L	ENST00000396033.2	37	c.445	CCDS7174.1	10	.	.	.	.	.	.	.	.	.	.	T	29.9	5.044383	0.93685	.	.	ENSG00000150093	ENST00000396033;ENST00000423113;ENST00000302278;ENST00000374956;ENST00000480226;ENST00000474568;ENST00000488494	D;D;D;D;D;D;D	0.94537	-3.45;-3.45;-3.45;-3.45;-3.45;-3.45;-3.45	6.07	6.07	0.98685	Integrin beta subunit, N-terminal (2);von Willebrand factor, type A (1);	0.000000	0.85682	D	0.000000	D	0.97015	0.9025	M	0.91510	3.215	0.80722	D	1	P;P;B;P;P	0.48089	0.492;0.654;0.415;0.905;0.565	B;B;B;P;B	0.52109	0.276;0.398;0.267;0.69;0.326	D	0.97628	1.0140	10	0.87932	D	0	.	16.6407	0.85098	0.0:0.0:0.0:1.0	.	149;149;149;149;149	P05556-2;P05556;P05556-5;P05556-3;P05556-4	.;ITB1_HUMAN;.;.;.	L	149;149;149;149;149;92;152	ENSP00000379350:M149L;ENSP00000388694:M149L;ENSP00000303351:M149L;ENSP00000364094:M149L;ENSP00000417537:M149L;ENSP00000420282:M92L;ENSP00000418725:M152L	ENSP00000303351:M149L	M	-	1	0	ITGB1	33257130	1.000000	0.71417	0.964000	0.40570	0.801000	0.45260	8.013000	0.88655	2.326000	0.78906	0.533000	0.62120	ATG	ITGB1	-	pirsf_Integrin_bsu,pfam_Integrin_bsu_N,smart_Integrin_bsu_N,prints_Integrin_bsu	ENSG00000150093		0.368	ITGB1-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	ITGB1	HGNC	protein_coding	OTTHUMT00000047496.1	347	0.00	0	T	NM_002211		33217124	33217124	-1	no_errors	ENST00000374956	ensembl	human	known	69_37n	missense	137	28.65	55	SNP	1.000	G
KCNK13	56659	genome.wustl.edu	37	14	90651284	90651285	+	Frame_Shift_Ins	INS	-	-	G			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr14:90651284_90651285insG	ENST00000282146.4	+	2	1605_1606	c.1164_1165insG	c.(1165-1167)gggfs	p.G389fs		NM_022054.2	NP_071337.2	Q9HB14	KCNKD_HUMAN	potassium channel, subfamily K, member 13	389			G -> A (in dbSNP:rs35909577).		synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)	p.G389W(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(12)|prostate(1)|skin(4)	25		all_cancers(154;0.186)				ATGAATTCTCAGGGGGGGTGGG	0.589																																						dbGAP											1	Substitution - Missense(1)	lung(1)																																								-	-	-	SO:0001589	frameshift_variant	0			AF287303	CCDS9889.1	14q32.11	2012-03-07				ENSG00000152315		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6275	protein-coding gene	gene with protein product		607367				11060316, 16382106	Standard	NM_022054		Approved	K2p13.1, THIK-1, THIK1	uc001xye.1	Q9HB14		ENST00000282146.4:c.1171dupG	14.37:g.90651291_90651291dupG	ENSP00000282146:p.Gly389fs	Somatic		WXS	Illumina GAIIx	Phase_IV	B5TJL8|Q96E79	Frame_Shift_Ins	INS	pfam_Ion_trans_2,prints_2pore_dom_K_chnl_THIK,prints_2pore_dom_K_chnl,prints_2pore_dom_K_chnl_TASK	p.V390fs	ENST00000282146.4	37	c.1164_1165	CCDS9889.1	14																																																																																			KCNK13	-	NULL	ENSG00000152315		0.589	KCNK13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KCNK13	HGNC	protein_coding	OTTHUMT00000411251.1	57	0.00	0	-	NM_022054		90651284	90651285	+1	no_errors	ENST00000282146	ensembl	human	known	69_37n	frame_shift_ins	36	10.00	4	INS	0.587:1.000	G
KIAA0907	22889	genome.wustl.edu	37	1	155886454	155886454	+	Silent	SNP	C	C	T			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr1:155886454C>T	ENST00000368321.3	-	12	1538	c.1515G>A	c.(1513-1515)aaG>aaA	p.K505K	KIAA0907_ENST00000368320.3_Silent_p.K505K	NM_014949.2	NP_055764.2	Q7Z7F0	K0907_HUMAN	KIAA0907	505							RNA binding (GO:0003723)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|urinary_tract(1)	21	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;8.82e-06)			AACTTGCTGGCTTCGATCCTG	0.413																																						dbGAP											0													152.0	160.0	157.0					1																	155886454		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			BC062637	CCDS30885.1	1q22	2012-11-30			ENSG00000132680	ENSG00000132680			29145	protein-coding gene	gene with protein product						10048485	Standard	NM_014949		Approved	BLOM7	uc001fmi.1	Q7Z7F0	OTTHUMG00000014103	ENST00000368321.3:c.1515G>A	1.37:g.155886454C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	O94981|Q7L7Q2|Q7Z7E9|Q8TBQ0	Silent	SNP	NULL	p.K505	ENST00000368321.3	37	c.1515	CCDS30885.1	1																																																																																			KIAA0907	-	NULL	ENSG00000132680		0.413	KIAA0907-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KIAA0907	HGNC	protein_coding	OTTHUMT00000039583.1	260	0.00	0	C	NM_014949		155886454	155886454	-1	no_errors	ENST00000368321	ensembl	human	known	69_37n	silent	201	28.87	82	SNP	1.000	T
LIMK1	3984	genome.wustl.edu	37	7	73520549	73520550	+	Missense_Mutation	DNP	GC	GC	TG			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	G|C	G|C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr7:73520549_73520550GC>TG	ENST00000336180.2	+	7	908_909	c.857_858GC>TG	c.(856-858)aGC>aTG	p.S286M	LIMK1_ENST00000418310.1_Missense_Mutation_p.S316M|LIMK1_ENST00000538333.3_Missense_Mutation_p.S252M	NM_002314.3	NP_002305.1	P53667	LIMK1_HUMAN	LIM domain kinase 1	286					actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|nervous system development (GO:0007399)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of axon extension (GO:0045773)|positive regulation of stress fiber assembly (GO:0051496)|protein phosphorylation (GO:0006468)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|nucleus (GO:0005634)	ATP binding (GO:0005524)|heat shock protein binding (GO:0031072)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	21		Lung NSC(55;0.137)			Dabrafenib(DB08912)	GAGGCGGGCAGCTCTGCCCGGC	0.653																																						dbGAP											0																																										-	-	-	SO:0001583	missense	0			D26309	CCDS5563.1, CCDS56491.1	7q11.23	2005-01-21			ENSG00000106683	ENSG00000106683			6613	protein-coding gene	gene with protein product		601329				8673124, 8812460	Standard	NM_002314		Approved	LIMK	uc003uaa.2	P53667	OTTHUMG00000023448	Exception_encountered	7.37:g.73520549_73520550delinsTG	ENSP00000336740:p.Ser286Met	Somatic		WXS	Illumina GAIIx	Phase_IV	B7Z6I8|D3DXF4|D3DXF5|O15283|Q15820|Q15821|Q75MU3|Q9Y5Q1	Missense_Mutation	SNP	pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_cat_dom,pfam_Znf_LIM,pfam_PDZ,pfam_LipoPS_kinase,superfamily_Kinase-like_dom,superfamily_PDZ,smart_Znf_LIM,smart_PDZ,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Znf_LIM,pfscan_PDZ,pfscan_Prot_kinase_cat_dom,prints_Ser-Thr/Tyr_kinase_cat_dom	p.S286I|p.S286R	ENST00000336180.2	37	c.857|c.858	CCDS5563.1	7																																																																																			LIMK1	-	NULL	ENSG00000106683		0.653	LIMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LIMK1	HGNC	protein_coding	OTTHUMT00000252335.2	73|74	0.00	0	G|C	NM_002314		73520549|73520550	73520549|73520550	+1	no_errors	ENST00000336180	ensembl	human	known	69_37n	missense	48|49	25.00|19.35	16|12	SNP	0.000	T|G
LMNB2	84823	genome.wustl.edu	37	19	2431861	2431862	+	Frame_Shift_Ins	INS	-	-	G	rs149126950	byFrequency	TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr19:2431861_2431862insG	ENST00000582871.1	-	10	1655_1656	c.1569_1570insC	c.(1567-1572)ccctcgfs	p.S524fs	LMNB2_ENST00000475819.1_5'Flank|LMNB2_ENST00000325327.3_Frame_Shift_Ins_p.S544fs	NM_032737.3	NP_116126.3	Q03252	LMNB2_HUMAN	lamin B2	524	LTD.|Tail.					lamin filament (GO:0005638)|nuclear inner membrane (GO:0005637)	structural molecule activity (GO:0005198)	p.S524fs*23(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18		Hepatocellular(1079;0.137)		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)		ACCAGCGTCGAGGGGGGGCTGT	0.678																																						dbGAP											1	Insertion - Frameshift(1)	large_intestine(1)																																								-	-	-	SO:0001589	frameshift_variant	0			M94362	CCDS12090.1, CCDS12090.2	19p13.3	2013-01-16			ENSG00000176619	ENSG00000176619		"""Intermediate filaments type V, lamins"""	6638	protein-coding gene	gene with protein product		150341		LMN2		1630457	Standard	NM_032737		Approved		uc002lvy.4	Q03252	OTTHUMG00000150626	ENST00000582871.1:c.1570dupC	19.37:g.2431868_2431868dupG	ENSP00000462730:p.Ser524fs	Somatic		WXS	Illumina GAIIx	Phase_IV	O75292|Q14734|Q96DF6	Frame_Shift_Ins	INS	pfam_F,pfam_Lamin_tail_dom,superfamily_Prefoldin	p.S543fs	ENST00000582871.1	37	c.1630_1629		19																																																																																			LMNB2	-	pfam_Lamin_tail_dom	ENSG00000176619		0.678	LMNB2-201	KNOWN	basic|appris_principal	protein_coding	LMNB2	HGNC	protein_coding		25	0.00	0	-	NM_032737		2431861	2431862	-1	no_errors	ENST00000325327	ensembl	human	known	69_37n	frame_shift_ins	5	37.50	3	INS	0.018:0.000	G
MAP1A	4130	genome.wustl.edu	37	15	43818899	43818899	+	Missense_Mutation	SNP	G	G	A			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr15:43818899G>A	ENST00000300231.5	+	4	5678	c.5228G>A	c.(5227-5229)cGg>cAg	p.R1743Q	MAP1A_ENST00000382031.1_Missense_Mutation_p.R1981Q|MAP1A_ENST00000399453.1_Missense_Mutation_p.R1743Q			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	1743					microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	GTACCCCTGCGGGAACACGCA	0.597																																						dbGAP											0													53.0	56.0	55.0					15																	43818899		1930	4135	6065	-	-	-	SO:0001583	missense	0			U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.5228G>A	15.37:g.43818899G>A	ENSP00000300231:p.Arg1743Gln	Somatic		WXS	Illumina GAIIx	Phase_IV	O95643|Q12973|Q15882|Q9UJT4	Missense_Mutation	SNP	NULL	p.R1743Q	ENST00000300231.5	37	c.5228	CCDS42031.1	15	.	.	.	.	.	.	.	.	.	.	g	1.152	-0.646339	0.03531	.	.	ENSG00000166963	ENST00000382031;ENST00000399453;ENST00000300231	T;T;T	0.01388	4.95;4.95;4.95	4.28	1.89	0.25635	.	.	.	.	.	T	0.00875	0.0029	N	0.08118	0	0.20074	N	0.999934	B	0.10296	0.003	B	0.04013	0.001	T	0.49254	-0.8959	9	0.20519	T	0.43	0.6865	6.1419	0.20265	0.1492:0.0:0.194:0.6567	.	1743	P78559	MAP1A_HUMAN	Q	1981;1743;1743	ENSP00000371462:R1981Q;ENSP00000382380:R1743Q;ENSP00000300231:R1743Q	ENSP00000300231:R1743Q	R	+	2	0	MAP1A	41606191	0.058000	0.20735	0.119000	0.21687	0.009000	0.06853	0.030000	0.13688	0.190000	0.20209	0.457000	0.33378	CGG	MAP1A	-	NULL	ENSG00000166963		0.597	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	MAP1A	HGNC	protein_coding	OTTHUMT00000132894.5	156	0.00	0	G	NM_002373		43818899	43818899	+1	no_errors	ENST00000399453	ensembl	human	known	69_37n	missense	125	26.90	46	SNP	0.478	A
