#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_Chromosome_hg18	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_End_position_hg18	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_Start_position_hg18	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	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_entrez_gene_id	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
NEUROD6	63974	hgsc.bcm.edu	37	7	31378715	31378715	+	Silent	SNP	G	G	A	rs563979318		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr7:31378715G>A	ENST00000297142.3	-	2	490	c.168C>T	c.(166-168)acC>acT	p.T56T		NM_022728.2	NP_073565.2	Q96NK8	NDF6_HUMAN	neuronal differentiation 6	56	Poly-Glu.				cell differentiation (GO:0030154)|dentate gyrus development (GO:0021542)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	32						cttctttctcggtttcttctc	0.458													G|||	1	0.000199681	0.0	0.0	5008	,	,		16244	0.001		0.0	False		,,,				2504	0.0																0			7											181.0	179.0	179.0					7																	31378715		2203	4300	6503	31345240	SO:0001819	synonymous_variant	63974			AF248954	CCDS5434.1	7p15.1	2013-05-21	2012-02-22		ENSG00000164600	ENSG00000164600		"""Basic helix-loop-helix proteins"""	13804	protein-coding gene	gene with protein product		611513	"""neurogenic differentiation 6"""			12357074	Standard	NM_022728		Approved	Atoh2, NEX1M, Math-2, bHLHa2, Nex1	uc003tch.4	Q96NK8	OTTHUMG00000022865	ENST00000297142.3:c.168C>T	7.37:g.31378715G>A		Somatic		Capture	Illumina HiSeq	Phase_I	31345240	Q548T9|Q9H3H6	Silent	SNP	ENST00000297142.3	37	CCDS5434.1																																																																																				NEUROD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215050.1	NM_022728	
AMPH	273	hgsc.bcm.edu	37	7	38534123	38534123	+	Missense_Mutation	SNP	C	C	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr7:38534123C>A	ENST00000356264.2	-	4	425	c.210G>T	c.(208-210)atG>atT	p.M70I	AMPH_ENST00000428293.2_Missense_Mutation_p.M70I|AMPH_ENST00000325590.5_Missense_Mutation_p.M70I	NM_001635.3	NP_001626.1	P49418	AMPH_HUMAN	amphiphysin	70	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				endocytosis (GO:0006897)|learning (GO:0007612)|synaptic transmission (GO:0007268)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|leading edge membrane (GO:0031256)|synaptic vesicle (GO:0008021)	phospholipid binding (GO:0005543)			breast(1)|endometrium(3)|kidney(3)|large_intestine(12)|liver(3)|lung(27)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)	62						AGGCCTCCTGCATGCCTAGTG	0.473																																																	0			7											149.0	130.0	137.0					7																	38534123		2203	4300	6503	38500648	SO:0001583	missense	273				CCDS5456.1, CCDS47574.1	7p14-p13	2007-06-19	2007-06-19		ENSG00000078053	ENSG00000078053			471	protein-coding gene	gene with protein product		600418	"""amphiphysin (Stiff-Mann syndrome with breast cancer 128kD autoantigen)"", ""amphiphysin (Stiff-Man syndrome with breast cancer 128kDa autoantigen)"""			8245793	Standard	NM_139316		Approved		uc003tgu.3	P49418	OTTHUMG00000023725	ENST00000356264.2:c.210G>T	7.37:g.38534123C>A	ENSP00000348602:p.Met70Ile	Somatic		Capture	Illumina HiSeq	Phase_I	38500648	A4D1X8|A4D1X9|O43538|Q75MJ8|Q75MK5|Q75MM3|Q8N4G0	Missense_Mutation	SNP	ENST00000356264.2	37	CCDS5456.1	.	.	.	.	.	.	.	.	.	.	C	33	5.238839	0.95240	.	.	ENSG00000078053	ENST00000325590;ENST00000356264;ENST00000428293;ENST00000544070	T;T;T	0.60548	0.18;0.18;0.18	6.07	6.07	0.98685	BAR (3);	0.000000	0.85682	D	0.000000	T	0.76428	0.3986	M	0.87180	2.865	0.80722	D	1	P;D	0.55605	0.877;0.972	B;P	0.56514	0.361;0.8	T	0.79708	-0.1690	10	0.72032	D	0.01	-30.9676	17.5761	0.87949	0.0:1.0:0.0:0.0	.	70;70	P49418-2;P49418	.;AMPH_HUMAN	I	70	ENSP00000317441:M70I;ENSP00000348602:M70I;ENSP00000390734:M70I	ENSP00000317441:M70I	M	-	3	0	AMPH	38500648	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.991000	0.76232	2.885000	0.99019	0.655000	0.94253	ATG		AMPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226953.2	NM_001635	
EGFR	1956	hgsc.bcm.edu	37	7	55249087	55249087	+	Silent	SNP	C	C	T	rs375332959		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr7:55249087C>T	ENST00000275493.2	+	20	2562	c.2385C>T	c.(2383-2385)ttC>ttT	p.F795F	EGFR_ENST00000442591.1_Intron|EGFR-AS1_ENST00000442411.1_RNA|EGFR_ENST00000455089.1_Silent_p.F750F|EGFR_ENST00000454757.2_Silent_p.F742F	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	795	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	TCATGCCCTTCGGCTGCCTCC	0.587		8	"""A, O, Mis"""		"""glioma, NSCLC"""	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																													yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"""epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"""		"""E, O"""	0			7						C		1,4405	2.1+/-5.4	0,1,2202	95.0	82.0	86.0		2385	-5.8	0.5	7		86	0,8600		0,0,4300	no	coding-synonymous	EGFR	NM_005228.3		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		795/1211	55249087	1,13005	2203	4300	6503	55216581	SO:0001819	synonymous_variant	1956	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"""erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"""	131550	"""epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"""	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.2385C>T	7.37:g.55249087C>T		Somatic		Capture	Illumina HiSeq	Phase_I	55216581	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Silent	SNP	ENST00000275493.2	37	CCDS5514.1																																																																																				EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228	
SEMA3D	223117	hgsc.bcm.edu	37	7	84644426	84644426	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr7:84644426T>C	ENST00000284136.6	-	14	1695	c.1652A>G	c.(1651-1653)tAc>tGc	p.Y551C	SEMA3D_ENST00000484038.1_5'UTR	NM_152754.2	NP_689967.2	O95025	SEM3D_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	551	PSI.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(1)|breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(19)|lung(29)|ovary(3)|pancreas(1)|prostate(4)|skin(2)	73						CCAGGCACAGTAGGGGTCTCT	0.468																																					Ovarian(63;442 1191 17318 29975 31528)												0			7											132.0	119.0	124.0					7																	84644426		2203	4300	6503	84482362	SO:0001583	missense	223117			BC029590	CCDS34676.1	7q21.11	2013-01-11			ENSG00000153993	ENSG00000153993		"""Semaphorins"", ""Immunoglobulin superfamily / V-set domain containing"""	10726	protein-coding gene	gene with protein product		609907					Standard	NM_152754		Approved	coll-2, Sema-Z2	uc003uic.3	O95025	OTTHUMG00000154569	ENST00000284136.6:c.1652A>G	7.37:g.84644426T>C	ENSP00000284136:p.Tyr551Cys	Somatic		Capture	Illumina HiSeq	Phase_I	84482362	A6NK46|Q6UW77|Q8NCQ1	Missense_Mutation	SNP	ENST00000284136.6	37	CCDS34676.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.597799	0.87055	.	.	ENSG00000153993	ENST00000284136	T	0.38240	1.15	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.73458	0.3589	H	0.97023	3.925	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.83406	0.0025	10	0.87932	D	0	.	16.0459	0.80720	0.0:0.0:0.0:1.0	.	551	O95025	SEM3D_HUMAN	C	551	ENSP00000284136:Y551C	ENSP00000284136:Y551C	Y	-	2	0	SEMA3D	84482362	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.040000	0.89188	2.196000	0.70406	0.459000	0.35465	TAC		SEMA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336084.2	NM_152754	
SAMD9L	219285	hgsc.bcm.edu	37	7	92760879	92760879	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr7:92760879G>A	ENST00000318238.4	-	5	5622	c.4406C>T	c.(4405-4407)tCc>tTc	p.S1469F	SAMD9L_ENST00000411955.1_Missense_Mutation_p.S1469F|SAMD9L_ENST00000437805.1_Missense_Mutation_p.S1469F	NM_152703.2	NP_689916.2	Q8IVG5	SAM9L_HUMAN	sterile alpha motif domain containing 9-like	1469					common myeloid progenitor cell proliferation (GO:0035726)|endosomal vesicle fusion (GO:0034058)|hematopoietic progenitor cell differentiation (GO:0002244)|regulation of protein catabolic process (GO:0042176)|spleen development (GO:0048536)|stem cell division (GO:0017145)	early endosome (GO:0005769)				central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(23)|liver(2)|lung(31)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	88	all_cancers(62;4.15e-11)|all_epithelial(64;2.29e-10)|Breast(17;0.000675)|Lung NSC(181;0.0755)|all_lung(186;0.0989)		STAD - Stomach adenocarcinoma(171;0.000302)			TGCCTGCTTGGACCTGCACAT	0.398																																																	0			7											150.0	140.0	144.0					7																	92760879		2203	4300	6503	92598815	SO:0001583	missense	219285			AB095926	CCDS34681.1	7q21.2	2013-01-10		2005-04-26	ENSG00000177409	ENSG00000177409		"""Sterile alpha motif (SAM) domain containing"""	1349	protein-coding gene	gene with protein product		611170	"""chromosome 7 open reading frame 6"""	C7orf6			Standard	NM_152703		Approved	KIAA2005, FLJ39885	uc003umh.1	Q8IVG5	OTTHUMG00000155807	ENST00000318238.4:c.4406C>T	7.37:g.92760879G>A	ENSP00000326247:p.Ser1469Phe	Somatic		Capture	Illumina HiSeq	Phase_I	92598815	A0JP23|A0JP24|A0PJG8|A4D1G8|D6W5Q6|Q2TV71|Q2TV75|Q2UZV8|Q8IWI4|Q8N3L9|Q8N875	Missense_Mutation	SNP	ENST00000318238.4	37	CCDS34681.1	.	.	.	.	.	.	.	.	.	.	G	13.98	2.398691	0.42512	.	.	ENSG00000177409	ENST00000318238;ENST00000411955;ENST00000437805;ENST00000394472	T;T;T	0.24908	1.83;1.83;1.83	5.22	4.26	0.50523	.	0.251965	0.32518	N	0.005995	T	0.27697	0.0681	L	0.56769	1.78	0.26349	N	0.977236	B	0.15473	0.013	B	0.14578	0.011	T	0.21008	-1.0258	10	0.72032	D	0.01	-7.544	14.055	0.64761	0.0851:0.0:0.9149:0.0	.	1469	Q8IVG5	SAM9L_HUMAN	F	1469;1469;1469;291	ENSP00000326247:S1469F;ENSP00000405760:S1469F;ENSP00000408796:S1469F	ENSP00000326247:S1469F	S	-	2	0	SAMD9L	92598815	0.014000	0.17966	0.986000	0.45419	0.848000	0.48234	1.075000	0.30716	2.716000	0.92895	0.467000	0.42956	TCC		SAMD9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341730.1	NM_152703	
CALCR	799	hgsc.bcm.edu	37	7	93055880	93055880	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr7:93055880G>A	ENST00000394441.1	-	13	1528	c.1213C>T	c.(1213-1215)Caa>Taa	p.Q405*	CALCR_ENST00000359558.2_Nonsense_Mutation_p.Q439*|CALCR_ENST00000421592.1_Nonsense_Mutation_p.Q421*|CALCR_ENST00000360249.4_Nonsense_Mutation_p.Q421*|CALCR_ENST00000426151.1_Nonsense_Mutation_p.Q405*	NM_001164738.1	NP_001158210.1	P30988	CALCR_HUMAN	calcitonin receptor	439					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|response to glucocorticoid (GO:0051384)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcitonin binding (GO:0032841)|calcitonin receptor activity (GO:0004948)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(3)	45	all_cancers(62;3.18e-12)|all_epithelial(64;1.34e-11)|Breast(17;0.000675)|Lung NSC(181;0.207)		STAD - Stomach adenocarcinoma(171;0.000244)		Pramlintide(DB01278)|Salmon Calcitonin(DB00017)	TGGGCCCATTGGCGCTTCACG	0.532																																																	0			7											35.0	40.0	39.0					7																	93055880		2203	4300	6503	92893816	SO:0001587	stop_gained	799			L00587	CCDS5631.1, CCDS55125.1	7q21.3	2012-08-10			ENSG00000004948	ENSG00000004948		"""GPCR / Class B : Calcitonin receptors"""	1440	protein-coding gene	gene with protein product		114131				1331173	Standard	NM_001742		Approved	CTR	uc003umw.2	P30988	OTTHUMG00000023599	ENST00000394441.1:c.1213C>T	7.37:g.93055880G>A	ENSP00000377959:p.Gln405*	Somatic		Capture	Illumina HiSeq	Phase_I	92893816	A4D1G6|F5H605|O14585|Q13941|Q5ZGL8|Q659U6|Q6DJU8|Q6T712	Nonsense_Mutation	SNP	ENST00000394441.1	37	CCDS5631.1	.	.	.	.	.	.	.	.	.	.	G	33	5.286164	0.95517	.	.	ENSG00000004948	ENST00000359558;ENST00000360249;ENST00000421592;ENST00000394441;ENST00000426151	.	.	.	4.92	4.92	0.64577	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11182	T	0.66	.	13.8286	0.63366	0.0:0.0:1.0:0.0	.	.	.	.	X	439;421;421;405;405	.	ENSP00000352561:Q439X	Q	-	1	0	CALCR	92893816	1.000000	0.71417	0.954000	0.39281	0.304000	0.27724	7.279000	0.78599	2.728000	0.93425	0.585000	0.79938	CAA		CALCR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254661.2	NM_001742	
TRIP6	7205	hgsc.bcm.edu	37	7	100470316	100470316	+	Nonsense_Mutation	SNP	A	A	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr7:100470316A>T	ENST00000200457.4	+	8	1609	c.1249A>T	c.(1249-1251)Aga>Tga	p.R417*	SRRT_ENST00000388793.4_5'Flank|SRRT_ENST00000347433.4_5'Flank|SRRT_ENST00000457580.2_5'Flank|SRRT_ENST00000432932.1_5'Flank	NM_003302.2	NP_003293.2	Q15654	TRIP6_HUMAN	thyroid hormone receptor interactor 6	417	LIM zinc-binding 3. {ECO:0000255|PROSITE- ProRule:PRU00125}.				focal adhesion assembly (GO:0048041)|positive regulation of cell migration (GO:0030335)|regulation of transcription, DNA-templated (GO:0006355)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|kinase binding (GO:0019900)|poly(A) RNA binding (GO:0044822)|thyroid hormone receptor binding (GO:0046966)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|liver(1)|lung(5)	14	Lung NSC(181;0.041)|all_lung(186;0.0581)					GGAGACTGTGAGAATTGTTGC	0.572																																																	0			7											149.0	110.0	123.0					7																	100470316		2203	4300	6503	100308252	SO:0001587	stop_gained	7205			L40374, AF000974	CCDS5708.1	7q22	2006-09-05			ENSG00000087077	ENSG00000087077			12311	protein-coding gene	gene with protein product		602933				9598321, 7776974	Standard	NM_003302		Approved	ZRP-1, OIP1, MGC10556, MGC10558, MGC29959, MGC3837, MGC4423	uc003uww.3	Q15654	OTTHUMG00000157029	ENST00000200457.4:c.1249A>T	7.37:g.100470316A>T	ENSP00000200457:p.Arg417*	Somatic		Capture	Illumina HiSeq	Phase_I	100308252	A4D2E7|F2ZC07|F2ZC08|O15170|O15275|Q9BTB2|Q9BUE5|Q9BXP3|Q9UNT4	Nonsense_Mutation	SNP	ENST00000200457.4	37	CCDS5708.1	.	.	.	.	.	.	.	.	.	.	A	38	6.924247	0.97940	.	.	ENSG00000087077	ENST00000200457	.	.	.	4.61	0.809	0.18725	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.0889	0.53713	0.5529:0.4471:0.0:0.0	.	.	.	.	X	417	.	ENSP00000200457:R417X	R	+	1	2	TRIP6	100308252	0.998000	0.40836	0.993000	0.49108	0.986000	0.74619	0.694000	0.25512	0.245000	0.21373	0.460000	0.39030	AGA		TRIP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347151.2	NM_003302	
NRCAM	4897	hgsc.bcm.edu	37	7	107816967	107816967	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr7:107816967A>G	ENST00000425651.2	-	24	3058	c.3059T>C	c.(3058-3060)tTc>tCc	p.F1020S	NRCAM_ENST00000379024.4_Missense_Mutation_p.F1001S|NRCAM_ENST00000351718.4_Missense_Mutation_p.F1004S|NRCAM_ENST00000413765.2_Missense_Mutation_p.F1001S|NRCAM_ENST00000379028.3_Missense_Mutation_p.F1020S|NRCAM_ENST00000379022.4_Missense_Mutation_p.F1020S	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	1020	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						TCGAGTGCTGAAATTTAAATT	0.363																																																	0			7											112.0	113.0	113.0					7																	107816967		2203	4300	6503	107604203	SO:0001583	missense	4897				CCDS5751.1, CCDS47686.1, CCDS55153.1, CCDS75652.1	7q31	2013-02-11			ENSG00000091129	ENSG00000091129		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7994	protein-coding gene	gene with protein product	"""NgCAM-related cell adhesion molecule"""	601581				8812479	Standard	NM_001037132		Approved	KIAA0343, Bravo	uc022aka.1	Q92823	OTTHUMG00000154973	ENST00000425651.2:c.3059T>C	7.37:g.107816967A>G	ENSP00000401244:p.Phe1020Ser	Somatic		Capture	Illumina HiSeq	Phase_I	107604203	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Missense_Mutation	SNP	ENST00000425651.2	37	CCDS47686.1	.	.	.	.	.	.	.	.	.	.	A	11.05	1.523389	0.27299	.	.	ENSG00000091129	ENST00000379032;ENST00000379028;ENST00000413765;ENST00000537765;ENST00000351718;ENST00000379024;ENST00000425651;ENST00000379022	T;T;T;T;T;T	0.55760	0.5;0.5;0.5;0.5;0.5;0.5	5.62	3.08	0.35506	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.441828	0.28971	N	0.013550	T	0.25005	0.0607	N	0.02674	-0.535	0.36472	D	0.867304	B;B;B;B;B	0.16603	0.018;0.0;0.0;0.0;0.007	B;B;B;B;B	0.18561	0.022;0.003;0.004;0.003;0.001	T	0.10753	-1.0616	10	0.32370	T	0.25	.	9.3702	0.38250	0.4325:0.0:0.0:0.5675	.	1020;1001;1001;1004;1020	Q92823-5;Q92823-3;E9PDA4;Q92823-4;Q92823	.;.;.;.;NRCAM_HUMAN	S	1020;1020;1001;1020;1004;1001;1020;1020	ENSP00000368314:F1020S;ENSP00000407858:F1001S;ENSP00000325269:F1004S;ENSP00000368310:F1001S;ENSP00000401244:F1020S;ENSP00000368308:F1020S	ENSP00000325269:F1004S	F	-	2	0	NRCAM	107604203	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.076000	0.50081	0.922000	0.37019	0.528000	0.53228	TTC		NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132	
