#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_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	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_default_gene_name	i_deletion_substructures	i_domain	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_name	i_gene_name_source	i_gene_type	i_havana_transcript	i_reference	i_refseq_mrna_id	i_secondary_variant_classification	i_stop	i_strand	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_type	i_ucsc_cons	i_variant
AKAP5	9495	genome.wustl.edu	37	14	64936170	64936170	+	Missense_Mutation	SNP	C	C	T			TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chr14:64936170C>T	ENST00000394718.4	+	2	1436	c.1058C>T	c.(1057-1059)aCa>aTa	p.T353I	ZBTB25_ENST00000555424.1_Intron|AKAP5_ENST00000320636.5_Missense_Mutation_p.T353I|ZBTB25_ENST00000555220.1_Intron	NM_004857.3	NP_004848.3	P24588	AKAP5_HUMAN	A kinase (PRKA) anchor protein 5	353					energy reserve metabolic process (GO:0006112)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|protein targeting (GO:0006605)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	adenylate cyclase binding (GO:0008179)|protein kinase A binding (GO:0051018)			endometrium(2)|kidney(1)|large_intestine(5)|lung(4)|stomach(1)	13				all cancers(60;0.00749)|OV - Ovarian serous cystadenocarcinoma(108;0.0095)|BRCA - Breast invasive adenocarcinoma(234;0.0449)		TTTGATGTTACAAAATCTAAA	0.328																																																	0													90.0	103.0	98.0					14																	64936170		2203	4299	6502	SO:0001583	missense	9495			M90359	CCDS9764.1	14q23.3	2012-05-16			ENSG00000179841	ENSG00000179841		"""A-kinase anchor proteins"""	375	protein-coding gene	gene with protein product		604688				1512224, 1618839	Standard	NM_004857		Approved	AKAP75, AKAP79	uc001xhd.4	P24588	OTTHUMG00000029634	ENST00000394718.4:c.1058C>T	14.37:g.64936170C>T	ENSP00000378207:p.Thr353Ile	Somatic		WXS	Illumina HiSeq	Phase_IV	A2RRB8	Missense_Mutation	SNP	pfam_Pkinase-A_anch_WSK-motif	p.T353I	ENST00000394718.4	37	c.1058	CCDS9764.1	14	.	.	.	.	.	.	.	.	.	.	C	9.444	1.088882	0.20390	.	.	ENSG00000179841	ENST00000394718;ENST00000320636	T;T	0.25085	1.82;1.82	5.51	1.4	0.22301	.	0.571549	0.16323	N	0.219492	T	0.16811	0.0404	N	0.19112	0.55	0.09310	N	1	B	0.27068	0.167	B	0.22386	0.039	T	0.19811	-1.0294	10	0.62326	D	0.03	-9.8958	13.1948	0.59732	0.5082:0.4918:0.0:0.0	.	353	P24588	AKAP5_HUMAN	I	353	ENSP00000378207:T353I;ENSP00000315615:T353I	ENSP00000315615:T353I	T	+	2	0	AKAP5	64005923	0.127000	0.22367	0.846000	0.33378	0.729000	0.41735	0.543000	0.23237	0.439000	0.26476	-0.346000	0.07831	ACA	AKAP5	-	NULL		0.328	AKAP5-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	AKAP5	HGNC	protein_coding	OTTHUMT00000268070.3	C			64936170	+1	no_errors	ENST00000320636	ensembl	human	known	70_37	missense	SNP	0.085	T
ALMS1	7840	genome.wustl.edu	37	2	73613031	73613032	+	In_Frame_Ins	INS	-	-	GGA	rs55889738|rs72319667|rs200709146|rs61156725|rs70965731|rs193922695|rs3074417	byFrequency	TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chr2:73613031_73613032insGGA	ENST00000264448.6	+	1	146_147	c.35_36insGGA	c.(34-39)ctggag>ctGGAggag	p.28_29insE	ALMS1_ENST00000409009.1_In_Frame_Ins_p.28_29insE|ALMS1_ENST00000377715.1_In_Frame_Ins_p.28_29insE	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	28	Glu-rich.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.E27_E28delEE(1)|p.E28_A29insE(1)		breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CCGGGCGAGCTggaggaggagg	0.698																																																	2	Insertion - In frame(1)|Deletion - In frame(1)	ovary(1)|breast(1)																																								SO:0001652	inframe_insertion	7840			AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.72_74dupGGA	2.37:g.73613038_73613040dupGGA	ENSP00000264448:p.Glu28_Glu28dup	Somatic		WXS	Illumina HiSeq	Phase_IV	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	In_Frame_Ins	INS	NULL	p.16in_frame_insE	ENST00000264448.6	37	c.35_36	CCDS42697.1	2																																																																																			ALMS1	-	NULL		0.698	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ALMS1	HGNC	protein_coding	OTTHUMT00000327776.1	-	NM_015120		73613032	+1	no_errors	ENST00000264448	ensembl	human	known	70_37	in_frame_ins	INS	0.999:0.989	GGA
ANXA1	301	genome.wustl.edu	37	9	75783796	75783797	+	Intron	INS	-	-	GTGT	rs71495355|rs10577190|rs3832643		TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chr9:75783796_75783797insGTGT	ENST00000376911.1	+	11	1743				ANXA1_ENST00000491192.1_3'UTR|ANXA1_ENST00000257497.6_Intron			P04083	ANXA1_HUMAN	annexin A1						alpha-beta T cell differentiation (GO:0046632)|arachidonic acid secretion (GO:0050482)|cell surface receptor signaling pathway (GO:0007166)|cellular component movement (GO:0006928)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to hydrogen peroxide (GO:0070301)|endocrine pancreas development (GO:0031018)|estrous cycle phase (GO:0060206)|gliogenesis (GO:0042063)|hepatocyte differentiation (GO:0070365)|inflammatory response (GO:0006954)|insulin secretion (GO:0030073)|keratinocyte differentiation (GO:0030216)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of apoptotic process (GO:0043066)|negative regulation of catalytic activity (GO:0043086)|negative regulation of interleukin-8 secretion (GO:2000483)|neutrophil clearance (GO:0097350)|neutrophil homeostasis (GO:0001780)|peptide cross-linking (GO:0018149)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of neutrophil apoptotic process (GO:0033031)|positive regulation of prostaglandin biosynthetic process (GO:0031394)|positive regulation of vesicle fusion (GO:0031340)|regulation of cell proliferation (GO:0042127)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to interleukin-1 (GO:0070555)|response to peptide hormone (GO:0043434)|response to X-ray (GO:0010165)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cilium (GO:0005929)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|phospholipase A2 inhibitor activity (GO:0019834)|phospholipid binding (GO:0005543)|protein binding, bridging (GO:0030674)|receptor binding (GO:0005102)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|large_intestine(1)|lung(5)	8		all_epithelial(88;2.54e-11)		OV - Ovarian serous cystadenocarcinoma(323;2.82e-06)|GBM - Glioblastoma multiforme(74;0.0325)	Amcinonide(DB00288)|Dexamethasone(DB01234)|Hydrocortisone(DB00741)	ATTCGTGTAAGgtgtgtgtgtg	0.366																																																	0																																										SO:0001627	intron_variant	301			X05908	CCDS6645.1	9q21.13	2013-02-25			ENSG00000135046	ENSG00000135046		"""Annexins"", ""Endogenous ligands"""	533	protein-coding gene	gene with protein product		151690		ANX1, LPC1		2936963	Standard	NM_000700		Approved		uc004ajf.1	P04083	OTTHUMG00000020016	ENST00000376911.1:c.862-151->GTGT	9.37:g.75783801_75783804dupGTGT		Somatic		WXS	Illumina HiSeq	Phase_IV		RNA	INS	-	NULL	ENST00000376911.1	37	NULL	CCDS6645.1	9																																																																																			ANXA1	-	-		0.366	ANXA1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	ANXA1	HGNC	protein_coding	OTTHUMT00000052665.1	-	NM_000700		75783797	+1	no_errors	ENST00000491192	ensembl	human	known	70_37	rna	INS	0.000:0.003	GTGT
ARHGAP22	58504	genome.wustl.edu	37	10	49791043	49791043	+	Silent	SNP	C	C	G			TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chr10:49791043C>G	ENST00000249601.4	-	2	485	c.189G>C	c.(187-189)ggG>ggC	p.G63G	ARHGAP22_ENST00000417912.2_Silent_p.G63G|ARHGAP22_ENST00000435790.2_Silent_p.G69G|ARHGAP22_ENST00000491108.1_5'UTR	NM_001256024.1|NM_021226.3	NP_001242953.1|NP_067049.2	Q7Z5H3	RHG22_HUMAN	Rho GTPase activating protein 22	63	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			endometrium(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						AAAGCTGATCCCCACGCAGCA	0.597																																																	0													132.0	118.0	123.0					10																	49791043		2203	4300	6503	SO:0001819	synonymous_variant	58504			AY324801	CCDS7227.1, CCDS58079.1, CCDS58080.1, CCDS58081.1	10q11.23	2013-01-10			ENSG00000128805	ENSG00000128805		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	30320	protein-coding gene	gene with protein product		610585				8619474	Standard	NM_021226		Approved	RhoGAP2	uc010qgm.3	Q7Z5H3	OTTHUMG00000018176	ENST00000249601.4:c.189G>C	10.37:g.49791043C>G		Somatic		WXS	Illumina HiSeq	Phase_IV	A0AVP7|A5YM75|B4DED8|B9EGA0|C9JDM2|O00152|Q6ZSB0	Silent	SNP	pfam_RhoGAP_dom,pfam_Pleckstrin_homology,superfamily_Rho_GTPase_activation_prot,smart_Pleckstrin_homology,smart_RhoGAP_dom,pfscan_Pleckstrin_homology,pfscan_RhoGAP_dom	p.G63	ENST00000249601.4	37	c.189	CCDS7227.1	10																																																																																			ARHGAP22	-	pfam_Pleckstrin_homology,smart_Pleckstrin_homology,pfscan_Pleckstrin_homology		0.597	ARHGAP22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	ARHGAP22	HGNC	protein_coding	OTTHUMT00000358767.1	C	NM_021226		49791043	-1	no_errors	ENST00000417912	ensembl	human	known	70_37	silent	SNP	1.000	G
BAZ2B	29994	genome.wustl.edu	37	2	160318094	160318094	+	Intron	SNP	G	G	T			TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chr2:160318094G>T	ENST00000392783.2	-	4	641				BAZ2B_ENST00000392782.1_Intron|BAZ2B_ENST00000343439.5_Intron|BAZ2B_ENST00000483316.1_5'UTR|BAZ2B_ENST00000355831.2_Intron	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(7)|liver(2)|lung(41)|ovary(3)|prostate(1)|skin(2)|soft_tissue(1)|urinary_tract(1)	82						CAAGATACCTGTTATTCCTTC	0.294																																																	0																																										SO:0001627	intron_variant	29994			AB032255	CCDS2209.2, CCDS74594.1	2q24.2	2013-01-28			ENSG00000123636	ENSG00000123636		"""Zinc fingers, PHD-type"""	963	protein-coding gene	gene with protein product		605683				10662543	Standard	XM_005246488		Approved	WALp4	uc002uao.3	Q9UIF8	OTTHUMG00000132027	ENST00000392783.2:c.146-7782C>A	2.37:g.160318094G>T		Somatic		WXS	Illumina HiSeq	Phase_IV	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	RNA	SNP	-	NULL	ENST00000392783.2	37	NULL	CCDS2209.2	2																																																																																			BAZ2B	-	-		0.294	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	BAZ2B	HGNC	protein_coding	OTTHUMT00000255037.2	G			160318094	-1	no_errors	ENST00000483316	ensembl	human	known	70_37	rna	SNP	0.964	T
BRIX1	55299	genome.wustl.edu	37	5	34925328	34925329	+	Intron	INS	-	-	A	rs112241293|rs66875519	byFrequency	TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chr5:34925328_34925329insA	ENST00000336767.5	+	10	1155				BRIX1_ENST00000506023.1_Intron	NM_018321.3	NP_060791.3	Q8TDN6	BRX1_HUMAN	BRX1, biogenesis of ribosomes, homolog (S. cerevisiae)						ribosome biogenesis (GO:0042254)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|large_intestine(2)|lung(1)	4						TTTTTTTTTTTAGCATCGGCGT	0.332													|||unknown(HR)	735	0.146765	0.0719	0.1455	5008	,	,		16270	0.1131		0.2058	False		,,,				2504	0.2229																0										312,517,55,3344		15,38,7,237,60,6,353,4,34,1360						0.4	0.3		dbSNP_130	11	1360,691,230,5903		125,93,69,948,47,18,486,8,127,2171	no	splice-3	BRIX1	NM_018321.3		140,131,76,1185,107,24,839,12,161,3531	A1A1,A1A2,A1A3,A1R,A2A2,A2A3,A2R,A3A3,A3R,RR		27.8715,20.9082,25.4995				1672,1208,285,9247				SO:0001627	intron_variant	55299				CCDS34143.1	5p13.2	2009-09-25	2009-09-25	2009-09-25	ENSG00000113460	ENSG00000113460			24170	protein-coding gene	gene with protein product			"""brix domain containing 2"""	BXDC2		12477932	Standard	NM_018321		Approved	BRIX, FLJ11100	uc003jja.3	Q8TDN6	OTTHUMG00000162021	ENST00000336767.5:c.793-2->A	5.37:g.34925329_34925329dupA		Somatic		WXS	Illumina HiSeq	Phase_IV	A8K0P5|Q3ZTT4|Q8N453|Q96DH1	Splice_Site	INS	-	e10-2	ENST00000336767.5	37	c.793-3_793-2	CCDS34143.1	5																																																																																			BRIX1	-	-		0.332	BRIX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	BRIX1	HGNC	protein_coding	OTTHUMT00000366826.2	-	NM_018321		34925329	+1	no_errors	ENST00000336767	ensembl	human	known	70_37	splice_site_ins	INS	0.213:0.997	A