MAPK4	5596	genome.wustl.edu	37	18	48190626	48190626	+	Missense_Mutation	SNP	G	G	A	rs199714690	byFrequency	TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr18:48190626G>A	ENST00000400384.2	+	2	1334	c.298G>A	c.(298-300)Gtg>Atg	p.V100M	MAPK4_ENST00000592595.1_Missense_Mutation_p.V100M|MAPK4_ENST00000588540.1_Missense_Mutation_p.V100M|MAPK4_ENST00000540640.1_Intron	NM_002747.3	NP_002738.2	P31152	MK04_HUMAN	mitogen-activated protein kinase 4	100	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|MAPK cascade (GO:0000165)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)			lung(4)|skin(3)|upper_aerodigestive_tract(1)	8		Colorectal(6;0.0297)		Colorectal(21;0.156)		CAAGTTCAGCGTGGCGTACAT	0.587													G|||	2	0.000399361	0.0	0.0	5008	,	,		19255	0.0		0.0	False		,,,				2504	0.002					dbGAP											0													78.0	80.0	80.0					18																	48190626		2199	4289	6488	-	-	-	SO:0001583	missense	0			X59727	CCDS42437.1	18q21.1	2012-10-02			ENSG00000141639	ENSG00000141639		"""Mitogen-activated protein kinase cascade / Kinases"""	6878	protein-coding gene	gene with protein product		176949		PRKM4		8290275	Standard	XM_005258299		Approved	Erk3-related, Erk4	uc002lev.3	P31152	OTTHUMG00000179853	ENST00000400384.2:c.298G>A	18.37:g.48190626G>A	ENSP00000383234:p.Val100Met	Somatic		WXS	Illumina GAIIx	Phase_IV	A1A4C4|Q0VG04	Missense_Mutation	SNP	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom,prints_MAPK_ERK3/4	p.V100M	ENST00000400384.2	37	c.298	CCDS42437.1	18	.	.	.	.	.	.	.	.	.	.	G	12.15	1.850416	0.32699	.	.	ENSG00000141639	ENST00000400384	T	0.65732	-0.17	5.86	3.76	0.43208	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.202341	0.35466	N	0.003200	T	0.41673	0.1169	N	0.16708	0.43	0.32096	N	0.591162	B;B	0.20459	0.045;0.045	B;B	0.23419	0.046;0.046	T	0.44967	-0.9293	10	0.46703	T	0.11	0.0675	5.1426	0.14967	0.2229:0.0:0.6148:0.1623	.	100;100	Q0VG04;P31152	.;MK04_HUMAN	M	100	ENSP00000383234:V100M	ENSP00000383234:V100M	V	+	1	0	MAPK4	46444624	0.943000	0.32029	1.000000	0.80357	0.975000	0.68041	0.556000	0.23438	1.487000	0.48415	0.555000	0.69702	GTG	MAPK4	-	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom	ENSG00000141639		0.587	MAPK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MAPK4	HGNC	protein_coding	OTTHUMT00000448631.2	200	0.00	0	G	NM_002747		48190626	48190626	+1	no_errors	ENST00000400384	ensembl	human	known	69_37n	missense	57	53.97	68	SNP	1.000	A
NREP	9315	genome.wustl.edu	37	5	111066712	111066712	+	Missense_Mutation	SNP	C	C	T	rs535738997		TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr5:111066712C>T	ENST00000379671.3	-	5	377	c.113G>A	c.(112-114)cGc>cAc	p.R38H	NREP_ENST00000515855.1_3'UTR|NREP_ENST00000509979.1_3'UTR|NREP_ENST00000395634.3_Missense_Mutation_p.R82H|NREP_ENST00000508870.1_Missense_Mutation_p.R38H|STARD4-AS1_ENST00000500779.2_RNA|NREP_ENST00000446294.2_Missense_Mutation_p.R38H|NREP_ENST00000419114.2_Missense_Mutation_p.R38H|NREP_ENST00000507742.1_5'UTR|NREP_ENST00000509427.1_Missense_Mutation_p.R38H|NREP_ENST00000447165.2_Missense_Mutation_p.R38H|STARD4-AS1_ENST00000513221.1_RNA|NREP_ENST00000455559.2_Missense_Mutation_p.R38H|NREP_ENST00000257435.7_Missense_Mutation_p.R38H|NREP_ENST00000509025.1_Intron|NREP_ENST00000450761.2_Missense_Mutation_p.R38H|NREP_ENST00000453526.2_Missense_Mutation_p.R38H	NM_001142478.1	NP_001135950.1	Q16612	NREP_HUMAN	neuronal regeneration related protein	38					axon regeneration (GO:0031103)|regulation of neuron differentiation (GO:0045664)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											GTTCTTCTTGCGGTTCACTTC	0.478													C|||	1	0.000199681	0.0	0.0	5008	,	,		18303	0.0		0.001	False		,,,				2504	0.0					dbGAP											0													154.0	125.0	135.0					5																	111066712		2202	4300	6502	-	-	-	SO:0001583	missense	0			AF119859	CCDS4105.1, CCDS47255.1	5q22.1	2012-12-07	2012-12-07	2012-01-23	ENSG00000134986	ENSG00000134986			16834	protein-coding gene	gene with protein product	"""neuronal protein 3.1"""	607332	"""chromosome 5 open reading frame 13"", ""neuronal regeneration related protein homolog (rat)"""	C5orf13		8261136, 10981724, 15485502	Standard	NM_004772		Approved	P311, D4S114, PRO1873, PTZ17, SEZ17	uc011cvr.2	Q16612	OTTHUMG00000128795	ENST00000379671.3:c.113G>A	5.37:g.111066712C>T	ENSP00000368993:p.Arg38His	Somatic		WXS	Illumina GAIIx	Phase_IV	B2RDN8|B7Z5D2|D3DSZ8	Missense_Mutation	SNP	pfam_Neuronal_3.1	p.R82H	ENST00000379671.3	37	c.245	CCDS4105.1	5	.	.	.	.	.	.	.	.	.	.	C	14.37	2.514497	0.44763	.	.	ENSG00000134986	ENST00000379671;ENST00000257435;ENST00000447165;ENST00000446294;ENST00000395634;ENST00000450761;ENST00000419114;ENST00000509427;ENST00000453526;ENST00000455559;ENST00000508870;ENST00000513100	T;T;T;T;T;T;T;T;T;T;T;T	0.63096	-0.02;-0.02;-0.02;-0.02;-0.02;-0.02;-0.02;-0.02;-0.02;-0.02;-0.02;-0.02	5.81	5.81	0.92471	.	0.093221	0.47852	N	0.000206	T	0.79009	0.4374	.	.	.	0.53005	D	0.999965	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.73917	-0.3831	9	0.27785	T	0.31	-6.3612	20.073	0.97731	0.0:1.0:0.0:0.0	.	38;82;38	D6RIC9;B7Z5D2;Q16612	.;.;NP311_HUMAN	H	38;38;38;38;82;38;38;38;38;38;38;38	ENSP00000368993:R38H;ENSP00000257435:R38H;ENSP00000408839:R38H;ENSP00000402965:R38H;ENSP00000378996:R82H;ENSP00000416617:R38H;ENSP00000399766:R38H;ENSP00000422630:R38H;ENSP00000403383:R38H;ENSP00000392559:R38H;ENSP00000427149:R38H;ENSP00000427476:R38H	ENSP00000257435:R38H	R	-	2	0	C5orf13	111094611	1.000000	0.71417	1.000000	0.80357	0.874000	0.50279	3.571000	0.53841	2.750000	0.94351	0.655000	0.94253	CGC	NREP	-	pfam_Neuronal_3.1	ENSG00000134986		0.478	NREP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NREP	HGNC	protein_coding	OTTHUMT00000250722.1	227	0.44	1	C	NM_004772		111066712	111066712	-1	no_errors	ENST00000395634	ensembl	human	known	69_37n	missense	204	16.39	40	SNP	1.000	T
OR4C12	283093	genome.wustl.edu	37	11	50003457	50003457	+	Missense_Mutation	SNP	C	C	T			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr11:50003457C>T	ENST00000335238.4	-	1	614	c.581G>A	c.(580-582)gGt>gAt	p.G194D		NM_001005270.2	NP_001005270.2	Q96R67	OR4CC_HUMAN	olfactory receptor, family 4, subfamily C, member 12	194						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|kidney(4)|large_intestine(3)|liver(1)|lung(19)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	36						AACAAAGAGACCAAGGGTATG	0.413																																						dbGAP											0													101.0	101.0	101.0					11																	50003457		2201	4296	6497	-	-	-	SO:0001583	missense	0			BK004413	CCDS31496.1	11p11.12	2012-08-09			ENSG00000221954	ENSG00000221954		"""GPCR / Class A : Olfactory receptors"""	15168	protein-coding gene	gene with protein product							Standard	NM_001005270		Approved		uc010ria.2	Q96R67	OTTHUMG00000166687	ENST00000335238.4:c.581G>A	11.37:g.50003457C>T	ENSP00000334418:p.Gly194Asp	Somatic		WXS	Illumina GAIIx	Phase_IV	B2RNF0|Q6IF49	Missense_Mutation	SNP	pfam_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam,prints_Olfact_rcpt,prints_7TM_GPCR_Rhodpsn	p.G194D	ENST00000335238.4	37	c.581	CCDS31496.1	11	.	.	.	.	.	.	.	.	.	.	.	14.85	2.659938	0.47572	.	.	ENSG00000221954	ENST00000335238	T	0.00063	8.78	2.45	2.45	0.29901	GPCR, rhodopsin-like superfamily (1);	0.160723	0.28577	N	0.014860	T	0.00241	0.0007	L	0.41415	1.275	0.39365	D	0.965996	D	0.67145	0.996	D	0.74023	0.982	D	0.86146	0.1584	10	0.87932	D	0	.	5.3443	0.16000	0.0:0.8394:0.0:0.1605	.	194	Q96R67	OR4CC_HUMAN	D	194	ENSP00000334418:G194D	ENSP00000334418:G194D	G	-	2	0	OR4C12	49960033	0.000000	0.05858	1.000000	0.80357	0.625000	0.37756	-0.045000	0.12003	1.698000	0.51180	0.398000	0.26397	GGT	OR4C12	-	pfam_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam	ENSG00000221954		0.413	OR4C12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR4C12	HGNC	protein_coding	OTTHUMT00000391104.1	625	0.00	0	C	NM_001005270		50003457	50003457	-1	no_errors	ENST00000335238	ensembl	human	known	69_37n	missense	194	23.02	58	SNP	1.000	T
OR5K2	402135	genome.wustl.edu	37	3	98216663	98216663	+	Missense_Mutation	SNP	G	G	A			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr3:98216663G>A	ENST00000427338.1	+	1	216	c.139G>A	c.(139-141)Gca>Aca	p.A47T		NM_001004737.1	NP_001004737.1	Q8NHB8	OR5K2_HUMAN	olfactory receptor, family 5, subfamily K, member 2	47						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(1)|lung(10)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						TAGTTTGGTGGCACTGATATT	0.468																																						dbGAP											0													229.0	231.0	230.0					3																	98216663		2203	4300	6503	-	-	-	SO:0001583	missense	0			AC021660	CCDS33804.1	3q11.2	2013-09-23			ENSG00000231861	ENSG00000231861		"""GPCR / Class A : Olfactory receptors"""	14774	protein-coding gene	gene with protein product							Standard	NM_001004737		Approved		uc011bgx.2	Q8NHB8	OTTHUMG00000160049	ENST00000427338.1:c.139G>A	3.37:g.98216663G>A	ENSP00000393889:p.Ala47Thr	Somatic		WXS	Illumina GAIIx	Phase_IV	B2RN70|Q6IF47	Missense_Mutation	SNP	pfam_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam,prints_Olfact_rcpt,prints_7TM_GPCR_Rhodpsn	p.A47T	ENST00000427338.1	37	c.139	CCDS33804.1	3	.	.	.	.	.	.	.	.	.	.	G	5.511	0.279165	0.10458	.	.	ENSG00000231861	ENST00000427338	T	0.01084	5.36	2.91	-3.95	0.04118	GPCR, rhodopsin-like superfamily (1);	2.020610	0.02825	N	0.125952	T	0.00967	0.0032	N	0.17838	0.53	0.09310	N	1	B	0.21452	0.056	B	0.23419	0.046	T	0.47699	-0.9097	10	0.20046	T	0.44	-0.0709	5.0476	0.14492	0.5366:0.0:0.3224:0.141	.	47	Q8NHB8	OR5K2_HUMAN	T	47	ENSP00000393889:A47T	ENSP00000393889:A47T	A	+	1	0	OR5K2	99699353	0.000000	0.05858	0.001000	0.08648	0.013000	0.08279	-2.788000	0.00768	-0.881000	0.03992	0.298000	0.19748	GCA	OR5K2	-	pfam_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam,prints_7TM_GPCR_Rhodpsn	ENSG00000231861		0.468	OR5K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR5K2	HGNC	protein_coding	OTTHUMT00000359020.2	476	0.00	0	G			98216663	98216663	+1	no_errors	ENST00000427338	ensembl	human	known	69_37n	missense	216	31.55	100	SNP	0.000	A