CTTNBP2	83992	hgsc.bcm.edu	37	7	117432610	117432610	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr7:117432610A>G	ENST00000160373.3	-	4	731	c.640T>C	c.(640-642)Tcc>Ccc	p.S214P	CTTNBP2_ENST00000487820.1_5'Flank	NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	214					brain development (GO:0007420)	cell projection (GO:0042995)|synaptic vesicle (GO:0008021)				breast(3)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(36)|ovary(4)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		TTCTCAGCGGAGAGTTCCTCT	0.478																																																	0			7											136.0	123.0	127.0					7																	117432610		2203	4300	6503	117219846	SO:0001583	missense	83992				CCDS5774.1	7q31	2013-01-10	2004-06-08	2004-06-09	ENSG00000077063	ENSG00000077063		"""Ankyrin repeat domain containing"""	15679	protein-coding gene	gene with protein product		609772	"""cortactin binding protein 2"""	CORTBP2, C7orf8		11707066	Standard	XM_005250635		Approved	KIAA1758, Orf4	uc003vjf.3	Q8WZ74	OTTHUMG00000022880	ENST00000160373.3:c.640T>C	7.37:g.117432610A>G	ENSP00000160373:p.Ser214Pro	Somatic		Capture	Illumina HiSeq	Phase_I	117219846	O43389|Q7LG11|Q9C0A5	Missense_Mutation	SNP	ENST00000160373.3	37	CCDS5774.1	.	.	.	.	.	.	.	.	.	.	A	7.250	0.603130	0.13939	.	.	ENSG00000077063	ENST00000160373	T	0.66099	-0.19	5.77	0.123	0.14709	.	0.534645	0.20899	N	0.083674	T	0.62865	0.2463	M	0.77820	2.39	0.19775	N	0.999952	P	0.36944	0.574	B	0.40228	0.323	T	0.58891	-0.7556	10	0.48119	T	0.1	0.8091	12.078	0.53655	0.3391:0.571:0.0:0.0899	.	214	Q8WZ74	CTTB2_HUMAN	P	214	ENSP00000160373:S214P	ENSP00000160373:S214P	S	-	1	0	CTTNBP2	117219846	0.994000	0.37717	0.150000	0.22450	0.019000	0.09904	1.203000	0.32284	0.141000	0.18875	0.528000	0.53228	TCC		CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427	
ZC3HAV1	56829	hgsc.bcm.edu	37	7	138763338	138763338	+	Missense_Mutation	SNP	T	T	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr7:138763338T>G	ENST00000242351.5	-	5	1849	c.1533A>C	c.(1531-1533)gaA>gaC	p.E511D	ZC3HAV1_ENST00000464606.1_Missense_Mutation_p.E633D|ZC3HAV1_ENST00000471652.1_Missense_Mutation_p.E511D	NM_020119.3	NP_064504.2	Q7Z2W4	ZCCHV_HUMAN	zinc finger CCCH-type, antiviral 1	511					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral genome replication (GO:0045071)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of mRNA catabolic process (GO:0061014)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(4)|skin(1)	37						CAAGACAAATTTCCTCTGAGT	0.388																																																	0			7											135.0	116.0	123.0					7																	138763338		2203	4300	6503	138413878	SO:0001583	missense	56829			BX571742	CCDS5851.1, CCDS55171.1	7q34	2012-07-05			ENSG00000105939	ENSG00000105939		"""Zinc fingers, CCCH-type domain containing"", ""Poly (ADP-ribose) polymerases"""	23721	protein-coding gene	gene with protein product	"""zinc finger antiviral protein"", "" CCCH-type zinc finger antiviral protein"""	607312				12215647, 12851707	Standard	NM_024625		Approved	ZAP, FLB6421, FLJ13288, MGC48898, ZC3HDC2, ZC3H2, PARP13	uc003vun.3	Q7Z2W4	OTTHUMG00000157471	ENST00000242351.5:c.1533A>C	7.37:g.138763338T>G	ENSP00000242351:p.Glu511Asp	Somatic		Capture	Illumina HiSeq	Phase_I	138413878	A4D1R2|A4D1S4|Q8IW57|Q8TAJ3|Q96N79|Q9H8R9|Q9P0Y7	Missense_Mutation	SNP	ENST00000242351.5	37	CCDS5851.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.68|12.68	2.009873|2.009873	0.35415|0.35415	.|.	.|.	ENSG00000105939|ENSG00000105939	ENST00000242351;ENST00000464606;ENST00000471652;ENST00000540247|ENST00000460845	T;T;T|.	0.23147|.	2.99;2.96;1.92|.	5.05|5.05	1.27|1.27	0.21489|0.21489	Zinc finger, CCCH-type (1);|.	0.993989|.	0.08164|.	N|.	0.987971|.	T|T	0.59307|0.59307	0.2184|0.2184	M|M	0.83012|0.83012	2.62|2.62	0.33722|0.33722	D|D	0.617178|0.617178	B;B|.	0.25904|.	0.004;0.137|.	B;B|.	0.23852|.	0.016;0.049|.	T|T	0.64829|0.64829	-0.6315|-0.6315	10|5	0.56958|.	D|.	0.05|.	.|.	3.1164|3.1164	0.06376|0.06376	0.0:0.2544:0.2226:0.5229|0.0:0.2544:0.2226:0.5229	.|.	511;511|.	Q7Z2W4-2;Q7Z2W4|.	.;ZCCHV_HUMAN|.	D|H	511;633;511;271|76	ENSP00000242351:E511D;ENSP00000418385:E633D;ENSP00000419855:E511D|.	ENSP00000242351:E511D|.	E|N	-|-	3|1	2|0	ZC3HAV1|ZC3HAV1	138413878|138413878	0.322000|0.322000	0.24634|0.24634	0.964000|0.964000	0.40570|0.40570	0.658000|0.658000	0.38924|0.38924	-0.024000|-0.024000	0.12435|0.12435	0.382000|0.382000	0.24878|0.24878	0.519000|0.519000	0.50382|0.50382	GAA|AAT		ZC3HAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348915.1	NM_020119	
BRAF	673	hgsc.bcm.edu	37	7	140500173	140500173	+	Silent	SNP	C	C	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr7:140500173C>T	ENST00000288602.6	-	7	1029	c.969G>A	c.(967-969)tcG>tcA	p.S323S		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	323					activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)		SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	CAATAGAGTCCGAGGCGGGTG	0.483		61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												Colon(40;35 892 2973 5743 27438)			Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	0			7											137.0	112.0	120.0					7																	140500173		2203	4300	6503	140146642	SO:0001819	synonymous_variant	673	Familial Cancer Database	CFC, CFCS	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"""v-raf murine sarcoma viral oncogene homolog B"""			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.969G>A	7.37:g.140500173C>T		Somatic		Capture	Illumina HiSeq	Phase_I	140146642	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Silent	SNP	ENST00000288602.6	37	CCDS5863.1																																																																																				BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333	
PCNA	5111	hgsc.bcm.edu	37	20	5099470	5099470	+	Silent	SNP	A	A	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr20:5099470A>T	ENST00000379160.3	-	3	506	c.264T>A	c.(262-264)atT>atA	p.I88I	SNORA26_ENST00000391215.1_RNA|PCNA_ENST00000379143.5_Silent_p.I88I	NM_002592.2	NP_002583.1	P12004	PCNA_HUMAN	proliferating cell nuclear antigen	88	Interaction with NUDT15.				base-excision repair (GO:0006284)|cell proliferation (GO:0008283)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|epithelial cell differentiation (GO:0030855)|G1/S transition of mitotic cell cycle (GO:0000082)|heart development (GO:0007507)|leading strand elongation (GO:0006272)|mismatch repair (GO:0006298)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of deoxyribonuclease activity (GO:0032077)|regulation of DNA replication (GO:0006275)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|response to cadmium ion (GO:0046686)|response to lipid (GO:0033993)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)|translesion synthesis (GO:0019985)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|DNA replication factor C complex (GO:0005663)|extracellular vesicular exosome (GO:0070062)|nuclear replication fork (GO:0043596)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCNA complex (GO:0043626)|PCNA-p21 complex (GO:0070557)	dinucleotide insertion or deletion binding (GO:0032139)|DNA polymerase binding (GO:0070182)|DNA polymerase processivity factor activity (GO:0030337)|identical protein binding (GO:0042802)|MutLalpha complex binding (GO:0032405)|purine-specific mismatch base pair DNA N-glycosylase activity (GO:0000701)|receptor tyrosine kinase binding (GO:0030971)			endometrium(2)|kidney(1)|large_intestine(4)|lung(2)	9						CCCTTAGTGTAATGATATCTT	0.428								DNA polymerases (catalytic subunits)																																									0			20											225.0	218.0	220.0					20																	5099470		2203	4300	6503	5047470	SO:0001819	synonymous_variant	5111			J04718	CCDS13087.1	20p13-p12.3	2013-09-19			ENSG00000132646	ENSG00000132646			8729	protein-coding gene	gene with protein product		176740				2565339	Standard	NM_002592		Approved		uc002wlp.3	P12004	OTTHUMG00000031798	ENST00000379160.3:c.264T>A	20.37:g.5099470A>T		Somatic		Capture	Illumina HiSeq	Phase_I	5047470	B2R897|D3DW02	Silent	SNP	ENST00000379160.3	37	CCDS13087.1																																																																																				PCNA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077852.2		
LRRN4	164312	hgsc.bcm.edu	37	20	6022178	6022178	+	Silent	SNP	G	G	T	rs555054750		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr20:6022178G>T	ENST00000378858.4	-	5	1937	c.1713C>A	c.(1711-1713)ccC>ccA	p.P571P		NM_152611.4	NP_689824.2	Q8WUT4	LRRN4_HUMAN	leucine rich repeat neuronal 4	571					long-term memory (GO:0007616)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				breast(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(2)	27						CGCTGAGGCCGGGGCACCGGC	0.697																																																	0			20											56.0	63.0	60.0					20																	6022178		2202	4298	6500	5970178	SO:0001819	synonymous_variant	164312			AL118505	CCDS13097.1	20p12.3	2013-02-11	2008-05-20	2008-05-20	ENSG00000125872	ENSG00000125872		"""Fibronectin type III domain containing"""	16208	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 75"""	C20orf75		15870286	Standard	NM_152611		Approved	dJ1056H1.1, NLRR4	uc002wmo.3	Q8WUT4	OTTHUMG00000031825	ENST00000378858.4:c.1713C>A	20.37:g.6022178G>T		Somatic		Capture	Illumina HiSeq	Phase_I	5970178	A8K258|Q5JWV6|Q9H419	Silent	SNP	ENST00000378858.4	37	CCDS13097.1																																																																																				LRRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077907.2	NM_152611	
TM9SF4	9777	hgsc.bcm.edu	37	20	30729599	30729599	+	Silent	SNP	G	G	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr20:30729599G>A	ENST00000398022.2	+	5	664	c.429G>A	c.(427-429)cgG>cgA	p.R143R	TM9SF4_ENST00000217315.5_Silent_p.R126R	NM_014742.3	NP_055557.2	Q92544	TM9S4_HUMAN	transmembrane 9 superfamily protein member 4	143						integral component of membrane (GO:0016021)				central_nervous_system(2)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			TGGCCACCCGGCTGGAGCTCT	0.577																																																	0			20											104.0	118.0	114.0					20																	30729599		2203	4300	6503	30193260	SO:0001819	synonymous_variant	9777			BC021107	CCDS13196.2	20q11.21	2004-04-19			ENSG00000101337	ENSG00000101337			30797	protein-coding gene	gene with protein product						9039502	Standard	NM_014742		Approved	KIAA0255, dJ836N17.2	uc002wxj.2	Q92544	OTTHUMG00000032206	ENST00000398022.2:c.429G>A	20.37:g.30729599G>A		Somatic		Capture	Illumina HiSeq	Phase_I	30193260	B0QYT7|Q9NUA3	Silent	SNP	ENST00000398022.2	37	CCDS13196.2																																																																																				TM9SF4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323568.1	NM_014742	
ERGIC3	51614	hgsc.bcm.edu	37	20	34136262	34136262	+	Splice_Site	SNP	G	G	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr20:34136262G>A	ENST00000348547.2	+	6	539	c.462G>A	c.(460-462)aaG>aaA	p.K154K	ERGIC3_ENST00000447986.1_Splice_Site_p.K154K|ERGIC3_ENST00000357394.4_Splice_Site_p.K154K|ERGIC3_ENST00000279052.6_Splice_Site_p.K154K|ERGIC3_ENST00000482338.1_3'UTR	NM_015966.2	NP_057050.1	Q9Y282	ERGI3_HUMAN	ERGIC and golgi 3	154					vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)	16	Lung NSC(9;0.00489)|all_lung(11;0.00729)		BRCA - Breast invasive adenocarcinoma(18;0.0127)			TGCCCTACAGGTGCTGTAACA	0.557																																																	0			20											58.0	55.0	56.0					20																	34136262		2203	4300	6503	33599676	SO:0001630	splice_region_variant	51614			AF077030	CCDS13257.1, CCDS13258.1	20q11.22	2013-09-19	2006-01-19	2006-01-19	ENSG00000125991	ENSG00000125991			15927	protein-coding gene	gene with protein product			"""serologically defined breast cancer antigen 84"", ""chromosome 20 open reading frame 47"""	SDBCAG84, C20orf47		10810093	Standard	NM_015966		Approved	CGI-54, PRO0989, NY-BR-84, Erv46	uc002xcs.3	Q9Y282	OTTHUMG00000032346	ENST00000348547.2:c.462-1G>A	20.37:g.34136262G>A		Somatic		Capture	Illumina HiSeq	Phase_I	33599676	Q5JWS3|Q6ZWP7|Q9H276|Q9P1L3	Silent	SNP	ENST00000348547.2	37	CCDS13257.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	10.51|10.51	1.371023|1.371023	0.24771|0.24771	.|.	.|.	ENSG00000125991|ENSG00000125991	ENST00000416206|ENST00000413587	.|.	.|.	.|.	4.74|4.74	2.38|2.38	0.29361|0.29361	.|.	.|.	.|.	.|.	.|.	T|T	0.55878|0.55878	0.1948|0.1948	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.50709|0.50709	-0.8796|-0.8796	4|4	.|.	.|.	.|.	.|.	7.7232|7.7232	0.28744|0.28744	0.2267:0.1292:0.644:0.0|0.2267:0.1292:0.644:0.0	.|.	.|.	.|.	.|.	N|M	153|156	.|.	.|.	S|V	+|+	2|1	0|0	ERGIC3|ERGIC3	33599676|33599676	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.831000|0.831000	0.47069|0.47069	1.628000|1.628000	0.37060|0.37060	1.006000|1.006000	0.39211|0.39211	-0.354000|-0.354000	0.07668|0.07668	AGT|GTG		ERGIC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078880.2	NM_015966	Silent
BCAS1	8537	hgsc.bcm.edu	37	20	52645320	52645320	+	Missense_Mutation	SNP	C	C	T	rs201371925		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr20:52645320C>T	ENST00000395961.3	-	4	500	c.334G>A	c.(334-336)Gca>Aca	p.A112T	BCAS1_ENST00000411563.1_Missense_Mutation_p.A15T|BCAS1_ENST00000371435.2_Missense_Mutation_p.A112T|BCAS1_ENST00000371440.3_Missense_Mutation_p.A112T	NM_003657.2	NP_003648.2	O75363	BCAS1_HUMAN	breast carcinoma amplified sequence 1	112						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(23)|ovary(2)|skin(2)|stomach(1)|urinary_tract(1)	37	Breast(2;9.53e-15)|Lung NSC(4;5.57e-06)|all_lung(4;1.44e-05)		STAD - Stomach adenocarcinoma(23;0.116)|Colorectal(105;0.198)			GATGAATCTGCGGCTTGGTCT	0.532																																																	0			20											71.0	68.0	69.0					20																	52645320		2203	4300	6503	52078727	SO:0001583	missense	8537			AF041260	CCDS13444.1	20q13.2	2006-11-10			ENSG00000064787	ENSG00000064787			974	protein-coding gene	gene with protein product		602968				9671742	Standard	NM_003657		Approved	NABC1, AIBC1	uc002xws.2	O75363	OTTHUMG00000032772	ENST00000395961.3:c.334G>A	20.37:g.52645320C>T	ENSP00000379290:p.Ala112Thr	Somatic		Capture	Illumina HiSeq	Phase_I	52078727	A0AVG5|Q68CZ3	Missense_Mutation	SNP	ENST00000395961.3	37	CCDS13444.1	.	.	.	.	.	.	.	.	.	.	C	1.524	-0.546098	0.04024	.	.	ENSG00000064787	ENST00000371440;ENST00000395961;ENST00000371435;ENST00000411563	T;T;T;T	0.04758	3.56;3.56;3.56;3.56	5.11	-3.93	0.04143	.	0.785958	0.11479	N	0.559912	T	0.00784	0.0026	N	0.00142	-2.005	0.09310	N	0.999999	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0;0.0	T	0.38520	-0.9657	10	0.02654	T	1	-0.4969	4.5089	0.11901	0.5014:0.2285:0.0:0.2701	.	15;112;112;112;112;112	B4E2C4;B2RCQ5;O75363-2;G3XAF7;A0AVG7;O75363	.;.;.;.;.;BCAS1_HUMAN	T	112;112;112;15	ENSP00000360495:A112T;ENSP00000379290:A112T;ENSP00000360490:A112T;ENSP00000397442:A15T	ENSP00000360490:A112T	A	-	1	0	BCAS1	52078727	0.082000	0.21442	0.548000	0.28192	0.660000	0.38997	-0.061000	0.11693	-1.046000	0.03246	-0.414000	0.06135	GCA		BCAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079766.2	NM_003657	
VAPB	9217	hgsc.bcm.edu	37	20	56993271	56993271	+	Silent	SNP	C	C	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr20:56993271C>T	ENST00000475243.1	+	2	401	c.63C>T	c.(61-63)ccC>ccT	p.P21P	VAPB_ENST00000265619.2_3'UTR|VAPB_ENST00000395802.3_Silent_p.P21P	NM_004738.4	NP_004729.1	O95292	VAPB_HUMAN	VAMP (vesicle-associated membrane protein)-associated protein B and C	21	MSP. {ECO:0000255|PROSITE- ProRule:PRU00132}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell death (GO:0008219)|cellular calcium ion homeostasis (GO:0006874)|endoplasmic reticulum unfolded protein response (GO:0030968)|modulation by virus of host morphology or physiology (GO:0019048)|positive regulation of viral genome replication (GO:0045070)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	beta-tubulin binding (GO:0048487)|enzyme binding (GO:0019899)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|structural molecule activity (GO:0005198)			kidney(2)|lung(3)|prostate(1)	6	Lung NSC(12;0.000615)|all_lung(29;0.00186)		BRCA - Breast invasive adenocarcinoma(13;6.2e-12)|Epithelial(14;3.7e-08)|all cancers(14;3.88e-07)			CTACAGGTCCCTTCACCGATG	0.448																																																	0			20											138.0	126.0	130.0					20																	56993271		2203	4300	6503	56426677	SO:0001819	synonymous_variant	9217			AF086628	CCDS33498.1, CCDS56198.1	20q13	2014-09-17			ENSG00000124164	ENSG00000124164			12649	protein-coding gene	gene with protein product		605704				9920726	Standard	NM_004738		Approved	VAP-B, VAP-C, ALS8	uc002xza.3	O95292	OTTHUMG00000032840	ENST00000475243.1:c.63C>T	20.37:g.56993271C>T		Somatic		Capture	Illumina HiSeq	Phase_I	56426677	A2A2F2|O95293|Q9P0H0	Silent	SNP	ENST00000475243.1	37	CCDS33498.1																																																																																				VAPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079875.2		