CACNA1E	777	genome.wustl.edu	37	1	181767481	181767481	+	Silent	SNP	C	C	A			TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chr1:181767481C>A	ENST00000367573.2	+	48	6453	c.6453C>A	c.(6451-6453)acC>acA	p.T2151T	CACNA1E_ENST00000367570.1_Silent_p.T2108T|CACNA1E_ENST00000360108.3_Silent_p.T2132T|CACNA1E_ENST00000367567.4_Silent_p.T1715T|CACNA1E_ENST00000357570.5_Silent_p.T2102T|CACNA1E_ENST00000526775.1_Silent_p.T2089T|CACNA1E_ENST00000358338.5_Silent_p.T2040T	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	2151					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						ACACCAGCACCCCAAGAAGAA	0.592																																																	0													116.0	127.0	123.0					1																	181767481		2025	4165	6190	SO:0001819	synonymous_variant	777			AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.6453C>A	1.37:g.181767481C>A		Somatic		WXS	Illumina HiSeq	Phase_IV	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Silent	SNP	pfam_Ion_trans_dom,pfam_VDCC_a1su_IQ,pfam_PKD1_2_channel,pfscan_EF_HAND_2,prints_VDCCAlpha1,prints_VDCC_R_a1su	p.T2151	ENST00000367573.2	37	c.6453	CCDS55664.1	1																																																																																			CACNA1E	-	NULL		0.592	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	CACNA1E	HGNC	protein_coding	OTTHUMT00000090793.2	C	NM_000721		181767481	+1	no_errors	ENST00000367573	ensembl	human	known	70_37	silent	SNP	1.000	A
MBD1	4152	genome.wustl.edu	37	18	47792730	47792730	+	IGR	SNP	G	G	T			TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chr18:47792730G>T	ENST00000591416.1	-	0	4905				CCDC11_ENST00000398545.4_Silent_p.G15G			Q9UIS9	MBD1_HUMAN	methyl-CpG binding domain protein 1						negative regulation of transcription, DNA-templated (GO:0045892)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methyl-CpG binding (GO:0008327)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36						TGGGGGTGGGGCCCTTAACCT	0.622																																																	0													99.0	108.0	105.0					18																	47792730		1968	4170	6138	SO:0001628	intergenic_variant	220136			Y10746	CCDS11941.1, CCDS11942.1, CCDS11943.1, CCDS11944.1, CCDS32832.1, CCDS56071.1, CCDS56072.1, CCDS56073.1, CCDS59318.1, CCDS59319.1, CCDS59320.1	18q21	2014-02-18			ENSG00000141644	ENSG00000141644			6916	protein-coding gene	gene with protein product		156535				9207790, 10441743	Standard	NM_015844		Approved	PCM1, CXXC3	uc002lem.4	Q9UIS9	OTTHUMG00000132669		18.37:g.47792730G>T		Somatic		WXS	Illumina HiSeq	Phase_IV	A4UTZ0|B4DXJ5|E9PEC5|K7ELI2|K7EQZ4|K7ESN0|O15248|O95241|Q7Z7B5|Q8N4W4|Q9UNZ6|Q9UNZ7|Q9UNZ8|Q9UNZ9	Silent	SNP	NULL	p.G15	ENST00000591416.1	37	c.45	CCDS11943.1	18																																																																																			CCDC11	-	NULL		0.622	MBD1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	CCDC11	HGNC	protein_coding	OTTHUMT00000255926.3	G	NM_015846		47792730	-1	no_errors	ENST00000398545	ensembl	human	known	70_37	silent	SNP	0.996	T
CCPG1	9236	genome.wustl.edu	37	15	55653051	55653051	+	Missense_Mutation	SNP	T	T	A			TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chr15:55653051T>A	ENST00000310958.6	-	8	1218	c.920A>T	c.(919-921)aAt>aTt	p.N307I	CCPG1_ENST00000569205.1_Missense_Mutation_p.N307I|CCPG1_ENST00000442196.3_Missense_Mutation_p.N307I|DYX1C1-CCPG1_ENST00000565113.1_RNA|CCPG1_ENST00000425574.3_Missense_Mutation_p.N307I	NM_001204450.1|NM_001204451.1|NM_004748.4|NM_020739.3	NP_001191379.1|NP_001191380.1|NP_004739.3|NP_065790.2	Q9ULG6	CCPG1_HUMAN	cell cycle progression 1	307	Interaction with MCF2L and SRC. {ECO:0000250}.				cell cycle (GO:0007049)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001106)	integral component of membrane (GO:0016021)				autonomic_ganglia(1)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|stomach(3)	30				all cancers(107;0.0354)		TAAATACTGATTTTCTGTAGC	0.348																																																	0													76.0	71.0	73.0					15																	55653051		1816	4079	5895	SO:0001583	missense	9236			AF212228	CCDS42039.1, CCDS55966.1, CCDS55967.1	15q21.1	2011-04-20				ENSG00000260916			24227	protein-coding gene	gene with protein product		611326				9383053, 10574462	Standard	NM_004748		Approved	KIAA1254, CPR8	uc010bfk.2	Q9ULG6		ENST00000310958.6:c.920A>T	15.37:g.55653051T>A	ENSP00000311656:p.Asn307Ile	Somatic		WXS	Illumina HiSeq	Phase_IV	A0PJH3|A8K9T0|O14712|Q05DG4|Q5U5S7|Q8IYV8|Q9BY53|Q9HA17	Missense_Mutation	SNP	NULL	p.N307I	ENST00000310958.6	37	c.920	CCDS42039.1	15	.	.	.	.	.	.	.	.	.	.	T	20.3	3.962917	0.74016	.	.	ENSG00000256061	ENST00000310958;ENST00000442196;ENST00000425574	T;T;T	0.39406	1.15;1.15;1.08	5.72	5.72	0.89469	.	0.086978	0.85682	D	0.000000	T	0.65770	0.2723	M	0.77820	2.39	0.58432	D	0.999999	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.999;0.999;0.999	T	0.67428	-0.5673	10	0.48119	T	0.1	.	15.484	0.75551	0.0:0.0:0.0:1.0	.	307;307;307;307;163	A8K9T0;Q9ULG6-3;Q9ULG6-4;Q9ULG6;Q9ULG6-2	.;.;.;CCPG1_HUMAN;.	I	307	ENSP00000311656:N307I;ENSP00000403400:N307I;ENSP00000415128:N307I	ENSP00000311656:N307I	N	-	2	0	DYX1C1	53440343	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.034000	0.76511	2.299000	0.77371	0.528000	0.53228	AAT	CCPG1	-	NULL		0.348	CCPG1-001	KNOWN	basic|CCDS	protein_coding	CCPG1	HGNC	protein_coding	OTTHUMT00000419850.1	T	NM_004748		55653051	-1	no_errors	ENST00000310958	ensembl	human	known	70_37	missense	SNP	1.000	A
CDC27	996	genome.wustl.edu	37	17	45234327	45234327	+	Missense_Mutation	SNP	C	C	T	rs7350889		TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chr17:45234327C>T	ENST00000066544.3	-	7	887	c.794G>A	c.(793-795)gGt>gAt	p.G265D	CDC27_ENST00000531206.1_Missense_Mutation_p.G265D|CDC27_ENST00000446365.2_Missense_Mutation_p.G204D|CDC27_ENST00000527547.1_Missense_Mutation_p.G265D|CDC27_ENST00000528748.1_5'Flank	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	265					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)	p.G265D(2)		NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TAAACTTCGACCAGTTTTTGG	0.368																																																	2	Substitution - Missense(2)	skin(2)											60.0	65.0	63.0					17																	45234327		2201	4295	6496	SO:0001583	missense	996			U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.794G>A	17.37:g.45234327C>T	ENSP00000066544:p.Gly265Asp	Somatic		WXS	Illumina HiSeq	Phase_IV	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	pfam_TPR-1,pfam_TPR_2,smart_TPR_repeat,pfscan_TPR_repeat,pfscan_TPR-contain_dom	p.G265D	ENST00000066544.3	37	c.794	CCDS11509.1	17	.	.	.	.	.	.	.	.	.	.	C	15.07	2.725453	0.48833	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547;ENST00000526866	T;T;T;T;T	0.68181	-0.31;-0.3;-0.11;-0.31;0.86	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.52853	0.1760	N	0.24115	0.695	0.80722	D	1	B;B;B;B	0.32350	0.251;0.366;0.247;0.251	B;B;B;B	0.27076	0.045;0.056;0.076;0.055	T	0.51694	-0.8673	10	0.33141	T	0.24	1.6987	17.2083	0.86924	0.0:1.0:0.0:0.0	rs7350889;rs7350889	204;265;265;265	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	D	265;265;204;265;265	ENSP00000066544:G265D;ENSP00000434614:G265D;ENSP00000392802:G204D;ENSP00000437339:G265D;ENSP00000432105:G265D	ENSP00000066544:G265D	G	-	2	0	CDC27	42589326	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.618000	0.67722	2.665000	0.90641	0.460000	0.39030	GGT	CDC27	-	NULL		0.368	CDC27-001	KNOWN	basic|CCDS	protein_coding	CDC27	HGNC	protein_coding	OTTHUMT00000389742.2	C			45234327	-1	no_errors	ENST00000531206	ensembl	human	known	70_37	missense	SNP	1.000	T
CHD4	1108	genome.wustl.edu	37	12	6701194	6701194	+	Missense_Mutation	SNP	T	T	G			TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chr12:6701194T>G	ENST00000357008.2	-	20	3141	c.2978A>C	c.(2977-2979)aAt>aCt	p.N993T	CHD4_ENST00000544040.1_Missense_Mutation_p.N986T|CHD4_ENST00000544484.1_Missense_Mutation_p.N990T|CHD4_ENST00000309577.6_Missense_Mutation_p.N993T	NM_001273.2	NP_001264.2	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	993					ATP-dependent chromatin remodeling (GO:0043044)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spindle assembly (GO:0051225)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|RNA polymerase II repressing transcription factor binding (GO:0001103)|zinc ion binding (GO:0008270)			central_nervous_system(2)	2						TGCTTCAAAATTTCGAGTGAG	0.453																																					Colon(32;586 792 4568 16848 45314)												0													150.0	147.0	148.0					12																	6701194		2203	4300	6503	SO:0001583	missense	1108			X86691	CCDS8552.1	12p13	2013-01-28				ENSG00000111642		"""Zinc fingers, PHD-type"""	1919	protein-coding gene	gene with protein product		603277				7575689, 8843877	Standard	XM_006718958		Approved	Mi-2b, Mi2-BETA	uc001qpo.3	Q14839		ENST00000357008.2:c.2978A>C	12.37:g.6701194T>G	ENSP00000349508:p.Asn993Thr	Somatic		WXS	Illumina HiSeq	Phase_IV	Q8IXZ5	Missense_Mutation	SNP	pfam_CHD_C2,pfam_DUF1086,pfam_SNF2_N,pfam_CHD_N,pfam_DUF1087,pfam_Znf_PHD-finger,pfam_Chromo_domain,pfam_Helicase_C,pfam_HDA_complex_subunit-2/3,pfam_Helicase/UvrB_dom,superfamily_Chromodomain-like,superfamily_Znf_FYVE_PHD,superfamily_HMG_superfamily,superfamily_Homeodomain-like,smart_Znf_PHD,smart_Chromo_domain/shadow,smart_Helicase_ATP-bd,smart_Helicase_C,pfscan_Znf_PHD-finger,pfscan_Helicase_ATP-bd,pfscan_Helicase_C,pfscan_Chromo_domain/shadow	p.N993T	ENST00000357008.2	37	c.2978	CCDS8552.1	12	.	.	.	.	.	.	.	.	.	.	T	18.01	3.528483	0.64860	.	.	ENSG00000111642	ENST00000544484;ENST00000544040;ENST00000309577;ENST00000357008;ENST00000537464	D;D;D;D	0.92911	-3.13;-3.13;-3.13;-3.13	4.59	4.59	0.56863	SNF2-related (1);	0.000000	0.85682	D	0.000000	D	0.94879	0.8345	M	0.63843	1.955	0.80722	D	1	D;D;D	0.67145	0.989;0.995;0.996	P;D;D	0.76071	0.805;0.93;0.987	D	0.95395	0.8485	10	0.87932	D	0	.	14.1276	0.65233	0.0:0.0:0.0:1.0	.	993;993;986	Q14839-2;Q14839;F5GWX5	.;CHD4_HUMAN;.	T	990;986;993;993;967	ENSP00000440392:N990T;ENSP00000440542:N986T;ENSP00000312419:N993T;ENSP00000349508:N993T	ENSP00000312419:N993T	N	-	2	0	CHD4	6571455	1.000000	0.71417	0.958000	0.39756	0.982000	0.71751	7.816000	0.86201	1.913000	0.55393	0.460000	0.39030	AAT	CHD4	-	pfam_SNF2_N		0.453	CHD4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	CHD4	HGNC	protein_coding		T	NM_001273		6701194	-1	no_errors	ENST00000309577	ensembl	human	known	70_37	missense	SNP	1.000	G