PCDHA5	56143	genome.wustl.edu	37	5	140202966	140202966	+	Missense_Mutation	SNP	G	G	A			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr5:140202966G>A	ENST00000529859.1	+	1	1606	c.1606G>A	c.(1606-1608)Gcg>Acg	p.A536T	PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529619.1_Missense_Mutation_p.A536T|PCDHA5_ENST00000378126.3_Missense_Mutation_p.A536T|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron	NM_018908.2	NP_061731.1	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5	536	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(3)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCAGGTGAGCGCGCGCGACGC	0.677																																						dbGAP											0													46.0	53.0	51.0					5																	140202966		2203	4298	6501	-	-	-	SO:0001583	missense	0			AF152483	CCDS54917.1	5q31	2010-11-26				ENSG00000204965		"""Cadherins / Protocadherins : Clustered"""	8671	other	complex locus constituent	"""ortholog of mouse CNR6"", ""KIAA0345-like 9"""	606311		CNRS6		10380929, 10662547	Standard	NM_018908		Approved	CNR6, CRNR6, CNRN6, PCDH-ALPHA5		Q9Y5H7		ENST00000529859.1:c.1606G>A	5.37:g.140202966G>A	ENSP00000436557:p.Ala536Thr	Somatic		WXS	Illumina GAIIx	Phase_IV	O75284|Q8N4R3	Missense_Mutation	SNP	pfam_Cadherin,pfam_Cadherin_N,superfamily_Cadherin-like,smart_Cadherin,prints_Cadherin,pfscan_Cadherin	p.A536T	ENST00000529859.1	37	c.1606	CCDS54917.1	5	.	.	.	.	.	.	.	.	.	.	G	18.92	3.725904	0.69074	.	.	ENSG00000204965	ENST00000529619;ENST00000529859;ENST00000378126	T;T;T	0.75589	-0.95;-0.95;-0.95	3.86	3.86	0.44501	Cadherin (5);Cadherin-like (1);	.	.	.	.	D	0.89901	0.6849	H	0.95574	3.69	0.45390	D	0.998374	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79784	0.993;0.979;0.991	D	0.93474	0.6821	9	0.87932	D	0	.	16.2179	0.82239	0.0:0.0:1.0:0.0	.	536;536;536	Q9Y5H7;Q9Y5H7-3;Q9Y5H7-2	PCDA5_HUMAN;.;.	T	536	ENSP00000433416:A536T;ENSP00000436557:A536T;ENSP00000367366:A536T	ENSP00000367366:A536T	A	+	1	0	PCDHA5	140183150	1.000000	0.71417	1.000000	0.80357	0.285000	0.27093	9.167000	0.94773	1.864000	0.54056	0.461000	0.40582	GCG	PCDHA5	-	pfam_Cadherin,superfamily_Cadherin-like,smart_Cadherin,prints_Cadherin,pfscan_Cadherin	ENSG00000204965		0.677	PCDHA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PCDHA5	HGNC	protein_coding	OTTHUMT00000372883.2	67	0.00	0	G	NM_018908		140202966	140202966	+1	no_errors	ENST00000529859	ensembl	human	known	69_37n	missense	41	24.07	13	SNP	1.000	A
PCNT	5116	genome.wustl.edu	37	21	47754627	47754627	+	Missense_Mutation	SNP	G	G	A			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr21:47754627G>A	ENST00000359568.5	+	3	691	c.584G>A	c.(583-585)cGt>cAt	p.R195H	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	195					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					CCAGAACAGCGTGGGATCTTC	0.483																																						dbGAP											0													184.0	139.0	154.0					21																	47754627		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.584G>A	21.37:g.47754627G>A	ENSP00000352572:p.Arg195His	Somatic		WXS	Illumina GAIIx	Phase_IV	O43152|Q7Z7C9	Missense_Mutation	SNP	pfam_PACT_domain	p.R195H	ENST00000359568.5	37	c.584	CCDS33592.1	21	.	.	.	.	.	.	.	.	.	.	G	2.313	-0.357453	0.05138	.	.	ENSG00000160299	ENST00000359568;ENST00000337772	T	0.01538	4.79	0.235	-0.47	0.12131	.	.	.	.	.	T	0.01523	0.0049	L	0.32530	0.975	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46652	-0.9176	8	0.42905	T	0.14	.	.	.	.	.	77;195	O95613-2;O95613	.;PCNT_HUMAN	H	195;182	ENSP00000352572:R195H	ENSP00000338675:R182H	R	+	2	0	PCNT	46579055	0.194000	0.23325	0.002000	0.10522	0.002000	0.02628	-0.224000	0.09164	-0.677000	0.05231	-0.671000	0.03813	CGT	PCNT	-	NULL	ENSG00000160299		0.483	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PCNT	HGNC	protein_coding	OTTHUMT00000207336.1	431	0.23	1	G	NM_006031		47754627	47754627	+1	no_errors	ENST00000359568	ensembl	human	known	69_37n	missense	221	40.11	148	SNP	0.008	A
POLR1A	25885	genome.wustl.edu	37	2	86258493	86258493	+	Missense_Mutation	SNP	T	T	C			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr2:86258493T>C	ENST00000263857.6	-	30	4916	c.4538A>G	c.(4537-4539)gAt>gGt	p.D1513G	POLR1A_ENST00000409681.1_Intron			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	1513					gene expression (GO:0010467)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase I complex (GO:0005736)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	63						CTGGTAGTCATCTATGAACGG	0.662																																						dbGAP											0													102.0	110.0	107.0					2																	86258493		2092	4212	6304	-	-	-	SO:0001583	missense	0			AK025568	CCDS42706.1	2p11.2	2013-01-21			ENSG00000068654	ENSG00000068654		"""RNA polymerase subunits"""	17264	protein-coding gene	gene with protein product						9236775	Standard	NM_015425		Approved	DKFZP586M0122, FLJ21915, RPO1-4, RPA1	uc002sqs.3	O95602	OTTHUMG00000153165	ENST00000263857.6:c.4538A>G	2.37:g.86258493T>C	ENSP00000263857:p.Asp1513Gly	Somatic		WXS	Illumina GAIIx	Phase_IV	B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Missense_Mutation	SNP	pfam_RNA_pol_Rpb1_5,pfam_RNA_pol_asu,pfam_RNA_pol_Rpb1_3,pfam_RNA_pol_Rpb1_4,pfam_RNA_pol_Rpb1_1,smart_RNA_pol_N	p.D1513G	ENST00000263857.6	37	c.4538	CCDS42706.1	2	.	.	.	.	.	.	.	.	.	.	T	15.42	2.826883	0.50739	.	.	ENSG00000068654	ENST00000263857	T	0.66280	-0.2	5.11	3.93	0.45458	RNA polymerase Rpb1, domain 5 (1);	0.307834	0.34725	N	0.003722	T	0.43010	0.1228	N	0.13098	0.295	0.80722	D	1	B	0.09022	0.002	B	0.04013	0.001	T	0.17745	-1.0359	10	0.27082	T	0.32	-18.2887	11.9209	0.52791	0.0:0.0:0.1461:0.8539	.	1513	O95602	RPA1_HUMAN	G	1513	ENSP00000263857:D1513G	ENSP00000263857:D1513G	D	-	2	0	POLR1A	86112004	0.998000	0.40836	0.864000	0.33941	0.711000	0.40976	3.941000	0.56607	0.861000	0.35504	0.454000	0.30748	GAT	POLR1A	-	pfam_RNA_pol_Rpb1_5	ENSG00000068654		0.662	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	POLR1A	HGNC	protein_coding	OTTHUMT00000329830.2	281	0.35	1	T	NM_015425		86258493	86258493	-1	no_errors	ENST00000263857	ensembl	human	known	69_37n	missense	153	20.31	39	SNP	0.983	C
PRKCQ	5588	genome.wustl.edu	37	10	6557003	6557004	+	In_Frame_Ins	INS	-	-	TTT			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr10:6557003_6557004insTTT	ENST00000263125.5	-	2	193_194	c.94_95insAAA	c.(94-96)ctc>cAAAtc	p.32_32L>QI	PRKCQ_ENST00000397176.2_In_Frame_Ins_p.32_32L>QI|PRKCQ_ENST00000539722.1_5'UTR	NM_001282644.1|NM_006257.3	NP_001269573.1|NP_006248.1	Q04759	KPCT_HUMAN	protein kinase C, theta	32	C2.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|membrane protein ectodomain proteolysis (GO:0006509)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of T cell apoptotic process (GO:0070233)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 17 type immune response (GO:2000318)|positive regulation of T-helper 2 cell activation (GO:2000570)|protein ubiquitination (GO:0016567)|regulation of cell growth (GO:0001558)|regulation of platelet aggregation (GO:0090330)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|regulation of transcription, DNA-templated (GO:0006355)|rhodopsin mediated signaling pathway (GO:0016056)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|immunological synapse (GO:0001772)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(2)	45					Tamoxifen(DB00675)	CTCTTTGACGAGCACAGCACAG	0.515																																					Ovarian(50;572 1126 10530 25349 30594)	dbGAP											0																																										-	-	-	SO:0001652	inframe_insertion	0			L07032	CCDS7079.1, CCDS55701.1, CCDS60482.1	10p15	2009-07-10			ENSG00000065675	ENSG00000065675	2.7.11.1		9410	protein-coding gene	gene with protein product		600448				8444877	Standard	NM_001282645		Approved		uc001ijj.2	Q04759	OTTHUMG00000017623	ENST00000263125.5:c.94_95insAAA	10.37:g.6557003_6557004insTTT	ENSP00000263125:p.Leu32delinsGlnIle	Somatic		WXS	Illumina GAIIx	Phase_IV	B4DF52|Q14DH6|Q3MJF1|Q64FY5|Q9H508|Q9H549	In_Frame_Ins	INS	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_Kinase_C-like_PE/DAG-bd,pfam_Pkinase_C,superfamily_Kinase-like_dom,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_Prot_Kinase_C-like_PE/DAG-bd,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,smart_AGC-kinase_C,pirsf_Prot_kin_PKC_delta,prints_DAG/PE-bd,prints_Ser-Thr/Tyr_kinase_cat_dom,pfscan_Prot_Kinase_C-like_PE/DAG-bd,pfscan_Prot_kinase_cat_dom	p.L32in_frame_insQI	ENST00000263125.5	37	c.95_94	CCDS7079.1	10																																																																																			PRKCQ	-	superfamily_C2_Ca/lipid-bd_dom_CaLB,pirsf_Prot_kin_PKC_delta	ENSG00000065675		0.515	PRKCQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PRKCQ	HGNC	protein_coding	OTTHUMT00000046665.1	268	0.00	0	-	NM_006257		6557003	6557004	-1	no_errors	ENST00000263125	ensembl	human	known	69_37n	in_frame_ins	107	31.85	50	INS	0.985:0.997	TTT
PRKCQ	5588	genome.wustl.edu	37	10	6557004	6557005	+	Frame_Shift_Ins	INS	-	-	C			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr10:6557004_6557005insC	ENST00000263125.5	-	2	192_193	c.93_94insG	c.(91-96)gtgctcfs	p.L32fs	PRKCQ_ENST00000397176.2_Frame_Shift_Ins_p.L32fs|PRKCQ_ENST00000539722.1_5'UTR	NM_001282644.1|NM_006257.3	NP_001269573.1|NP_006248.1	Q04759	KPCT_HUMAN	protein kinase C, theta	32	C2.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|membrane protein ectodomain proteolysis (GO:0006509)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of T cell apoptotic process (GO:0070233)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 17 type immune response (GO:2000318)|positive regulation of T-helper 2 cell activation (GO:2000570)|protein ubiquitination (GO:0016567)|regulation of cell growth (GO:0001558)|regulation of platelet aggregation (GO:0090330)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|regulation of transcription, DNA-templated (GO:0006355)|rhodopsin mediated signaling pathway (GO:0016056)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|immunological synapse (GO:0001772)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(2)	45					Tamoxifen(DB00675)	TCTTTGACGAGCACAGCACAGT	0.515																																					Ovarian(50;572 1126 10530 25349 30594)	dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			L07032	CCDS7079.1, CCDS55701.1, CCDS60482.1	10p15	2009-07-10			ENSG00000065675	ENSG00000065675	2.7.11.1		9410	protein-coding gene	gene with protein product		600448				8444877	Standard	NM_001282645		Approved		uc001ijj.2	Q04759	OTTHUMG00000017623	ENST00000263125.5:c.94dupG	10.37:g.6557005_6557005dupC	ENSP00000263125:p.Leu32fs	Somatic		WXS	Illumina GAIIx	Phase_IV	B4DF52|Q14DH6|Q3MJF1|Q64FY5|Q9H508|Q9H549	Frame_Shift_Ins	INS	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_Kinase_C-like_PE/DAG-bd,pfam_Pkinase_C,superfamily_Kinase-like_dom,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_Prot_Kinase_C-like_PE/DAG-bd,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,smart_AGC-kinase_C,pirsf_Prot_kin_PKC_delta,prints_DAG/PE-bd,prints_Ser-Thr/Tyr_kinase_cat_dom,pfscan_Prot_Kinase_C-like_PE/DAG-bd,pfscan_Prot_kinase_cat_dom	p.L31fs	ENST00000263125.5	37	c.94_93	CCDS7079.1	10																																																																																			PRKCQ	-	superfamily_C2_Ca/lipid-bd_dom_CaLB,pirsf_Prot_kin_PKC_delta	ENSG00000065675		0.515	PRKCQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PRKCQ	HGNC	protein_coding	OTTHUMT00000046665.1	263	0.00	0	-	NM_006257		6557004	6557005	-1	no_errors	ENST00000263125	ensembl	human	known	69_37n	frame_shift_ins	96	34.25	50	INS	0.997:1.000	C