ADORA2A	135	hgsc.bcm.edu	37	22	24836656	24836656	+	Silent	SNP	C	C	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr22:24836656C>T	ENST00000337539.7	+	3	897	c.438C>T	c.(436-438)tgC>tgT	p.C146C	ADORA2A-AS1_ENST00000427813.2_RNA|ADORA2A_ENST00000496497.1_3'UTR|ADORA2A-AS1_ENST00000326341.4_RNA|ADORA2A-AS1_ENST00000543438.1_RNA|SPECC1L-ADORA2A_ENST00000358654.2_3'UTR	NM_000675.4|NM_001278497.1|NM_001278498.1|NM_001278499.1|NM_001278500.1	NP_000666.2|NP_001265426.1|NP_001265427.1|NP_001265428.1|NP_001265429.1	P29274	AA2AR_HUMAN	adenosine A2a receptor	146					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|apoptotic process (GO:0006915)|blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cAMP biosynthetic process (GO:0006171)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|central nervous system development (GO:0007417)|inflammatory response (GO:0006954)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phagocytosis (GO:0006909)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|sensory perception (GO:0007600)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|G-protein coupled adenosine receptor activity (GO:0001609)|identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(1)|lung(7)|skin(1)	21	Colorectal(2;0.196)				Adenosine(DB00640)|Caffeine(DB00201)|Defibrotide(DB04932)|Dyphylline(DB00651)|Enprofylline(DB00824)|Mefloquine(DB00358)|Oxtriphylline(DB01303)|Pentoxifylline(DB00806)|Regadenoson(DB06213)|Theobromine(DB01412)|Theophylline(DB00277)	GGAACAACTGCGGTCAGCCAA	0.587																																																	0			22											189.0	184.0	186.0					22																	24836656		2203	4300	6503	23166656	SO:0001819	synonymous_variant	135			X68486	CCDS13826.1	22q11.23	2012-08-08			ENSG00000128271	ENSG00000128271		"""GPCR / Class A : Adenosine receptors"""	263	protein-coding gene	gene with protein product		102776		ADORA2		1662665, 2541503	Standard	NM_001278497		Approved	RDC8	uc002zzy.4	P29274	OTTHUMG00000150761	ENST00000337539.7:c.438C>T	22.37:g.24836656C>T		Somatic		Capture	Illumina HiSeq	Phase_I	23166656	B2R7E0	Silent	SNP	ENST00000337539.7	37	CCDS13826.1																																																																																				ADORA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319971.2	NM_000675	
THOC5	8563	hgsc.bcm.edu	37	22	29921864	29921864	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr22:29921864T>C	ENST00000490103.1	-	12	1260	c.1138A>G	c.(1138-1140)Aca>Gca	p.T380A	THOC5_ENST00000397872.1_Missense_Mutation_p.T380A|THOC5_ENST00000397873.2_Missense_Mutation_p.T380A|CTA-256D12.11_ENST00000411969.1_RNA|THOC5_ENST00000397871.1_Missense_Mutation_p.T380A	NM_003678.4	NP_003669.4	Q13769	THOC5_HUMAN	THO complex 5	380			T -> K (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		blastocyst development (GO:0001824)|cell morphogenesis (GO:0000902)|monocyte differentiation (GO:0030224)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|negative regulation of DNA damage checkpoint (GO:2000002)|negative regulation of macrophage differentiation (GO:0045650)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|primitive hemopoiesis (GO:0060215)|regulation of mRNA export from nucleus (GO:0010793)|regulation of stem cell division (GO:2000035)|RNA splicing (GO:0008380)|stem cell division (GO:0017145)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	mRNA binding (GO:0003729)			NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(4)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						ATGGCAGTTGTCACTTTGGCT	0.507																																																	0			22											193.0	154.0	167.0					22																	29921864		2203	4300	6503	28251864	SO:0001583	missense	8563			AB023200	CCDS13859.1	22q12	2013-02-11			ENSG00000100296	ENSG00000100296		"""THO complex subunits"""	19074	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 79"""	612733	"""chromosome 22 open reading frame 19"""	C22orf19		11979277, 8242058, 10231032, 19015024, 18373705	Standard	NM_003678		Approved	PK1.3, KIAA0983, Fmip, fSAP79	uc003afs.3	Q13769	OTTHUMG00000151291	ENST00000490103.1:c.1138A>G	22.37:g.29921864T>C	ENSP00000420306:p.Thr380Ala	Somatic		Capture	Illumina HiSeq	Phase_I	28251864	O60839|Q9UPZ5	Missense_Mutation	SNP	ENST00000490103.1	37	CCDS13859.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	8.441|8.441	0.850758|0.850758	0.17034|0.17034	.|.	.|.	ENSG00000100296|ENSG00000100296	ENST00000443089|ENST00000490103;ENST00000397872;ENST00000397871;ENST00000397873	.|T;T;T;T	.|0.23147	.|1.92;1.92;1.92;1.92	6.07|6.07	5.03|5.03	0.67393|0.67393	.|.	.|0.198934	.|0.56097	.|D	.|0.000039	T|T	0.17323|0.17323	0.0416|0.0416	L|L	0.34521|0.34521	1.04|1.04	0.35455|0.35455	D|D	0.796031|0.796031	.|B	.|0.20164	.|0.042	.|B	.|0.21917	.|0.037	T|T	0.17930|0.17930	-1.0353|-1.0353	5|10	.|0.11485	.|T	.|0.65	-11.7893|-11.7893	8.6602|8.6602	0.34088|0.34088	0.1285:0.0:0.1348:0.7367|0.1285:0.0:0.1348:0.7367	.|.	.|380	.|Q13769	.|THOC5_HUMAN	G|A	250|380	.|ENSP00000420306:T380A;ENSP00000380970:T380A;ENSP00000380969:T380A;ENSP00000380971:T380A	.|ENSP00000380969:T380A	D|T	-|-	2|1	0|0	THOC5|THOC5	28251864|28251864	1.000000|1.000000	0.71417|0.71417	0.989000|0.989000	0.46669|0.46669	0.390000|0.390000	0.30446|0.30446	2.973000|2.973000	0.49264|0.49264	1.093000|1.093000	0.41377|0.41377	-0.333000|-0.333000	0.08304|0.08304	GAC|ACA		THOC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322097.1	NM_003678	
SGSM3	27352	hgsc.bcm.edu	37	22	40802178	40802178	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr22:40802178A>G	ENST00000248929.9	+	9	1100	c.911A>G	c.(910-912)gAg>gGg	p.E304G	SGSM3_ENST00000454798.2_Missense_Mutation_p.E237G	NM_015705.4	NP_056520.2			small G protein signaling modulator 3											cervix(1)|endometrium(4)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)|skin(6)	19						TTTTTCTACGAGGGCTCCCGG	0.627																																																	0			22											83.0	73.0	76.0					22																	40802178		2203	4300	6503	39132124	SO:0001583	missense	27352			AL022238	CCDS14002.1	22q13.1-q13.2	2013-07-09	2007-08-14	2007-08-14	ENSG00000100359	ENSG00000100359		"""Small G protein signaling modulators"""	25228	protein-coding gene	gene with protein product	"""RUN and SH3 containing 3"""	610440	"""RUN and TBC1 domain containing 3"""	RUTBC3		11214971, 17509819	Standard	XM_005261572		Approved	DJ1042K10.2, RUSC3, RabGAP-5, RABGAP5	uc003ayu.1	Q96HU1	OTTHUMG00000151141	ENST00000248929.9:c.911A>G	22.37:g.40802178A>G	ENSP00000248929:p.Glu304Gly	Somatic		Capture	Illumina HiSeq	Phase_I	39132124		Missense_Mutation	SNP	ENST00000248929.9	37	CCDS14002.1	.	.	.	.	.	.	.	.	.	.	A	25.3	4.628349	0.87560	.	.	ENSG00000100359	ENST00000457767;ENST00000248929;ENST00000545416;ENST00000454798	T;T;T	0.15487	2.42;2.42;2.42	4.85	4.85	0.62838	Rab-GAP/TBC domain (4);	0.107661	0.64402	D	0.000006	T	0.46521	0.1397	H	0.94183	3.505	0.58432	D	0.999993	P;B;P;P;P	0.50443	0.51;0.29;0.921;0.935;0.935	B;B;P;P;P	0.54174	0.312;0.375;0.735;0.744;0.744	T	0.63341	-0.6659	10	0.72032	D	0.01	.	15.1445	0.72641	1.0:0.0:0.0:0.0	.	241;237;304;304;304	B4DVE3;B4DMS2;Q96HU1-2;B9A6J5;Q96HU1	.;.;.;.;SGSM3_HUMAN	G	237;304;247;237	ENSP00000399249:E237G;ENSP00000248929:E304G;ENSP00000390998:E237G	ENSP00000248929:E304G	E	+	2	0	SGSM3	39132124	1.000000	0.71417	1.000000	0.80357	0.813000	0.45954	5.648000	0.67930	2.129000	0.65627	0.260000	0.18958	GAG		SGSM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321504.2	NM_015705	
PHF21B	112885	hgsc.bcm.edu	37	22	45312408	45312408	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr22:45312408C>T	ENST00000313237.5	-	4	466	c.316G>A	c.(316-318)Gtc>Atc	p.V106I	PHF21B_ENST00000396103.3_Missense_Mutation_p.V106I|PHF21B_ENST00000403565.1_5'UTR|PHF21B_ENST00000404079.2_Missense_Mutation_p.V94I|PHF21B_ENST00000447824.3_Missense_Mutation_p.V94I	NM_138415.4	NP_612424.1	Q96EK2	PF21B_HUMAN	PHD finger protein 21B	106							zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(14)|ovary(2)|prostate(1)|skin(2)	25		all_neural(38;0.00802)|Glioma(61;0.0353)|Ovarian(80;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0203)		GGGTTCTTGACGCTGACCACG	0.697																																																	0			22											43.0	47.0	46.0					22																	45312408		2202	4300	6502	43691072	SO:0001583	missense	112885			AK091480	CCDS14061.1, CCDS56234.1, CCDS63504.1	22q13.31	2013-01-28			ENSG00000056487	ENSG00000056487		"""Zinc fingers, PHD-type"""	25161	protein-coding gene	gene with protein product			"""PHD finger protein 4"""	PHF4		12477932	Standard	NM_138415		Approved	BHC80L, FLJ34161	uc011aql.2	Q96EK2	OTTHUMG00000151199	ENST00000313237.5:c.316G>A	22.37:g.45312408C>T	ENSP00000324403:p.Val106Ile	Somatic		Capture	Illumina HiSeq	Phase_I	43691072	B0QYW3|B0QYW4|B3KRU4|B7Z4F8|Q5TFL2|Q6ICC0	Missense_Mutation	SNP	ENST00000313237.5	37	CCDS14061.1	.	.	.	.	.	.	.	.	.	.	C	3.658	-0.070121	0.07228	.	.	ENSG00000056487	ENST00000313237;ENST00000396103;ENST00000404079;ENST00000447824;ENST00000420689	T;T;T;T;T	0.21932	1.98;1.98;1.98;1.98;1.98	5.21	0.465	0.16711	.	0.325833	0.28718	N	0.014369	T	0.06371	0.0164	N	0.02916	-0.46	0.19575	N	0.999966	B;B;B;B	0.06786	0.0;0.0;0.0;0.001	B;B;B;B	0.04013	0.001;0.001;0.0;0.001	T	0.41805	-0.9488	10	0.02654	T	1	-24.1219	9.6005	0.39601	0.0:0.263:0.0:0.737	.	94;106;94;106	B7Z657;Q96EK2-3;B7Z4F8;Q96EK2	.;.;.;PF21B_HUMAN	I	106;106;94;94;94	ENSP00000324403:V106I;ENSP00000379410:V106I;ENSP00000385105:V94I;ENSP00000388619:V94I;ENSP00000401294:V94I	ENSP00000324403:V106I	V	-	1	0	PHF21B	43691072	1.000000	0.71417	0.959000	0.39883	0.982000	0.71751	1.657000	0.37366	-0.238000	0.09724	-0.982000	0.02568	GTC		PHF21B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321731.2	NM_138415	
MOV10L1	54456	hgsc.bcm.edu	37	22	50538027	50538027	+	Silent	SNP	C	C	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr22:50538027C>T	ENST00000262794.5	+	3	521	c.438C>T	c.(436-438)tgC>tgT	p.C146C	MOV10L1_ENST00000395858.3_Silent_p.C146C|MOV10L1_ENST00000475190.1_3'UTR|MOV10L1_ENST00000545383.1_Silent_p.C146C|MOV10L1_ENST00000540615.1_Silent_p.C126C|MOV10L1_ENST00000395843.1_5'UTR	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	146					ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		AGAGTGTGTGCGAAGGTATGC	0.512																																																	0			22											113.0	94.0	101.0					22																	50538027		2203	4300	6503	48880154	SO:0001819	synonymous_variant	54456			AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"""cardiac helicase activated by MEF2C protein"""	605794	"""Mov10 (mouse)-like 1"", ""Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"""			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.438C>T	22.37:g.50538027C>T		Somatic		Capture	Illumina HiSeq	Phase_I	48880154	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Silent	SNP	ENST00000262794.5	37	CCDS14084.1																																																																																				MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995	
OR4K5	79317	hgsc.bcm.edu	37	14	20389054	20389054	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr14:20389054T>C	ENST00000315915.4	+	1	314	c.289T>C	c.(289-291)Tgc>Cgc	p.C97R		NM_001005483.1	NP_001005483.1	Q8NGD3	OR4K5_HUMAN	olfactory receptor, family 4, subfamily K, member 5	97						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(6)|liver(1)|lung(27)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	47	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TTTCAGTGGCTGCATAGCCCA	0.428																																																	0			14											251.0	268.0	263.0					14																	20389054		2203	4299	6502	19458894	SO:0001583	missense	79317			BK004355	CCDS32024.1	14q11.22	2012-08-09				ENSG00000176281		"""GPCR / Class A : Olfactory receptors"""	14745	protein-coding gene	gene with protein product						14983052	Standard	NM_001005483		Approved		uc010tkw.2	Q8NGD3		ENST00000315915.4:c.289T>C	14.37:g.20389054T>C	ENSP00000319511:p.Cys97Arg	Somatic		Capture	Illumina HiSeq	Phase_I	19458894	Q6IFA7	Missense_Mutation	SNP	ENST00000315915.4	37	CCDS32024.1	.	.	.	.	.	.	.	.	.	.	.	19.61	3.859049	0.71834	.	.	ENSG00000176281	ENST00000315915	T	0.00545	6.67	4.41	4.41	0.53225	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000036	T	0.04363	0.0120	H	0.98256	4.185	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.00420	-1.1750	10	0.87932	D	0	.	11.614	0.51078	0.0:0.0:0.0:1.0	.	97	Q8NGD3	OR4K5_HUMAN	R	97	ENSP00000319511:C97R	ENSP00000319511:C97R	C	+	1	0	OR4K5	19458894	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.152000	0.77419	1.838000	0.53458	0.533000	0.62120	TGC		OR4K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409867.1	NM_001005483	
CHD8	57680	hgsc.bcm.edu	37	14	21870224	21870224	+	Silent	SNP	T	T	C			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr14:21870224T>C	ENST00000557364.1	-	20	4217	c.3954A>G	c.(3952-3954)gaA>gaG	p.E1318E	CHD8_ENST00000555962.1_5'UTR|CHD8_ENST00000430710.3_Silent_p.E1039E|CHD8_ENST00000399982.2_Silent_p.E1318E			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	1318					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|canonical Wnt signaling pathway (GO:0060070)|DNA duplex unwinding (GO:0032508)|in utero embryonic development (GO:0001701)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	MLL1 complex (GO:0071339)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(33)|ovary(6)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	85	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)		CTTCATCATCTTCCTCCATGA	0.388																																																	0			14											142.0	135.0	137.0					14																	21870224		2027	4222	6249	20940064	SO:0001819	synonymous_variant	57680			AB046784	CCDS45081.1, CCDS53885.1	14q11.2	2008-02-05	2004-06-22	2004-06-23		ENSG00000100888			20153	protein-coding gene	gene with protein product		610528	"""helicase with SNF2 domain 1"""	HELSNF1		10997877	Standard	NM_020920		Approved	KIAA1564, DUPLIN	uc001war.2	Q9HCK8		ENST00000557364.1:c.3954A>G	14.37:g.21870224T>C		Somatic		Capture	Illumina HiSeq	Phase_I	20940064	Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Silent	SNP	ENST00000557364.1	37	CCDS53885.1	.	.	.	.	.	.	.	.	.	.	T	6.292	0.422062	0.11928	.	.	ENSG00000100888	ENST00000555935	.	.	.	6.17	5.03	0.67393	.	.	.	.	.	T	0.60183	0.2249	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57694	-0.7767	4	.	.	.	-22.9691	9.2637	0.37627	0.0:0.1448:0.0:0.8552	.	.	.	.	G	544	.	.	R	-	1	2	CHD8	20940064	0.995000	0.38212	1.000000	0.80357	0.999000	0.98932	0.377000	0.20552	1.148000	0.42385	0.533000	0.62120	AGA		CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920	
SLC35F4	341880	hgsc.bcm.edu	37	14	58056021	58056021	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr14:58056021G>A	ENST00000339762.6	-	3	607	c.608C>T	c.(607-609)aCa>aTa	p.T203I	SLC35F4_ENST00000556826.1_Missense_Mutation_p.T167I|SLC35F4_ENST00000554729.1_Missense_Mutation_p.T44I			A4IF30	S35F4_HUMAN	solute carrier family 35, member F4	203					transport (GO:0006810)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|large_intestine(3)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						GTTCCAGTTTGTTGAAAACCA	0.343																																																	0			14											99.0	99.0	99.0					14																	58056021		1845	4089	5934	57125774	SO:0001583	missense	341880					14q22.3	2013-05-22		2003-11-28	ENSG00000151812	ENSG00000151812		"""Solute carriers"""	19845	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 36"""	C14orf36			Standard	NM_001206920		Approved	FLJ37712	uc021rtp.1	A4IF30	OTTHUMG00000171317	ENST00000339762.6:c.608C>T	14.37:g.58056021G>A	ENSP00000342518:p.Thr203Ile	Somatic		Capture	Illumina HiSeq	Phase_I	57125774	A6NDQ3	Missense_Mutation	SNP	ENST00000339762.6	37		.	.	.	.	.	.	.	.	.	.	G	21.0	4.087633	0.76642	.	.	ENSG00000151812	ENST00000556826;ENST00000339762;ENST00000554729	T;T;T	0.54479	0.62;0.57;0.69	5.92	5.92	0.95590	.	0.041863	0.85682	D	0.000000	T	0.73822	0.3636	M	0.74647	2.275	0.80722	D	1	D	0.69078	0.997	D	0.69479	0.964	T	0.73927	-0.3828	10	0.59425	D	0.04	-14.8536	20.3167	0.98654	0.0:0.0:1.0:0.0	.	203	A4IF30	S35F4_HUMAN	I	167;203;44	ENSP00000452086:T167I;ENSP00000342518:T203I;ENSP00000451990:T44I	ENSP00000342518:T203I	T	-	2	0	SLC35F4	57125774	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.058000	0.76676	2.809000	0.96659	0.557000	0.71058	ACA		SLC35F4-201	KNOWN	basic	protein_coding	protein_coding		XM_292260	