DOPEY1	23033	genome.wustl.edu	37	6	83877984	83877984	+	3'UTR	SNP	C	C	T			TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chr6:83877984C>T	ENST00000349129.2	+	0	7756				DOPEY1_ENST00000484282.1_3'UTR|DOPEY1_ENST00000369739.3_3'UTR|DOPEY1_ENST00000237163.5_3'UTR|PGM3_ENST00000513973.1_3'UTR|PGM3_ENST00000512866.1_Intron	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1						protein transport (GO:0015031)					breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(16)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	67		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		TTGTATGTAACAGAACACATT	0.308																																																	0																																										SO:0001624	3_prime_UTR_variant	23033			AK027030	CCDS4996.1, CCDS64467.1	6q15	2013-03-05	2006-02-02	2006-02-02	ENSG00000083097	ENSG00000083097			21194	protein-coding gene	gene with protein product			"""KIAA1117"""	KIAA1117		16301316, 16303751, 10931277	Standard	NM_015018		Approved	dJ202D23.2	uc011dyy.2	Q5JWR5	OTTHUMG00000016365	ENST00000349129.2:c.*98C>T	6.37:g.83877984C>T		Somatic		WXS	Illumina HiSeq	Phase_IV	Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	RNA	SNP	-	NULL	ENST00000349129.2	37	NULL	CCDS4996.1	6																																																																																			DOPEY1	-	-		0.308	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	DOPEY1	HGNC	protein_coding	OTTHUMT00000043785.2	C	NM_015018		83877984	+1	no_errors	ENST00000484282	ensembl	human	known	70_37	rna	SNP	1.000	T
TUBB8P12	260334	genome.wustl.edu	37	18	49208	49208	+	Missense_Mutation	SNP	G	G	A			TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chr18:49208G>A	ENST00000573909.1	-	2	543	c.11C>T	c.(10-12)cCa>cTa	p.P4L	RP11-683L23.1_ENST00000594555.1_5'Flank|RP11-683L23.1_ENST00000308911.6_Silent_p.A29A																							CGGAGTCGATGGCATGTTCAT	0.677																																																	0																																										SO:0001583	missense	0																														ENST00000573909.1:c.11C>T	18.37:g.49208G>A	ENSP00000459638:p.Pro4Leu	Somatic		WXS	Illumina HiSeq	Phase_IV		Missense_Mutation	SNP	pfam_Tubulin/FtsZ_2-layer-sand-dom,pfam_Tubulin_FtsZ_GTPase,superfamily_Tub_FtsZ_C,superfamily_Tubulin_FtsZ_GTPase,smart_Tubulin_FtsZ_GTPase,smart_Tubulin/FtsZ_2-layer-sand-dom,prints_Beta_tubulin,prints_Tubulin,prints_Epsilon_tubulin,prints_Gamma_tubulin,prints_Delta_tubulin	p.P4L	ENST00000573909.1	37	c.11		18																																																																																			RP11-683L23.1	-	NULL		0.677	RP11-683L23.1-002	PUTATIVE	not_best_in_genome_evidence|basic	protein_coding	ENSG00000173213	Clone_based_vega_gene	protein_coding	OTTHUMT00000439819.1	G			49208	-1	no_errors	ENST00000573909	ensembl	human	putative	70_37	missense	SNP	0.997	A
ROBO2	6092	genome.wustl.edu	37	3	76467129	76467129	+	Intron	SNP	A	A	C			TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chr3:76467129A>C	ENST00000487694.3	+	2	388				AC026877.1_ENST00000390815.1_RNA	NM_001128929.2	NP_001122401.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)						apoptotic process involved in luteolysis (GO:0061364)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|cellular response to hormone stimulus (GO:0032870)|central nervous system development (GO:0007417)|homophilic cell adhesion (GO:0007156)|metanephros development (GO:0001656)|negative regulation of negative chemotaxis (GO:0050925)|negative regulation of synapse assembly (GO:0051964)|olfactory bulb interneuron development (GO:0021891)|positive regulation of axonogenesis (GO:0050772)|retinal ganglion cell axon guidance (GO:0031290)|ureteric bud development (GO:0001657)	axolemma (GO:0030673)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)			NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		accaacctttaataaaatgag	0.333																																																	0																																										SO:0001627	intron_variant	0			AF040991	CCDS43109.1, CCDS54609.1	3p12.3	2013-02-11	2001-11-28		ENSG00000185008	ENSG00000185008		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	10250	protein-coding gene	gene with protein product		602431	"""roundabout (axon guidance receptor, Drosophila) homolog 2"""			9458045	Standard	NM_002942		Approved	KIAA1568	uc003dpy.4	Q9HCK4	OTTHUMG00000158935	ENST00000487694.3:c.109+480376A>C	3.37:g.76467129A>C		Somatic		WXS	Illumina HiSeq	Phase_IV	O43608|Q19AB4|Q19AB5	RNA	SNP	-	NULL	ENST00000487694.3	37	NULL	CCDS54609.1	3																																																																																			AC026877.1	-	-		0.333	ROBO2-013	NOVEL	basic|CCDS	protein_coding	ENSG00000212104	Clone_based_ensembl_gene	protein_coding	OTTHUMT00000467720.1	A	XM_031246		76467129	-1	no_errors	ENST00000390815	ensembl	human	novel	70_37	rna	SNP	0.283	C
ERCC6	2074	genome.wustl.edu	37	10	50740702	50740702	+	Silent	SNP	G	G	A			TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chr10:50740702G>A	ENST00000355832.5	-	2	387	c.309C>T	c.(307-309)gaC>gaT	p.D103D	ERCC6-PGBD3_ENST00000447839.2_Silent_p.D103D|PGBD3_ENST00000603152.1_Silent_p.D103D|ERCC6-PGBD3_ENST00000515869.1_Silent_p.D103D	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	103					activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|photoreceptor cell maintenance (GO:0045494)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of protein tyrosine kinase activity (GO:0061098)|pyrimidine dimer repair (GO:0006290)|regulation of DNA-templated transcription, elongation (GO:0032784)|response to gamma radiation (GO:0010332)|response to oxidative stress (GO:0006979)|response to superoxide (GO:0000303)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase II promoter (GO:0006366)|transcription-coupled nucleotide-excision repair (GO:0006283)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein N-terminus binding (GO:0047485)|protein tyrosine kinase activator activity (GO:0030296)			breast(5)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						GTTCCAGCACGTCCTGGTCAT	0.612								Direct reversal of damage;Nucleotide excision repair (NER)																																									0													140.0	116.0	124.0					10																	50740702		2203	4300	6503	SO:0001819	synonymous_variant	2074			L04791	CCDS7229.1	10q11	2014-09-17	2014-03-07		ENSG00000225830	ENSG00000225830			3438	protein-coding gene	gene with protein product	"""Cockayne syndrome B protein"""	609413	"""excision repair cross-complementing rodent repair deficiency, complementation group 6"""	CKN2		1339317, 19179336	Standard	NM_000124		Approved	CSB, RAD26, ARMD5	uc001jhs.5	Q03468	OTTHUMG00000018195	ENST00000355832.5:c.309C>T	10.37:g.50740702G>A		Somatic		WXS	Illumina HiSeq	Phase_IV	D3DX94|Q5W0L9	Silent	SNP	pfam_SNF2_N,pfam_Helicase_C,smart_Helicase_ATP-bd,smart_Helicase_C,pfscan_Helicase_ATP-bd,pfscan_Helicase_C	p.D103	ENST00000355832.5	37	c.309	CCDS7229.1	10																																																																																			ERCC6	-	NULL		0.612	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ERCC6	HGNC	protein_coding	OTTHUMT00000047990.1	G	NM_000124		50740702	-1	no_errors	ENST00000355832	ensembl	human	known	70_37	silent	SNP	0.013	A
ERICH2	285141	genome.wustl.edu	37	2	171649410	171649411	+	Frame_Shift_Ins	INS	-	-	A			TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chr2:171649410_171649411insA	ENST00000409885.1	+	3	307_308	c.254_255insA	c.(253-258)gcaaaafs	p.AK85fs				A1L162	ERIC2_HUMAN	glutamate-rich 2	85																	TACCAGCTGGCAAAAAAATTAT	0.312																																																	0																																										SO:0001589	frameshift_variant	285141			BC127676, BC150546		2q31.1	2012-09-25			ENSG00000204334	ENSG00000204334			44395	protein-coding gene	gene with protein product							Standard	XM_001714892		Approved		uc002ugg.3	A1L162	OTTHUMG00000154074	ENST00000409885.1:c.261dupA	2.37:g.171649417_171649417dupA	ENSP00000387298:p.Ala85fs	Somatic		WXS	Illumina HiSeq	Phase_IV	A7E2T7	Frame_Shift_Ins	INS	NULL	p.L88fs	ENST00000409885.1	37	c.254_255		2																																																																																			ERICH2	-	NULL		0.312	ERICH2-001	NOVEL	basic|appris_principal|exp_conf	protein_coding	ERICH2	HGNC	protein_coding	OTTHUMT00000333723.1	-			171649411	+1	no_errors	ENST00000409885	ensembl	human	novel	70_37	frame_shift_ins	INS	1.000:1.000	A
F9	2158	genome.wustl.edu	37	X	138633355	138633355	+	Missense_Mutation	SNP	C	C	A	rs137852239		TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chrX:138633355C>A	ENST00000218099.2	+	6	662	c.655C>A	c.(655-657)Caa>Aaa	p.Q219K	F9_ENST00000394090.2_Missense_Mutation_p.Q181K	NM_000133.3	NP_000124.1	P00740	FA9_HUMAN	coagulation factor IX	219					blood coagulation (GO:0007596)|blood coagulation, extrinsic pathway (GO:0007598)|blood coagulation, intrinsic pathway (GO:0007597)|cellular protein metabolic process (GO:0044267)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(7)|lung(19)|ovary(1)|skin(1)	35	Acute lymphoblastic leukemia(192;0.000127)				Antihemophilic Factor(DB00025)|Menadione(DB00170)	TCAAAGCACCCAATCATTTAA	0.423																																																	0			GRCh37	CM940539	F9	M	rs137852239						142.0	120.0	127.0					X																	138633355		2203	4300	6503	SO:0001583	missense	2158			M11309	CCDS14666.1	Xq26.3-q27.1	2014-09-17	2008-08-01		ENSG00000101981	ENSG00000101981	3.4.21.22		3551	protein-coding gene	gene with protein product	"""Factor IX"", ""plasma thromboplastic component"", ""Christmas disease"", ""hemophilia B"""	300746					Standard	NM_000133		Approved	FIX	uc004fas.1	P00740	OTTHUMG00000022536	ENST00000218099.2:c.655C>A	X.37:g.138633355C>A	ENSP00000218099:p.Gln219Lys	Somatic		WXS	Illumina HiSeq	Phase_IV	A8K9N4|F2RM36|Q5FBE1|Q5JYJ8	Missense_Mutation	SNP	pfam_Peptidase_S1_S6,pfam_GLA_domain,pfam_EG-like_dom,superfamily_Pept_cys/ser_Trypsin-like,superfamily_GLA_domain,smart_GLA_domain,smart_EGF-like_Ca-bd,smart_EG-like_dom,smart_Peptidase_S1_S6,pirsf_Pept_S1A_FX,pfscan_EG-like_dom,pfscan_GLA_domain,pfscan_Peptidase_S1_S6,prints_Peptidase_S1A,prints_GLA_domain	p.Q219K	ENST00000218099.2	37	c.655	CCDS14666.1	X	.	.	.	.	.	.	.	.	.	.	C	0.004	-2.316758	0.00235	.	.	ENSG00000101981	ENST00000218099;ENST00000394090	D;D	0.94417	-3.42;-3.42	5.31	-1.93	0.07594	Peptidase cysteine/serine, trypsin-like (1);	1.074810	0.07060	N	0.833529	D	0.86117	0.5856	N	0.25647	0.755	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.002;0.003	T	0.72456	-0.4288	10	0.06891	T	0.86	.	4.6169	0.12432	0.1163:0.1992:0.5142:0.1703	.	181;219	Q5FBE1;P00740	.;FA9_HUMAN	K	219;181	ENSP00000218099:Q219K;ENSP00000377650:Q181K	ENSP00000218099:Q219K	Q	+	1	0	F9	138461021	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.347000	0.07750	-1.048000	0.03238	-0.218000	0.12543	CAA	F9	-	superfamily_Pept_cys/ser_Trypsin-like,pirsf_Pept_S1A_FX		0.423	F9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	F9	HGNC	protein_coding	OTTHUMT00000058557.1	C			138633355	+1	no_errors	ENST00000218099	ensembl	human	known	70_37	missense	SNP	0.000	A
FBN1	2200	genome.wustl.edu	37	15	48760655	48760655	+	Silent	SNP	G	G	A			TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chr15:48760655G>A	ENST00000316623.5	-	37	4991	c.4536C>T	c.(4534-4536)gaC>gaT	p.D1512D		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	1512	EGF-like 26; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		CAGGTGGGCAGTCACAGATAT	0.438																																																	0													122.0	101.0	108.0					15																	48760655		2198	4296	6494	SO:0001819	synonymous_variant	2200			X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"""Marfan syndrome"""	134797	"""fibrillin 1 (Marfan syndrome)"""	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.4536C>T	15.37:g.48760655G>A		Somatic		WXS	Illumina HiSeq	Phase_IV	B2RUU0|D2JYH6|Q15972|Q75N87	Silent	SNP	pfam_EGF-like_Ca-bd,pfam_EG-like_dom,pfam_TB_dom,superfamily_TB_dom,superfamily_Growth_fac_rcpt,smart_EG-like_dom,smart_EGF-like_Ca-bd,pirsf_FBN,pfscan_EG-like_dom	p.D1512	ENST00000316623.5	37	c.4536	CCDS32232.1	15																																																																																			FBN1	-	pfam_EGF-like_Ca-bd,smart_EGF-like_Ca-bd,smart_EG-like_dom,pirsf_FBN,pfscan_EG-like_dom		0.438	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FBN1	HGNC	protein_coding	OTTHUMT00000417355.1	G			48760655	-1	no_errors	ENST00000316623	ensembl	human	known	70_37	silent	SNP	0.238	A