PRKCQ	5588	genome.wustl.edu	37	10	6557011	6557012	+	Frame_Shift_Ins	INS	-	-	G			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr10:6557011_6557012insG	ENST00000263125.5	-	2	185_186	c.86_87insC	c.(85-87)tgtfs	p.C29fs	PRKCQ_ENST00000397176.2_Frame_Shift_Ins_p.C29fs|PRKCQ_ENST00000539722.1_5'UTR	NM_001282644.1|NM_006257.3	NP_001269573.1|NP_006248.1	Q04759	KPCT_HUMAN	protein kinase C, theta	29	C2.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|membrane protein ectodomain proteolysis (GO:0006509)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of T cell apoptotic process (GO:0070233)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 17 type immune response (GO:2000318)|positive regulation of T-helper 2 cell activation (GO:2000570)|protein ubiquitination (GO:0016567)|regulation of cell growth (GO:0001558)|regulation of platelet aggregation (GO:0090330)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|regulation of transcription, DNA-templated (GO:0006355)|rhodopsin mediated signaling pathway (GO:0016056)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|immunological synapse (GO:0001772)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(2)	45					Tamoxifen(DB00675)	CGAGCACAGCACAGTAAGGGTT	0.52																																					Ovarian(50;572 1126 10530 25349 30594)	dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			L07032	CCDS7079.1, CCDS55701.1, CCDS60482.1	10p15	2009-07-10			ENSG00000065675	ENSG00000065675	2.7.11.1		9410	protein-coding gene	gene with protein product		600448				8444877	Standard	NM_001282645		Approved		uc001ijj.2	Q04759	OTTHUMG00000017623	ENST00000263125.5:c.86_87insC	10.37:g.6557011_6557012insG	ENSP00000263125:p.Cys29fs	Somatic		WXS	Illumina GAIIx	Phase_IV	B4DF52|Q14DH6|Q3MJF1|Q64FY5|Q9H508|Q9H549	Frame_Shift_Ins	INS	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_Kinase_C-like_PE/DAG-bd,pfam_Pkinase_C,superfamily_Kinase-like_dom,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_Prot_Kinase_C-like_PE/DAG-bd,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,smart_AGC-kinase_C,pirsf_Prot_kin_PKC_delta,prints_DAG/PE-bd,prints_Ser-Thr/Tyr_kinase_cat_dom,pfscan_Prot_Kinase_C-like_PE/DAG-bd,pfscan_Prot_kinase_cat_dom	p.A30fs	ENST00000263125.5	37	c.87_86	CCDS7079.1	10																																																																																			PRKCQ	-	superfamily_C2_Ca/lipid-bd_dom_CaLB,pirsf_Prot_kin_PKC_delta	ENSG00000065675		0.520	PRKCQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PRKCQ	HGNC	protein_coding	OTTHUMT00000046665.1	258	0.00	0	-	NM_006257		6557011	6557012	-1	no_errors	ENST00000263125	ensembl	human	known	69_37n	frame_shift_ins	95	34.48	50	INS	0.661:1.000	G
RAB25	57111	genome.wustl.edu	37	1	156038083	156038083	+	Missense_Mutation	SNP	G	G	A			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr1:156038083G>A	ENST00000361084.5	+	3	503	c.262G>A	c.(262-264)Gcc>Acc	p.A88T	RAB25_ENST00000487325.1_3'UTR	NM_020387.2	NP_065120.2	P57735	RAB25_HUMAN	RAB25, member RAS oncogene family	88					positive regulation of cell proliferation (GO:0008284)|protein transport (GO:0015031)|pseudopodium organization (GO:0031268)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	GTP binding (GO:0005525)|myosin V binding (GO:0031489)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	5	Hepatocellular(266;0.158)|all_neural(408;0.195)					TGCAGTGGGGGCCCTCCTGGT	0.557																																						dbGAP											0													109.0	106.0	107.0					1																	156038083		2113	4264	6377	-	-	-	SO:0001583	missense	0			AF083124	CCDS41413.1	1q22	2008-07-03			ENSG00000132698	ENSG00000132698		"""RAB, member RAS oncogene"""	18238	protein-coding gene	gene with protein product		612942				11697911	Standard	NM_020387		Approved	CATX-8	uc001fnc.3	P57735	OTTHUMG00000017457	ENST00000361084.5:c.262G>A	1.37:g.156038083G>A	ENSP00000354376:p.Ala88Thr	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5VYA2|Q8NG24|Q96GB1|Q9BT12	Missense_Mutation	SNP	pfam_Small_GTPase,pfam_MIRO-like,pfam_Small_GTPase_ARF/SAR,pfam_Gtr1_RagA,smart_Small_GTPase_Ras,smart_Small_GTPase_Rab_type,smart_Small_GTPase_Rho,smart_Ran_GTPase,prints_Small_GTPase,tigrfam_Small_GTP-bd_dom	p.A88T	ENST00000361084.5	37	c.262	CCDS41413.1	1	.	.	.	.	.	.	.	.	.	.	G	35	5.595812	0.96602	.	.	ENSG00000132698	ENST00000361084	T	0.81163	-1.46	5.19	5.19	0.71726	Small GTP-binding protein domain (1);	0.106823	0.64402	D	0.000006	D	0.92851	0.7726	H	0.97131	3.945	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.94704	0.7886	10	0.87932	D	0	.	17.4443	0.87574	0.0:0.0:1.0:0.0	.	88	P57735	RAB25_HUMAN	T	88	ENSP00000354376:A88T	ENSP00000354376:A88T	A	+	1	0	RAB25	154304707	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.520000	0.98027	2.686000	0.91538	0.655000	0.94253	GCC	RAB25	-	pfam_Small_GTPase,pfam_MIRO-like,pfam_Small_GTPase_ARF/SAR,pfam_Gtr1_RagA,smart_Small_GTPase_Ras,smart_Small_GTPase_Rab_type,smart_Small_GTPase_Rho,smart_Ran_GTPase,tigrfam_Small_GTP-bd_dom	ENSG00000132698		0.557	RAB25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RAB25	HGNC	protein_coding	OTTHUMT00000046185.1	213	0.00	0	G			156038083	156038083	+1	no_errors	ENST00000361084	ensembl	human	known	69_37n	missense	357	14.15	59	SNP	1.000	A
RASGRP1	10125	genome.wustl.edu	37	15	38805032	38805032	+	Silent	SNP	C	C	T	rs200086434	byFrequency	TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr15:38805032C>T	ENST00000310803.5	-	7	978	c.801G>A	c.(799-801)acG>acA	p.T267T	RASGRP1_ENST00000561180.1_Silent_p.T318T|RASGRP1_ENST00000450598.2_Silent_p.T267T|RASGRP1_ENST00000539159.1_Silent_p.T219T|RASGRP1_ENST00000558164.1_Silent_p.T267T|RASGRP1_ENST00000559830.1_Silent_p.T267T	NM_001128602.1|NM_005739.3	NP_001122074.1|NP_005730.2	O95267	GRP1_HUMAN	RAS guanyl releasing protein 1 (calcium and DAG-regulated)	267	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				activation of Rho GTPase activity (GO:0032862)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response to antigenic stimulus (GO:0002437)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|platelet activation (GO:0030168)|Ras protein signal transduction (GO:0007265)|regulation of phosphatidylinositol 3-kinase signaling (GO:0014066)|secretory granule localization (GO:0032252)|signal transduction (GO:0007165)|vesicle transport along microtubule (GO:0047496)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20		all_cancers(109;6.38e-17)|all_epithelial(112;5.51e-15)|Lung NSC(122;2.12e-11)|all_lung(180;5.63e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;1.97e-07)|BRCA - Breast invasive adenocarcinoma(123;0.00248)		GGAGCTGCGGCGTGGGGCGGC	0.493													C|||	3	0.000599042	0.0	0.0	5008	,	,		18912	0.003		0.0	False		,,,				2504	0.0					dbGAP											0													56.0	61.0	59.0					15																	38805032		1979	4164	6143	-	-	-	SO:0001819	synonymous_variant	0			AF106071	CCDS45221.1, CCDS45222.1	15q15	2013-01-10				ENSG00000172575		"""EF-hand domain containing"""	9878	protein-coding gene	gene with protein product		603962				10087292, 9789079	Standard	NM_005739		Approved	CalDAG-GEFII, RASGRP	uc001zke.4	O95267		ENST00000310803.5:c.801G>A	15.37:g.38805032C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q56CZ0|Q58G75|Q59HB1|Q5I3A8|Q6GV31|Q6NX39|Q7LDG6|Q9UI94|Q9UNN9	Silent	SNP	pfam_RasGRF_CDC25,pfam_Prot_Kinase_C-like_PE/DAG-bd,superfamily_Ras_GEF_dom,smart_Ras-like_Gua-exchang_fac_N,smart_RasGRF_CDC25,smart_EF_hand_Ca-bd,smart_Prot_Kinase_C-like_PE/DAG-bd,prints_DAG/PE-bd,pfscan_EF_HAND_2,pfscan_Prot_Kinase_C-like_PE/DAG-bd,pfscan_RasGRF_CDC25,pfscan_Ras-like_Gua-exchang_fac_N	p.T267	ENST00000310803.5	37	c.801	CCDS45222.1	15																																																																																			RASGRP1	-	pfam_RasGRF_CDC25,superfamily_Ras_GEF_dom,smart_RasGRF_CDC25,pfscan_RasGRF_CDC25	ENSG00000172575		0.493	RASGRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RASGRP1	HGNC	protein_coding	OTTHUMT00000418223.1	49	0.00	0	C	NM_005739		38805032	38805032	-1	no_errors	ENST00000310803	ensembl	human	known	69_37n	silent	46	14.81	8	SNP	1.000	T