ZFYVE26	23503	hgsc.bcm.edu	37	14	68268904	68268904	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr14:68268904G>A	ENST00000347230.4	-	10	1669	c.1531C>T	c.(1531-1533)Ctc>Ttc	p.L511F	ZFYVE26_ENST00000555452.1_Missense_Mutation_p.L511F	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	511					cell death (GO:0008219)|cytokinesis (GO:0000910)|double-strand break repair via homologous recombination (GO:0000724)	centrosome (GO:0005813)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	94				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		TTTACACAGAGGGCATAGATG	0.547																																																	0			14											143.0	128.0	133.0					14																	68268904		2203	4300	6503	67338657	SO:0001583	missense	23503			AB002319	CCDS9788.1	14q23.3	2012-11-23				ENSG00000072121		"""Zinc fingers, FYVE domain containing"""	20761	protein-coding gene	gene with protein product	"""spastizin"", ""FYVE-CENT"""	612012	"""spastic paraplegia 15 (complicated, autosomal recessive)"""	SPG15		9205841, 18394578	Standard	NM_015346		Approved	KIAA0321	uc001xka.2	Q68DK2		ENST00000347230.4:c.1531C>T	14.37:g.68268904G>A	ENSP00000251119:p.Leu511Phe	Somatic		Capture	Illumina HiSeq	Phase_I	67338657	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Missense_Mutation	SNP	ENST00000347230.4	37	CCDS9788.1	.	.	.	.	.	.	.	.	.	.	G	19.25	3.791400	0.70452	.	.	ENSG00000072121	ENST00000347230;ENST00000411699;ENST00000555452	T;T	0.36699	1.4;1.24	5.83	4.93	0.64822	.	0.230823	0.35646	N	0.003061	T	0.48840	0.1522	L	0.60455	1.87	0.43919	D	0.996563	D;D;D	0.63046	0.973;0.992;0.986	P;P;P	0.60068	0.811;0.868;0.741	T	0.45323	-0.9269	10	0.42905	T	0.14	-9.9359	9.6924	0.40136	0.0696:0.0:0.7883:0.142	.	511;511;511	Q68DK2-4;G3V2D8;Q68DK2	.;.;ZFY26_HUMAN	F	511;490;511	ENSP00000251119:L511F;ENSP00000450603:L511F	ENSP00000251119:L511F	L	-	1	0	ZFYVE26	67338657	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	3.505000	0.53356	1.447000	0.47661	-0.182000	0.12963	CTC		ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346	
ADAM20	8748	hgsc.bcm.edu	37	14	70989383	70989383	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr14:70989383A>G	ENST00000256389.3	-	2	2486	c.2242T>C	c.(2242-2244)Tgc>Cgc	p.C748R	RP11-486O13.4_ENST00000556646.1_lincRNA	NM_003814.4	NP_003805.3	O43506	ADA20_HUMAN	ADAM metallopeptidase domain 20	698					binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(1)|skin(2)	27			KIRC - Kidney renal clear cell carcinoma(12;0.133)|Kidney(31;0.188)	all cancers(60;0.00294)|BRCA - Breast invasive adenocarcinoma(234;0.00668)|OV - Ovarian serous cystadenocarcinoma(108;0.0344)		GGAAGAAGGCACAATAGTGAC	0.393																																																	0			14											225.0	188.0	201.0					14																	70989383		2203	4300	6503	70059136	SO:0001583	missense	8748			AF029899	CCDS32111.1	14q24.2	2012-04-30	2005-08-18		ENSG00000134007	ENSG00000134007		"""ADAM metallopeptidase domain containing"""	199	protein-coding gene	gene with protein product		603712	"""a disintegrin and metalloproteinase domain 20"""			9469942	Standard	NM_003814		Approved		uc001xme.3	O43506	OTTHUMG00000167548	ENST00000256389.3:c.2242T>C	14.37:g.70989383A>G	ENSP00000256389:p.Cys748Arg	Somatic		Capture	Illumina HiSeq	Phase_I	70059136	Q6GTZ1|Q9UKJ9	Missense_Mutation	SNP	ENST00000256389.3	37	CCDS32111.1	.	.	.	.	.	.	.	.	.	.	A	8.748	0.920573	0.17982	.	.	ENSG00000134007	ENST00000256389	T	0.00912	5.55	3.66	3.66	0.41972	.	3.514400	0.01092	U	0.005201	T	0.00815	0.0027	N	0.19112	0.55	0.09310	N	0.999994	P	0.36144	0.539	B	0.22880	0.042	T	0.44267	-0.9339	10	0.23891	T	0.37	.	6.584	0.22610	0.7863:0.0:0.0:0.2137	.	698	O43506	ADA20_HUMAN	R	748	ENSP00000256389:C748R	ENSP00000256389:C748R	C	-	1	0	ADAM20	70059136	0.014000	0.17966	0.032000	0.17829	0.066000	0.16364	1.280000	0.33202	1.441000	0.47550	0.477000	0.44152	TGC		ADAM20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395004.2		
SAMD15	161394	hgsc.bcm.edu	37	14	77845074	77845074	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr14:77845074A>G	ENST00000216471.4	+	1	1599	c.1313A>G	c.(1312-1314)gAg>gGg	p.E438G	SAMD15_ENST00000533095.2_Intron|TMED8_ENST00000216468.7_5'Flank	NM_001010860.1	NP_001010860.1	Q9P1V8	SAM15_HUMAN	sterile alpha motif domain containing 15	438										breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						GGAAACGATGAGCTAGAGCAC	0.393																																																	0			14											71.0	68.0	69.0					14																	77845074		2203	4300	6503	76914827	SO:0001583	missense	0			AK093282	CCDS32126.1	14q24.3	2013-01-10	2010-10-20	2010-10-20	ENSG00000100583	ENSG00000100583		"""Sterile alpha motif (SAM) domain containing"""	18631	protein-coding gene	gene with protein product			"""family with sequence similarity 15, member A"", ""chromosome 14 open reading frame 174"""	FAM15A, C14orf174			Standard	XM_006720069		Approved	FLJ35963	uc001xtq.1	Q9P1V8		ENST00000216471.4:c.1313A>G	14.37:g.77845074A>G	ENSP00000216471:p.Glu438Gly	Somatic		Capture	Illumina HiSeq	Phase_I	76914827	Q2M3P3	Missense_Mutation	SNP	ENST00000216471.4	37	CCDS32126.1	.	.	.	.	.	.	.	.	.	.	A	15.24	2.775707	0.49786	.	.	ENSG00000100583	ENST00000216471	T	0.20881	2.04	4.7	3.57	0.40892	.	.	.	.	.	T	0.26846	0.0657	L	0.58810	1.83	0.09310	N	1	P	0.51791	0.948	P	0.48815	0.591	T	0.11591	-1.0581	9	0.62326	D	0.03	0.2598	6.5641	0.22503	0.8928:0.0:0.1072:0.0	.	438	Q9P1V8	SAM15_HUMAN	G	438	ENSP00000216471:E438G	ENSP00000216471:E438G	E	+	2	0	SAMD15	76914827	0.004000	0.15560	0.004000	0.12327	0.004000	0.04260	1.769000	0.38522	0.860000	0.35481	0.454000	0.30748	GAG		SAMD15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394587.2	NM_001010860	
REXO1	57455	hgsc.bcm.edu	37	19	1827578	1827578	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr19:1827578G>A	ENST00000170168.4	-	2	1304	c.1210C>T	c.(1210-1212)Cga>Tga	p.R404*	REXO1_ENST00000587524.1_5'Flank	NM_020695.3	NP_065746.3	Q8N1G1	REXO1_HUMAN	REX1, RNA exonuclease 1 homolog (S. cerevisiae)	404						nucleus (GO:0005634)	exonuclease activity (GO:0004527)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	16		Ovarian(11;1.78e-06)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGCCGCCCTCGGCCCTTGTCC	0.672																																																	0			19											14.0	17.0	16.0					19																	1827578		2194	4273	6467	1778578	SO:0001587	stop_gained	57455			AB032964	CCDS32866.1	19p13.3	2014-05-28	2005-08-22	2005-08-22	ENSG00000079313	ENSG00000079313			24616	protein-coding gene	gene with protein product	"""elongin A binding protein 1"""	609614	"""transcription elongation factor B polypeptide 3 binding protein 1"""	TCEB3BP1		10574461	Standard	NM_020695		Approved	EloA-BP1, KIAA1138	uc002lua.4	Q8N1G1	OTTHUMG00000179991	ENST00000170168.4:c.1210C>T	19.37:g.1827578G>A	ENSP00000170168:p.Arg404*	Somatic		Capture	Illumina HiSeq	Phase_I	1778578	Q9ULT2	Nonsense_Mutation	SNP	ENST00000170168.4	37	CCDS32866.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.080879	0.76528	.	.	ENSG00000079313	ENST00000170168	.	.	.	4.12	1.8	0.24995	.	1.275950	0.05319	N	0.526203	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15066	T	0.55	-1.0924	2.5034	0.04639	0.1731:0.1454:0.5129:0.1685	.	.	.	.	X	404	.	ENSP00000170168:R404X	R	-	1	2	REXO1	1778578	0.000000	0.05858	0.001000	0.08648	0.225000	0.24961	0.552000	0.23376	0.942000	0.37525	-0.273000	0.10243	CGA		REXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449200.1	NM_020695	
TMPRSS9	360200	hgsc.bcm.edu	37	19	2396635	2396635	+	Missense_Mutation	SNP	C	C	T	rs552048658		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr19:2396635C>T	ENST00000332578.3	+	2	241	c.241C>T	c.(241-243)Cgc>Tgc	p.R81C	TMPRSS9_ENST00000592650.1_3'UTR	NM_182973.1	NP_892018.1	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	81					plasminogen activation (GO:0031639)	integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGACTATCACCGCACGCTGAC	0.662													C|||	1	0.000199681	0.0	0.0	5008	,	,		12114	0.001		0.0	False		,,,				2504	0.0																0			19											28.0	24.0	25.0					19																	2396635		2203	4299	6502	2347635	SO:0001583	missense	360200			AJ488946	CCDS12088.1	19p13.3	2010-04-13						"""Serine peptidases / Transmembrane"""	30079	protein-coding gene	gene with protein product	"""polyserase 1"""	610477				12886014	Standard	NM_182973		Approved		uc010xgx.2	Q7Z410		ENST00000332578.3:c.241C>T	19.37:g.2396635C>T	ENSP00000330264:p.Arg81Cys	Somatic		Capture	Illumina HiSeq	Phase_I	2347635	Q6ZND6|Q7Z411	Missense_Mutation	SNP	ENST00000332578.3	37	CCDS12088.1	.	.	.	.	.	.	.	.	.	.	C	15.91	2.971224	0.53614	.	.	ENSG00000178297	ENST00000395264;ENST00000332578	D	0.90788	-2.73	3.98	1.58	0.23477	.	0.119241	0.36932	N	0.002337	D	0.92331	0.7567	M	0.65498	2.005	0.19945	N	0.999941	D;D	0.89917	0.999;1.0	P;D	0.69824	0.826;0.966	D	0.83490	0.0069	10	0.72032	D	0.01	.	5.5525	0.17099	0.194:0.6968:0.0:0.1092	.	81;81	Q7Z410;E7EMP4	TMPS9_HUMAN;.	C	81	ENSP00000330264:R81C	ENSP00000330264:R81C	R	+	1	0	TMPRSS9	2347635	0.003000	0.15002	0.034000	0.17996	0.002000	0.02628	0.065000	0.14466	0.798000	0.33994	-0.266000	0.10368	CGC		TMPRSS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451330.3	NM_182973	
XAB2	56949	hgsc.bcm.edu	37	19	7690922	7690922	+	Missense_Mutation	SNP	G	G	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr19:7690922G>T	ENST00000358368.4	-	6	703	c.666C>A	c.(664-666)caC>caA	p.H222Q	XAB2_ENST00000534844.1_Missense_Mutation_p.H219Q	NM_020196.2	NP_064581.2	Q9HCS7	SYF1_HUMAN	XPA binding protein 2	222					blastocyst development (GO:0001824)|DNA repair (GO:0006281)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	26						CGCACAGCTCGTGCCACAGCT	0.672								Direct reversal of damage;Nucleotide excision repair (NER)																																									0			19											55.0	53.0	54.0					19																	7690922		2203	4300	6503	7596922	SO:0001583	missense	56949			AB026111	CCDS32892.1	19p13.3	2013-08-21				ENSG00000076924			14089	protein-coding gene	gene with protein product	"""SYF1 homolog, RNA splicing factor (S. cerevisiae)"", ""SYF1 pre-mRNA-splicing factor"""	610850				10944529	Standard	NM_020196		Approved	HCNP, HCRN, SYF1, NTC90	uc002mgx.3	Q9HCS7		ENST00000358368.4:c.666C>A	19.37:g.7690922G>T	ENSP00000351137:p.His222Gln	Somatic		Capture	Illumina HiSeq	Phase_I	7596922	Q8TET6|Q96HB0|Q96IW0|Q9NRG6|Q9ULP3	Missense_Mutation	SNP	ENST00000358368.4	37	CCDS32892.1	.	.	.	.	.	.	.	.	.	.	G	10.26	1.301505	0.23736	.	.	ENSG00000076924	ENST00000358368;ENST00000534844	T;T	0.62498	0.02;0.02	4.61	-1.35	0.09114	.	0.065141	0.64402	D	0.000012	T	0.30324	0.0761	N	0.03608	-0.345	0.44956	D	0.997971	B	0.09022	0.002	B	0.09377	0.004	T	0.02202	-1.1196	10	0.25751	T	0.34	-45.9916	7.5803	0.27961	0.6209:0.0:0.3791:0.0	.	222	Q9HCS7	SYF1_HUMAN	Q	222;219	ENSP00000351137:H222Q;ENSP00000438225:H219Q	ENSP00000351137:H222Q	H	-	3	2	XAB2	7596922	0.177000	0.23109	0.997000	0.53966	0.968000	0.65278	-0.545000	0.06069	-0.024000	0.13941	-0.266000	0.10368	CAC		XAB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461021.1	NM_020196	
ZNF490	57474	hgsc.bcm.edu	37	19	12691348	12691348	+	Nonsense_Mutation	SNP	G	G	C			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr19:12691348G>C	ENST00000311437.6	-	5	1663	c.1541C>G	c.(1540-1542)tCa>tGa	p.S514*	CTD-2192J16.20_ENST00000593682.1_Missense_Mutation_p.Q148E|ZNF490_ENST00000465656.1_5'Flank	NM_020714.2	NP_065765.1	Q9ULM2	ZN490_HUMAN	zinc finger protein 490	514					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	18						CAAAGACTTTGAGTAACTGAA	0.383																																																	0			19											181.0	162.0	168.0					19																	12691348		2203	4300	6503	12552348	SO:0001587	stop_gained	57474			AB033024	CCDS12272.1	19p13.2	2013-01-08			ENSG00000188033	ENSG00000188033		"""Zinc fingers, C2H2-type"", ""-"""	23705	protein-coding gene	gene with protein product							Standard	NM_020714		Approved	KIAA1198	uc002mtz.2	Q9ULM2	OTTHUMG00000156398	ENST00000311437.6:c.1541C>G	19.37:g.12691348G>C	ENSP00000311521:p.Ser514*	Somatic		Capture	Illumina HiSeq	Phase_I	12552348		Nonsense_Mutation	SNP	ENST00000311437.6	37	CCDS12272.1	.	.	.	.	.	.	.	.	.	.	G	14.57	2.575083	0.45902	.	.	ENSG00000188033	ENST00000311437	.	.	.	0.832	-1.35	0.09114	.	.	.	.	.	.	.	.	.	.	.	0.29708	N	0.839658	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	.	3.9343	0.09299	0.4162:0.0:0.5838:0.0	.	.	.	.	X	514	.	ENSP00000311521:S514X	S	-	2	0	ZNF490	12552348	0.000000	0.05858	0.000000	0.03702	0.053000	0.15095	-0.549000	0.06041	-0.512000	0.06505	0.313000	0.20887	TCA		ZNF490-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344073.1	NM_020714	
AKAP8	10270	hgsc.bcm.edu	37	19	15469828	15469828	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr19:15469828T>C	ENST00000269701.2	-	13	1633	c.1573A>G	c.(1573-1575)Agt>Ggt	p.S525G		NM_005858.3	NP_005849.1	O43823	AKAP8_HUMAN	A kinase (PRKA) anchor protein 8	525					mitotic chromosome condensation (GO:0007076)|mitotic nuclear division (GO:0007067)|signal transduction (GO:0007165)	condensed chromosome (GO:0000793)|female pronucleus (GO:0001939)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)	26						TTCAAAACACTCTTAGCCACA	0.403																																					GBM(190;1671 2163 3274 27186 30476)												0			19											161.0	145.0	150.0					19																	15469828		2203	4300	6503	15330828	SO:0001583	missense	10270			Y11997	CCDS12329.1	19p13.12	2012-05-16			ENSG00000105127	ENSG00000105127		"""A-kinase anchor proteins"""	378	protein-coding gene	gene with protein product	"""A-kinase anchor protein, 95kDa"""	604692				9473338	Standard	NM_005858		Approved	AKAP95, DKFZp586B1222	uc002nav.3	O43823		ENST00000269701.2:c.1573A>G	19.37:g.15469828T>C	ENSP00000269701:p.Ser525Gly	Somatic		Capture	Illumina HiSeq	Phase_I	15330828		Missense_Mutation	SNP	ENST00000269701.2	37	CCDS12329.1	.	.	.	.	.	.	.	.	.	.	T	19.72	3.879773	0.72294	.	.	ENSG00000105127	ENST00000269701	T	0.50813	0.73	5.84	5.84	0.93424	.	0.000000	0.64402	D	0.000015	T	0.51143	0.1657	L	0.47190	1.495	0.80722	D	1	P	0.52842	0.956	P	0.49799	0.622	T	0.54820	-0.8236	10	0.72032	D	0.01	-25.2211	13.7399	0.62840	0.0:0.0:0.0:1.0	.	525	O43823	AKAP8_HUMAN	G	525	ENSP00000269701:S525G	ENSP00000269701:S525G	S	-	1	0	AKAP8	15330828	1.000000	0.71417	1.000000	0.80357	0.620000	0.37586	6.284000	0.72652	2.234000	0.73211	0.460000	0.39030	AGT		AKAP8-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461293.3	NM_005858	
ZNF253	56242	hgsc.bcm.edu	37	19	20002521	20002521	+	Silent	SNP	G	G	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr19:20002521G>A	ENST00000589717.1	+	4	557	c.465G>A	c.(463-465)aaG>aaA	p.K155K	AC011477.1_ENST00000578823.1_RNA|ZNF253_ENST00000355650.4_Silent_p.K79K|CTC-559E9.8_ENST00000585571.1_RNA	NM_021047.2	NP_066385.2	O75346	ZN253_HUMAN	zinc finger protein 253	155					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TCTTTCATAAGTTTTCAAATT	0.308																																																	0			19											43.0	45.0	44.0					19																	20002521		2058	4240	6298	19863521	SO:0001819	synonymous_variant	56242			AF038951	CCDS42532.1	19p12	2014-02-12	2003-12-17		ENSG00000256771	ENSG00000256771		"""Zinc fingers, C2H2-type"", ""-"""	13497	protein-coding gene	gene with protein product		606954	"""zinc finger protein 411"""	ZNF411		10585455	Standard	NM_021047		Approved	BMZF-1, FLJ90391	uc002noj.3	O75346	OTTHUMG00000182369	ENST00000589717.1:c.465G>A	19.37:g.20002521G>A		Somatic		Capture	Illumina HiSeq	Phase_I	19863521	A4FVA7|Q0P6G3|Q6P0L2|Q8NCA3|Q8NCF9	Silent	SNP	ENST00000589717.1	37	CCDS42532.1																																																																																				ZNF253-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460802.1	NM_021047	
ZNF626	199777	hgsc.bcm.edu	37	19	20807776	20807776	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr19:20807776G>A	ENST00000601440.1	-	4	1053	c.907C>T	c.(907-909)Cat>Tat	p.H303Y	CTC-513N18.7_ENST00000595094.1_lincRNA	NM_001076675.2	NP_001070143.1	Q68DY1	ZN626_HUMAN	zinc finger protein 626	303					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|lung(3)|skin(1)	6						ATTATCTTATGTGTAGTAAGG	0.368																																																	0			19											85.0	94.0	91.0					19																	20807776		2180	4288	6468	20599616	SO:0001583	missense	199777			BC007116	CCDS32976.1, CCDS42535.1	19p13.11	2013-01-08				ENSG00000188171		"""Zinc fingers, C2H2-type"", ""-"""	30461	protein-coding gene	gene with protein product						12477932	Standard	NM_145297		Approved		uc002npb.1	Q68DY1		ENST00000601440.1:c.907C>T	19.37:g.20807776G>A	ENSP00000469958:p.His303Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	20599616	Q8N8T4|Q96QM1	Missense_Mutation	SNP	ENST00000601440.1	37	CCDS42535.1	.	.	.	.	.	.	.	.	.	.	N	11.32	1.604238	0.28534	.	.	ENSG00000188171	ENST00000392298;ENST00000453075;ENST00000305570	T	0.67523	-0.27	0.865	0.865	0.19074	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.83825	0.5338	H	0.95884	3.735	0.80722	D	1	D	0.69078	0.997	D	0.72982	0.979	T	0.82184	-0.0583	9	0.72032	D	0.01	.	7.1124	0.25399	0.0:0.0:1.0:0.0	.	303	Q68DY1	ZN626_HUMAN	Y	303;227;303	ENSP00000445201:H303Y	ENSP00000445201:H303Y	H	-	1	0	ZNF626	20599616	1.000000	0.71417	0.306000	0.25113	0.305000	0.27757	6.564000	0.73969	0.277000	0.22141	0.282000	0.19409	CAT		ZNF626-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447845.2	NM_145297	