FLNB	2317	genome.wustl.edu	37	3	58127612	58127612	+	Nonsense_Mutation	SNP	G	G	T			TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chr3:58127612G>T	ENST00000295956.4	+	30	5302	c.5137G>T	c.(5137-5139)Gag>Tag	p.E1713*	FLNB_ENST00000490882.1_Nonsense_Mutation_p.E1744*|FLNB_ENST00000358537.3_Intron|FLNB_ENST00000357272.4_Nonsense_Mutation_p.E1713*|FLNB_ENST00000348383.5_Nonsense_Mutation_p.E1713*|FLNB_ENST00000419752.2_Nonsense_Mutation_p.E1544*|FLNB_ENST00000429972.2_Nonsense_Mutation_p.E1713*|FLNB_ENST00000493452.1_Intron	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	1713	Hinge 1. {ECO:0000250}.				actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		CACAGCCGTGGAGGAGGCACC	0.488																																																	0													230.0	198.0	209.0					3																	58127612		2203	4300	6503	SO:0001587	stop_gained	2317			AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068			3755	protein-coding gene	gene with protein product	"""actin binding protein 278"""	603381	"""filamin B, beta (actin binding protein 278)"", ""Larsen syndrome 1 (autosomal dominant)"""	FLN1L, LRS1		8327473, 10449914, 14991055, 16801345	Standard	NM_001457		Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000295956.4:c.5137G>T	3.37:g.58127612G>T	ENSP00000295956:p.Glu1713*	Somatic		WXS	Illumina HiSeq	Phase_IV	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Nonsense_Mutation	SNP	pfam_Filamin/ABP280_repeat-like,pfam_CH-domain,superfamily_CH-domain,superfamily_Ig_E-set,smart_CH-domain,smart_Filamin,pfscan_CH-domain,pfscan_Filamin/ABP280_repeat-like	p.E1713*	ENST00000295956.4	37	c.5137	CCDS2885.1	3	.	.	.	.	.	.	.	.	.	.	G	45	11.452211	0.99562	.	.	ENSG00000136068	ENST00000295956;ENST00000490882;ENST00000429972;ENST00000348383;ENST00000357272;ENST00000419752	.	.	.	5.84	2.69	0.31865	.	0.837087	0.11127	N	0.596764	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.24483	T	0.36	.	2.5435	0.04731	0.2346:0.2012:0.4535:0.1107	.	.	.	.	X	1713;1744;1713;1713;1713;1544	.	ENSP00000295956:E1713X	E	+	1	0	FLNB	58102652	1.000000	0.71417	1.000000	0.80357	0.625000	0.37756	0.564000	0.23563	0.828000	0.34709	-0.136000	0.14681	GAG	FLNB	-	pfscan_Filamin/ABP280_repeat-like		0.488	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	FLNB	HGNC	protein_coding	OTTHUMT00000353569.1	G	NM_001457		58127612	+1	no_errors	ENST00000295956	ensembl	human	known	70_37	nonsense	SNP	0.963	T
GABRD	2563	genome.wustl.edu	37	1	1961008	1961008	+	Missense_Mutation	SNP	C	C	T			TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chr1:1961008C>T	ENST00000378585.4	+	8	949	c.866C>T	c.(865-867)aCg>aTg	p.T289M		NM_000815.4	NP_000806.2	O14764	GBRD_HUMAN	gamma-aminobutyric acid (GABA) A receptor, delta	289					signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			central_nervous_system(2)|endometrium(3)|kidney(2)|lung(8)|ovary(2)|prostate(1)|skin(2)	20	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;2.7e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;2.19e-38)|OV - Ovarian serous cystadenocarcinoma(86;3.17e-24)|GBM - Glioblastoma multiforme(42;9.56e-08)|Colorectal(212;4.12e-05)|COAD - Colon adenocarcinoma(227;0.000194)|Kidney(185;0.00231)|BRCA - Breast invasive adenocarcinoma(365;0.00441)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0344)|Lung(427;0.2)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|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)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	ACGGTGCTGACGATGACCACG	0.617																																																	0													86.0	72.0	77.0					1																	1961008		2202	4299	6501	SO:0001583	missense	2563			BC033801	CCDS36.1	1p36.3	2012-06-22			ENSG00000187730	ENSG00000187730		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4084	protein-coding gene	gene with protein product	"""GABA(A) receptor, delta"""	137163				2176788, 10965146	Standard	NM_000815		Approved		uc001aip.2	O14764	OTTHUMG00000041064	ENST00000378585.4:c.866C>T	1.37:g.1961008C>T	ENSP00000367848:p.Thr289Met	Somatic		WXS	Illumina HiSeq	Phase_IV	Q8N4N9	Missense_Mutation	SNP	pfam_Neur_chan_lig-bd,pfam_Neurotrans-gated_channel_TM,superfamily_Neur_chan_lig-bd,superfamily_Neurotrans-gated_channel_TM,prints_GABAA_rcpt,prints_GABAAd_rcpt,prints_Neur_channel,tigrfam_Neur_channel	p.T289M	ENST00000378585.4	37	c.866	CCDS36.1	1	.	.	.	.	.	.	.	.	.	.	C	17.04	3.287135	0.59867	.	.	ENSG00000187730	ENST00000378585	D	0.87887	-2.31	4.62	4.62	0.57501	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.057809	0.64402	D	0.000001	D	0.94381	0.8193	M	0.88842	2.985	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95491	0.8569	10	0.87932	D	0	-13.5048	16.8444	0.85976	0.0:1.0:0.0:0.0	.	289	O14764	GBRD_HUMAN	M	289	ENSP00000367848:T289M	ENSP00000367848:T289M	T	+	2	0	GABRD	1950868	1.000000	0.71417	0.999000	0.59377	0.926000	0.56050	7.546000	0.82137	2.297000	0.77311	0.561000	0.74099	ACG	GABRD	-	pfam_Neurotrans-gated_channel_TM,superfamily_Neurotrans-gated_channel_TM,prints_GABAA_rcpt,tigrfam_Neur_channel		0.617	GABRD-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	GABRD	HGNC	protein_coding	OTTHUMT00000098493.1	C	NM_000815		1961008	+1	no_errors	ENST00000378585	ensembl	human	known	70_37	missense	SNP	1.000	T
GABRD	2563	genome.wustl.edu	37	1	1961652	1961652	+	Silent	SNP	C	C	T			TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chr1:1961652C>T	ENST00000378585.4	+	9	1373	c.1290C>T	c.(1288-1290)taC>taT	p.Y430Y		NM_000815.4	NP_000806.2	O14764	GBRD_HUMAN	gamma-aminobutyric acid (GABA) A receptor, delta	430					signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.Y430Y(1)		central_nervous_system(2)|endometrium(3)|kidney(2)|lung(8)|ovary(2)|prostate(1)|skin(2)	20	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;2.7e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;2.19e-38)|OV - Ovarian serous cystadenocarcinoma(86;3.17e-24)|GBM - Glioblastoma multiforme(42;9.56e-08)|Colorectal(212;4.12e-05)|COAD - Colon adenocarcinoma(227;0.000194)|Kidney(185;0.00231)|BRCA - Breast invasive adenocarcinoma(365;0.00441)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0344)|Lung(427;0.2)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|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)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TTGACATTTACGCCCGCGCTG	0.647																																																	1	Substitution - coding silent(1)	ovary(1)											65.0	64.0	64.0					1																	1961652		2203	4296	6499	SO:0001819	synonymous_variant	2563			BC033801	CCDS36.1	1p36.3	2012-06-22			ENSG00000187730	ENSG00000187730		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4084	protein-coding gene	gene with protein product	"""GABA(A) receptor, delta"""	137163				2176788, 10965146	Standard	NM_000815		Approved		uc001aip.2	O14764	OTTHUMG00000041064	ENST00000378585.4:c.1290C>T	1.37:g.1961652C>T		Somatic		WXS	Illumina HiSeq	Phase_IV	Q8N4N9	Silent	SNP	pfam_Neur_chan_lig-bd,pfam_Neurotrans-gated_channel_TM,superfamily_Neur_chan_lig-bd,superfamily_Neurotrans-gated_channel_TM,prints_GABAA_rcpt,prints_GABAAd_rcpt,prints_Neur_channel,tigrfam_Neur_channel	p.Y430	ENST00000378585.4	37	c.1290	CCDS36.1	1																																																																																			GABRD	-	superfamily_Neurotrans-gated_channel_TM,prints_GABAA_rcpt		0.647	GABRD-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	GABRD	HGNC	protein_coding	OTTHUMT00000098493.1	C	NM_000815		1961652	+1	no_errors	ENST00000378585	ensembl	human	known	70_37	silent	SNP	0.902	T
GIT2	9815	genome.wustl.edu	37	12	110427511	110427511	+	Missense_Mutation	SNP	G	G	T			TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chr12:110427511G>T	ENST00000355312.3	-	3	282	c.283C>A	c.(283-285)Cca>Aca	p.P95T	GIT2_ENST00000457474.2_Missense_Mutation_p.P95T|GIT2_ENST00000354574.4_Missense_Mutation_p.P95T|GIT2_ENST00000553118.1_Missense_Mutation_p.P95T|GIT2_ENST00000338373.5_Missense_Mutation_p.P95T|GIT2_ENST00000551209.1_Missense_Mutation_p.P95T|GIT2_ENST00000361006.5_Missense_Mutation_p.P95T|GIT2_ENST00000343646.5_Missense_Mutation_p.P95T|GIT2_ENST00000547815.1_Missense_Mutation_p.P95T|GIT2_ENST00000356259.4_Missense_Mutation_p.P95T|GIT2_ENST00000360185.4_Missense_Mutation_p.P95T|GIT2_ENST00000320063.9_Missense_Mutation_p.P95T	NM_057169.3	NP_476510.1	Q14161	GIT2_HUMAN	G protein-coupled receptor kinase interacting ArfGAP 2	95	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.				behavioral response to pain (GO:0048266)|regulation of ARF GTPase activity (GO:0032312)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(8)|skin(4)	27						TTATCCTGTGGATTAGCTTTA	0.393																																																	0													122.0	112.0	115.0					12																	110427511		2203	4300	6503	SO:0001583	missense	9815			AF124491	CCDS9138.1, CCDS9139.1, CCDS44968.1, CCDS44969.1, CCDS55884.1	12q24.1	2013-01-10	2008-09-05			ENSG00000139436		"""ADP-ribosylation factor GTPase activating proteins"", ""Ankyrin repeat domain containing"""	4273	protein-coding gene	gene with protein product		608564	"""G protein-coupled receptor kinase interactor 2"""			9826657, 10896954	Standard	NM_139201		Approved	KIAA0148	uc001tps.2	Q14161	OTTHUMG00000169313	ENST00000355312.3:c.283C>A	12.37:g.110427511G>T	ENSP00000347464:p.Pro95Thr	Somatic		WXS	Illumina HiSeq	Phase_IV	Q86U59|Q96CI2|Q9BV91|Q9Y5V2	Missense_Mutation	SNP	pfam_GIT1_C,pfam_GIT_SHD,pfam_ArfGAP,superfamily_Ankyrin_rpt-contain_dom,smart_ArfGAP,smart_Ankyrin_rpt,smart_GIT_SHD,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom,pfscan_ArfGAP,prints_ArfGAP	p.P95T	ENST00000355312.3	37	c.283	CCDS9138.1	12	.	.	.	.	.	.	.	.	.	.	G	32	5.193326	0.94960	.	.	ENSG00000139436	ENST00000355312;ENST00000360185;ENST00000354574;ENST00000338373;ENST00000343646;ENST00000356259;ENST00000457474;ENST00000361006;ENST00000553118;ENST00000551209;ENST00000542273;ENST00000547815;ENST00000320063;ENST00000551494	T;T;T;T;T;T;T;T;T;T;T;T	0.40756	1.02;1.02;1.02;1.02;1.02;1.02;1.02;1.02;1.02;1.02;1.02;1.02	5.87	5.87	0.94306	Ankyrin repeat-containing domain (1);	0.093432	0.85682	D	0.000000	T	0.67050	0.2852	M	0.75150	2.29	0.80722	D	1	P;P;P;P;P;D;D	0.65815	0.753;0.863;0.815;0.815;0.924;0.96;0.995	P;P;P;P;P;P;D	0.73380	0.701;0.842;0.688;0.688;0.669;0.827;0.98	T	0.67601	-0.5629	10	0.87932	D	0	.	19.5705	0.95413	0.0:0.0:1.0:0.0	.	95;95;95;95;95;95;95	B4E2E7;Q6FI58;Q14161-10;F8WAK2;Q14161-11;Q14161;Q14161-5	.;.;.;.;.;GIT2_HUMAN;.	T	95;95;95;95;95;95;95;95;95;95;33;95;95;9	ENSP00000347464:P95T;ENSP00000353312:P95T;ENSP00000346585:P95T;ENSP00000340342:P95T;ENSP00000340938:P95T;ENSP00000348595:P95T;ENSP00000391813:P95T;ENSP00000354282:P95T;ENSP00000447465:P95T;ENSP00000448832:P95T;ENSP00000450348:P95T;ENSP00000323833:P95T	ENSP00000323833:P95T	P	-	1	0	GIT2	108911894	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.813000	0.99286	2.941000	0.99782	0.655000	0.94253	CCA	GIT2	-	pfam_ArfGAP,superfamily_Ankyrin_rpt-contain_dom,smart_ArfGAP,pfscan_ArfGAP		0.393	GIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GIT2	HGNC	protein_coding	OTTHUMT00000403407.1	G	NM_057169		110427511	-1	no_errors	ENST00000355312	ensembl	human	known	70_37	missense	SNP	1.000	T