RBM33	155435	genome.wustl.edu	37	7	155493674	155493674	+	Intron	SNP	C	C	G			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr7:155493674C>G	ENST00000401878.3	+	6	937				RBM33_ENST00000392759.3_Missense_Mutation_p.L299V|RBM33_ENST00000287912.3_Missense_Mutation_p.L259V	NM_053043.2	NP_444271.2	Q96EV2	RBM33_HUMAN	RNA binding motif protein 33								nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	27	all_neural(206;0.101)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)		CTCCTTTACTCTCATTTCAAC	0.428																																						dbGAP											0													40.0	37.0	38.0					7																	155493674		1883	4120	6003	-	-	-	SO:0001627	intron_variant	0			AL832196	CCDS5941.2	7q36.3	2013-02-12			ENSG00000184863	ENSG00000184863		"""RNA binding motif (RRM) containing"""	27223	protein-coding gene	gene with protein product			"""proline rich 8"""	PRR8			Standard	NM_053043		Approved	DKFZp686F102, MGC20460, DKFZp434D1319	uc010lqk.1	Q96EV2	OTTHUMG00000150260	ENST00000401878.3:c.739+36C>G	7.37:g.155493674C>G		Somatic		WXS	Illumina GAIIx	Phase_IV	A4D244|B5MC24|Q52LF5|Q75LN9|Q75ML5|Q9NSV0	Missense_Mutation	SNP	NULL	p.L259V	ENST00000401878.3	37	c.775	CCDS5941.2	7	.	.	.	.	.	.	.	.	.	.	C	0.001	-3.186709	0.00026	.	.	ENSG00000184863	ENST00000287912;ENST00000392759	.	.	.	3.8	-3.7	0.04437	.	.	.	.	.	T	0.14700	0.0355	.	.	.	0.09310	N	1	B	0.13594	0.008	B	0.11329	0.006	T	0.31724	-0.9933	7	0.12103	T	0.63	.	5.0272	0.14391	0.0:0.2499:0.2834:0.4667	.	259	Q96EV2-2	.	V	259;299	.	ENSP00000287912:L259V	L	+	1	0	RBM33	155186435	0.000000	0.05858	0.000000	0.03702	0.052000	0.14988	-1.001000	0.03690	-0.919000	0.03803	-1.084000	0.02203	CTC	RBM33	-	NULL	ENSG00000184863		0.428	RBM33-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	RBM33	HGNC	protein_coding	OTTHUMT00000317225.3	48	0.00	0	C	NM_001008408		155493674	155493674	+1	no_errors	ENST00000287912	ensembl	human	known	69_37n	missense	28	17.65	6	SNP	0.001	G
RPH3A	22895	genome.wustl.edu	37	12	113314581	113314581	+	Missense_Mutation	SNP	G	G	T			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr12:113314581G>T	ENST00000389385.4	+	13	1578	c.1081G>T	c.(1081-1083)Gca>Tca	p.A361S	RPH3A_ENST00000548866.1_Missense_Mutation_p.A312S|RPH3A_ENST00000420983.2_Missense_Mutation_p.A361S|RPH3A_ENST00000447659.2_Missense_Mutation_p.A312S|RPH3A_ENST00000551052.1_Missense_Mutation_p.A357S|RPH3A_ENST00000549913.2_3'UTR|RPH3A_ENST00000543106.2_Missense_Mutation_p.A361S|RPH3A_ENST00000415485.3_Missense_Mutation_p.A361S	NM_001143854.1|NM_014954.3	NP_001137326.1|NP_055769.2	Q9Y2J0	RP3A_HUMAN	rabphilin 3A	361	Pro-rich.				intracellular protein transport (GO:0006886)	cell junction (GO:0030054)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylinositol phosphate binding (GO:1901981)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(16)|ovary(3)|prostate(4)|skin(6)|urinary_tract(1)	47				BRCA - Breast invasive adenocarcinoma(302;0.00453)		CCAAGCATCTGCAGCTGCCCC	0.637																																						dbGAP											0													43.0	43.0	43.0					12																	113314581		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB023202	CCDS31904.1, CCDS44979.1	12q24.13	2014-07-02	2014-07-02		ENSG00000089169	ENSG00000089169		"""Synaptotagmins"""	17056	protein-coding gene	gene with protein product		612159	"""rabphilin 3A homolog (mouse)"""			10231032, 7822236	Standard	NM_014954		Approved	KIAA0985, rabphilin, exophilin-1	uc001ttz.3	Q9Y2J0	OTTHUMG00000169713	ENST00000389385.4:c.1081G>T	12.37:g.113314581G>T	ENSP00000374036:p.Ala361Ser	Somatic		WXS	Illumina GAIIx	Phase_IV	B7Z3C3|Q96AE0	Missense_Mutation	SNP	pfam_C2_Ca-dep,pfam_Rabphilin3A_effector_Zn-bd,superfamily_C2_Ca/lipid-bd_dom_CaLB,superfamily_Znf_FYVE_PHD,smart_C2_Ca-dep,prints_Synaptotagmin,prints_C2_dom,pfscan_C2_membr_targeting,pfscan_Rab-bd_domain,pfscan_Znf_FYVE-rel	p.A361S	ENST00000389385.4	37	c.1081	CCDS44979.1	12	.	.	.	.	.	.	.	.	.	.	G	11.92	1.783500	0.31593	.	.	ENSG00000089169	ENST00000543106;ENST00000389385;ENST00000447659;ENST00000551052;ENST00000415485;ENST00000548866;ENST00000420983;ENST00000549913;ENST00000552755	T;T;T;T;T;T;T	0.16457	2.34;2.34;2.34;2.34;2.34;2.34;2.34	4.99	4.99	0.66335	.	0.422897	0.18994	N	0.125521	T	0.14098	0.0341	L	0.44542	1.39	0.22851	N	0.998659	B;B;B;B	0.17038	0.019;0.02;0.011;0.004	B;B;B;B	0.18871	0.023;0.01;0.01;0.007	T	0.26985	-1.0087	10	0.08599	T	0.76	.	12.1831	0.54223	0.0:0.0:0.8288:0.1712	.	312;361;361;357	F8VP47;B7Z9Z7;Q9Y2J0;Q9Y2J0-2	.;.;RP3A_HUMAN;.	S	361;361;312;357;361;312;361;13;13	ENSP00000440384:A361S;ENSP00000374036:A361S;ENSP00000413254:A312S;ENSP00000448297:A357S;ENSP00000405357:A361S;ENSP00000450347:A312S;ENSP00000408889:A361S	ENSP00000374036:A361S	A	+	1	0	RPH3A	111798964	0.743000	0.28239	0.221000	0.23827	0.023000	0.10783	1.945000	0.40273	2.297000	0.77311	0.511000	0.50034	GCA	RPH3A	-	NULL	ENSG00000089169		0.637	RPH3A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	RPH3A	HGNC	protein_coding	OTTHUMT00000405561.1	50	0.00	0	G	NM_014954		113314581	113314581	+1	no_errors	ENST00000389385	ensembl	human	known	69_37n	missense	33	13.16	5	SNP	0.920	T
SARDH	1757	genome.wustl.edu	37	9	136594964	136594964	+	Silent	SNP	G	G	T			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr9:136594964G>T	ENST00000371872.4	-	6	1095	c.838C>A	c.(838-840)Cgg>Agg	p.R280R	SARDH_ENST00000298628.5_Silent_p.R280R|SARDH_ENST00000371867.1_Silent_p.R191R|SARDH_ENST00000422262.2_Silent_p.R112R|SARDH_ENST00000439388.1_Silent_p.R280R	NM_007101.3	NP_009032.2	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase	280					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|sarcosine dehydrogenase activity (GO:0008480)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(13)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	44				OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)		CCAGCCATCCGGCCCACAGCA	0.642																																						dbGAP											0													81.0	67.0	71.0					9																	136594964		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0				CCDS6978.1	9q33-q34	2008-02-05			ENSG00000123453	ENSG00000123453	1.5.99.2		10536	protein-coding gene	gene with protein product		604455		DMGDHL1		10444331	Standard	NM_007101		Approved	SDH	uc004cep.4	Q9UL12	OTTHUMG00000020879	ENST00000371872.4:c.838C>A	9.37:g.136594964G>T		Somatic		WXS	Illumina GAIIx	Phase_IV	B2RMR5|B4DPI2|B7ZLT6|Q5SYV0|Q9Y280|Q9Y2Y3	Silent	SNP	pfam_FAD-dep_OxRdtase,pfam_GCV_T_N,pfam_GCV_T_C	p.R280	ENST00000371872.4	37	c.838	CCDS6978.1	9																																																																																			SARDH	-	pfam_FAD-dep_OxRdtase	ENSG00000123453		0.642	SARDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SARDH	HGNC	protein_coding	OTTHUMT00000054931.1	89	0.00	0	G			136594964	136594964	-1	no_errors	ENST00000371872	ensembl	human	known	69_37n	silent	79	15.05	14	SNP	0.661	T
SEC24B	10427	genome.wustl.edu	37	4	110442693	110442693	+	Missense_Mutation	SNP	C	C	G			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr4:110442693C>G	ENST00000265175.5	+	14	2474	c.2419C>G	c.(2419-2421)Cgt>Ggt	p.R807G	SEC24B_ENST00000504968.2_Missense_Mutation_p.R837G|SEC24B_ENST00000399100.2_Missense_Mutation_p.R772G	NM_006323.2	NP_006314.2	O95487	SC24B_HUMAN	SEC24 family member B	807					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|aorta morphogenesis (GO:0035909)|auditory receptor cell stereocilium organization (GO:0060088)|cellular protein metabolic process (GO:0044267)|cochlear nucleus development (GO:0021747)|COPII vesicle coating (GO:0048208)|coronary artery morphogenesis (GO:0060982)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|lung lobe morphogenesis (GO:0060463)|membrane organization (GO:0061024)|neural tube closure (GO:0001843)|outflow tract morphogenesis (GO:0003151)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|pulmonary artery morphogenesis (GO:0061156)|regulation of cargo loading into COPII-coated vesicle (GO:1901301)|regulation of establishment of planar polarity involved in neural tube closure (GO:0090178)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|membrane (GO:0016020)	transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.03e-05)		AACAGGTGGCCGTGTGTCTGT	0.433																																						dbGAP											0													93.0	85.0	87.0					4																	110442693		1900	4118	6018	-	-	-	SO:0001583	missense	0			AJ131245	CCDS43260.1, CCDS47124.1, CCDS75179.1	4q25	2013-10-21	2013-10-21		ENSG00000138802	ENSG00000138802			10704	protein-coding gene	gene with protein product		607184	"""SEC24 (S. cerevisiae) related gene family, member B"", ""SEC24 family, member B (S. cerevisiae)"""			10075675, 10329445	Standard	XM_005262688		Approved		uc003hzk.3	O95487	OTTHUMG00000161372	ENST00000265175.5:c.2419C>G	4.37:g.110442693C>G	ENSP00000265175:p.Arg807Gly	Somatic		WXS	Illumina GAIIx	Phase_IV	B7ZKM8|B7ZKN4|Q0VG08	Missense_Mutation	SNP	pfam_Sec23/24_trunk_dom,pfam_Sec23/24_helical_dom,pfam_Sec23_24_beta_S,pfam_Znf_Sec23_Sec24,pfam_Gelsolin_dom,superfamily_Sec23/24_helical_dom,superfamily_Znf_Sec23_Sec24	p.R807G	ENST00000265175.5	37	c.2419	CCDS47124.1	4	.	.	.	.	.	.	.	.	.	.	C	23.8	4.463518	0.84425	.	.	ENSG00000138802	ENST00000504968;ENST00000399100;ENST00000265175	T;T;T	0.79940	-1.32;-1.32;-1.32	5.91	5.91	0.95273	Sec23/Sec24, trunk domain (1);	0.000000	0.85682	D	0.000000	D	0.92459	0.7606	M	0.91717	3.235	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	D	0.93178	0.6572	10	0.87932	D	0	-18.4839	20.2985	0.98592	0.0:1.0:0.0:0.0	.	721;406;837;772;807	B4DTM6;B4E2E1;B7ZKM8;O95487-2;O95487	.;.;.;.;SC24B_HUMAN	G	837;772;807	ENSP00000428564:R837G;ENSP00000382051:R772G;ENSP00000265175:R807G	ENSP00000265175:R807G	R	+	1	0	SEC24B	110662142	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	4.839000	0.62810	2.793000	0.96121	0.655000	0.94253	CGT	SEC24B	-	pfam_Sec23/24_trunk_dom	ENSG00000138802		0.433	SEC24B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	SEC24B	HGNC	protein_coding	OTTHUMT00000364693.2	81	0.00	0	C			110442693	110442693	+1	no_errors	ENST00000265175	ensembl	human	known	69_37n	missense	54	18.18	12	SNP	1.000	G