TMEM91	641649	hgsc.bcm.edu	37	19	41884236	41884236	+	Missense_Mutation	SNP	G	G	C	rs192256295		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr19:41884236G>C	ENST00000392002.2	+	2	682	c.22G>C	c.(22-24)Gag>Cag	p.E8Q	TMEM91_ENST00000544232.1_Missense_Mutation_p.E8Q|TMEM91_ENST00000413014.2_Missense_Mutation_p.E8Q|TMEM91_ENST00000436170.2_Missense_Mutation_p.E8Q|TMEM91_ENST00000604123.1_Missense_Mutation_p.E65Q|CTC-435M10.3_ENST00000604424.1_Intron|BCKDHA_ENST00000595085.1_Missense_Mutation_p.E8Q|TMEM91_ENST00000447302.2_Missense_Mutation_p.E8Q|TMEM91_ENST00000542945.1_Missense_Mutation_p.E8Q|CTC-435M10.3_ENST00000540732.1_Missense_Mutation_p.E8Q|TMEM91_ENST00000539627.1_Missense_Mutation_p.E8Q|TMEM91_ENST00000356385.4_Missense_Mutation_p.E8Q	NM_001098821.1	NP_001092291.1	Q6ZNR0	TMM91_HUMAN	transmembrane protein 91	8					hematopoietic progenitor cell differentiation (GO:0002244)|response to biotic stimulus (GO:0009607)	integral component of membrane (GO:0016021)				lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	5						TAGTCTTCGTGAGCTTCAACA	0.547																																																	0			19											67.0	66.0	67.0					19																	41884236		1881	4116	5997	46576076	SO:0001583	missense	641649			AK130820, BC063705	CCDS42571.1, CCDS42572.1, CCDS46082.1, CCDS46083.1, CCDS46084.1	19q13.2	2009-10-16							32393	protein-coding gene	gene with protein product	"""interferon induced transmembrane protein domain containing 6"""					12477932	Standard	NM_001098824		Approved	FLJ27310, IFITMD6		Q6ZNR0		ENST00000392002.2:c.22G>C	19.37:g.41884236G>C	ENSP00000375859:p.Glu8Gln	Somatic		Capture	Illumina HiSeq	Phase_I	46576076	C9J9D1|C9JZ62|C9K046|Q6P434	Missense_Mutation	SNP	ENST00000392002.2	37	CCDS42571.1	.	.	.	.	.	.	.	.	.	.	G	14.09	2.432733	0.43224	.	.	ENSG00000142046;ENSG00000142046;ENSG00000142046;ENSG00000142046;ENSG00000142046;ENSG00000142046;ENSG00000142046;ENSG00000142046;ENSG00000142046;ENSG00000142046;ENSG00000255730	ENST00000539627;ENST00000413014;ENST00000392002;ENST00000436170;ENST00000447302;ENST00000544232;ENST00000542945;ENST00000537354;ENST00000342187;ENST00000356385;ENST00000540732	D;D	0.99113	-4.33;-5.44	4.44	4.44	0.53790	.	0.000000	0.39759	N	0.001274	D	0.97108	0.9055	L	0.27053	0.805	0.09310	N	1	P;P;P;P;B;P;P	0.52061	0.917;0.917;0.917;0.917;0.13;0.629;0.95	B;B;B;B;B;B;P	0.46718	0.401;0.401;0.326;0.401;0.102;0.137;0.525	D	0.93403	0.6762	10	0.56958	D	0.05	.	12.7892	0.57523	0.0:0.0:1.0:0.0	.	8;8;8;8;8;8;8	C9J9D1;C9JZ62;C9K046;Q6P434;F5H5P2;Q6ZNR0;F5GWC9	.;.;.;.;.;TMM91_HUMAN;.	Q	8	ENSP00000375859:E8Q;ENSP00000443246:E8Q	ENSP00000443246:E8Q	E	+	1	0	CTC-435M10.3;TMEM91	46576076	0.553000	0.26513	0.270000	0.24601	0.242000	0.25591	3.821000	0.55700	2.488000	0.83962	0.561000	0.74099	GAG		TMEM91-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398302.2		
BCL3	602	hgsc.bcm.edu	37	19	45262731	45262731	+	Silent	SNP	C	C	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr19:45262731C>A	ENST00000164227.5	+	9	1468	c.1224C>A	c.(1222-1224)ccC>ccA	p.P408P		NM_005178.4	NP_005169.2	P20749	BCL3_HUMAN	B-cell CLL/lymphoma 3	408	Pro/Ser-rich.				antimicrobial humoral response (GO:0019730)|cellular response to DNA damage stimulus (GO:0006974)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|extracellular matrix organization (GO:0030198)|follicular dendritic cell differentiation (GO:0002268)|germinal center formation (GO:0002467)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of protein location in nucleus (GO:0051457)|marginal zone B cell differentiation (GO:0002315)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-8 biosynthetic process (GO:0045415)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 biosynthetic process (GO:0045082)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|protein import into nucleus, translocation (GO:0000060)|regulation of apoptotic process (GO:0042981)|regulation of DNA binding (GO:0051101)|regulation of NF-kappaB import into nucleus (GO:0042345)|response to UV-C (GO:0010225)|response to virus (GO:0009615)|spleen development (GO:0048536)|T-helper 1 type immune response (GO:0042088)|T-helper 2 cell differentiation (GO:0045064)|transcription, DNA-templated (GO:0006351)	Bcl3-Bcl10 complex (GO:0032996)|Bcl3/NF-kappaB2 complex (GO:0033257)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			kidney(1)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10	Lung NSC(12;0.000698)|all_lung(12;0.002)	Ovarian(192;0.0728)				AGTCTCCCCCCAGGGACCCCC	0.627			T	IGH@	CLL																																			Dom	yes		19	19q13	602	B-cell CLL/lymphoma 3		L	0			19											190.0	205.0	200.0					19																	45262731		2203	4300	6503	49954571	SO:0001819	synonymous_variant	602			M31732	CCDS12642.2	19q13.1-q13.2	2013-01-10			ENSG00000069399	ENSG00000069399		"""Ankyrin repeat domain containing"""	998	protein-coding gene	gene with protein product	"""B-cell lymphoma 3-encoded protein"", ""B-cell leukemia/lymphoma 3"", ""chronic lymphatic leukemia protein"""	109560		D19S37, BCL4		1501714, 2180580	Standard	NM_005178		Approved		uc010xxe.2	P20749	OTTHUMG00000151517	ENST00000164227.5:c.1224C>A	19.37:g.45262731C>A		Somatic		Capture	Illumina HiSeq	Phase_I	49954571		Silent	SNP	ENST00000164227.5	37	CCDS12642.2																																																																																				BCL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322976.1	NM_005178	
GRIN2D	2906	hgsc.bcm.edu	37	19	48922494	48922494	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr19:48922494C>T	ENST00000263269.3	+	8	1827	c.1739C>T	c.(1738-1740)cCc>cTc	p.P580L		NM_000836.2	NP_000827.2	O15399	NMDE4_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2D	580					adult locomotory behavior (GO:0008344)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|regulation of sensory perception of pain (GO:0051930)|signal transduction (GO:0007165)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)			autonomic_ganglia(1)|breast(6)|endometrium(2)|large_intestine(9)|lung(12)|ovary(5)|pancreas(1)|prostate(1)	37		all_epithelial(76;1.11e-06)|all_lung(116;5.79e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		all cancers(93;0.00014)|OV - Ovarian serous cystadenocarcinoma(262;0.000233)|Epithelial(262;0.0112)|GBM - Glioblastoma multiforme(486;0.0161)	Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	TCCCCAGAGCCCTACAGCCCC	0.577																																																	0			19											121.0	85.0	97.0					19																	48922494		2203	4300	6503	53614306	SO:0001583	missense	2906			U77783	CCDS12719.1	19q13.33	2012-08-29			ENSG00000105464	ENSG00000105464		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4588	protein-coding gene	gene with protein product	"""N-methyl-d-aspartate receptor subunit 2D"""	602717		NMDAR2D		9480759, 9418891	Standard	NM_000836		Approved	GluN2D, EB11, NR2D	uc002pjc.4	O15399		ENST00000263269.3:c.1739C>T	19.37:g.48922494C>T	ENSP00000263269:p.Pro580Leu	Somatic		Capture	Illumina HiSeq	Phase_I	53614306		Missense_Mutation	SNP	ENST00000263269.3	37	CCDS12719.1	.	.	.	.	.	.	.	.	.	.	C	29.4	4.999137	0.93227	.	.	ENSG00000105464	ENST00000263269	T	0.56941	0.43	4.33	4.33	0.51752	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (1);	0.000000	0.85682	D	0.000000	T	0.79305	0.4423	M	0.93241	3.395	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85509	0.1196	10	0.87932	D	0	.	16.1361	0.81490	0.0:1.0:0.0:0.0	.	580	O15399	NMDE4_HUMAN	L	580	ENSP00000263269:P580L	ENSP00000263269:P580L	P	+	2	0	GRIN2D	53614306	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.605000	0.82844	2.421000	0.82119	0.655000	0.94253	CCC		GRIN2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466121.1		
ZNF547	284306	hgsc.bcm.edu	37	19	57889115	57889115	+	Silent	SNP	A	A	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr19:57889115A>G	ENST00000282282.3	+	4	921	c.771A>G	c.(769-771)acA>acG	p.T257T	AC003002.4_ENST00000597658.1_Intron	NM_173631.2	NP_775902.2	Q8IVP9	ZN547_HUMAN	zinc finger protein 547	257					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	12		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		CACTCATTACACATCAGAGGG	0.433																																																	0			19											125.0	114.0	118.0					19																	57889115		2203	4300	6503	62580927	SO:0001819	synonymous_variant	284306			AK055662	CCDS33131.1	19q13.43	2013-01-08				ENSG00000152433		"""Zinc fingers, C2H2-type"", ""-"""	26432	protein-coding gene	gene with protein product							Standard	NM_173631		Approved	FLJ31100	uc002qol.3	Q8IVP9		ENST00000282282.3:c.771A>G	19.37:g.57889115A>G		Somatic		Capture	Illumina HiSeq	Phase_I	62580927	A8K5Z9|Q96NC4	Silent	SNP	ENST00000282282.3	37	CCDS33131.1																																																																																				ZNF547-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465787.1	NM_173631	
ZNF134	7693	hgsc.bcm.edu	37	19	58131715	58131715	+	Silent	SNP	A	A	G	rs373945795		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr19:58131715A>G	ENST00000396161.5	+	3	538	c.228A>G	c.(226-228)aaA>aaG	p.K76K	ZNF134_ENST00000597975.1_3'UTR	NM_003435.3	NP_003426.3	P52741	ZN134_HUMAN	zinc finger protein 134	76					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(3)|prostate(1)	11		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0265)		ATGGACTGAAACTTCACACAT	0.478																																																	0			19						A		1,4087		0,1,2043	103.0	100.0	101.0		228	1.8	0.0	19		101	0,8446		0,0,4223	no	coding-synonymous	ZNF134	NM_003435.3		0,1,6266	GG,GA,AA		0.0,0.0245,0.0080		76/428	58131715	1,12533	2044	4223	6267	62823527	SO:0001819	synonymous_variant	7693			U09412	CCDS42638.1	19q13.4	2013-01-08	2006-06-13			ENSG00000213762		"""Zinc fingers, C2H2-type"""	12918	protein-coding gene	gene with protein product		604076	"""zinc finger protein 134 (clone pHZ-15)"""			7557990	Standard	NM_003435		Approved	pHZ-15	uc002qpn.2	P52741		ENST00000396161.5:c.228A>G	19.37:g.58131715A>G		Somatic		Capture	Illumina HiSeq	Phase_I	62823527	Q9Y4B2	Silent	SNP	ENST00000396161.5	37	CCDS42638.1																																																																																				ZNF134-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466808.1	NM_003435	
ADRA1A	148	hgsc.bcm.edu	37	8	26722324	26722324	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr8:26722324G>A	ENST00000519229.1	-	1	169	c.163C>T	c.(163-165)Cga>Tga	p.R55*	ADRA1A_ENST00000380582.3_Nonsense_Mutation_p.R55*|ADRA1A_ENST00000354550.4_Nonsense_Mutation_p.R55*|ADRA1A_ENST00000380573.3_Nonsense_Mutation_p.R55*|ADRA1A_ENST00000276393.4_Nonsense_Mutation_p.R55*|ADRA1A_ENST00000380581.2_Nonsense_Mutation_p.R55*|ADRA1A_ENST00000380587.1_Nonsense_Mutation_p.R55*|ADRA1A_ENST00000380586.1_Nonsense_Mutation_p.R55*|ADRA1A_ENST00000380572.3_Nonsense_Mutation_p.R55*|ADRA1A_ENST00000358857.5_Nonsense_Mutation_p.R55*			P25100	ADA1D_HUMAN	adrenoceptor alpha 1A	125				MTFRDLLSVSFEGPRPDSSAGGSSAGGGGGSAGGAAPSEGP AVGGVPGGAGGGGGVVGAGSGEDNRSSAGEPGSAGAGGDVN G -> MAAALRSVMMAGYLSEWRTPTYRSTEMVQRLRMEAV QHSTS (in Ref. 1). {ECO:0000305}.	adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|DNA metabolic process (GO:0006259)|G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)|negative regulation of the force of heart contraction involved in baroreceptor response to increased systemic arterial blood pressure (GO:0001986)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|positive regulation of cell proliferation (GO:0008284)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alpha1-adrenergic receptor activity (GO:0004937)			breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(17)|ovary(1)|prostate(1)|skin(1)	36		all_cancers(63;0.122)|Ovarian(32;2.61e-05)|all_epithelial(46;0.118)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;4.92e-10)|Colorectal(74;0.0132)|READ - Rectum adenocarcinoma(644;0.115)	Alfuzosin(DB00346)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Dapiprazole(DB00298)|Desipramine(DB01151)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|Labetalol(DB00598)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Mianserin(DB06148)|Midodrine(DB00211)|Mirtazapine(DB00370)|Nicardipine(DB00622)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Oxymetazoline(DB00935)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Phenylephrine(DB00388)|Prazosin(DB00457)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Sertindole(DB06144)|Silodosin(DB06207)|Tamsulosin(DB00706)|Terazosin(DB01162)|Xylometazoline(DB06694)	TGCAGGTGTCGGTGACAGGCT	0.587																																																	0			8											255.0	266.0	262.0					8																	26722324		2203	4300	6503	26778241	SO:0001587	stop_gained	148			L31774	CCDS6052.1, CCDS6053.1, CCDS6054.1, CCDS34869.1	8p21.2	2012-08-08	2012-05-09		ENSG00000120907	ENSG00000120907		"""GPCR / Class A : Adrenoceptors : alpha"""	277	protein-coding gene	gene with protein product		104221	"""adrenergic, alpha-1A-, receptor"""	ADRA1C			Standard	NM_033303		Approved	ADRA1L1	uc003xfh.1	P35348	OTTHUMG00000099459	ENST00000519229.1:c.163C>T	8.37:g.26722324G>A	ENSP00000430793:p.Arg55*	Somatic		Capture	Illumina HiSeq	Phase_I	26778241	Q9NPY0	Nonsense_Mutation	SNP	ENST00000519229.1	37		.	.	.	.	.	.	.	.	.	.	G	40	8.009688	0.98607	.	.	ENSG00000120907	ENST00000380586;ENST00000380587;ENST00000380582;ENST00000380581;ENST00000519229;ENST00000354550;ENST00000276393;ENST00000380573;ENST00000380572;ENST00000358857	.	.	.	4.83	4.83	0.62350	.	0.067670	0.64402	D	0.000012	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.9988	0.58664	0.0:0.0:0.7953:0.2047	.	.	.	.	X	55	.	ENSP00000276393:R55X	R	-	1	2	ADRA1A	26778241	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	2.116000	0.41930	2.365000	0.80145	0.563000	0.77884	CGA		ADRA1A-009	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000376207.1	NM_033303	
PNOC	5368	hgsc.bcm.edu	37	8	28186709	28186709	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr8:28186709G>A	ENST00000301908.3	+	2	243	c.35G>A	c.(34-36)aGt>aAt	p.S12N	RP11-380I10.4_ENST00000521731.1_RNA	NM_006228.3	NP_006219.1	Q13519	PNOC_HUMAN	prepronociceptin	12					neuropeptide signaling pathway (GO:0007218)|sensory perception (GO:0007600)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	extracellular region (GO:0005576)	neuropeptide hormone activity (GO:0005184)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)	5		Ovarian(32;0.000953)		KIRC - Kidney renal clear cell carcinoma(542;0.104)|Kidney(114;0.125)|Colorectal(74;0.145)|BRCA - Breast invasive adenocarcinoma(99;0.245)		CTGCTGCTCAGTCTCTTCTCC	0.552																																																	0			8											164.0	137.0	146.0					8																	28186709		2203	4300	6503	28242628	SO:0001583	missense	5368				CCDS6066.1, CCDS64862.1	8p21	2013-02-26			ENSG00000168081	ENSG00000168081		"""Endogenous ligands"""	9163	protein-coding gene	gene with protein product	"""nocistatin"""	601459				8710928, 10101606	Standard	XM_005273532		Approved	PPNOC	uc003xgp.3	Q13519	OTTHUMG00000102125	ENST00000301908.3:c.35G>A	8.37:g.28186709G>A	ENSP00000301908:p.Ser12Asn	Somatic		Capture	Illumina HiSeq	Phase_I	28242628	B7Z749|Q6FH16	Missense_Mutation	SNP	ENST00000301908.3	37	CCDS6066.1	.	.	.	.	.	.	.	.	.	.	G	16.13	3.036041	0.54896	.	.	ENSG00000168081	ENST00000518479;ENST00000301908	T;T	0.78364	0.74;-1.17	4.57	4.57	0.56435	.	0.307857	0.34245	N	0.004121	T	0.72277	0.3440	L	0.54323	1.7	0.80722	D	1	P	0.45044	0.849	B	0.39617	0.305	T	0.76495	-0.2938	10	0.56958	D	0.05	-14.4077	13.025	0.58810	0.0:0.0:1.0:0.0	.	12	Q13519	PNOC_HUMAN	N	12	ENSP00000428059:S12N;ENSP00000301908:S12N	ENSP00000301908:S12N	S	+	2	0	PNOC	28242628	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	2.977000	0.49297	2.526000	0.85167	0.491000	0.48974	AGT		PNOC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219964.2	NM_006228	