IFI16	3428	genome.wustl.edu	37	1	158988186	158988186	+	Missense_Mutation	SNP	C	C	A			TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chr1:158988186C>A	ENST00000295809.7	+	5	972	c.717C>A	c.(715-717)ttC>ttA	p.F239L	IFI16_ENST00000368131.4_Missense_Mutation_p.F239L|IFI16_ENST00000368132.3_Missense_Mutation_p.F239L|IFI16_ENST00000359709.3_Missense_Mutation_p.F183L|IFI16_ENST00000448393.2_Missense_Mutation_p.F239L|IFI16_ENST00000430894.2_Missense_Mutation_p.F187L|IFI16_ENST00000340979.6_Missense_Mutation_p.F239L			Q16666	IF16_HUMAN	interferon, gamma-inducible protein 16	239	HIN-200 1. {ECO:0000255|PROSITE- ProRule:PRU00106}.|Interaction with TP53 C-terminus.				activation of cysteine-type endopeptidase activity (GO:0097202)|activation of innate immune response (GO:0002218)|autophagy (GO:0006914)|cell proliferation (GO:0008283)|cellular response to glucose starvation (GO:0042149)|cellular response to ionizing radiation (GO:0071479)|defense response to virus (GO:0051607)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|monocyte differentiation (GO:0030224)|myeloid cell differentiation (GO:0030099)|negative regulation of cysteine-type endopeptidase activity (GO:2000117)|negative regulation of DNA binding (GO:0043392)|negative regulation of innate immune response (GO:0045824)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral genome replication (GO:0045071)|positive regulation of cytokine production (GO:0001819)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of autophagy (GO:0010506)|regulation of gene expression, epigenetic (GO:0040029)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter binding (GO:0001047)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)	p.F239F(1)		cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_hematologic(112;0.0429)					AGACACAGTTCTTCCATGTGA	0.363																																																	1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)											82.0	83.0	82.0					1																	158988186		2203	4300	6503	SO:0001583	missense	3428			M63838	CCDS1180.3, CCDS58039.1	1q22	2008-02-05			ENSG00000163565	ENSG00000163565			5395	protein-coding gene	gene with protein product		147586				1526658, 7959953	Standard	NM_005531		Approved	IFNGIP1, PYHIN2	uc010pis.2	Q16666	OTTHUMG00000037108	ENST00000295809.7:c.717C>A	1.37:g.158988186C>A	ENSP00000295809:p.Phe239Leu	Somatic		WXS	Illumina HiSeq	Phase_IV	B4DJT8|H3BLV7|Q59GX0|Q5T3W7|Q5T3W8|Q5T3X0|Q5T3X1|Q5T3X2|Q8N9E5|Q8NEQ7|Q96AJ5|Q9UH78	Missense_Mutation	SNP	pfam_HIN200/IF120x,pfam_DAPIN,superfamily_DEATH-like,pfscan_DAPIN,pfscan_HIN200/IF120x	p.F239L	ENST00000295809.7	37	c.717		1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.70|12.70	2.015513|2.015513	0.35511|0.35511	.|.	.|.	ENSG00000163565|ENSG00000163565	ENST00000359709;ENST00000295809;ENST00000340979;ENST00000368131;ENST00000368132;ENST00000430894|ENST00000448393	T;T;T;T;T|.	0.21543|.	2.0;2.0;2.0;2.0;2.0|.	2.9|2.9	-2.4|-2.4	0.06583|0.06583	HIN-200/IF120x (2);Nucleic acid-binding, OB-fold (1);|.	.|.	.|.	.|.	.|.	T|T	0.25232|0.25232	0.0613|0.0613	M|M	0.79011|0.79011	2.435|2.435	0.09310|0.09310	N|N	1|1	B;B;B|.	0.21520|.	0.057;0.046;0.055|.	B;B;B|.	0.19666|.	0.014;0.008;0.026|.	T|T	0.38908|0.38908	-0.9639|-0.9639	9|5	0.48119|.	T|.	0.1|.	.|.	2.5684|2.5684	0.04789|0.04789	0.2172:0.3104:0.0:0.4723|0.2172:0.3104:0.0:0.4723	.|.	187;239;239|.	E7EPR3;Q16666-2;Q16666|.	.;.;IF16_HUMAN|.	L|Y	239;239;239;239;239;187|60	ENSP00000295809:F239L;ENSP00000342741:F239L;ENSP00000357113:F239L;ENSP00000357114:F239L;ENSP00000394935:F187L|.	ENSP00000295809:F239L|.	F|S	+|+	3|2	2|0	IFI16|IFI16	157254810|157254810	0.000000|0.000000	0.05858|0.05858	0.076000|0.076000	0.20297|0.20297	0.396000|0.396000	0.30629|0.30629	-2.554000|-2.554000	0.00926|0.00926	-0.719000|-0.719000	0.04942|0.04942	0.555000|0.555000	0.69702|0.69702	TTC|TCT	IFI16	-	pfam_HIN200/IF120x,pfscan_HIN200/IF120x		0.363	IFI16-013	KNOWN	basic	protein_coding	IFI16	HGNC	protein_coding	OTTHUMT00000421720.1	C	NM_005531		158988186	+1	no_errors	ENST00000295809	ensembl	human	known	70_37	missense	SNP	0.072	A
KRT72	140807	genome.wustl.edu	37	12	52980755	52980755	+	Silent	SNP	G	G	A	rs140936315		TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chr12:52980755G>A	ENST00000537672.2	-	8	1330	c.1320C>T	c.(1318-1320)ggC>ggT	p.G440G	KRT72_ENST00000398066.3_Silent_p.G252G|KRT72_ENST00000354310.4_Silent_p.G398G|KRT72_ENST00000293745.2_Silent_p.G440G	NM_001146225.1	NP_001139697.1	Q14CN4	K2C72_HUMAN	keratin 72	440	Tail.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.G440G(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(14)|ovary(5)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(357;0.195)		TTGGATATTCGCCAGACATCC	0.453																																																	1	Substitution - coding silent(1)	pancreas(1)						G	,,	0,4406		0,0,2203	115.0	103.0	107.0		1320,1194,1320	-6.6	0.8	12	dbSNP_134	107	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	KRT72	NM_001146225.1,NM_001146226.1,NM_080747.2	,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,	440/512,398/470,440/512	52980755	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	140807			AY033495	CCDS8833.1, CCDS53795.1	12q13.13	2013-06-25			ENSG00000170486	ENSG00000170486		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28932	protein-coding gene	gene with protein product		608246				12648212, 11703281, 16831889	Standard	NM_080747		Approved	K6IRS2, KRT6IRS2, KRT6, K6irs	uc001saq.2	Q14CN4	OTTHUMG00000169744	ENST00000537672.2:c.1320C>T	12.37:g.52980755G>A		Somatic		WXS	Illumina HiSeq	Phase_IV	B4DEI8|H9KV51|Q8NA87|Q8WWY9|Q8WWZ0	Silent	SNP	pfam_F,superfamily_Prefoldin,prints_Keratin_II	p.G440	ENST00000537672.2	37	c.1320	CCDS8833.1	12																																																																																			KRT72	-	NULL		0.453	KRT72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KRT72	HGNC	protein_coding	OTTHUMT00000405693.1	G	NM_080747		52980755	-1	no_errors	ENST00000293745	ensembl	human	known	70_37	silent	SNP	0.857	A
LIMK1	3984	genome.wustl.edu	37	7	73520242	73520242	+	Missense_Mutation	SNP	T	T	A			TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chr7:73520242T>A	ENST00000336180.2	+	6	697	c.646T>A	c.(646-648)Tcc>Acc	p.S216T	LIMK1_ENST00000538333.3_Missense_Mutation_p.S182T|LIMK1_ENST00000418310.1_Missense_Mutation_p.S246T	NM_002314.3	NP_002305.1	P53667	LIMK1_HUMAN	LIM domain kinase 1	216	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				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)	TGTGAAGAATTCCATCCACGT	0.602																																																	0													80.0	70.0	74.0					7																	73520242		2203	4300	6503	SO:0001583	missense	3984			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	ENST00000336180.2:c.646T>A	7.37:g.73520242T>A	ENSP00000336740:p.Ser216Thr	Somatic		WXS	Illumina HiSeq	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.S216T	ENST00000336180.2	37	c.646	CCDS5563.1	7	.	.	.	.	.	.	.	.	.	.	T	14.74	2.625180	0.46840	.	.	ENSG00000106683	ENST00000418310;ENST00000419043;ENST00000336180;ENST00000423685;ENST00000538333	T;T;T;T	0.57273	0.58;0.58;0.41;0.58	4.35	4.35	0.52113	PDZ/DHR/GLGF (4);	0.178504	0.51477	D	0.000096	T	0.42653	0.1212	L	0.46157	1.445	0.42068	D	0.991198	B;B;B	0.27068	0.134;0.167;0.167	B;B;B	0.30572	0.027;0.117;0.117	T	0.32455	-0.9906	10	0.25751	T	0.34	-34.2923	7.2109	0.25933	0.1979:0.0:0.0:0.802	.	111;182;216	Q59FA3;B7Z6I8;P53667	.;.;LIMK1_HUMAN	T	246;216;216;182;182	ENSP00000409717:S246T;ENSP00000336740:S216T;ENSP00000396480:S182T;ENSP00000444452:S182T	ENSP00000336740:S216T	S	+	1	0	LIMK1	73158178	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.859000	0.39418	1.852000	0.53769	0.524000	0.50904	TCC	LIMK1	-	pfam_PDZ,superfamily_PDZ,smart_PDZ,pfscan_PDZ		0.602	LIMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LIMK1	HGNC	protein_coding	OTTHUMT00000252335.2	T	NM_002314		73520242	+1	no_errors	ENST00000336180	ensembl	human	known	70_37	missense	SNP	1.000	A
LINC00303	284573	genome.wustl.edu	37	1	204006330	204006330	+	lincRNA	SNP	G	G	C			TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chr1:204006330G>C	ENST00000367207.3	-	0	690							Q3SY05	CA157_HUMAN	long intergenic non-protein coding RNA 303																		AGGAAGGGATGGGATTTATTC	0.522																																																	0																																												284573			AK097662		1q32.1	2012-10-12	2011-08-10	2011-08-10	ENSG00000176754	ENSG00000176754		"""Long non-coding RNAs"""	26865	non-coding RNA	RNA, long non-coding			"""chromosome 1 open reading frame 157"", ""non-protein coding RNA 303"""	C1orf157, NCRNA00303			Standard	NR_027902		Approved	FLJ40343	uc010pqo.1	Q3SY05	OTTHUMG00000036054		1.37:g.204006330G>C		Somatic		WXS	Illumina HiSeq	Phase_IV	Q3SY06|Q8N7U1	RNA	SNP	-	NULL	ENST00000367207.3	37	NULL		1																																																																																			LINC00303	-	-		0.522	LINC00303-001	KNOWN	basic	lincRNA	LINC00303	HGNC	lincRNA	OTTHUMT00000087885.3	G	NR_027902		204006330	-1	no_errors	ENST00000367207	ensembl	human	known	70_37	rna	SNP	0.019	C
MAP1A	4130	genome.wustl.edu	37	15	43814937	43814937	+	Missense_Mutation	SNP	G	G	C			TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chr15:43814937G>C	ENST00000300231.5	+	4	1716	c.1266G>C	c.(1264-1266)gaG>gaC	p.E422D	MAP1A_ENST00000382031.1_Missense_Mutation_p.E660D|MAP1A_ENST00000399453.1_Missense_Mutation_p.E422D			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	422	9 X 3 AA repeats of K-K-[DE].|Lys-rich (basic).				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)	agaaaaaagagatcaaaaagg	0.418																																																	0													33.0	34.0	34.0					15																	43814937		1838	4090	5928	SO:0001583	missense	4130			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.1266G>C	15.37:g.43814937G>C	ENSP00000300231:p.Glu422Asp	Somatic		WXS	Illumina HiSeq	Phase_IV	O95643|Q12973|Q15882|Q9UJT4	Missense_Mutation	SNP	NULL	p.E422D	ENST00000300231.5	37	c.1266	CCDS42031.1	15	.	.	.	.	.	.	.	.	.	.	G	11.72	1.721612	0.30503	.	.	ENSG00000166963	ENST00000382031;ENST00000399453;ENST00000300231;ENST00000442025	T;T;T	0.19938	2.11;2.11;2.11	5.4	5.4	0.78164	.	0.000000	0.34507	N	0.003920	T	0.30417	0.0764	M	0.71581	2.175	0.40048	D	0.975732	P	0.51537	0.946	P	0.48677	0.586	T	0.04203	-1.0969	10	0.54805	T	0.06	-17.5847	9.2878	0.37769	0.073:0.0:0.7817:0.1453	.	422	P78559	MAP1A_HUMAN	D	660;422;422;422	ENSP00000371462:E660D;ENSP00000382380:E422D;ENSP00000300231:E422D	ENSP00000300231:E422D	E	+	3	2	MAP1A	41602229	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.111000	0.41883	2.833000	0.97629	0.650000	0.86243	GAG	MAP1A	-	NULL		0.418	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	MAP1A	HGNC	protein_coding	OTTHUMT00000132894.5	G	NM_002373		43814937	+1	no_errors	ENST00000399453	ensembl	human	known	70_37	missense	SNP	1.000	C