SERPINB7	8710	genome.wustl.edu	37	18	61463607	61463607	+	Silent	SNP	T	T	C			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr18:61463607T>C	ENST00000398019.2	+	5	769	c.444T>C	c.(442-444)aaT>aaC	p.N148N	SERPINB7_ENST00000336429.2_Silent_p.N148N|SERPINB7_ENST00000546027.1_Silent_p.N148N|SERPINB7_ENST00000540675.1_Silent_p.N131N	NM_003784.3	NP_003775.1	O75635	SPB7_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 7	148					negative regulation of endopeptidase activity (GO:0010951)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of glomerular mesangial cell proliferation (GO:0072126)|positive regulation of platelet-derived growth factor production (GO:0090362)|positive regulation of transforming growth factor beta1 production (GO:0032914)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(14)|prostate(1)|skin(3)	27		Esophageal squamous(42;0.129)				GGGTTGAAAATGAAACACATG	0.348																																						dbGAP											0													77.0	79.0	78.0					18																	61463607		2203	4299	6502	-	-	-	SO:0001819	synonymous_variant	0			AF027866	CCDS11988.1, CCDS58633.1	18q21.33	2014-02-18	2005-08-18		ENSG00000166396	ENSG00000166396		"""Serine (or cysteine) peptidase inhibitors"""	13902	protein-coding gene	gene with protein product		603357	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 7"""			24172014	Standard	NM_003784		Approved	MEGSIN	uc002ljl.4	O75635	OTTHUMG00000060591	ENST00000398019.2:c.444T>C	18.37:g.61463607T>C		Somatic		WXS	Illumina GAIIx	Phase_IV	B4DUW8|F5GZC0|Q1ED45|Q3KPG4	Silent	SNP	pfam_Sepin_dom,superfamily_Sepin_dom,smart_Sepin_dom	p.N148	ENST00000398019.2	37	c.444	CCDS11988.1	18																																																																																			SERPINB7	-	pfam_Sepin_dom,superfamily_Sepin_dom,smart_Sepin_dom	ENSG00000166396		0.348	SERPINB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SERPINB7	HGNC	protein_coding	OTTHUMT00000134007.1	163	0.00	0	T	NM_003784		61463607	61463607	+1	no_errors	ENST00000336429	ensembl	human	known	69_37n	silent	67	11.84	9	SNP	0.085	C
SPEG	10290	genome.wustl.edu	37	2	220312900	220312901	+	Frame_Shift_Ins	INS	-	-	C			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr2:220312900_220312901insC	ENST00000312358.7	+	4	1152_1153	c.1020_1021insC	c.(1021-1023)gagfs	p.E341fs	SPEG_ENST00000396695.2_5'UTR|SPEG_ENST00000485813.1_3'UTR|SPEG_ENST00000396698.1_Frame_Shift_Ins_p.E237fs	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	341	Pro-rich.				cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		GTCGCACTCAGGAGCCTGTGCT	0.748																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"""Immunoglobulin superfamily / I-set domain containing"""	16901	protein-coding gene	gene with protein product		615950	"""aortic preferentially expressed gene 1"""	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	Exception_encountered	2.37:g.220312900_220312901insC	ENSP00000311684:p.Glu341fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Frame_Shift_Ins	INS	pfam_Ig_I-set,pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,superfamily_Fibronectin_type3,smart_Ig_sub,smart_Ig_sub2,smart_Fibronectin_type3,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Fibronectin_type3,pfscan_Prot_kinase_cat_dom,pfscan_Ig-like	p.E340fs	ENST00000312358.7	37	c.1020_1021	CCDS42824.1	2																																																																																			SPEG	-	NULL	ENSG00000072195		0.748	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	SPEG	HGNC	protein_coding	OTTHUMT00000130252.2	14	0.00	0	-	NM_005876		220312900	220312901	+1	no_errors	ENST00000312358	ensembl	human	novel	69_37n	frame_shift_ins	1	66.67	2	INS	0.813:0.864	C
STRBP	55342	genome.wustl.edu	37	9	125923337	125923337	+	Silent	SNP	C	C	T	rs150511866		TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr9:125923337C>T	ENST00000348403.5	-	7	975	c.546G>A	c.(544-546)tcG>tcA	p.S182S	STRBP_ENST00000447404.2_Silent_p.S182S|STRBP_ENST00000360998.3_Silent_p.S168S	NM_018387.4	NP_060857.2	Q96SI9	STRBP_HUMAN	spermatid perinuclear RNA binding protein	182	DZF. {ECO:0000255|PROSITE- ProRule:PRU01040}.				cellular component movement (GO:0006928)|mechanosensory behavior (GO:0007638)|multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)	p.S182S(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(6)|prostate(1)|skin(2)	26						GATCTTTCATCGAAACATTTT	0.358																																						dbGAP											1	Substitution - coding silent(1)	skin(1)											35.0	34.0	35.0					9																	125923337		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AK002169	CCDS6851.1, CCDS55337.1	9q33.1-q33.3	2008-08-29	2001-11-28		ENSG00000165209	ENSG00000165209			16462	protein-coding gene	gene with protein product		611138	"""spermatid perinuclear RNA-binding protein"", ""interleukin enhancer binding factor 3-like"""	ILF3L			Standard	NM_018387		Approved	FLJ11307, SPNR	uc004bns.3	Q96SI9	OTTHUMG00000020636	ENST00000348403.5:c.546G>A	9.37:g.125923337C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q32NB9|Q9BUE1|Q9BXG4|Q9H0B4|Q9H7V1|Q9NUK4	Silent	SNP	pfam_DZF,pfam_Ds-RNA-bd,smart_DZF,smart_Ds-RNA-bd,pfscan_Ds-RNA-bd	p.S182	ENST00000348403.5	37	c.546	CCDS6851.1	9																																																																																			STRBP	-	pfam_DZF,smart_DZF	ENSG00000165209		0.358	STRBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	STRBP	HGNC	protein_coding	OTTHUMT00000053982.1	81	0.00	0	C			125923337	125923337	-1	no_errors	ENST00000348403	ensembl	human	known	69_37n	silent	19	42.42	14	SNP	1.000	T
TATDN2	9797	genome.wustl.edu	37	3	10301826	10301826	+	Silent	SNP	T	T	C			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr3:10301826T>C	ENST00000287652.4	+	3	1471	c.420T>C	c.(418-420)gaT>gaC	p.D140D	RP11-438J1.1_ENST00000450534.1_Intron|TATDN2_ENST00000448281.2_Silent_p.D140D	NM_014760.3	NP_055575.3	Q93075	TATD2_HUMAN	TatD DNase domain containing 2	140					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|DNA catabolic process (GO:0006308)|endoplasmic reticulum unfolded protein response (GO:0030968)	intracellular organelle (GO:0043229)|nucleoplasm (GO:0005654)	deoxyribonuclease activity (GO:0004536)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(9)|pancreas(2)|prostate(1)|stomach(2)	28						CCCAGGTTGATTCCAAAGATA	0.408																																						dbGAP											0													51.0	53.0	52.0					3																	10301826		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			D86972	CCDS33698.1	3p25.3	2010-11-24			ENSG00000157014	ENSG00000157014			28988	protein-coding gene	gene with protein product						9039502	Standard	NM_014760		Approved	KIAA0218	uc003bvf.3	Q93075	OTTHUMG00000155361	ENST00000287652.4:c.420T>C	3.37:g.10301826T>C		Somatic		WXS	Illumina GAIIx	Phase_IV	Q3MIL9|Q5BKU0	Silent	SNP	pfam_TatD_superfamily	p.D140	ENST00000287652.4	37	c.420	CCDS33698.1	3																																																																																			TATDN2	-	NULL	ENSG00000157014		0.408	TATDN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TATDN2	HGNC	protein_coding	OTTHUMT00000339641.1	196	0.51	1	T	XM_376203		10301826	10301826	+1	no_errors	ENST00000287652	ensembl	human	known	69_37n	silent	110	44.16	87	SNP	1.000	C
TFPI2	7980	genome.wustl.edu	37	7	93518420	93518420	+	Frame_Shift_Del	DEL	C	C	-			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr7:93518420delC	ENST00000222543.5	-	3	699	c.387delG	c.(385-387)gggfs	p.G129fs	AC002076.10_ENST00000435257.1_RNA|TFPI2_ENST00000545378.1_Intron|GNGT1_ENST00000455502.1_Intron	NM_001271003.1|NM_001271004.1|NM_006528.3	NP_001257932.1|NP_001257933.1|NP_006519.1	P48307	TFPI2_HUMAN	tissue factor pathway inhibitor 2	129	BPTI/Kunitz inhibitor 2. {ECO:0000255|PROSITE-ProRule:PRU00031}.				blood coagulation (GO:0007596)	nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(1)|large_intestine(5)|lung(5)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14	all_cancers(62;4.45e-10)|all_epithelial(64;2.92e-09)|Lung NSC(181;0.218)		STAD - Stomach adenocarcinoma(171;0.000967)			TCCGGTGACACCCACCGGAAA	0.438																																						dbGAP											0													84.0	94.0	91.0					7																	93518420		2203	4300	6503	-	-	-	SO:0001589	frameshift_variant	0			L27624	CCDS5632.1	7q	2008-07-18			ENSG00000105825	ENSG00000105825			11761	protein-coding gene	gene with protein product		600033				7896752, 8945635	Standard	NM_006528		Approved	PP5, TFPI-2, REF1	uc003umy.2	P48307	OTTHUMG00000022963	ENST00000222543.5:c.387delG	7.37:g.93518420delC	ENSP00000222543:p.Gly129fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q66ME8|Q8NAK6|Q9UC86	Frame_Shift_Del	DEL	pirsf_Prot_inhib_I2_TFPI,pfam_Prot_inh_Kunz-m,superfamily_Prot_inh_Kunz-m,smart_Prot_inh_Kunz-m,prints_Prot_inh_Kunz-m,pfscan_Prot_inh_Kunz-m	p.C130fs	ENST00000222543.5	37	c.387	CCDS5632.1	7																																																																																			TFPI2	-	pirsf_Prot_inhib_I2_TFPI,pfam_Prot_inh_Kunz-m,superfamily_Prot_inh_Kunz-m,smart_Prot_inh_Kunz-m,pfscan_Prot_inh_Kunz-m	ENSG00000105825		0.438	TFPI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TFPI2	HGNC	protein_coding	OTTHUMT00000254720.2	297	0.00	0	C	NM_006528		93518420	93518420	-1	no_errors	ENST00000222543	ensembl	human	known	69_37n	frame_shift_del	131	17.61	28	DEL	0.000	-
TIGD2	166815	genome.wustl.edu	37	4	90035623	90035623	+	Missense_Mutation	SNP	C	C	A			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr4:90035623C>A	ENST00000317005.2	+	1	1656	c.1498C>A	c.(1498-1500)Ctg>Atg	p.L500M	RP11-84C13.1_ENST00000603357.1_lincRNA	NM_145715.2	NP_663761.1	Q4W5G0	TIGD2_HUMAN	tigger transposable element derived 2	500						nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	14		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;3.86e-05)		TGACATGCTTCTGTCTGATAA	0.328																																						dbGAP											0													65.0	70.0	68.0					4																	90035623		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK027653	CCDS3633.1	4q21.3	2013-02-21			ENSG00000180346	ENSG00000180346			18333	protein-coding gene	gene with protein product		612973					Standard	NM_145715		Approved		uc003hsk.3	Q4W5G0	OTTHUMG00000130946	ENST00000317005.2:c.1498C>A	4.37:g.90035623C>A	ENSP00000317170:p.Leu500Met	Somatic		WXS	Illumina GAIIx	Phase_IV		Missense_Mutation	SNP	pfam_DDE_SF_endonuclease_CENPB-like,pfam_HTH_CenpB_DNA-bd_dom,pfam_HTH_Psq,superfamily_Homeodomain-like,smart_HTH_CenpB_DNA-bd_dom,pfscan_HTH_Psq	p.L500M	ENST00000317005.2	37	c.1498	CCDS3633.1	4	.	.	.	.	.	.	.	.	.	.	C	7.266	0.606258	0.14002	.	.	ENSG00000180346	ENST00000317005	T	0.23754	1.89	4.49	2.67	0.31697	.	0.000000	0.36034	N	0.002824	T	0.17534	0.0421	L	0.28115	0.83	0.25747	N	0.98509	D	0.54772	0.968	P	0.46389	0.515	T	0.06427	-1.0827	10	0.30078	T	0.28	-2.5366	5.6814	0.17778	0.1907:0.7064:0.0:0.1029	.	500	Q4W5G0	TIGD2_HUMAN	M	500	ENSP00000317170:L500M	ENSP00000317170:L500M	L	+	1	2	TIGD2	90254646	1.000000	0.71417	1.000000	0.80357	0.866000	0.49608	1.423000	0.34837	1.101000	0.41535	0.467000	0.42956	CTG	TIGD2	-	NULL	ENSG00000180346		0.328	TIGD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TIGD2	HGNC	protein_coding	OTTHUMT00000253545.2	216	0.00	0	C	NM_145715		90035623	90035623	+1	no_errors	ENST00000317005	ensembl	human	known	69_37n	missense	125	11.35	16	SNP	0.998	A