PLAG1	5324	hgsc.bcm.edu	37	8	57079860	57079860	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr8:57079860C>T	ENST00000316981.3	-	5	924	c.445G>A	c.(445-447)Gac>Aac	p.D149N	PLAG1_ENST00000423799.2_Missense_Mutation_p.D67N|PLAG1_ENST00000429357.2_Missense_Mutation_p.D149N	NM_001114634.1|NM_002655.2	NP_001108106.1|NP_002646.2	Q6DJT9	PLAG1_HUMAN	pleiomorphic adenoma gene 1	149	Decreased nuclear import with localization in the nucleus but also in the cytoplasm.				gland morphogenesis (GO:0022612)|multicellular organism growth (GO:0035264)|negative regulation of gene expression (GO:0010629)|organ growth (GO:0035265)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland growth (GO:0060736)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)		CTNNB1/PLAG1(60)|LIFR_ENST00000263409/PLAG1(10)|HAS2/PLAG1(10)|FGFR1_ENST00000447712/PLAG1(28)|COL1A2/PLAG1(3)|CHCHD7/PLAG1(12)|TCEA1_ENST00000521604/PLAG1(3)	breast(3)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(7)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28		all_lung(136;0.0548)|Lung NSC(129;0.0718)|all_epithelial(80;0.125)	Epithelial(17;0.00179)|all cancers(17;0.0125)			CAGGTGAGGTCACCACTTGTT	0.463			T	"""TCEA1, LIFR, CTNNB1, CHCHD7"""	salivary adenoma																																			Dom	yes		8	8q12	5324	pleiomorphic adenoma gene 1		E	0			8											117.0	90.0	99.0					8																	57079860		2203	4300	6503	57242414	SO:0001583	missense	5324			U65002	CCDS6165.1, CCDS47860.1	8q12	2010-07-30				ENSG00000181690		"""Zinc fingers, C2H2-type"""	9045	protein-coding gene	gene with protein product		603026				9268638	Standard	NM_002655		Approved	ZNF912	uc010lyi.3	Q6DJT9		ENST00000316981.3:c.445G>A	8.37:g.57079860C>T	ENSP00000325546:p.Asp149Asn	Somatic		Capture	Illumina HiSeq	Phase_I	57242414	B4DLC2|Q59GH8|Q9Y4L2	Missense_Mutation	SNP	ENST00000316981.3	37	CCDS6165.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.477940	0.84747	.	.	ENSG00000181690	ENST00000316981;ENST00000423799;ENST00000429357	T;T;T	0.27557	1.66;3.39;1.66	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.42585	0.1209	N	0.17564	0.495	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.40327	-0.9569	10	0.46703	T	0.11	-22.9455	19.5003	0.95091	0.0:1.0:0.0:0.0	.	149	Q6DJT9	PLAG1_HUMAN	N	149;67;149	ENSP00000325546:D149N;ENSP00000404067:D67N;ENSP00000416537:D149N	ENSP00000325546:D149N	D	-	1	0	PLAG1	57242414	1.000000	0.71417	0.993000	0.49108	0.984000	0.73092	7.818000	0.86416	2.594000	0.87642	0.585000	0.79938	GAC		PLAG1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378212.1	NM_002655	
GGH	8836	hgsc.bcm.edu	37	8	63951237	63951237	+	Missense_Mutation	SNP	C	C	T	rs11545077	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr8:63951237C>T	ENST00000260118.6	-	1	493	c.91G>A	c.(91-93)Gcc>Acc	p.A31T		NM_003878.2	NP_003869.1	Q92820	GGH_HUMAN	gamma-glutamyl hydrolase (conjugase, folylpolygammaglutamyl hydrolase)	31	Gamma-glutamyl hydrolase. {ECO:0000255|PROSITE-ProRule:PRU00607}.		A -> T (in dbSNP:rs11545077).		glutamine metabolic process (GO:0006541)|proteolysis (GO:0006508)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to insulin (GO:0032868)|response to zinc ion (GO:0010043)	cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	exopeptidase activity (GO:0008238)|gamma-glutamyl-peptidase activity (GO:0034722)|omega peptidase activity (GO:0008242)			breast(1)|kidney(1)|large_intestine(1)|liver(1)|lung(6)|stomach(1)	11	Breast(64;0.0716)	all_cancers(86;0.189)|Lung NSC(129;0.0324)|all_lung(136;0.0593)|all_epithelial(80;0.131)			Folic Acid(DB00158)|Methotrexate(DB00563)	GGCTTCTTGGCGGTGTCGCCG	0.726													C|||	1005	0.200679	0.1051	0.2046	5008	,	,		11929	0.2183		0.2505	False		,,,				2504	0.2577																0			8						C	THR/ALA	573,3819		35,503,1658	15.0	15.0	15.0		91	-8.0	0.0	8	dbSNP_120	15	2151,6439		264,1623,2408	yes	missense	GGH	NM_003878.2	58	299,2126,4066	TT,TC,CC		25.0407,13.0464,20.9829	benign	31/319	63951237	2724,10258	2196	4295	6491	64113791	SO:0001583	missense	8836			U55206	CCDS6177.1	8q12.3	2008-02-05			ENSG00000137563	ENSG00000137563	3.4.19.9		4248	protein-coding gene	gene with protein product		601509				8816764, 10570974	Standard	NM_003878		Approved		uc003xuw.3	Q92820	OTTHUMG00000164365	ENST00000260118.6:c.91G>A	8.37:g.63951237C>T	ENSP00000260118:p.Ala31Thr	Somatic		Capture	Illumina HiSeq	Phase_I	64113791		Missense_Mutation	SNP	ENST00000260118.6	37	CCDS6177.1	443	0.20283882783882784	46	0.09349593495934959	74	0.20441988950276244	127	0.22202797202797203	196	0.25857519788918204	C	8.288	0.817065	0.16607	0.130464	0.250407	ENSG00000137563	ENST00000260118	T	0.21543	2.0	4.08	-7.97	0.01139	.	0.792035	0.11203	N	0.588636	T	0.00012	0.0000	N	0.04090	-0.28	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.39921	-0.9590	9	0.26408	T	0.33	-13.8596	0.7201	0.00939	0.2962:0.13:0.3164:0.2574	rs11545077;rs13270305;rs58961784;rs13270305	31	Q92820	GGH_HUMAN	T	31	ENSP00000260118:A31T	ENSP00000260118:A31T	A	-	1	0	GGH	64113791	0.000000	0.05858	0.000000	0.03702	0.653000	0.38743	-1.288000	0.02783	-1.754000	0.01321	0.313000	0.20887	GCC		GGH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378453.1		
LRRCC1	85444	hgsc.bcm.edu	37	8	86035726	86035726	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr8:86035726T>C	ENST00000360375.3	+	7	1158	c.1009T>C	c.(1009-1011)Tat>Cat	p.Y337H	LRRCC1_ENST00000414626.2_Missense_Mutation_p.Y317H	NM_033402.4	NP_208325.3	Q9C099	LRCC1_HUMAN	leucine rich repeat and coiled-coil centrosomal protein 1	337					mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(4)|kidney(9)|large_intestine(7)|lung(16)|skin(1)|upper_aerodigestive_tract(2)	43						TGAAAGTGACTATGGAAACAG	0.323																																																	0			8											81.0	81.0	81.0					8																	86035726		1806	4071	5877	86222978	SO:0001583	missense	85444			BC030701	CCDS43750.1	8q21.2	2012-04-10	2012-04-10		ENSG00000133739	ENSG00000133739			29373	protein-coding gene	gene with protein product	"""centrosomal leucine-rich repeat and coiled-coil containing protein"", ""variable number of flagella 1 homolog (Chlamydomonas)"""		"""leucine rich repeat and coiled-coil domain containing 1"""			11214970, 18728398	Standard	NM_033402		Approved	KIAA1764, CLERC, VFL1	uc003ycw.3	Q9C099	OTTHUMG00000164784	ENST00000360375.3:c.1009T>C	8.37:g.86035726T>C	ENSP00000353538:p.Tyr337His	Somatic		Capture	Illumina HiSeq	Phase_I	86222978	B4DYX6|B5RI11|Q8N768|Q96DK7|Q96N01	Missense_Mutation	SNP	ENST00000360375.3	37	CCDS43750.1	.	.	.	.	.	.	.	.	.	.	T	8.252	0.809206	0.16537	.	.	ENSG00000133739	ENST00000426019;ENST00000360375;ENST00000414626	T;T	0.31769	1.48;1.48	5.83	4.64	0.57946	.	1.012730	0.07950	N	0.980698	T	0.23014	0.0556	L	0.40543	1.245	0.09310	N	1	B;B;B;B	0.15473	0.013;0.007;0.013;0.005	B;B;B;B	0.18561	0.022;0.011;0.012;0.005	T	0.39461	-0.9613	10	0.14252	T	0.57	0.1053	3.718	0.08445	0.1214:0.0682:0.2528:0.5576	.	244;317;244;337	B4DV06;Q9C099-2;E9PE41;Q9C099	.;.;.;LRCC1_HUMAN	H	244;337;317	ENSP00000353538:Y337H;ENSP00000394695:Y317H	ENSP00000353538:Y337H	Y	+	1	0	LRRCC1	86222978	0.028000	0.19301	0.383000	0.26132	0.995000	0.86356	1.656000	0.37355	1.000000	0.39049	0.528000	0.53228	TAT		LRRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380267.1	NM_033402	
PSKH2	85481	hgsc.bcm.edu	37	8	87081681	87081681	+	Silent	SNP	G	G	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr8:87081681G>A	ENST00000276616.2	-	1	245	c.171C>T	c.(169-171)ccC>ccT	p.P57P	PSKH2_ENST00000517981.1_Intron	NM_033126.1	NP_149117.1	Q96QS6	KPSH2_HUMAN	protein serine kinase H2	57							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|kidney(11)|large_intestine(2)|lung(26)|ovary(1)|prostate(1)|stomach(3)|urinary_tract(1)	47			STAD - Stomach adenocarcinoma(118;0.129)			CAAGGACCCGGGGGTCGAACT	0.672																																																	0			8											15.0	19.0	18.0					8																	87081681		2201	4297	6498	87150797	SO:0001819	synonymous_variant	85481			AY037806	CCDS6240.1	8q21.13	2004-06-03				ENSG00000147613			18997	protein-coding gene	gene with protein product							Standard	NM_033126		Approved		uc011lfy.2	Q96QS6		ENST00000276616.2:c.171C>T	8.37:g.87081681G>A		Somatic		Capture	Illumina HiSeq	Phase_I	87150797	A0AV22	Silent	SNP	ENST00000276616.2	37	CCDS6240.1																																																																																				PSKH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374628.1	NM_033126	
PLEKHF2	79666	hgsc.bcm.edu	37	8	96166991	96166991	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr8:96166991A>G	ENST00000315367.3	+	2	960	c.719A>G	c.(718-720)gAt>gGt	p.D240G	PLEKHF2_ENST00000519516.1_Missense_Mutation_p.D240G	NM_024613.3	NP_078889.1	Q9H8W4	PKHF2_HUMAN	pleckstrin homology domain containing, family F (with FYVE domain) member 2	240					protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|membrane (GO:0016020)|transport vesicle (GO:0030133)	metal ion binding (GO:0046872)			breast(1)|large_intestine(1)|lung(1)|ovary(2)	5	Breast(36;3.18e-05)					GATATGTCTGATGATGATGAC	0.433																																																	0			8											77.0	74.0	75.0					8																	96166991		2203	4300	6503	96236167	SO:0001583	missense	79666			AF434819	CCDS6267.1	8q22.1	2013-01-10				ENSG00000175895		"""Zinc fingers, FYVE domain containing"", ""Pleckstrin homology (PH) domain containing"""	20757	protein-coding gene	gene with protein product		615208					Standard	NM_024613		Approved	ZFYVE18, PHAFIN2, FLJ13187	uc003yhn.2	Q9H8W4		ENST00000315367.3:c.719A>G	8.37:g.96166991A>G	ENSP00000322373:p.Asp240Gly	Somatic		Capture	Illumina HiSeq	Phase_I	96236167		Missense_Mutation	SNP	ENST00000315367.3	37	CCDS6267.1	.	.	.	.	.	.	.	.	.	.	A	12.99	2.103495	0.37145	.	.	ENSG00000175895	ENST00000315367;ENST00000519516	T;T	0.81078	-1.45;-1.45	5.81	5.81	0.92471	.	0.090894	0.64402	D	0.000001	T	0.76962	0.4061	N	0.08118	0	0.80722	D	1	D	0.57571	0.98	P	0.57009	0.811	T	0.81387	-0.0956	10	0.51188	T	0.08	-19.809	16.179	0.81887	1.0:0.0:0.0:0.0	.	240	Q9H8W4	PKHF2_HUMAN	G	240	ENSP00000322373:D240G;ENSP00000427792:D240G	ENSP00000322373:D240G	D	+	2	0	PLEKHF2	96236167	1.000000	0.71417	0.997000	0.53966	0.975000	0.68041	8.590000	0.90821	2.225000	0.72522	0.455000	0.32223	GAT		PLEKHF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379666.1	NM_024613	
SPAG1	6674	hgsc.bcm.edu	37	8	101237453	101237453	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr8:101237453T>C	ENST00000388798.2	+	14	1932	c.1741T>C	c.(1741-1743)Tca>Cca	p.S581P	SPAG1_ENST00000251809.3_Missense_Mutation_p.S581P|SPAG1_ENST00000523302.1_3'UTR	NM_003114.4	NP_003105.2	Q07617	SPAG1_HUMAN	sperm associated antigen 1	581					axonemal dynein complex assembly (GO:0070286)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	GTP binding (GO:0005525)|hydrolase activity (GO:0016787)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	all_cancers(14;2.35e-05)|all_epithelial(15;5.2e-08)|Lung NSC(17;0.000283)|all_lung(17;0.000823)	Breast(495;0.195)	Epithelial(11;1.12e-09)|all cancers(13;1.26e-07)|OV - Ovarian serous cystadenocarcinoma(57;4.37e-05)|STAD - Stomach adenocarcinoma(118;0.0525)	KIRC - Kidney renal clear cell carcinoma(542;0.00178)|READ - Rectum adenocarcinoma(644;0.236)		GGAGAAGCTGTCACCTATTCC	0.453																																																	0			8											63.0	59.0	61.0					8																	101237453		2203	4300	6503	101306629	SO:0001583	missense	6674			AF311312	CCDS34930.1	8q22	2014-01-21			ENSG00000104450	ENSG00000104450		"""Tetratricopeptide (TTC) repeat domain containing"""	11212	protein-coding gene	gene with protein product		603395				16368546	Standard	NM_172218		Approved	SP75, FLJ32920, HSD-3.8, TPIS, CT140	uc003yjh.2	Q07617	OTTHUMG00000164706	ENST00000388798.2:c.1741T>C	8.37:g.101237453T>C	ENSP00000373450:p.Ser581Pro	Somatic		Capture	Illumina HiSeq	Phase_I	101306629	A6NP70|B3KQ58|G3XAM3|Q7Z5G1	Missense_Mutation	SNP	ENST00000388798.2	37	CCDS34930.1	.	.	.	.	.	.	.	.	.	.	T	14.02	2.410763	0.42817	.	.	ENSG00000104450	ENST00000251809;ENST00000388798	T;T	0.59772	0.24;0.24	5.46	-1.44	0.08856	.	0.281448	0.39985	N	0.001218	T	0.23572	0.0570	N	0.02685	-0.53	0.27830	N	0.941496	B	0.06786	0.001	B	0.08055	0.003	T	0.35126	-0.9801	10	0.02654	T	1	-0.0026	11.0949	0.48139	0.0:0.6141:0.0:0.3859	.	581	Q07617	SPAG1_HUMAN	P	581	ENSP00000251809:S581P;ENSP00000373450:S581P	ENSP00000251809:S581P	S	+	1	0	SPAG1	101306629	0.598000	0.26882	0.986000	0.45419	0.993000	0.82548	0.578000	0.23773	-0.170000	0.10816	0.528000	0.53228	TCA		SPAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379853.2	NM_172218	
RNF19A	25897	hgsc.bcm.edu	37	8	101299869	101299869	+	Silent	SNP	T	T	C			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr8:101299869T>C	ENST00000519449.1	-	3	850	c.534A>G	c.(532-534)gaA>gaG	p.E178E	RNF19A_ENST00000341084.2_Silent_p.E178E	NM_001280539.1|NM_015435.3	NP_001267468.1|NP_056250.3	Q9NV58	RN19A_HUMAN	ring finger protein 19A, RBR E3 ubiquitin protein ligase	178					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(11)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	30	all_cancers(14;3.5e-05)|all_epithelial(15;8.91e-08)|Lung NSC(17;0.000615)|all_lung(17;0.00166)		Epithelial(11;3.06e-11)|all cancers(13;5.78e-09)|OV - Ovarian serous cystadenocarcinoma(57;2.24e-05)|STAD - Stomach adenocarcinoma(118;0.0525)			GTTCAGTACATTCTGGGCAAC	0.358																																																	0			8											120.0	124.0	122.0					8																	101299869		2203	4300	6503	101369045	SO:0001819	synonymous_variant	25897			AB029316	CCDS6286.1	8q22	2013-10-03	2013-10-03	2007-08-20		ENSG00000034677		"""RING-type (C3HC4) zinc fingers"""	13432	protein-coding gene	gene with protein product		607119	"""ring finger protein 19"", ""ring finger protein 19A"", ""ring finger protein 19A, E3 ubiquitin protein ligase"""	RNF19		11237715, 10976766	Standard	NM_183419		Approved	dorfin, DKFZp566B1346	uc003yjj.1	Q9NV58		ENST00000519449.1:c.534A>G	8.37:g.101299869T>C		Somatic		Capture	Illumina HiSeq	Phase_I	101369045	A3KCU9|Q52LG1|Q9H5H9|Q9H8M8|Q9UFG0|Q9UFX6|Q9Y4Y1	Silent	SNP	ENST00000519449.1	37	CCDS6286.1																																																																																				RNF19A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380004.1	NM_015435	
CSMD3	114788	hgsc.bcm.edu	37	8	113402946	113402946	+	Missense_Mutation	SNP	T	T	C	rs375988803	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr8:113402946T>C	ENST00000297405.5	-	36	6125	c.5881A>G	c.(5881-5883)Aac>Gac	p.N1961D	CSMD3_ENST00000343508.3_Missense_Mutation_p.N1921D|CSMD3_ENST00000352409.3_Missense_Mutation_p.N1891D|CSMD3_ENST00000455883.2_Missense_Mutation_p.N1857D	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1961	CUB 11. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TTCAGATTGTTGTCATAAGGC	0.408										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			T|||	8	0.00159744	0.0	0.0	5008	,	,		17211	0.0		0.0	False		,,,				2504	0.0082																0			8											90.0	84.0	86.0					8																	113402946		2203	4300	6503	113472122	SO:0001583	missense	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.5881A>G	8.37:g.113402946T>C	ENSP00000297405:p.Asn1961Asp	Somatic		Capture	Illumina HiSeq	Phase_I	113472122	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.608830	0.87258	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.30448	1.53;1.53;1.53;1.53;1.53	5.14	5.14	0.70334	CUB (5);	0.000000	0.85682	D	0.000000	T	0.51024	0.1650	L	0.56396	1.775	0.52099	D	0.999942	D;P;D	0.76494	0.999;0.948;0.999	D;D;D	0.85130	0.997;0.93;0.986	T	0.44952	-0.9294	10	0.36615	T	0.2	.	15.1178	0.72416	0.0:0.0:0.0:1.0	.	1857;1961;1921	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	D	1921;1961;1231;1857;1891	ENSP00000345799:N1921D;ENSP00000297405:N1961D;ENSP00000341558:N1231D;ENSP00000412263:N1857D;ENSP00000343124:N1891D	ENSP00000297405:N1961D	N	-	1	0	CSMD3	113472122	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.857000	0.86963	2.162000	0.67917	0.383000	0.25322	AAC		CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
CPSF1	29894	hgsc.bcm.edu	37	8	145625387	145625387	+	Silent	SNP	G	G	A	rs144467510	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr8:145625387G>A	ENST00000349769.3	-	10	1120	c.1026C>T	c.(1024-1026)ggC>ggT	p.G342G	MIR1234_ENST00000408875.1_RNA	NM_013291.2	NP_037423.2	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1, 160kDa	342					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	mRNA 3'-UTR binding (GO:0003730)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			CTCACATCTCGCCGCCCTTGA	0.672													G|||	5	0.000998403	0.0038	0.0	5008	,	,		8530	0.0		0.0	False		,,,				2504	0.0				NSCLC(133;1088 1848 27708 34777 35269)												0			8						G		9,4395		0,9,2193	25.0	21.0	23.0		1026	-11.3	0.0	8	dbSNP_134	23	0,8596		0,0,4298	no	coding-synonymous	CPSF1	NM_013291.2		0,9,6491	AA,AG,GG		0.0,0.2044,0.0692		342/1444	145625387	9,12991	2202	4298	6500	145596195	SO:0001819	synonymous_variant	29894			U37012	CCDS34966.1	8q24	2014-05-06	2002-08-29		ENSG00000071894	ENSG00000071894			2324	protein-coding gene	gene with protein product		606027	"""cleavage and polyadenylation specific factor 1, 160kD subunit"""			7651824, 7590244	Standard	NM_013291		Approved		uc003zcj.3	Q10570	OTTHUMG00000174612	ENST00000349769.3:c.1026C>T	8.37:g.145625387G>A		Somatic		Capture	Illumina HiSeq	Phase_I	145596195	Q96AF0	Silent	SNP	ENST00000349769.3	37	CCDS34966.1																																																																																				CPSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382422.2	NM_013291	