MMP25	64386	genome.wustl.edu	37	16	3105840	3105840	+	3'UTR	SNP	C	C	T			TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chr16:3105840C>T	ENST00000570755.1	+	0	456				RP11-473M20.7_ENST00000570949.1_RNA|RP11-473M20.7_ENST00000573878.1_RNA|RP11-473M20.7_ENST00000573953.1_RNA|RP11-473M20.7_ENST00000572222.1_RNA|RP11-473M20.7_ENST00000572574.1_RNA|RP11-473M20.7_ENST00000576250.1_RNA|RP11-473M20.7_ENST00000573130.1_RNA|MMP25_ENST00000336577.4_Intron|RP11-473M20.7_ENST00000597579.1_RNA|RP11-473M20.7_ENST00000572427.1_RNA|RP11-473M20.7_ENST00000572930.1_RNA			Q9H239	MMP28_HUMAN	matrix metallopeptidase 25						negative regulation of macrophage chemotaxis (GO:0010760)	cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)|skin(1)	14					Marimastat(DB00786)	GGCCTCTCAGCAGCTGGAGCA	0.627																																					NSCLC(147;665 1067 3888 6863 19894 30469 40247 45633 51336)												0																																										SO:0001624	3_prime_UTR_variant	64386			AF145442	CCDS10492.1	16p13.3	2008-02-05	2005-08-08			ENSG00000008516			14246	protein-coding gene	gene with protein product		608482	"""matrix metalloproteinase 25"", ""matrix metallopeptidase-like 1"""	MMPL1, MMP20		10628838, 10706098	Standard	NM_022468		Approved	MT6-MMP	uc002cth.3	Q9NPA2		ENST00000570755.1:c.*453C>T	16.37:g.3105840C>T		Somatic		WXS	Illumina HiSeq	Phase_IV	Q96F04|Q96TE2	RNA	SNP	-	NULL	ENST00000570755.1	37	NULL		16	.	.	.	.	.	.	.	.	.	.	c	3.229	-0.157887	0.06544	.	.	ENSG00000008516	ENST00000325800	.	.	.	2.05	-1.46	0.08800	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	2.7839	0.05368	0.0:0.393:0.248:0.359	.	.	.	.	X	151	.	ENSP00000324953:Q151X	Q	+	1	0	MMP25	3045841	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-2.260000	0.01177	-0.322000	0.08615	-0.497000	0.04613	CAG	MMP25	-	-		0.627	MMP25-003	KNOWN	basic	processed_transcript	MMP25	HGNC	protein_coding	OTTHUMT00000437118.1	C	NM_022468		3105840	+1	no_errors	ENST00000570755	ensembl	human	known	70_37	rna	SNP	0.000	T
MTOR	2475	genome.wustl.edu	37	1	11273502	11273502	+	Missense_Mutation	SNP	C	C	G			TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chr1:11273502C>G	ENST00000361445.4	-	21	3315	c.3239G>C	c.(3238-3240)cGt>cCt	p.R1080P		NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	1080					cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	CATGAAGACACGCAGCATGTG	0.488																																																	0													121.0	116.0	118.0					1																	11273502		2203	4300	6503	SO:0001583	missense	2475			L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"""FK506 binding protein 12-rapamycin associated protein 2"", ""rapamycin target protein"", ""FKBP12-rapamycin complex-associated protein 1"", ""FKBP-rapamycin associated protein"", ""rapamycin associated protein FRAP2"", ""dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)"", ""rapamycin and FKBP12 target 1"", ""mammalian target of rapamycin"""	601231	"""FK506 binding protein 12-rapamycin associated protein 1"""	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.3239G>C	1.37:g.11273502C>G	ENSP00000354558:p.Arg1080Pro	Somatic		WXS	Illumina HiSeq	Phase_IV	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Missense_Mutation	SNP	pfam_PIK-rel_kinase_FAT,pfam_PI3/4_kinase_cat_dom,pfam_DUF3385_TOR,pfam_Rapamycin-bd_dom,pfam_FATC,superfamily_ARM-type_fold,superfamily_Kinase-like_dom,superfamily_Rapamycin-bd_dom,smart_PI3/4_kinase_cat_dom,pfscan_PIK_FAT,pfscan_FATC,pfscan_PI3/4_kinase_cat_dom	p.R1080P	ENST00000361445.4	37	c.3239	CCDS127.1	1	.	.	.	.	.	.	.	.	.	.	C	17.02	3.283072	0.59867	.	.	ENSG00000198793	ENST00000361445;ENST00000539766	T	0.64991	-0.13	5.99	5.08	0.68730	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.68632	0.3022	M	0.88450	2.955	0.80722	D	1	P	0.49447	0.924	B	0.40375	0.327	T	0.76515	-0.2931	10	0.54805	T	0.06	-17.3662	15.4334	0.75121	0.0:0.9336:0.0:0.0664	.	1080	P42345	MTOR_HUMAN	P	1080	ENSP00000354558:R1080P	ENSP00000354558:R1080P	R	-	2	0	MTOR	11196089	1.000000	0.71417	0.483000	0.27378	0.713000	0.41058	7.365000	0.79537	1.540000	0.49301	0.655000	0.94253	CGT	MTOR	-	superfamily_ARM-type_fold		0.488	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MTOR	HGNC	protein_coding	OTTHUMT00000005558.1	C	NM_004958		11273502	-1	no_errors	ENST00000361445	ensembl	human	known	70_37	missense	SNP	0.998	G
NYNRIN	57523	genome.wustl.edu	37	14	24879175	24879175	+	Silent	SNP	C	C	T			TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chr14:24879175C>T	ENST00000382554.3	+	4	2493	c.2175C>T	c.(2173-2175)ccC>ccT	p.P725P		NM_025081.2	NP_079357.2	Q9P2P1	NYNRI_HUMAN	NYN domain and retroviral integrase containing	725					DNA integration (GO:0015074)	integral component of membrane (GO:0016021)	nucleic acid binding (GO:0003676)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(8)|lung(21)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	56						GGCAGGGTCCCCAGTCCAGTG	0.627																																																	0													25.0	29.0	28.0					14																	24879175		1967	4144	6111	SO:0001819	synonymous_variant	57523			AB037726	CCDS45090.1	14q11.2	2009-10-14	2009-10-14	2009-10-14		ENSG00000205978			20165	protein-coding gene	gene with protein product	"""Cousin of GIN1"""		"""KIAA1305"""	KIAA1305		19561090, 17114934	Standard	NM_025081		Approved	FLJ11811, CGIN1	uc001wpf.4	Q9P2P1		ENST00000382554.3:c.2175C>T	14.37:g.24879175C>T		Somatic		WXS	Illumina HiSeq	Phase_IV	Q6P153|Q86TR3|Q9HAC4	Silent	SNP	pfam_RNase_Zc3h12,superfamily_RNaseH-like_dom,pfscan_Integrase_cat-core	p.P725	ENST00000382554.3	37	c.2175	CCDS45090.1	14																																																																																			NYNRIN	-	NULL		0.627	NYNRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NYNRIN	HGNC	protein_coding	OTTHUMT00000412939.1	C			24879175	+1	no_errors	ENST00000382554	ensembl	human	known	70_37	silent	SNP	0.002	T
OTOA	146183	genome.wustl.edu	37	16	21742211	21742211	+	Missense_Mutation	SNP	T	T	C			TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chr16:21742211T>C	ENST00000286149.4	+	20	2304	c.2303T>C	c.(2302-2304)gTa>gCa	p.V768A	OTOA_ENST00000388957.3_Missense_Mutation_p.V430A|OTOA_ENST00000388956.4_Missense_Mutation_p.V675A|OTOA_ENST00000388958.3_Missense_Mutation_p.V754A			Q7RTW8	OTOAN_HUMAN	otoancorin	768					cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)	46				GBM - Glioblastoma multiforme(48;0.0414)		CCCTTTCTAGTACTTTTCTCA	0.443																																																	0													59.0	50.0	53.0					16																	21742211		2195	4279	6474	SO:0001583	missense	146183			AK057335	CCDS10600.2, CCDS32403.1, CCDS53994.1	16p12.2	2009-08-18	2002-07-05		ENSG00000155719	ENSG00000155719			16378	protein-coding gene	gene with protein product	"""cancer/testis antigen 108"""	607038	"""deafness, autosomal recessive 22"""	DFNB22		11972037, 19088187	Standard	NM_170664		Approved	CT108	uc002djh.3	Q7RTW8	OTTHUMG00000090721	ENST00000286149.4:c.2303T>C	16.37:g.21742211T>C	ENSP00000286149:p.Val768Ala	Somatic		WXS	Illumina HiSeq	Phase_IV	A1L3A8|A2VDI0|B3KWU3|E9PF51|Q8NA86|Q96M76	Missense_Mutation	SNP	NULL	p.V768A	ENST00000286149.4	37	c.2303		16	.	.	.	.	.	.	.	.	.	.	T	0.439	-0.899394	0.02472	.	.	ENSG00000155719	ENST00000388958;ENST00000286149;ENST00000388956;ENST00000388957;ENST00000338456	T;T;T;T	0.62232	2.56;2.56;2.56;0.04	4.11	0.586	0.17434	.	0.621797	0.15076	N	0.281916	T	0.38825	0.1055	L	0.28740	0.885	0.09310	N	1	B;B;B;B	0.10296	0.002;0.002;0.003;0.002	B;B;B;B	0.09377	0.003;0.004;0.002;0.003	T	0.28744	-1.0034	10	0.02654	T	1	-0.2871	5.9483	0.19232	0.0:0.3563:0.0:0.6437	.	768;675;430;754	Q7RTW8;B3KWU3;Q7RTW8-2;E9PF51	OTOAN_HUMAN;.;.;.	A	754;768;675;430;163	ENSP00000373610:V754A;ENSP00000286149:V768A;ENSP00000373608:V675A;ENSP00000373609:V430A	ENSP00000286149:V768A	V	+	2	0	OTOA	21649712	0.000000	0.05858	0.004000	0.12327	0.993000	0.82548	-0.364000	0.07583	-0.019000	0.14055	0.496000	0.49642	GTA	OTOA	-	NULL		0.443	OTOA-003	KNOWN	basic	protein_coding	OTOA	HGNC	protein_coding	OTTHUMT00000430021.1	T			21742211	+1	no_errors	ENST00000286149	ensembl	human	known	70_37	missense	SNP	0.015	C
PTEN	5728	genome.wustl.edu	37	10	89685305	89685306	+	Frame_Shift_Ins	INS	-	-	A			TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chr10:89685305_89685306insA	ENST00000371953.3	+	3	1557_1558	c.200_201insA	c.(199-204)atatacfs	p.Y68fs		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	68	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.		Y -> H (in CWS1 and BRRS; loss of phosphatase activity towards Ins(1,3,4,5)P4 and PtdIns(3,4,5)P3; retains the ability to bind phospholipid membranes). {ECO:0000269|PubMed:10400993, ECO:0000269|PubMed:11494117, ECO:0000269|PubMed:9600246}.		activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(6)|p.R55fs*1(5)|p.Y27fs*1(2)|p.I67K(1)|p.I67T(1)|p.I67_Y68insY(1)|p.I67del(1)|p.V54fs*29(1)|p.I67R(1)|p.R55_L70>S(1)|p.F56fs*2(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		CATTACAAGATATACAATCTGT	0.277		31	"""D, Mis, N, F, S"""		"""glioma,  prostate, endometrial"""	"""harmartoma, glioma,  prostate, endometrial"""			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																													yes	Rec	yes	"""Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"""	10	10q23.3	5728	phosphatase and tensin homolog gene		"""L, E, M, O"""	58	Whole gene deletion(37)|Deletion - Frameshift(9)|Unknown(6)|Substitution - Missense(3)|Deletion - In frame(1)|Insertion - In frame(1)|Complex - deletion inframe(1)	prostate(16)|central_nervous_system(13)|skin(7)|lung(5)|haematopoietic_and_lymphoid_tissue(4)|endometrium(4)|ovary(3)|urinary_tract(2)|breast(2)|stomach(1)|soft_tissue(1)	GRCh37	CM981666	PTEN	M																																				SO:0001589	frameshift_variant	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	9588	protein-coding gene	gene with protein product	"""mutated in multiple advanced cancers 1"""	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.201dupA	10.37:g.89685306_89685306dupA	ENSP00000361021:p.Tyr68fs	Somatic		WXS	Illumina HiSeq	Phase_IV	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Frame_Shift_Ins	INS	pfam_Tensin_phosphatase_C2-dom,pfam_Dual-sp_phosphatase_cat-dom,pfam_Tyr_Pase_rcpt/non-rcpt,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_Tyr_Pase_cat,pirsf_Bifunc_PIno_P3_Pase/Pase_PTEN,pfscan_Tyr/Dual-specificity_Pase,pfscan_Phosphatase_tensin-typ,pfscan_Tensin_phosphatase_C2-dom	p.Y68fs	ENST00000371953.3	37	c.200_201	CCDS31238.1	10																																																																																			PTEN	-	pfam_Tyr_Pase_rcpt/non-rcpt,smart_Tyr_Pase_cat,pirsf_Bifunc_PIno_P3_Pase/Pase_PTEN,pfscan_Phosphatase_tensin-typ		0.277	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PTEN	HGNC	protein_coding	OTTHUMT00000049241.1	-	NM_000314		89685306	+1	no_errors	ENST00000371953	ensembl	human	known	70_37	frame_shift_ins	INS	1.000:1.000	A
RPS4X	6191	genome.wustl.edu	37	X	71493751	71493751	+	Silent	SNP	G	G	A			TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chrX:71493751G>A	ENST00000316084.6	-	5	536	c.432C>T	c.(430-432)gcC>gcT	p.A144A	RPS4X_ENST00000486733.1_5'UTR	NM_001007.4	NP_000998.1	P62701	RS4X_HUMAN	ribosomal protein S4, X-linked	144					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|multicellular organismal development (GO:0007275)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of cell proliferation (GO:0008284)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|ribosome (GO:0005840)|small ribosomal subunit (GO:0015935)	poly(A) RNA binding (GO:0044822)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			NS(1)|large_intestine(1)	2	Renal(35;0.156)					GGATGGTGCGGGCATCATGAG	0.448																																																	0													61.0	50.0	54.0					X																	71493751		2203	4300	6503	SO:0001819	synonymous_variant	6191				CCDS14418.1	Xq13.1	2011-04-05			ENSG00000198034	ENSG00000198034		"""S ribosomal proteins"""	10424	protein-coding gene	gene with protein product	"""40S ribosomal protein S4, X isoform"", ""ribosomal protein S4X isoform"", ""single-copy abundant mRNA"", ""cell cycle gene 2"""	312760				1795030, 8139551	Standard	NM_001007		Approved	DXS306, CCG2, SCAR, SCR10, FLJ40595, RPS4, S4	uc004ear.3	P62701	OTTHUMG00000021813	ENST00000316084.6:c.432C>T	X.37:g.71493751G>A		Somatic		WXS	Illumina HiSeq	Phase_IV	P12631|P12750|P27576|P55831|Q14727|Q6IPY4	Silent	SNP	pfam_Ribosomal_S4e_central,pfam_Ribosomal_S4e_N,pfam_S4_RNA-bd,pfam_KOW,smart_S4_RNA-bd,pirsf_Ribosomal_S4e,pfscan_S4_RNA-bd	p.A144	ENST00000316084.6	37	c.432	CCDS14418.1	X																																																																																			RPS4X	-	pfam_Ribosomal_S4e_central,pirsf_Ribosomal_S4e		0.448	RPS4X-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RPS4X	HGNC	protein_coding	OTTHUMT00000057188.1	G	NM_001007		71493751	-1	no_errors	ENST00000316084	ensembl	human	known	70_37	silent	SNP	0.995	A