NDC1	55706	genome.wustl.edu	37	1	54293701	54293701	+	Missense_Mutation	SNP	A	A	C			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr1:54293701A>C	ENST00000371429.3	-	4	1024	c.426T>G	c.(424-426)ttT>ttG	p.F142L	NDC1_ENST00000480952.1_5'UTR|AL049745.1_ENST00000578163.1_RNA|NDC1_ENST00000540001.1_Missense_Mutation_p.F142L|NDC1_ENST00000537333.1_5'UTR|NDC1_ENST00000234725.8_Missense_Mutation_p.F27L	NM_001168551.1|NM_018087.4	NP_001162023.1|NP_060557.3	Q9BTX1	NDC1_HUMAN	NDC1 transmembrane nucleoporin	142					mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nuclear pore distribution (GO:0031081)|protein transport (GO:0015031)|spermatogenesis (GO:0007283)|synapsis (GO:0007129)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)										GAACCACAAGAAAGCTGTACT	0.413																																						dbGAP											0													77.0	70.0	72.0					1																	54293701		2203	4300	6503	-	-	-	SO:0001583	missense	0			AL354613	CCDS583.1	1p32.3	2014-01-28	2013-05-23	2013-05-23	ENSG00000058804	ENSG00000058804			25525	protein-coding gene	gene with protein product	"""nuclear division cycle 1 homolog (S. cerevisiae)"""	610115	"""transmembrane protein 48"""	TMEM48		16779818, 12958361	Standard	NR_033142		Approved	FLJ10407, NET3		Q9BTX1	OTTHUMG00000008073	ENST00000371429.3:c.426T>G	1.37:g.54293701A>C	ENSP00000360483:p.Phe142Leu	Somatic		WXS	Illumina GAIIx	Phase_IV	B4DHA3|B4DQQ5|G3XA81|Q8NB76|Q9H9T6|Q9NSG3|Q9NSG4|Q9NVZ7	Missense_Mutation	SNP	pfam_Nucleoporin_prot_Ndc1/Nup	p.F142L	ENST00000371429.3	37	c.426	CCDS583.1	1	.	.	.	.	.	.	.	.	.	.	A	1.595	-0.527951	0.04112	.	.	ENSG00000058804	ENST00000371429;ENST00000360494;ENST00000540001;ENST00000234725	T;T;T	0.35973	1.28;1.28;1.28	5.41	-7.75	0.01236	.	0.423937	0.27650	N	0.018424	T	0.12561	0.0305	N	0.12182	0.205	0.09310	N	0.999991	B;B	0.09022	0.001;0.002	B;B	0.13407	0.007;0.009	T	0.36578	-0.9742	10	0.05721	T	0.95	.	11.426	0.50012	0.3586:0.1071:0.5342:0.0	.	102;142	B4DHA3;Q9BTX1	.;NDC1_HUMAN	L	142;142;142;27	ENSP00000360483:F142L;ENSP00000440873:F142L;ENSP00000234725:F27L	ENSP00000234725:F27L	F	-	3	2	TMEM48	54066289	0.771000	0.28555	0.410000	0.26471	0.182000	0.23217	-0.122000	0.10627	-1.174000	0.02754	-0.478000	0.04885	TTT	TMEM48	-	pfam_Nucleoporin_prot_Ndc1/Nup	ENSG00000058804		0.413	NDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TMEM48	HGNC	protein_coding	OTTHUMT00000022101.1	176	0.00	0	A	NM_018087		54293701	54293701	-1	no_errors	ENST00000371429	ensembl	human	known	69_37n	missense	79	20.20	20	SNP	0.166	C
TPM1	7168	genome.wustl.edu	37	15	63336291	63336291	+	Frame_Shift_Del	DEL	C	C	-	rs17850194	byFrequency	TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr15:63336291delC	ENST00000403994.3	+	2	260	c.180delC	c.(178-180)tacfs	p.Y60fs	TPM1_ENST00000560445.1_Frame_Shift_Del_p.Y60fs|RP11-244F12.3_ENST00000561241.1_RNA|TPM1_ENST00000267996.7_Intron|TPM1_ENST00000358278.3_Frame_Shift_Del_p.Y60fs|TPM1_ENST00000357980.4_Frame_Shift_Del_p.Y102fs|TPM1_ENST00000559397.1_Intron|TPM1_ENST00000559556.1_Frame_Shift_Del_p.Y60fs|TPM1_ENST00000288398.6_Frame_Shift_Del_p.Y60fs	NM_001018005.1	NP_001018005.1	P09493	TPM1_HUMAN	tropomyosin 1 (alpha)	60					cardiac muscle contraction (GO:0060048)|cellular component movement (GO:0006928)|cellular response to reactive oxygen species (GO:0034614)|cytoskeleton organization (GO:0007010)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|negative regulation of cell migration (GO:0030336)|positive regulation of ATPase activity (GO:0032781)|positive regulation of cell adhesion (GO:0045785)|positive regulation of heart rate by epinephrine (GO:0003065)|positive regulation of stress fiber assembly (GO:0051496)|regulation of heart contraction (GO:0008016)|regulation of muscle contraction (GO:0006937)|ruffle organization (GO:0031529)|sarcomere organization (GO:0045214)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|wound healing (GO:0042060)	bleb (GO:0032059)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|muscle thin filament tropomyosin (GO:0005862)|ruffle membrane (GO:0032587)|sarcomere (GO:0030017)|stress fiber (GO:0001725)	actin binding (GO:0003779)|cytoskeletal protein binding (GO:0008092)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			endometrium(1)|large_intestine(1)|lung(2)	4						TGGACAAATACTCTGAGGCTC	0.557																																						dbGAP											0													61.0	60.0	61.0					15																	63336291		2203	4300	6503	-	-	-	SO:0001589	frameshift_variant	0			AB209041	CCDS10181.1, CCDS32262.1, CCDS32263.1, CCDS32264.1, CCDS45273.1, CCDS58368.1, CCDS58369.1	15q22.1	2014-09-17			ENSG00000140416	ENSG00000140416		"""Tropomyosins"""	12010	protein-coding gene	gene with protein product		191010	"""chromosome 15 open reading frame 13"", ""cardiomyopathy, hypertrophic 3"""	C15orf13, CMH3		10343096, 8205619	Standard	XM_005254637		Approved		uc002all.3	P09493	OTTHUMG00000132803	ENST00000403994.3:c.180delC	15.37:g.63336291delC	ENSP00000385107:p.Tyr60fs	Somatic		WXS	Illumina GAIIx	Phase_IV	B7Z5T7|D9YZV2|D9YZV3|D9YZV8|P09494|P10469|Q6DV89|Q6DV90|Q7Z6L8|Q86W64|Q96IK2|Q9UCI1|Q9UCI2|Q9UCY9|Q9Y427	Frame_Shift_Del	DEL	pfam_Tropomyosin,prints_Tropomyosin	p.S61fs	ENST00000403994.3	37	c.180	CCDS45273.1	15																																																																																			TPM1	-	pfam_Tropomyosin	ENSG00000140416		0.557	TPM1-002	KNOWN	basic|CCDS	protein_coding	TPM1	HGNC	protein_coding	OTTHUMT00000417083.2	72	0.00	0	C	NM_001018004		63336291	63336291	+1	no_errors	ENST00000288398	ensembl	human	known	69_37n	frame_shift_del	23	29.41	10	DEL	1.000	-
TRAF6	7189	genome.wustl.edu	37	11	36518753	36518753	+	Missense_Mutation	SNP	T	T	C			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr11:36518753T>C	ENST00000526995.1	-	4	757	c.511A>G	c.(511-513)Aaa>Gaa	p.K171E	TRAF6_ENST00000348124.5_Missense_Mutation_p.K171E|TRAF6_ENST00000529150.1_5'Flank	NM_004620.3	NP_004611.1	Q9Y4K3	TRAF6_HUMAN	TNF receptor-associated factor 6, E3 ubiquitin protein ligase	171	Interaction with TAX1BP1.				activation of MAPK activity (GO:0000187)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|activation of protein kinase activity (GO:0032147)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|apoptotic signaling pathway (GO:0097190)|bone resorption (GO:0045453)|cell development (GO:0048468)|cellular response to lipopolysaccharide (GO:0071222)|Fc-epsilon receptor signaling pathway (GO:0038095)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|JNK cascade (GO:0007254)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|osteoclast differentiation (GO:0030316)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|protein autoubiquitination (GO:0051865)|protein complex assembly (GO:0006461)|protein K63-linked ubiquitination (GO:0070534)|protein polyubiquitination (GO:0000209)|regulation of immunoglobulin secretion (GO:0051023)|response to interleukin-1 (GO:0070555)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|lipid particle (GO:0005811)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	histone deacetylase binding (GO:0042826)|ligase activity (GO:0016874)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein kinase B binding (GO:0043422)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin conjugating enzyme binding (GO:0031624)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(13)|ovary(2)|pancreas(1)	27	all_lung(20;0.211)	all_hematologic(20;0.107)				ATATGGAATTTTTGGAAGGGA	0.383																																						dbGAP											0													70.0	74.0	73.0					11																	36518753		2202	4298	6500	-	-	-	SO:0001583	missense	0				CCDS7901.1	11p12	2013-01-09	2012-02-23		ENSG00000175104	ENSG00000175104		"""RING-type (C3HC4) zinc fingers"""	12036	protein-coding gene	gene with protein product		602355	"""TNF receptor-associated factor 6"""			8837778	Standard	NM_004620		Approved	RNF85	uc001mws.2	Q9Y4K3	OTTHUMG00000166391	ENST00000526995.1:c.511A>G	11.37:g.36518753T>C	ENSP00000433623:p.Lys171Glu	Somatic		WXS	Illumina GAIIx	Phase_IV	A6NKI7|A8KAB3|D3DR16|Q8NEH5	Missense_Mutation	SNP	pfam_MATH,pfam_Znf_C3HC4_RING-type,superfamily_TRAF-like,smart_Znf_RING,smart_MATH,pirsf_TNF_rcpt--assoc_TRAF,pfscan_MATH,pfscan_Znf_RING,pfscan_Znf_TRAF	p.K171E	ENST00000526995.1	37	c.511	CCDS7901.1	11	.	.	.	.	.	.	.	.	.	.	T	11.95	1.792404	0.31685	.	.	ENSG00000175104	ENST00000526995;ENST00000348124	T;T	0.36520	1.25;1.25	5.38	4.23	0.50019	Zinc finger, TRAF-type (1);	0.046274	0.85682	D	0.000000	T	0.39784	0.1091	M	0.78801	2.425	0.47547	D	0.999453	B	0.25809	0.135	B	0.20184	0.028	T	0.32348	-0.9910	10	0.66056	D	0.02	-27.5375	11.6052	0.51029	0.1336:0.0:0.0:0.8664	.	171	Q9Y4K3	TRAF6_HUMAN	E	171	ENSP00000433623:K171E;ENSP00000337853:K171E	ENSP00000337853:K171E	K	-	1	0	TRAF6	36475329	1.000000	0.71417	0.272000	0.24630	0.067000	0.16453	7.045000	0.76585	0.859000	0.35456	0.528000	0.53228	AAA	TRAF6	-	pirsf_TNF_rcpt--assoc_TRAF,pfscan_Znf_TRAF	ENSG00000175104		0.383	TRAF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TRAF6	HGNC	protein_coding	OTTHUMT00000389530.1	108	0.00	0	T	NM_145803		36518753	36518753	-1	no_errors	ENST00000348124	ensembl	human	known	69_37n	missense	86	28.33	34	SNP	0.987	C