ATAD3B	83858	hgsc.bcm.edu	37	1	1421550	1421550	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:1421550C>T	ENST00000308647.7	+	10	1140	c.1024C>T	c.(1024-1026)Cgg>Tgg	p.R342W		NM_031921.4	NP_114127.3	Q5T9A4	ATD3B_HUMAN	ATPase family, AAA domain containing 3B	342						mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)	p.R342W(1)		endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(2)|urinary_tract(1)	10	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		CAAGAAGAACCGGGGCCTGTA	0.647																																																	1	Substitution - Missense(1)	endometrium(1)	1											81.0	89.0	86.0					1																	1421550		2203	4299	6502	1411413	SO:0001583	missense	83858			AL834179	CCDS30.1	1p36.33	2010-04-21		2007-02-08	ENSG00000160072	ENSG00000160072		"""ATPases / AAA-type"""	24007	protein-coding gene	gene with protein product		612317				10574462	Standard	XM_005244806		Approved	TOB3, KIAA1273	uc001afv.3	Q5T9A4	OTTHUMG00000000577	ENST00000308647.7:c.1024C>T	1.37:g.1421550C>T	ENSP00000311766:p.Arg342Trp	Somatic		Capture	Illumina HiSeq	Phase_I	1411413	A8K3H1|Q6ZRB5|Q9BUK4|Q9ULE7	Missense_Mutation	SNP	ENST00000308647.7	37	CCDS30.1	.	.	.	.	.	.	.	.	.	.	.	9.510	1.105557	0.20632	.	.	ENSG00000160072	ENST00000360489;ENST00000378737;ENST00000308647	D	0.94966	-3.57	2.26	-2.86	0.05717	.	0.616433	0.16127	N	0.228367	D	0.94420	0.8205	M	0.73217	2.22	0.48830	D	0.999719	D;D	0.76494	0.999;0.997	P;P	0.61275	0.886;0.696	D	0.90218	0.4269	10	0.72032	D	0.01	.	4.022	0.09670	0.5905:0.1843:0.2252:0.0	.	296;342	Q5T9A4-3;Q5T9A4	.;ATD3B_HUMAN	W	237;159;342	ENSP00000311766:R342W	ENSP00000311766:R342W	R	+	1	2	ATAD3B	1411413	0.141000	0.22595	0.015000	0.15790	0.001000	0.01503	0.777000	0.26718	-0.801000	0.04427	-1.027000	0.02421	CGG		ATAD3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001369.2	NM_031921	
KDM1A	23028	hgsc.bcm.edu	37	1	23395124	23395124	+	Silent	SNP	C	C	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:23395124C>T	ENST00000356634.3	+	9	1349	c.1200C>T	c.(1198-1200)gtC>gtT	p.V400V	KDM1A_ENST00000542151.1_Silent_p.V424V|RP1-184J9.2_ENST00000427154.1_RNA|KDM1A_ENST00000400181.4_Silent_p.V424V	NM_015013.3	NP_055828.2	O60341	KDM1A_HUMAN	lysine (K)-specific demethylase 1A	400	Demethylase activity.				blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|granulocyte differentiation (GO:0030851)|histone H3-K4 demethylation (GO:0034720)|histone H3-K9 demethylation (GO:0033169)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of DNA binding (GO:0043392)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of protein binding (GO:0032091)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pituitary gland development (GO:0021983)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein demethylation (GO:0006482)|regulation of primitive erythrocyte differentiation (GO:0010725)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|demethylase activity (GO:0032451)|enzyme binding (GO:0019899)|flavin adenine dinucleotide binding (GO:0050660)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-K4 specific) (GO:0032453)|histone demethylase activity (H3-K9 specific) (GO:0032454)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|MRF binding (GO:0043426)|oxidoreductase activity (GO:0016491)|p53 binding (GO:0002039)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(2)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23						ACTTCAATGTCCTCAATAATA	0.383																																																	0			1											101.0	85.0	90.0					1																	23395124		2203	4300	6503	23267711	SO:0001819	synonymous_variant	0			AL031428	CCDS30627.1, CCDS53278.1	1p36.12	2011-07-01	2009-09-29	2009-09-29	ENSG00000004487	ENSG00000004487		"""Chromatin-modifying enzymes / K-demethylases"""	29079	protein-coding gene	gene with protein product		609132	"""amine oxidase (flavin containing) domain 2"", ""lysine (K)-specific demethylase 1"""	AOF2, KDM1		9628581, 12493763	Standard	NM_015013		Approved	KIAA0601, BHC110, LSD1	uc001bgj.2	O60341	OTTHUMG00000003220	ENST00000356634.3:c.1200C>T	1.37:g.23395124C>T		Somatic		Capture	Illumina HiSeq	Phase_I	23267711	A8MWP9|Q5TH94|Q5TH95|Q86VT7|Q8IXK4|Q8NDP6|Q8TAZ3|Q96AW4	Silent	SNP	ENST00000356634.3	37	CCDS30627.1																																																																																				KDM1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008880.3	NM_015013	
ARID1A	8289	hgsc.bcm.edu	37	1	27105552	27105552	+	Silent	SNP	A	A	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:27105552A>G	ENST00000324856.7	+	20	5534	c.5163A>G	c.(5161-5163)cgA>cgG	p.R1721R	ARID1A_ENST00000374152.2_Silent_p.R1338R|ARID1A_ENST00000540690.1_Silent_p.R49R|ARID1A_ENST00000457599.2_Silent_p.R1504R	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1721					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		AATATTTCCGACGATGCCTGA	0.438			"""Mis, N, F, S, D"""		"""clear cell ovarian carcinoma, RCC"""																																			Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	0			1											182.0	200.0	194.0					1																	27105552		2203	4300	6503	26978139	SO:0001819	synonymous_variant	8289			AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"""-"""	11110	protein-coding gene	gene with protein product		603024	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1"", ""AT rich interactive domain 1A (SWI- like)"""	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.5163A>G	1.37:g.27105552A>G		Somatic		Capture	Illumina HiSeq	Phase_I	26978139	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Silent	SNP	ENST00000324856.7	37	CCDS285.1	.	.	.	.	.	.	.	.	.	.	A	7.472	0.646786	0.14516	.	.	ENSG00000117713	ENST00000430799	.	.	.	4.71	-0.765	0.11023	.	.	.	.	.	T	0.42988	0.1227	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.26780	-1.0093	4	.	.	.	-6.2012	3.4497	0.07494	0.4185:0.0:0.2933:0.2882	.	.	.	.	A	618	.	.	T	+	1	0	ARID1A	26978139	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	0.866000	0.27954	0.057000	0.16193	0.482000	0.46254	ACG		ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135	
ZSCAN20	7579	hgsc.bcm.edu	37	1	33945203	33945203	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:33945203G>A	ENST00000361328.3	+	2	467	c.314G>A	c.(313-315)aGg>aAg	p.R105K	ZSCAN20_ENST00000480917.1_3'UTR|ZSCAN20_ENST00000373413.2_Missense_Mutation_p.R105K	NM_145238.3	NP_660281	P17040	ZSC20_HUMAN	zinc finger and SCAN domain containing 20	105	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(11)|ovary(2)|pancreas(1)|stomach(1)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				ATCTTGCCTAGGGAGGTCCAG	0.617																																																	0			1											38.0	42.0	41.0					1																	33945203		2202	4300	6502	33717790	SO:0001583	missense	7579			X52360	CCDS41300.1	1p34.3	2013-01-08	2007-02-20	2007-02-20	ENSG00000121903	ENSG00000121903		"""-"", ""Zinc fingers, C2H2-type"""	13093	protein-coding gene	gene with protein product		611315	"""zinc finger protein 31 (KOX 29)"", ""zinc finger protein 31"""	ZNF360, ZNF31		2288909	Standard	NM_145238		Approved	KOX29	uc001bxj.4	P17040	OTTHUMG00000004173	ENST00000361328.3:c.314G>A	1.37:g.33945203G>A	ENSP00000355053:p.Arg105Lys	Somatic		Capture	Illumina HiSeq	Phase_I	33717790	A8K2D0|B1ALI4|B1ALI5|B1ALI6|Q6ZN23|Q96FA9|Q96H84	Missense_Mutation	SNP	ENST00000361328.3	37	CCDS41300.1	.	.	.	.	.	.	.	.	.	.	G	5.293	0.239466	0.10023	.	.	ENSG00000121903	ENST00000373411;ENST00000326544;ENST00000373413;ENST00000361328;ENST00000401072	T	0.03982	3.74	4.97	-1.63	0.08345	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	0.954791	0.08671	N	0.910918	T	0.02610	0.0079	L	0.31065	0.9	0.20703	N	0.999861	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.10450	0.003;0.005;0.003	T	0.47156	-0.9139	10	0.02654	T	1	-1.4394	1.4869	0.02449	0.4132:0.1385:0.3065:0.1419	.	105;105;105	P17040-3;P17040-4;P17040	.;.;ZSC20_HUMAN	K	105;105;105;39;39	ENSP00000362512:R105K	ENSP00000324450:R105K	R	+	2	0	ZSCAN20	33717790	0.000000	0.05858	0.597000	0.28824	0.974000	0.67602	-0.340000	0.07821	-0.497000	0.06641	0.637000	0.83480	AGG		ZSCAN20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277003.2	NM_145238	
AGBL4	84871	hgsc.bcm.edu	37	1	49128842	49128842	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:49128842A>G	ENST00000371839.1	-	7	822	c.706T>C	c.(706-708)Tca>Cca	p.S236P	AGBL4_ENST00000334103.7_5'UTR|AGBL4_ENST00000371838.1_Missense_Mutation_p.S236P	NM_032785.3	NP_116174.3	Q5VU57	CBPC6_HUMAN	ATP/GTP binding protein-like 4	236					C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytosol (GO:0005829)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)	p.S236A(1)		NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)	15				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)		ACAAATGATGAGGGTGTTTCC	0.493																																																	1	Substitution - Missense(1)	breast(1)	1											181.0	179.0	179.0					1																	49128842		2034	4186	6220	48901429	SO:0001583	missense	84871			AK027348	CCDS44137.1	1p33	2014-06-23			ENSG00000186094	ENSG00000186094			25892	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase 6"""					21074048	Standard	NM_032785		Approved	FLJ14442, CCP6	uc001cru.2	Q5VU57	OTTHUMG00000007793	ENST00000371839.1:c.706T>C	1.37:g.49128842A>G	ENSP00000360905:p.Ser236Pro	Somatic		Capture	Illumina HiSeq	Phase_I	48901429	B3KT26|B4DG37	Missense_Mutation	SNP	ENST00000371839.1	37	CCDS44137.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.985204	0.74474	.	.	ENSG00000186094	ENST00000371839;ENST00000411952;ENST00000371838	T;T	0.12879	2.64;2.64	5.51	5.51	0.81932	Peptidase M14, carboxypeptidase A (1);	0.052765	0.85682	D	0.000000	T	0.42426	0.1202	M	0.86740	2.835	0.80722	D	1	D;D;D	0.57899	0.958;0.981;0.981	P;D;D	0.69142	0.563;0.953;0.962	T	0.44832	-0.9302	9	.	.	.	-21.0301	15.0959	0.72235	1.0:0.0:0.0:0.0	.	248;81;236	Q5VU57-2;B1AMW2;Q5VU57	.;.;CBPC6_HUMAN	P	236;230;236	ENSP00000360905:S236P;ENSP00000360904:S236P	.	S	-	1	0	AGBL4	48901429	1.000000	0.71417	0.999000	0.59377	0.892000	0.51952	5.655000	0.67981	2.216000	0.71823	0.533000	0.62120	TCA		AGBL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021346.4	NM_032785	
USP24	23358	hgsc.bcm.edu	37	1	55591073	55591073	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:55591073A>G	ENST00000294383.6	-	34	3879	c.3880T>C	c.(3880-3882)Tcc>Ccc	p.S1294P	USP24_ENST00000407756.1_Missense_Mutation_p.S1134P	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	1294					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)	p.S1211T(1)		breast(4)|cervix(1)|endometrium(8)|kidney(13)|large_intestine(7)|lung(16)|ovary(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	60						TGTCGGTAGGATGACTTTTCT	0.463																																																	1	Substitution - Missense(1)	ovary(1)	1											169.0	159.0	162.0					1																	55591073		1927	4140	6067	55363661	SO:0001583	missense	23358			AB028980	CCDS44154.1, CCDS44154.2	1p32.3	2008-04-11	2005-08-08		ENSG00000162402	ENSG00000162402		"""Ubiquitin-specific peptidases"""	12623	protein-coding gene	gene with protein product		610569	"""ubiquitin specific protease 24"""			12838346	Standard	NM_015306		Approved	KIAA1057	uc021onw.1	Q9UPU5	OTTHUMG00000008135	ENST00000294383.6:c.3880T>C	1.37:g.55591073A>G	ENSP00000294383:p.Ser1294Pro	Somatic		Capture	Illumina HiSeq	Phase_I	55363661	Q6ZSY2|Q8N2Y4|Q9NXD1	Missense_Mutation	SNP	ENST00000294383.6	37	CCDS44154.2	.	.	.	.	.	.	.	.	.	.	A	19.35	3.810148	0.70797	.	.	ENSG00000162402	ENST00000294383;ENST00000407756	T;T	0.02709	4.21;4.19	5.13	5.13	0.70059	.	0.052612	0.85682	D	0.000000	T	0.02929	0.0087	L	0.34521	1.04	0.58432	D	0.999991	P	0.38922	0.651	B	0.30855	0.121	T	0.58352	-0.7651	10	0.45353	T	0.12	.	14.9324	0.70926	1.0:0.0:0.0:0.0	.	1134	B7WPF4	.	P	1294;1134	ENSP00000294383:S1294P;ENSP00000385700:S1134P	ENSP00000294383:S1294P	S	-	1	0	USP24	55363661	1.000000	0.71417	0.998000	0.56505	0.983000	0.72400	8.923000	0.92808	1.938000	0.56188	0.460000	0.39030	TCC		USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2		
USP24	23358	hgsc.bcm.edu	37	1	55623038	55623038	+	Silent	SNP	G	G	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:55623038G>A	ENST00000294383.6	-	11	1232	c.1233C>T	c.(1231-1233)acC>acT	p.T411T	USP24_ENST00000407756.1_Silent_p.T299T	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	411					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(4)|cervix(1)|endometrium(8)|kidney(13)|large_intestine(7)|lung(16)|ovary(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	60						CTATTAGTTTGGTTACCTAAA	0.284																																																	0			1											67.0	63.0	64.0					1																	55623038		1807	4063	5870	55395626	SO:0001819	synonymous_variant	23358			AB028980	CCDS44154.1, CCDS44154.2	1p32.3	2008-04-11	2005-08-08		ENSG00000162402	ENSG00000162402		"""Ubiquitin-specific peptidases"""	12623	protein-coding gene	gene with protein product		610569	"""ubiquitin specific protease 24"""			12838346	Standard	NM_015306		Approved	KIAA1057	uc021onw.1	Q9UPU5	OTTHUMG00000008135	ENST00000294383.6:c.1233C>T	1.37:g.55623038G>A		Somatic		Capture	Illumina HiSeq	Phase_I	55395626	Q6ZSY2|Q8N2Y4|Q9NXD1	Silent	SNP	ENST00000294383.6	37	CCDS44154.2																																																																																				USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2		
RBMXL1	494115	hgsc.bcm.edu	37	1	89449223	89449223	+	Missense_Mutation	SNP	G	G	A	rs530375965	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:89449223G>A	ENST00000321792.5	-	2	714	c.287C>T	c.(286-288)cCg>cTg	p.P96L	CCBL2_ENST00000370485.2_Intron|CCBL2_ENST00000446900.2_Intron|CCBL2_ENST00000370491.3_Intron|CCBL2_ENST00000260508.4_Intron|RBMXL1_ENST00000399794.2_Missense_Mutation_p.P96L|RBMXL1_ENST00000413769.1_5'UTR	NM_019610.5	NP_062556.2	Q96E39	RMXL1_HUMAN	RNA binding motif protein, X-linked-like 1	96					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)										AGGTGGGGGCGGTCCATGTCT	0.512											OREG0013593	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	.|||	3	0.000599042	0.0	0.0	5008	,	,		17899	0.0		0.0	False		,,,				2504	0.0031																0			1											92.0	97.0	95.0					1																	89449223		2203	4300	6503	89221811	SO:0001583	missense	56267			BC012942	CCDS716.1	1p22.2	2013-02-12	2007-01-04	2007-01-04	ENSG00000213516	ENSG00000213516		"""RNA binding motif (RRM) containing"""	25073	protein-coding gene	gene with protein product	"""kynurenine aminotransferase III"""					10441733	Standard	NM_019610		Approved	KAT3	uc001dms.3	Q96E39	OTTHUMG00000010661	ENST00000321792.5:c.287C>T	1.37:g.89449223G>A	ENSP00000318415:p.Pro96Leu	Somatic	1267	Capture	Illumina HiSeq	Phase_I	89221811		Missense_Mutation	SNP	ENST00000321792.5	37	CCDS716.1	.	.	.	.	.	.	.	.	.	.	G	9.954	1.220967	0.22457	.	.	ENSG00000213516	ENST00000321792;ENST00000399794	T;T	0.73897	-0.79;-0.79	1.76	0.688	0.18027	.	0.000000	0.85682	U	0.000000	T	0.40815	0.1132	L	0.39898	1.24	0.34839	D	0.740515	B	0.27351	0.176	B	0.16722	0.016	T	0.09930	-1.0652	10	0.54805	T	0.06	-5.7204	5.0541	0.14524	0.0:0.0:0.6507:0.3493	.	96	Q96E39	RBMXL_HUMAN	L	96	ENSP00000318415:P96L;ENSP00000446099:P96L	ENSP00000318415:P96L	P	-	2	0	RBMXL1	89221811	1.000000	0.71417	0.132000	0.22025	0.147000	0.21601	4.379000	0.59575	0.042000	0.15717	0.306000	0.20318	CCG		RBMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029403.3	NM_019610	
GFI1	2672	hgsc.bcm.edu	37	1	92944146	92944146	+	Splice_Site	SNP	A	A	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:92944146A>G	ENST00000370332.1	-	6	1407	c.1089T>C	c.(1087-1089)acT>acC	p.T363T	GFI1_ENST00000427103.1_Splice_Site_p.T363T|GFI1_ENST00000294702.5_Splice_Site_p.T363T	NM_001127215.1	NP_001120687.1	Q99684	GFI1_HUMAN	growth factor independent 1 transcription repressor	363					auditory receptor cell differentiation (GO:0042491)|cell fate commitment (GO:0045165)|cellular response to lipopolysaccharide (GO:0071222)|inner ear morphogenesis (GO:0042472)|mechanosensory behavior (GO:0007638)|negative regulation of calcidiol 1-monooxygenase activity (GO:0010956)|negative regulation of cell fate specification (GO:0009996)|negative regulation of neuron projection development (GO:0010977)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vitamin D biosynthetic process (GO:0010957)|positive regulation of cell fate specification (GO:0042660)|positive regulation of interleukin-6-mediated signaling pathway (GO:0070105)|regulation of toll-like receptor signaling pathway (GO:0034121)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|viral process (GO:0016032)	nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.T363T(1)		autonomic_ganglia(1)|endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	15		all_lung(203;0.00292)|Lung NSC(277;0.0115)|all_neural(321;0.185)|Glioma(108;0.203)		OV - Ovarian serous cystadenocarcinoma(397;9.04e-07)|Epithelial(280;1.17e-05)|all cancers(265;5.61e-05)|GBM - Glioblastoma multiforme(16;0.0191)		TTAGCTCACCAGTGTGGATGA	0.507																																																	1	Substitution - coding silent(1)	large_intestine(1)	1											189.0	163.0	172.0					1																	92944146		2203	4300	6503	92716734	SO:0001630	splice_region_variant	2672			U67369	CCDS30773.1	1p22	2014-09-17	2007-10-04		ENSG00000162676	ENSG00000162676		"""Zinc fingers, C2H2-type"""	4237	protein-coding gene	gene with protein product		600871	"""growth factor independent 1"""	ZNF163		7789186	Standard	NM_005263		Approved	GFI1A, GFI-1	uc001dov.4	Q99684	OTTHUMG00000010897	ENST00000370332.1:c.1090+1T>C	1.37:g.92944146A>G		Somatic		Capture	Illumina HiSeq	Phase_I	92716734	Q8N564	Silent	SNP	ENST00000370332.1	37	CCDS30773.1																																																																																				GFI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030054.1	NM_005263	Silent