SCRIB	23513	genome.wustl.edu	37	8	144887379	144887379	+	Missense_Mutation	SNP	C	C	T			TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chr8:144887379C>T	ENST00000320476.3	-	19	2579	c.2573G>A	c.(2572-2574)cGt>cAt	p.R858H	SCRIB_ENST00000377533.3_Missense_Mutation_p.R777H|SCRIB_ENST00000356994.2_Missense_Mutation_p.R858H	NM_015356.4	NP_056171	Q14160	SCRIB_HUMAN	scribbled planar cell polarity protein	858	Interaction with ARHGEF7.				activation of Rac GTPase activity (GO:0032863)|apoptotic process involved in morphogenesis (GO:0060561)|astrocyte cell migration (GO:0043615)|asymmetric protein localization (GO:0008105)|auditory receptor cell stereocilium organization (GO:0060088)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cochlear nucleus development (GO:0021747)|establishment of apical/basal cell polarity (GO:0035089)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of mitotic cell cycle (GO:0045930)|neural tube closure (GO:0001843)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of receptor recycling (GO:0001921)|protein localization to adherens junction (GO:0071896)|single organismal cell-cell adhesion (GO:0016337)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle targeting (GO:0016080)|viral process (GO:0016032)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)|Scrib-APC-beta-catenin complex (GO:0034750)				NS(1)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(20)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	42	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			GTGGCGCTGACGGAGGGGCCC	0.721																																					Pancreas(51;966 1133 10533 14576 29674)												0																																										SO:0001583	missense	23513			AY062238	CCDS6411.1, CCDS6412.1	8q24.3	2013-03-05	2013-03-05		ENSG00000180900	ENSG00000180900			30377	protein-coding gene	gene with protein product		607733	"""scribbled homolog (Drosophila)"""			11027293, 14681682	Standard	NM_182706		Approved	KIAA0147, SCRB1, Vartul	uc003yzo.1	Q14160	OTTHUMG00000165154	ENST00000320476.3:c.2573G>A	8.37:g.144887379C>T	ENSP00000322938:p.Arg858His	Somatic		WXS	Illumina HiSeq	Phase_IV	Q6P496|Q7Z5D1|Q8WWV8|Q96C69|Q96GG1	Missense_Mutation	SNP	pfam_PDZ,pfam_Leu-rich_rpt,superfamily_PDZ,smart_Leu-rich_rpt_typical-subtyp,smart_PDZ,pfscan_PDZ	p.R858H	ENST00000320476.3	37	c.2573	CCDS6411.1	8	.	.	.	.	.	.	.	.	.	.	C	8.519	0.868230	0.17250	.	.	ENSG00000180900	ENST00000356994;ENST00000320476;ENST00000377533;ENST00000377539	T;T;T	0.39056	1.1;1.1;1.1	4.18	4.18	0.49190	PDZ/DHR/GLGF (1);	.	.	.	.	T	0.29158	0.0725	N	0.24115	0.695	0.09310	N	1	B;B	0.17268	0.012;0.021	B;B	0.14578	0.003;0.011	T	0.12451	-1.0547	9	0.45353	T	0.12	.	9.4034	0.38447	0.0:0.8862:0.0:0.1138	.	858;858	Q14160;Q14160-3	SCRIB_HUMAN;.	H	858;858;777;227	ENSP00000349486:R858H;ENSP00000322938:R858H;ENSP00000366756:R777H	ENSP00000322938:R858H	R	-	2	0	SCRIB	144959367	0.102000	0.21896	0.508000	0.27688	0.090000	0.18270	0.769000	0.26604	1.876000	0.54355	0.442000	0.29010	CGT	SCRIB	-	superfamily_PDZ		0.721	SCRIB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	SCRIB	HGNC	protein_coding	OTTHUMT00000382215.1	C	NM_015356		144887379	-1	no_errors	ENST00000320476	ensembl	human	known	70_37	missense	SNP	0.109	T
SERPINB7	8710	genome.wustl.edu	37	18	61449742	61449742	+	Missense_Mutation	SNP	G	G	C			TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chr18:61449742G>C	ENST00000398019.2	+	2	461	c.136G>C	c.(136-138)Gct>Cct	p.A46P	SERPINB7_ENST00000546027.1_Missense_Mutation_p.A46P|SERPINB7_ENST00000540675.1_Missense_Mutation_p.A46P|SERPINB7_ENST00000336429.2_Missense_Mutation_p.A46P	NM_003784.3	NP_003775.1	O75635	SPB7_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 7	46					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)				CCGCTTGGGCGCTCAAGATGA	0.473																																																	0													106.0	91.0	96.0					18																	61449742		2203	4300	6503	SO:0001583	missense	8710			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.136G>C	18.37:g.61449742G>C	ENSP00000381101:p.Ala46Pro	Somatic		WXS	Illumina HiSeq	Phase_IV	B4DUW8|F5GZC0|Q1ED45|Q3KPG4	Missense_Mutation	SNP	pfam_Serpin_dom,superfamily_Serpin_dom,smart_Serpin_dom	p.A46P	ENST00000398019.2	37	c.136	CCDS11988.1	18	.	.	.	.	.	.	.	.	.	.	G	12.36	1.914638	0.33815	.	.	ENSG00000166396	ENST00000425392;ENST00000336429;ENST00000398019;ENST00000540675;ENST00000447428;ENST00000546027;ENST00000431370	D;D;D;D;D;D;D	0.91792	-2.91;-2.46;-2.46;-2.46;-2.47;-2.46;-2.91	5.88	2.78	0.32641	Serpin domain (3);	0.672301	0.13747	N	0.365564	D	0.97306	0.9119	H	0.98664	4.295	0.31324	N	0.68565	D;D	0.76494	0.998;0.999	D;D	0.72075	0.958;0.976	D	0.93973	0.7251	10	0.87932	D	0	.	9.2999	0.37838	0.0772:0.0:0.6539:0.2689	.	46;46	F5GZC0;O75635	.;SPB7_HUMAN	P	46	ENSP00000397301:A46P;ENSP00000337212:A46P;ENSP00000381101:A46P;ENSP00000444572:A46P;ENSP00000402362:A46P;ENSP00000444861:A46P;ENSP00000393947:A46P	ENSP00000337212:A46P	A	+	1	0	SERPINB7	59600722	0.993000	0.37304	0.021000	0.16686	0.017000	0.09413	2.512000	0.45485	0.806000	0.34183	0.491000	0.48974	GCT	SERPINB7	-	pfam_Serpin_dom,superfamily_Serpin_dom,smart_Serpin_dom		0.473	SERPINB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SERPINB7	HGNC	protein_coding	OTTHUMT00000134007.1	G	NM_003784		61449742	+1	no_errors	ENST00000336429	ensembl	human	known	70_37	missense	SNP	0.436	C
SLC25A5	292	genome.wustl.edu	37	X	118603742	118603742	+	Missense_Mutation	SNP	A	A	C	rs148294496		TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chrX:118603742A>C	ENST00000317881.8	+	2	346	c.230A>C	c.(229-231)aAt>aCt	p.N77T	SLC25A5_ENST00000460013.1_3'UTR|SLC25A5-AS1_ENST00000446986.1_RNA	NM_001152.4	NP_001143.2	P05141	ADT2_HUMAN	solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 5	77					adenine transport (GO:0015853)|chromosome segregation (GO:0007059)|energy reserve metabolic process (GO:0006112)|negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901029)|positive regulation of cell proliferation (GO:0008284)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|MMXD complex (GO:0071817)|nucleus (GO:0005634)	adenine transmembrane transporter activity (GO:0015207)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|stomach(2)	12					Clodronate(DB00720)	AACCTGGCCAATGTCATCAGA	0.493																																																	0													137.0	131.0	133.0					X																	118603742		2203	4300	6503	SO:0001583	missense	292			BC068199	CCDS14578.1	Xq24	2013-08-09			ENSG00000005022	ENSG00000005022		"""Solute carriers"""	10991	protein-coding gene	gene with protein product		300150		ANT2		2168878, 2829183	Standard	NM_001152		Approved	T2, 2F1, T3	uc004erh.4	P05141	OTTHUMG00000022715	ENST00000317881.8:c.230A>C	X.37:g.118603742A>C	ENSP00000360671:p.Asn77Thr	Somatic		WXS	Illumina HiSeq	Phase_IV	B2RCV1|O43350	Missense_Mutation	SNP	pfam_Mitochondrial_sb/sol_carrier,superfamily_Mt_carrier_dom,pfscan_Mitochondrial_sb/sol_carrier,prints_Mit_carrier,prints_Aden_trnslctor	p.N77T	ENST00000317881.8	37	c.230	CCDS14578.1	X	.	.	.	.	.	.	.	.	.	.	A	19.69	3.874563	0.72180	.	.	ENSG00000005022	ENST00000317881	T	0.79141	-1.24	4.18	4.18	0.49190	Mitochondrial carrier domain (2);	0.042780	0.85682	D	0.000000	D	0.86752	0.6008	M	0.79343	2.45	0.09310	P	0.999999815679	D	0.89917	1.0	D	0.76071	0.987	D	0.90798	0.4692	9	0.87932	D	0	.	12.1849	0.54231	1.0:0.0:0.0:0.0	.	77	P05141	ADT2_HUMAN	T	77	ENSP00000360671:N77T	ENSP00000360671:N77T	N	+	2	0	SLC25A5	118487770	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.811000	0.91954	1.622000	0.50330	0.430000	0.28490	AAT	SLC25A5	-	pfam_Mitochondrial_sb/sol_carrier,superfamily_Mt_carrier_dom,pfscan_Mitochondrial_sb/sol_carrier,prints_Mit_carrier		0.493	SLC25A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC25A5	HGNC	protein_coding	OTTHUMT00000058952.2	A	NM_001152		118603742	+1	no_errors	ENST00000317881	ensembl	human	known	70_37	missense	SNP	1.000	C
SLC25A5	292	genome.wustl.edu	37	X	118603747	118603747	+	Missense_Mutation	SNP	A	A	T	rs141428607		TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chrX:118603747A>T	ENST00000317881.8	+	2	351	c.235A>T	c.(235-237)Atc>Ttc	p.I79F	SLC25A5_ENST00000460013.1_3'UTR|SLC25A5-AS1_ENST00000446986.1_RNA	NM_001152.4	NP_001143.2	P05141	ADT2_HUMAN	solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 5	79					adenine transport (GO:0015853)|chromosome segregation (GO:0007059)|energy reserve metabolic process (GO:0006112)|negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901029)|positive regulation of cell proliferation (GO:0008284)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|MMXD complex (GO:0071817)|nucleus (GO:0005634)	adenine transmembrane transporter activity (GO:0015207)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|stomach(2)	12					Clodronate(DB00720)	GGCCAATGTCATCAGATACTT	0.493																																																	0													131.0	126.0	128.0					X																	118603747		2203	4300	6503	SO:0001583	missense	292			BC068199	CCDS14578.1	Xq24	2013-08-09			ENSG00000005022	ENSG00000005022		"""Solute carriers"""	10991	protein-coding gene	gene with protein product		300150		ANT2		2168878, 2829183	Standard	NM_001152		Approved	T2, 2F1, T3	uc004erh.4	P05141	OTTHUMG00000022715	ENST00000317881.8:c.235A>T	X.37:g.118603747A>T	ENSP00000360671:p.Ile79Phe	Somatic		WXS	Illumina HiSeq	Phase_IV	B2RCV1|O43350	Missense_Mutation	SNP	pfam_Mitochondrial_sb/sol_carrier,superfamily_Mt_carrier_dom,pfscan_Mitochondrial_sb/sol_carrier,prints_Mit_carrier,prints_Aden_trnslctor	p.I79F	ENST00000317881.8	37	c.235	CCDS14578.1	X	.	.	.	.	.	.	.	.	.	.	A	23.3	4.400958	0.83120	.	.	ENSG00000005022	ENST00000317881	T	0.79749	-1.3	4.18	4.18	0.49190	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.89904	0.6850	M	0.93550	3.43	0.09310	P	0.99999999248091	D	0.62365	0.991	P	0.58172	0.834	D	0.94173	0.7425	9	0.87932	D	0	.	12.1849	0.54231	1.0:0.0:0.0:0.0	.	79	P05141	ADT2_HUMAN	F	79	ENSP00000360671:I79F	ENSP00000360671:I79F	I	+	1	0	SLC25A5	118487775	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.811000	0.91954	1.622000	0.50330	0.430000	0.28490	ATC	SLC25A5	-	pfam_Mitochondrial_sb/sol_carrier,superfamily_Mt_carrier_dom,pfscan_Mitochondrial_sb/sol_carrier,prints_Mit_carrier		0.493	SLC25A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC25A5	HGNC	protein_coding	OTTHUMT00000058952.2	A	NM_001152		118603747	+1	no_errors	ENST00000317881	ensembl	human	known	70_37	missense	SNP	1.000	T