TRAPPC12	51112	genome.wustl.edu	37	2	3428379	3428379	+	Silent	SNP	T	T	C			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr2:3428379T>C	ENST00000324266.5	+	5	1557	c.1362T>C	c.(1360-1362)ctT>ctC	p.L454L	TRAPPC12_ENST00000469147.1_3'UTR|TRAPPC12_ENST00000382110.2_Silent_p.L454L	NM_016030.5	NP_057114.5	Q8WVT3	TPC12_HUMAN	trafficking protein particle complex 12	454					vesicle-mediated transport (GO:0016192)												TCGGAAATCTTGATCAGCCAG	0.448																																						dbGAP											0													203.0	201.0	202.0					2																	3428379		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			BC017475	CCDS1652.1	2p25.3	2013-01-10	2011-12-12	2011-12-12	ENSG00000171853	ENSG00000171853		"""Trafficking protein particle complex"", ""Tetratricopeptide (TTC) repeat domain containing"""	24284	protein-coding gene	gene with protein product		614139	"""tetratricopeptide repeat domain 15"""	TTC15		10810093, 21525244, 20562859	Standard	NM_016030		Approved	CGI-87, TTC-15	uc002qxm.1	Q8WVT3	OTTHUMG00000090328	ENST00000324266.5:c.1362T>C	2.37:g.3428379T>C		Somatic		WXS	Illumina GAIIx	Phase_IV	B3KV01|D6W4Y2|Q8WVW1|Q9Y395	Missense_Mutation	SNP	NULL	p.L134S	ENST00000324266.5	37	c.401	CCDS1652.1	2	.	.	.	.	.	.	.	.	.	.	T	10.60	1.394360	0.25205	.	.	ENSG00000171853	ENST00000441983	.	.	.	5.73	-4.7	0.03288	.	0.000000	0.64402	D	0.000001	T	0.50274	0.1606	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50800	-0.8785	6	0.87932	D	0	.	1.2816	0.02042	0.4444:0.1772:0.1695:0.209	.	.	.	.	S	134	.	ENSP00000409960:L134S	L	+	2	0	TTC15	3407386	0.406000	0.25344	0.156000	0.22583	0.983000	0.72400	-0.355000	0.07671	-1.480000	0.01865	0.533000	0.62120	TTG	TRAPPC12	-	NULL	ENSG00000171853		0.448	TRAPPC12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	TRAPPC12	HGNC	protein_coding	OTTHUMT00000206693.2	142	0.00	0	T	NM_016030		3428379	3428379	+1	no_start_codon:pseudogene:bad_bp_length_for_coding_region	ENST00000441983	ensembl	human	putative	69_37n	missense	127	21.12	34	SNP	0.857	C
TRPM6	140803	genome.wustl.edu	37	9	77423061	77423061	+	Silent	SNP	G	G	T			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr9:77423061G>T	ENST00000360774.1	-	14	1764	c.1527C>A	c.(1525-1527)acC>acA	p.T509T	TRPM6_ENST00000376871.3_Intron|TRPM6_ENST00000451710.3_Silent_p.T509T|TRPM6_ENST00000376864.4_Silent_p.T509T|TRPM6_ENST00000449912.2_Silent_p.T504T|TRPM6_ENST00000376872.3_Silent_p.T509T|TRPM6_ENST00000361255.3_Silent_p.T504T	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	509					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						TGTCAATCAAGGTTATTCGGT	0.383																																						dbGAP											0													184.0	175.0	178.0					9																	77423061		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AK026281	CCDS6647.1, CCDS55318.1, CCDS55319.1	9q21.13	2011-12-14	2003-12-02		ENSG00000119121	ENSG00000119121		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17995	protein-coding gene	gene with protein product		607009	"""hypomagnesemia, secondary hypocalcemia"""	HOMG, HSH		10021370, 12032570, 16382100	Standard	NM_017662		Approved	CHAK2, FLJ22628	uc004ajk.1	Q9BX84	OTTHUMG00000020027	ENST00000360774.1:c.1527C>A	9.37:g.77423061G>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Silent	SNP	pfam_MHCK_EF2_kinase,pfam_Ion_trans_dom,superfamily_Kinase-like_dom,smart_MHCK_EF2_kinase,pfscan_MHCK_EF2_kinase	p.T509	ENST00000360774.1	37	c.1527	CCDS6647.1	9																																																																																			TRPM6	-	NULL	ENSG00000119121		0.383	TRPM6-001	KNOWN	basic|CCDS	protein_coding	TRPM6	HGNC	protein_coding	OTTHUMT00000052693.1	175	0.00	0	G	NM_017662		77423061	77423061	-1	no_errors	ENST00000451710	ensembl	human	known	69_37n	silent	54	34.15	28	SNP	0.013	T
VAC14	55697	genome.wustl.edu	37	16	70834801	70834802	+	Start_Codon_Del	DEL	CA	CA	-			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	CA	CA					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr16:70834801_70834802delCA	ENST00000261776.5	-	0	262_263				RP11-424M24.5_ENST00000574178.1_lincRNA	NM_018052.3	NP_060522.3	Q08AM6	VAC14_HUMAN	Vac14 homolog (S. cerevisiae)						phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|regulation of lipid kinase activity (GO:0043550)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|PAS complex (GO:0070772)	receptor activity (GO:0004872)			breast(2)|endometrium(2)|kidney(10)|large_intestine(1)|lung(10)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	33		Ovarian(137;0.0699)				TCTCGGGGTTCATGGTGGCAGC	0.693																																						dbGAP											0																																										-	-	-	SO:0001582	initiator_codon_variant	0			AK056433	CCDS10896.1	16q22.1	2010-03-23	2005-02-09		ENSG00000103043	ENSG00000103043			25507	protein-coding gene	gene with protein product		604632	"""Tax1 (human T-cell leukemia virus type I) binding protein 2"""	TAX1BP2		15542851, 12719380	Standard	NM_018052		Approved	FLJ10305, ArPIKfyve	uc002ezm.3	Q08AM6	OTTHUMG00000137583		16.37:g.70834801_70834802delCA		Somatic		WXS	Illumina GAIIx	Phase_IV	B3KPJ5|B3KSM8|Q13174|Q6IA12|Q7L4Y1|Q9BW96|Q9H6V6	Frame_Shift_Del	DEL	pfam_DUF3434,pfam_HEAT,superfamily_ARM-type_fold	p.M1fs	ENST00000261776.5	37	c.3_2	CCDS10896.1	16																																																																																			VAC14	-	superfamily_ARM-type_fold	ENSG00000103043		0.693	VAC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	VAC14	HGNC	protein_coding	OTTHUMT00000268973.3	18	0.00	0	CA	NM_018052		70834801	70834802	-1	no_errors	ENST00000261776	ensembl	human	known	69_37n	frame_shift_del	5	50.00	6	DEL	1.000:1.000	-
WDR62	284403	genome.wustl.edu	37	19	36584983	36584983	+	Missense_Mutation	SNP	G	G	A			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr19:36584983G>A	ENST00000270301.7	+	20	2384	c.2384G>A	c.(2383-2385)gGa>gAa	p.G795E	WDR62_ENST00000401500.2_Missense_Mutation_p.G795E			O43379	WDR62_HUMAN	WD repeat domain 62	795					cerebral cortex development (GO:0021987)|neurogenesis (GO:0022008)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle pole (GO:0000922)				cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(15)|prostate(4)|stomach(2)|urinary_tract(3)	43	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			CTGAGCCCTGGAGAGCAAACA	0.507																																						dbGAP											0													157.0	146.0	150.0					19																	36584983		2203	4300	6503	-	-	-	SO:0001583	missense	0			BX647726	CCDS33001.1, CCDS46059.1	19q13.12	2013-01-09	2005-05-09	2005-05-09	ENSG00000075702	ENSG00000075702		"""WD repeat domain containing"""	24502	protein-coding gene	gene with protein product		613583	"""chromosome 19 open reading frame 14"", ""microcephaly, primary autosomal recessive 2"""	C19orf14, MCPH2		19910486, 20729831, 20890278, 21496009	Standard	NM_001083961		Approved	DKFZP434J046, FLJ33298	uc002odd.2	O43379	OTTHUMG00000048139	ENST00000270301.7:c.2384G>A	19.37:g.36584983G>A	ENSP00000270301:p.Gly795Glu	Somatic		WXS	Illumina GAIIx	Phase_IV	Q63HP9|Q659D7|Q8NBF7|Q96AD9	Missense_Mutation	SNP	pfam_WD40_repeat,superfamily_WD40_repeat_dom,smart_WD40_repeat,pfscan_WD40_repeat,pfscan_WD40_repeat_dom	p.G795E	ENST00000270301.7	37	c.2384	CCDS33001.1	19	.	.	.	.	.	.	.	.	.	.	G	16.17	3.047460	0.55110	.	.	ENSG00000075702	ENST00000401500;ENST00000270301	T;T	0.44083	0.93;0.93	5.06	5.06	0.68205	.	0.295751	0.27016	N	0.021354	T	0.53126	0.1777	L	0.55103	1.725	0.80722	D	1	D;P	0.89917	1.0;0.911	D;B	0.97110	1.0;0.376	T	0.48445	-0.9035	10	0.02654	T	1	-12.2911	13.7967	0.63175	0.0:0.0:1.0:0.0	.	795;795	O43379-4;O43379	.;WDR62_HUMAN	E	795	ENSP00000384792:G795E;ENSP00000270301:G795E	ENSP00000270301:G795E	G	+	2	0	WDR62	41276823	1.000000	0.71417	1.000000	0.80357	0.798000	0.45092	2.142000	0.42177	2.641000	0.89580	0.563000	0.77884	GGA	WDR62	-	NULL	ENSG00000075702		0.507	WDR62-006	NOVEL	basic|appris_candidate|CCDS	protein_coding	WDR62	HGNC	protein_coding	OTTHUMT00000457436.1	165	0.00	0	G	NM_015671		36584983	36584983	+1	no_errors	ENST00000401500	ensembl	human	known	69_37n	missense	97	53.59	112	SNP	1.000	A
ZC3H4	23211	genome.wustl.edu	37	19	47570533	47570534	+	Frame_Shift_Ins	INS	-	-	G	rs369502892		TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr19:47570533_47570534insG	ENST00000253048.5	-	15	3028_3029	c.2991_2992insC	c.(2989-2994)cccgtgfs	p.V998fs	ZC3H4_ENST00000594019.1_5'UTR	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	998							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	41		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)		GCCGCGGGCACGGGGGGCACTG	0.738																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AB028987	CCDS42582.1	19q13.33	2012-07-05	2007-10-18	2007-10-18		ENSG00000130749		"""Zinc fingers, CCCH-type domain containing"""	17808	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 7"""	C19orf7			Standard	NM_015168		Approved	KIAA1064	uc002pga.4	Q9UPT8		ENST00000253048.5:c.2992dupC	19.37:g.47570539_47570539dupG	ENSP00000253048:p.Val998fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q9Y420	Frame_Shift_Ins	INS	pfam_Znf_CCCH,smart_Znf_CCCH	p.V997fs	ENST00000253048.5	37	c.2992_2991	CCDS42582.1	19																																																																																			ZC3H4	-	NULL	ENSG00000130749		0.738	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	ZC3H4	HGNC	protein_coding	OTTHUMT00000466667.1	63	0.00	0	-			47570533	47570534	-1	no_errors	ENST00000253048	ensembl	human	known	69_37n	frame_shift_ins	16	11.11	2	INS	0.128:0.006	G
ZNF227	7770	genome.wustl.edu	37	19	44738970	44738970	+	Silent	SNP	G	G	A			TCGA-BH-A0B1-01A-12W-A071-09	TCGA-BH-A0B1-10A-01W-A071-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	de20290a-1560-41fd-896b-a3ae1103423e	eb76d20f-0575-49c2-a173-c370be9eef44	g.chr19:44738970G>A	ENST00000313040.7	+	6	592	c.387G>A	c.(385-387)agG>agA	p.R129R	ZNF227_ENST00000589707.1_3'UTR|ZNF227_ENST00000586228.1_3'UTR|ZNF227_ENST00000391961.2_Silent_p.R78R|ZNF227_ENST00000589005.1_Silent_p.R78R	NM_182490.1	NP_872296.1	Q86WZ6	ZN227_HUMAN	zinc finger protein 227	129					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(2)|stomach(1)|urinary_tract(1)	24		Prostate(69;0.0435)				AATTAACCAGGTGTCTTCAGG	0.373																																						dbGAP											0													82.0	87.0	85.0					19																	44738970		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AK092253	CCDS12636.1, CCDS74388.1	19q13.32	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	13020	protein-coding gene	gene with protein product							Standard	XM_005259232		Approved		uc002oyu.3	Q86WZ6		ENST00000313040.7:c.387G>A	19.37:g.44738970G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	B3KRU7|B7Z5P9	Silent	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.R129	ENST00000313040.7	37	c.387	CCDS12636.1	19																																																																																			ZNF227	-	NULL	ENSG00000131115		0.373	ZNF227-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ZNF227	HGNC	protein_coding	OTTHUMT00000460720.1	200	0.00	0	G	NM_182490		44738970	44738970	+1	no_errors	ENST00000313040	ensembl	human	known	69_37n	silent	236	14.18	39	SNP	0.000	A