SMIM1	388588	genome.wustl.edu	37	1	3692044	3692044	+	Missense_Mutation	SNP	G	G	A			TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chr1:3692044G>A	ENST00000444870.2	+	3	355	c.107G>A	c.(106-108)cGc>cAc	p.R36H	SMIM1_ENST00000561886.1_Missense_Mutation_p.R36H	NM_001163724.1	NP_001157196.1	B2RUZ4	SMIM1_HUMAN	small integral membrane protein 1 (Vel blood group)	36						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											TCACGCTGCCGCAGGTGAGGG	0.667																																																	0													19.0	25.0	24.0					1																	3692044		691	1591	2282	SO:0001583	missense	388588				CCDS57966.1	1p36.32	2014-07-18	2014-01-02		ENSG00000235169	ENSG00000235169		"""Blood group antigens"""	44204	protein-coding gene	gene with protein product		615242	"""small integral membrane protein 1"""			23505126, 23563606, 23563608	Standard	NM_001163724		Approved	Vel	uc001akw.4	B2RUZ4	OTTHUMG00000003505	ENST00000444870.2:c.107G>A	1.37:g.3692044G>A	ENSP00000457386:p.Arg36His	Somatic		WXS	Illumina HiSeq	Phase_IV		Missense_Mutation	SNP	NULL	p.R36H	ENST00000444870.2	37	c.107	CCDS57966.1	1																																																																																			SMIM1	-	NULL		0.667	SMIM1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	SMIM1	HGNC	protein_coding	OTTHUMT00000009742.2	G	NM_001163724		3692044	+1	no_errors	ENST00000561886	ensembl	human	putative	70_37	missense	SNP	0.031	A
SUCLG1	8802	genome.wustl.edu	37	2	84668457	84668457	+	Nonsense_Mutation	SNP	G	G	A			TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chr2:84668457G>A	ENST00000393868.2	-	4	655	c.445C>T	c.(445-447)Cag>Tag	p.Q149*		NM_003849.3	NP_003840.2	P53597	SUCA_HUMAN	succinate-CoA ligase, alpha subunit	149					cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|succinyl-CoA metabolic process (GO:0006104)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|succinate-CoA ligase complex (GDP-forming) (GO:0045244)	ATP citrate synthase activity (GO:0003878)|cofactor binding (GO:0048037)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|poly(A) RNA binding (GO:0044822)|succinate-CoA ligase (ADP-forming) activity (GO:0004775)|succinate-CoA ligase (GDP-forming) activity (GO:0004776)			kidney(4)|large_intestine(4)|lung(2)	10					Succinic acid(DB00139)	ATGTCCTGCTGGGGAATTCCT	0.473																																					Ovarian(48;203 1101 37206 40305 50790)												0													115.0	105.0	109.0					2																	84668457		2203	4300	6503	SO:0001587	stop_gained	8802			Z68204	CCDS1967.2	2p11.3	2008-02-05	2008-01-08		ENSG00000163541	ENSG00000163541	6.2.1.4		11449	protein-coding gene	gene with protein product		611224	"""succinate-CoA ligase, GDP-forming, alpha subunit"""			9128182	Standard	NM_003849		Approved		uc002son.3	P53597	OTTHUMG00000130023	ENST00000393868.2:c.445C>T	2.37:g.84668457G>A	ENSP00000377446:p.Gln149*	Somatic		WXS	Illumina HiSeq	Phase_IV	Q9BWB0|Q9UNP6	Nonsense_Mutation	SNP	pfam_CoA-bd,pfam_CoA_ligase,superfamily_Succinyl-CoA_synth-like,smart_CoA-bd,pirsf_CoA_lig_alpha,prints_CoA_lig_alpha,tigrfam_CoA_lig_alpha	p.Q149*	ENST00000393868.2	37	c.445	CCDS1967.2	2	.	.	.	.	.	.	.	.	.	.	G	37	6.037881	0.97226	.	.	ENSG00000163541	ENST00000393868	.	.	.	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	-9.9411	17.4491	0.87587	0.0:0.0:1.0:0.0	.	.	.	.	X	149	.	ENSP00000377446:Q149X	Q	-	1	0	SUCLG1	84521968	1.000000	0.71417	0.993000	0.49108	0.650000	0.38633	9.804000	0.99143	2.793000	0.96121	0.561000	0.74099	CAG	SUCLG1	-	pirsf_CoA_lig_alpha,tigrfam_CoA_lig_alpha		0.473	SUCLG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SUCLG1	HGNC	protein_coding	OTTHUMT00000252298.2	G	NM_003849		84668457	-1	no_errors	ENST00000393868	ensembl	human	known	70_37	nonsense	SNP	1.000	A
TAF9B	51616	genome.wustl.edu	37	X	77393273	77393273	+	Silent	SNP	G	G	A			TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chrX:77393273G>A	ENST00000341864.5	-	4	472	c.378C>T	c.(376-378)aaC>aaT	p.N126N		NM_015975.4	NP_057059.2	Q9HBM6	TAF9B_HUMAN	TAF9B RNA polymerase II, TATA box binding protein (TBP)-associated factor, 31kDa	126					DNA-templated transcription, initiation (GO:0006352)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell growth (GO:0030307)|programmed cell death (GO:0012501)|protein stabilization (GO:0050821)|response to organic cyclic compound (GO:0014070)	transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	transcription corepressor activity (GO:0003714)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	14						TCAGCCTATAGTTTGGAGCTG	0.373																																																	0													81.0	72.0	75.0					X																	77393273		2203	4296	6499	SO:0001819	synonymous_variant	51616			AF220509	CCDS35340.1	Xq13.1-q21.1	2010-08-16	2006-01-04	2006-01-04	ENSG00000187325	ENSG00000187325			17306	protein-coding gene	gene with protein product		300754	"""TAF9-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 31kDa"""	TAF9L		15899866	Standard	XM_005262142		Approved	TAFII31L, DN-7, DN7, TFIID-31	uc004eda.3	Q9HBM6	OTTHUMG00000021887	ENST00000341864.5:c.378C>T	X.37:g.77393273G>A		Somatic		WXS	Illumina HiSeq	Phase_IV	B2RUZ9|Q9Y2S3	Silent	SNP	pfam_TFIID-31,superfamily_Histone-fold	p.N126	ENST00000341864.5	37	c.378	CCDS35340.1	X																																																																																			TAF9B	-	pfam_TFIID-31		0.373	TAF9B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TAF9B	HGNC	protein_coding	OTTHUMT00000057308.1	G	NM_015975		77393273	-1	no_errors	ENST00000341864	ensembl	human	known	70_37	silent	SNP	1.000	A
TFDP1	7027	genome.wustl.edu	37	13	114286076	114286076	+	Intron	SNP	G	G	C	rs370954362		TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chr13:114286076G>C	ENST00000375370.5	+	5	520				TFDP1_ENST00000544902.1_Intron|TFDP1_ENST00000538138.1_Intron|TFDP1_ENST00000465174.1_3'UTR	NM_007111.4	NP_009042.1	Q14186	TFDP1_HUMAN	transcription factor Dp-1						anoikis (GO:0043276)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|epidermis development (GO:0008544)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic cell cycle (GO:0000278)|Notch signaling pathway (GO:0007219)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA biosynthetic process (GO:2000278)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(10)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	26	Lung NSC(43;0.0113)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.132)|all_epithelial(44;0.0731)|all_lung(25;0.149)|Breast(118;0.153)	all cancers(43;0.0576)			ACTTCCCTCTGGACCCTTAGA	0.617										TSP Lung(29;0.18)																																							0													107.0	78.0	88.0					13																	114286076		2203	4300	6503	SO:0001627	intron_variant	7027			BC011685	CCDS9538.1	13q34	2008-07-18			ENSG00000198176	ENSG00000198176			11749	protein-coding gene	gene with protein product		189902				8413592, 9027491	Standard	NM_007111		Approved	Dp-1, DRTF1, DP1	uc001vtw.3	Q14186	OTTHUMG00000017388	ENST00000375370.5:c.308+17G>C	13.37:g.114286076G>C		Somatic		WXS	Illumina HiSeq	Phase_IV	B4DLQ9|Q5JSB4|Q8IZL5	RNA	SNP	-	NULL	ENST00000375370.5	37	NULL	CCDS9538.1	13																																																																																			TFDP1	-	-		0.617	TFDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TFDP1	HGNC	protein_coding	OTTHUMT00000045918.3	G	NM_007111		114286076	+1	no_errors	ENST00000465174	ensembl	human	known	70_37	rna	SNP	0.454	C
UACA	55075	genome.wustl.edu	37	15	70959464	70959464	+	Silent	SNP	A	A	G			TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chr15:70959464A>G	ENST00000322954.6	-	16	3744	c.3559T>C	c.(3559-3561)Ttg>Ctg	p.L1187L	UACA_ENST00000379983.2_Silent_p.L1174L|UACA_ENST00000539319.1_Silent_p.L1078L|UACA_ENST00000560441.1_Silent_p.L1172L	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	1187					intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of protein import into nucleus (GO:0042307)|response to UV (GO:0009411)	apoptosome (GO:0043293)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				breast(2)|endometrium(7)|kidney(4)|large_intestine(13)|lung(17)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	50						TTTTCTCTCAAGCTGGCTTTT	0.368																																																	0													149.0	144.0	146.0					15																	70959464		2199	4298	6497	SO:0001819	synonymous_variant	55075			AF322916	CCDS10235.1, CCDS32280.1	15q22-q24	2013-01-10			ENSG00000137831	ENSG00000137831		"""Ankyrin repeat domain containing"""	15947	protein-coding gene	gene with protein product		612516				11162650, 10997877	Standard	NM_001008224		Approved	FLJ10128, KIAA1561	uc002asr.3	Q9BZF9	OTTHUMG00000133363	ENST00000322954.6:c.3559T>C	15.37:g.70959464A>G		Somatic		WXS	Illumina HiSeq	Phase_IV	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Silent	SNP	pfam_Ankyrin_rpt,superfamily_Ankyrin_rpt-contain_dom,superfamily_Prefoldin,smart_Ankyrin_rpt,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom,pfscan_T_SNARE_dom,prints_Ankyrin_rpt	p.L1187	ENST00000322954.6	37	c.3559	CCDS10235.1	15																																																																																			UACA	-	NULL		0.368	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	UACA	HGNC	protein_coding	OTTHUMT00000257199.2	A			70959464	-1	no_errors	ENST00000322954	ensembl	human	known	70_37	silent	SNP	0.061	G
WDR62	284403	genome.wustl.edu	37	19	36590358	36590358	+	Missense_Mutation	SNP	C	C	G	rs200490970		TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chr19:36590358C>G	ENST00000270301.7	+	22	2578	c.2578C>G	c.(2578-2580)Ccc>Gcc	p.P860A	WDR62_ENST00000401500.2_Missense_Mutation_p.P860A			O43379	WDR62_HUMAN	WD repeat domain 62	860					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)			CAGCTACCAGCCCCACGGCCG	0.622																																																	0													37.0	37.0	37.0					19																	36590358		2203	4300	6503	SO:0001583	missense	284403			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.2578C>G	19.37:g.36590358C>G	ENSP00000270301:p.Pro860Ala	Somatic		WXS	Illumina HiSeq	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.P860A	ENST00000270301.7	37	c.2578	CCDS33001.1	19	.	.	.	.	.	.	.	.	.	.	C	20.6	4.014613	0.75161	.	.	ENSG00000075702	ENST00000401500;ENST00000270301	T;T	0.30448	1.53;1.53	5.31	5.31	0.75309	.	0.000000	0.64402	D	0.000001	T	0.52885	0.1762	M	0.72894	2.215	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.45760	-0.9239	10	0.27082	T	0.32	-15.9409	14.4721	0.67523	0.0:1.0:0.0:0.0	.	860;860	O43379-4;O43379	.;WDR62_HUMAN	A	860	ENSP00000384792:P860A;ENSP00000270301:P860A	ENSP00000270301:P860A	P	+	1	0	WDR62	41282198	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	4.845000	0.62853	2.490000	0.84030	0.655000	0.94253	CCC	WDR62	-	NULL		0.622	WDR62-006	NOVEL	basic|appris_candidate|CCDS	protein_coding	WDR62	HGNC	protein_coding	OTTHUMT00000457436.1	C	NM_015671		36590358	+1	no_errors	ENST00000401500	ensembl	human	known	70_37	missense	SNP	1.000	G
ZNF595	152687	genome.wustl.edu	37	4	85969	85970	+	3'UTR	INS	-	-	A			TCGA-EA-A556-01A-11D-A26G-09	TCGA-EA-A556-10A-01D-A26G-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c425e47-7f54-4c68-9be6-d58b4b980740	e6f0f4ac-02bd-44c2-9190-a1f437b2f83c	g.chr4:85969_85970insA	ENST00000339368.6	+	0	778_779							Q8IYB9	ZN595_HUMAN	zinc finger protein 595						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|kidney(1)|large_intestine(1)|lung(11)|prostate(2)	20		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173)		TCAACATACAGGAATTCATGCT	0.376																																																	0																																										SO:0001624	3_prime_UTR_variant	152687			BX537887	CCDS75075.1, CCDS75076.1, CCDS75077.1	4p16.3	2013-01-08				ENSG00000272602		"""Zinc fingers, C2H2-type"", ""-"""	27196	protein-coding gene	gene with protein product						12477932	Standard	NM_182524		Approved	FLJ31740		Q8IYB9		ENST00000339368.6:c.*776->A	4.37:g.85969_85970insA		Somatic		WXS	Illumina HiSeq	Phase_IV		RNA	INS	-	NULL	ENST00000339368.6	37	NULL		4																																																																																			ZNF595	-	-		0.376	ZNF595-001	KNOWN	basic	processed_transcript	ZNF595	HGNC	protein_coding	OTTHUMT00000357814.2	-	NM_182524		85970	+1	no_errors	ENST00000339368	ensembl	human	known	70_37	rna	INS	0.614:0.715	A