AGL	178	hgsc.bcm.edu	37	1	100343239	100343239	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:100343239A>G	ENST00000294724.4	+	12	1944	c.1466A>G	c.(1465-1467)gAc>gGc	p.D489G	AGL_ENST00000370161.2_Missense_Mutation_p.D473G|AGL_ENST00000370165.3_Missense_Mutation_p.D489G|AGL_ENST00000370163.3_Missense_Mutation_p.D489G|AGL_ENST00000361302.3_Missense_Mutation_p.D473G|AGL_ENST00000361915.3_Missense_Mutation_p.D489G|AGL_ENST00000361522.4_Missense_Mutation_p.D472G	NM_000028.2	NP_000019.2	P35573	GDE_HUMAN	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	489					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|inclusion body (GO:0016234)|isoamylase complex (GO:0043033)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)	4-alpha-glucanotransferase activity (GO:0004134)|amylo-alpha-1,6-glucosidase activity (GO:0004135)|glycogen debranching enzyme activity (GO:0004133)|polysaccharide binding (GO:0030247)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(9)|lung(35)|ovary(1)|prostate(4)|skin(3)|urinary_tract(1)	69		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)		TGCTGGGGAGACAGTGTTAAA	0.363																																																	0			1											102.0	99.0	100.0					1																	100343239		2203	4300	6503	100115827	SO:0001583	missense	178			BC078663	CCDS759.1, CCDS760.1, CCDS761.1	1p21	2010-04-27	2010-04-27		ENSG00000162688	ENSG00000162688	2.4.1.25, 3.2.1.33		321	protein-coding gene	gene with protein product	"""glycogen debranching enzyme"", ""glycogen storage disease type III"""	610860	"""amylo-1, 6-glucosidase, 4-alpha-glucanotransferase"""			1505983	Standard	NM_000028		Approved		uc001dsi.1	P35573	OTTHUMG00000010803	ENST00000294724.4:c.1466A>G	1.37:g.100343239A>G	ENSP00000294724:p.Asp489Gly	Somatic		Capture	Illumina HiSeq	Phase_I	100115827	A6NCX7|A6NEK2|D3DT51|P78354|P78544|Q59H92|Q6AZ90|Q9UF08	Missense_Mutation	SNP	ENST00000294724.4	37	CCDS759.1	.	.	.	.	.	.	.	.	.	.	A	27.5	4.838082	0.91117	.	.	ENSG00000162688	ENST00000361915;ENST00000370165;ENST00000370163;ENST00000294724;ENST00000361302;ENST00000370161;ENST00000361522	D;D;D;D;D;D;D	0.92858	-3.12;-3.12;-3.12;-3.12;-3.12;-3.12;-3.12	5.97	5.97	0.96955	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.85682	D	0.000000	D	0.96787	0.8951	M	0.92507	3.315	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.97687	1.0176	10	0.87932	D	0	.	16.4608	0.84044	1.0:0.0:0.0:0.0	.	472;473;489	P35573-2;P35573-3;P35573	.;.;GDE_HUMAN	G	489;489;489;489;473;473;472	ENSP00000355106:D489G;ENSP00000359184:D489G;ENSP00000359182:D489G;ENSP00000294724:D489G;ENSP00000354971:D473G;ENSP00000359180:D473G;ENSP00000354635:D472G	ENSP00000294724:D489G	D	+	2	0	AGL	100115827	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	8.896000	0.92521	2.288000	0.76882	0.533000	0.62120	GAC		AGL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029778.1	NM_000028	
C1orf162	128346	hgsc.bcm.edu	37	1	112020640	112020640	+	Silent	SNP	C	C	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:112020640C>T	ENST00000343534.5	+	6	613	c.363C>T	c.(361-363)gcC>gcT	p.A121A	C1orf162_ENST00000369718.3_Silent_p.A96A|C1orf162_ENST00000464591.1_3'UTR	NM_174896.2	NP_777556.1	Q8NEQ5	CA162_HUMAN	chromosome 1 open reading frame 162	121						integral component of membrane (GO:0016021)				NS(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)	5		all_cancers(81;0.00116)|all_epithelial(167;0.000761)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0236)|Colorectal(144;0.0286)|all cancers(265;0.0572)|Epithelial(280;0.0862)|COAD - Colon adenocarcinoma(174;0.112)|LUSC - Lung squamous cell carcinoma(189;0.134)		TTACCTATGCCAGCACAACTT	0.438																																																	0			1											103.0	98.0	100.0					1																	112020640		2203	4300	6503	111822163	SO:0001819	synonymous_variant	128346			BC017973	CCDS837.1, CCDS72837.1	1p13.2	2008-02-05			ENSG00000143110	ENSG00000143110			28344	protein-coding gene	gene with protein product						12477932	Standard	XM_005270475		Approved	MGC24133	uc001ebe.3	Q8NEQ5	OTTHUMG00000011750	ENST00000343534.5:c.363C>T	1.37:g.112020640C>T		Somatic		Capture	Illumina HiSeq	Phase_I	111822163	Q5QNZ1	Silent	SNP	ENST00000343534.5	37	CCDS837.1																																																																																				C1orf162-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000032471.1	NM_174896	
VANGL1	81839	hgsc.bcm.edu	37	1	116206712	116206712	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:116206712G>A	ENST00000355485.2	+	4	906	c.635G>A	c.(634-636)cGg>cAg	p.R212Q	VANGL1_ENST00000369510.4_Missense_Mutation_p.R210Q|VANGL1_ENST00000310260.3_Missense_Mutation_p.R212Q|VANGL1_ENST00000369509.1_Missense_Mutation_p.R212Q	NM_001172411.1|NM_138959.2	NP_001165882.1|NP_620409.1	Q8TAA9	VANG1_HUMAN	VANGL planar cell polarity protein 1	212					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|liver(2)|lung(13)|urinary_tract(1)	27	Lung SC(450;0.211)	all_cancers(81;1.24e-06)|all_epithelial(167;1.02e-06)|all_lung(203;7.95e-06)|Lung NSC(69;4.97e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		TTGGACTCTCGGGACCGGAAT	0.517																																																	0			1											195.0	197.0	196.0					1																	116206712		2203	4300	6503	116008235	SO:0001583	missense	81839			AB075805	CCDS883.1, CCDS53350.1	1p13.1	2013-03-05	2013-03-05		ENSG00000173218	ENSG00000173218			15512	protein-coding gene	gene with protein product		610132	"""vang (van gogh, Drosophila)-like 1, vang, van gogh-like 1 (Drosophila)"", ""vang-like 1 (van gogh, Drosophila)"""			11956595, 12011995	Standard	NM_001172411		Approved	STB2	uc001efv.1	Q8TAA9	OTTHUMG00000011971	ENST00000355485.2:c.635G>A	1.37:g.116206712G>A	ENSP00000347672:p.Arg212Gln	Somatic		Capture	Illumina HiSeq	Phase_I	116008235	Q5T1D3|Q5T1D4|Q86WG8|Q8N559	Missense_Mutation	SNP	ENST00000355485.2	37	CCDS883.1	.	.	.	.	.	.	.	.	.	.	G	13.56	2.274091	0.40194	.	.	ENSG00000173218	ENST00000355485;ENST00000369510;ENST00000310260;ENST00000369509	T;T;T;T	0.80824	-1.42;-1.42;-1.42;-1.42	5.73	4.82	0.62117	.	0.120688	0.64402	D	0.000018	T	0.51449	0.1675	N	0.25890	0.77	0.39974	D	0.974838	B;B	0.15930	0.012;0.015	B;B	0.15052	0.007;0.012	T	0.50939	-0.8768	10	0.21014	T	0.42	2.8345	9.7263	0.40333	0.197:0.0:0.803:0.0	.	210;212	Q8TAA9-2;Q8TAA9	.;VANG1_HUMAN	Q	212;210;212;212	ENSP00000347672:R212Q;ENSP00000358523:R210Q;ENSP00000310800:R212Q;ENSP00000358522:R212Q	ENSP00000310800:R212Q	R	+	2	0	VANGL1	116008235	1.000000	0.71417	0.996000	0.52242	0.952000	0.60782	4.819000	0.62664	1.582000	0.49881	-0.142000	0.14014	CGG		VANGL1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033096.1		
GJA8	2703	hgsc.bcm.edu	37	1	147380779	147380779	+	Missense_Mutation	SNP	C	C	T	rs140512440		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:147380779C>T	ENST00000369235.1	+	1	697	c.697C>T	c.(697-699)Cgg>Tgg	p.R233W	GJA8_ENST00000240986.4_Missense_Mutation_p.R233W			P48165	CXA8_HUMAN	gap junction protein, alpha 8, 50kDa	233					cell-cell signaling (GO:0007267)|lens development in camera-type eye (GO:0002088)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of plasma membrane (GO:0005887)	channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)	37	all_hematologic(923;0.0276)					GAAGGGGATCCGGTCTGCCTT	0.557													C|||	1	0.000199681	0.0	0.0	5008	,	,		17208	0.0		0.0	False		,,,				2504	0.001				Melanoma(76;1255 1795 8195 52096)												0			1						C	TRP/ARG	0,4406		0,0,2203	83.0	75.0	78.0		697	4.4	0.5	1	dbSNP_134	78	2,8598	2.2+/-6.3	0,2,4298	no	missense	GJA8	NM_005267.4	101	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging	233/434	147380779	2,13004	2203	4300	6503	145847403	SO:0001583	missense	2703			U34802	CCDS30834.1	1q21.1	2008-02-05	2007-01-16		ENSG00000121634	ENSG00000121634		"""Ion channels / Gap junction proteins (connexins)"""	4281	protein-coding gene	gene with protein product	"""connexin 50"""	600897	"""gap junction protein, alpha 8, 50kD (connexin 50)"", ""gap junction protein, alpha 8, 50kDa (connexin 50)"""	CAE1, CZP1, CAE		9497259, 7796604	Standard	NM_005267		Approved	CX50	uc001epu.2	P48165	OTTHUMG00000024085	ENST00000369235.1:c.697C>T	1.37:g.147380779C>T	ENSP00000358238:p.Arg233Trp	Somatic		Capture	Illumina HiSeq	Phase_I	145847403	A7L5M5|Q5VVN9|Q9NP25	Missense_Mutation	SNP	ENST00000369235.1	37	CCDS30834.1	.	.	.	.	.	.	.	.	.	.	c	16.89	3.246117	0.59103	0.0	2.33E-4	ENSG00000121634	ENST00000240986;ENST00000369235	D;D	0.97831	-4.56;-4.56	4.4	4.4	0.53042	.	0.065730	0.64402	D	0.000007	D	0.97170	0.9075	L	0.32530	0.975	0.58432	D	0.999997	D	0.89917	1.0	D	0.65573	0.936	D	0.98521	1.0623	10	0.87932	D	0	.	17.1387	0.86747	0.0:1.0:0.0:0.0	.	233	P48165	CXA8_HUMAN	W	233	ENSP00000240986:R233W;ENSP00000358238:R233W	ENSP00000240986:R233W	R	+	1	2	GJA8	145847403	1.000000	0.71417	0.520000	0.27837	0.478000	0.33099	5.842000	0.69417	2.267000	0.75376	0.313000	0.20887	CGG		GJA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060647.1	NM_005267	
FLG2	388698	hgsc.bcm.edu	37	1	152324056	152324056	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:152324056T>C	ENST00000388718.5	-	3	6278	c.6206A>G	c.(6205-6207)cAc>cGc	p.H2069R	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000445097.1_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	2069					establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			AGTAGTTCCGTGTCTCTCATG	0.532																																																	0			1											549.0	483.0	506.0					1																	152324056		2203	4300	6503	150590680	SO:0001583	missense	388698			AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"""EF-hand domain containing"""	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.6206A>G	1.37:g.152324056T>C	ENSP00000373370:p.His2069Arg	Somatic		Capture	Illumina HiSeq	Phase_I	150590680	Q9H4U1	Missense_Mutation	SNP	ENST00000388718.5	37	CCDS30861.1	.	.	.	.	.	.	.	.	.	.	T	4.716	0.133155	0.09032	.	.	ENSG00000143520	ENST00000388718	T	0.03635	3.86	4.32	3.21	0.36854	.	.	.	.	.	T	0.01156	0.0038	L	0.50333	1.59	0.09310	N	1	B	0.15930	0.015	B	0.12156	0.007	T	0.47861	-0.9084	9	0.11485	T	0.65	.	6.0272	0.19662	0.0:0.1144:0.0:0.8856	.	2069	Q5D862	FILA2_HUMAN	R	2069	ENSP00000373370:H2069R	ENSP00000373370:H2069R	H	-	2	0	FLG2	150590680	0.021000	0.18746	0.167000	0.22817	0.006000	0.05464	1.485000	0.35519	1.961000	0.56991	0.524000	0.50904	CAC		FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342	
LCE2B	26239	hgsc.bcm.edu	37	1	152659458	152659458	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:152659458T>C	ENST00000368780.3	+	2	193	c.139T>C	c.(139-141)Tgc>Cgc	p.C47R	LCE2B_ENST00000417924.2_Missense_Mutation_p.C47R	NM_014357.4	NP_055172.1	O14633	LCE2B_HUMAN	late cornified envelope 2B	47	Cys-rich.				epidermis development (GO:0008544)|keratinization (GO:0031424)					endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	11	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			AGTCTCTTCTTGCTGTGGTCC	0.622																																																	0			1											139.0	149.0	146.0					1																	152659458		2203	4300	6503	150926082	SO:0001583	missense	26239			BI670514	CCDS1020.1	1q21	2008-02-05	2004-10-11	2004-10-15	ENSG00000159455	ENSG00000159455		"""Late cornified envelopes"""	16610	protein-coding gene	gene with protein product		612610	"""small proline rich-like (epidermal differentiation complex) 1B"""	SPRL1B		11698679, 9344646	Standard	NM_014357		Approved	LEP10, XP5	uc001fai.3	O14633	OTTHUMG00000012404	ENST00000368780.3:c.139T>C	1.37:g.152659458T>C	ENSP00000357769:p.Cys47Arg	Somatic		Capture	Illumina HiSeq	Phase_I	150926082	Q5TA80	Missense_Mutation	SNP	ENST00000368780.3	37	CCDS1020.1	.	.	.	.	.	.	.	.	.	.	T	0.305	-0.971704	0.02215	.	.	ENSG00000159455	ENST00000417924;ENST00000368780	T;T	0.05382	3.45;3.45	2.26	2.26	0.28386	.	.	.	.	.	T	0.12518	0.0304	M	0.82323	2.585	0.41513	D	0.988354	D	0.62365	0.991	D	0.68039	0.955	T	0.01198	-1.1421	9	0.87932	D	0	.	6.3311	0.21270	0.0:0.0:0.0:1.0	.	47	O14633	LCE2B_HUMAN	R	47	ENSP00000414043:C47R;ENSP00000357769:C47R	ENSP00000357769:C47R	C	+	1	0	LCE2B	150926082	0.910000	0.30920	0.805000	0.32314	0.027000	0.11550	0.988000	0.29616	1.029000	0.39812	0.260000	0.18958	TGC		LCE2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034524.1	NM_014357	
LMNA	4000	hgsc.bcm.edu	37	1	156106818	156106818	+	Splice_Site	SNP	C	C	T	rs200466188		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:156106818C>T	ENST00000368300.4	+	8	1699	c.1487C>T	c.(1486-1488)aCg>aTg	p.T496M	LMNA_ENST00000347559.2_Splice_Site_p.T496M|LMNA_ENST00000392353.3_Splice_Site_p.T415M|LMNA_ENST00000361308.4_Splice_Site_p.T496M|LMNA_ENST00000368299.3_Splice_Site_p.T496M|LMNA_ENST00000496738.1_3'UTR|LMNA_ENST00000473598.2_Splice_Site_p.T397M|LMNA_ENST00000448611.2_Splice_Site_p.T384M|LMNA_ENST00000368297.1_Splice_Site_p.T415M|LMNA_ENST00000368301.2_Splice_Site_p.T496M	NM_170707.3	NP_733821.1	P02545	LMNA_HUMAN	lamin A/C	496	LTD.|Tail.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular protein metabolic process (GO:0044267)|cellular response to hypoxia (GO:0071456)|endoplasmic reticulum unfolded protein response (GO:0030968)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic nuclear envelope reassembly (GO:0007084)|muscle organ development (GO:0007517)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|positive regulation of cell aging (GO:0090343)|protein localization to nucleus (GO:0034504)|regulation of cell migration (GO:0030334)|regulation of protein localization to nucleus (GO:1900180)|sterol regulatory element binding protein import into nucleus (GO:0035105)|ventricular cardiac muscle cell development (GO:0055015)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament (GO:0005882)|lamin filament (GO:0005638)|nuclear envelope (GO:0005635)|nuclear lamina (GO:0005652)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	structural molecule activity (GO:0005198)			NS(1)|endometrium(1)|kidney(1)|lung(3)|ovary(4)	10	Hepatocellular(266;0.158)					CAGGTGGTGACGGTGAGTGGC	0.597									Werner syndrome;Hutchinson-Gilford Progeria Syndrome																																								0			1											48.0	49.0	48.0					1																	156106818		2203	4300	6503	154373442	SO:0001630	splice_region_variant	4000	Familial Cancer Database	WS, Adult Progeria;HGPS, Progeria	BC014507	CCDS1129.1, CCDS1131.1, CCDS58038.1, CCDS72941.1, CCDS72942.1	1q22	2014-09-17			ENSG00000160789	ENSG00000160789		"""Intermediate filaments type V, lamins"""	6636	protein-coding gene	gene with protein product		150330	"""cardiomyopathy, dilated 1A (autosomal dominant)"", ""limb girdle muscular dystrophy 1B (autosomal dominant)"", ""progeria 1 (Hutchinson-Gilford type)"", ""lamin A/C-like 1"""	LMN1, CMD1A, LGMD1B, PRO1, LMNL1		8511676, 8838815, 12702809	Standard	NM_005572		Approved	HGPS	uc001fni.3	P02545	OTTHUMG00000013961	ENST00000368300.4:c.1488+1C>T	1.37:g.156106818C>T		Somatic		Capture	Illumina HiSeq	Phase_I	154373442	B4DI32|D3DVB0|D6RAQ3|E7EUI9|P02546|Q5I6Y4|Q5I6Y6|Q5TCJ2|Q5TCJ3|Q6UYC3|Q969I8|Q96JA2	Missense_Mutation	SNP	ENST00000368300.4	37	CCDS1129.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.814232	0.90790	.	.	ENSG00000160789	ENST00000368301;ENST00000347559;ENST00000361308;ENST00000368300;ENST00000368299;ENST00000448611;ENST00000368297;ENST00000473598;ENST00000392353;ENST00000508500	D;D;D;D;D;D;D;D;D;D	0.98649	-5.05;-5.05;-5.05;-5.05;-5.05;-5.05;-5.05;-5.05;-5.05;-5.05	5.4	5.4	0.78164	Intermediate filament, C-terminal (1);	0.000000	0.56097	D	0.000029	D	0.99196	0.9721	M	0.87547	2.89	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.97110	0.999;0.997;1.0;0.999;0.999;0.999;0.998;1.0	D	0.99376	1.0921	10	0.59425	D	0.04	.	16.7143	0.85394	0.0:1.0:0.0:0.0	.	152;384;496;397;415;496;496;496	B4DFR3;E7EUI9;Q6UYC3;D6RAQ3;Q5TCI8;P02545;P02545-3;P02545-2	.;.;.;.;.;LMNA_HUMAN;.;.	M	496;496;496;496;496;384;415;397;415;122	ENSP00000357284:T496M;ENSP00000292304:T496M;ENSP00000355292:T496M;ENSP00000357283:T496M;ENSP00000357282:T496M;ENSP00000395597:T384M;ENSP00000357280:T415M;ENSP00000421821:T397M;ENSP00000376164:T415M;ENSP00000424977:T122M	ENSP00000292304:T496M	T	+	2	0	LMNA	154373442	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.448000	0.80631	2.797000	0.96272	0.655000	0.94253	ACG		LMNA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039200.2	NM_170707	Missense_Mutation
LAMC1	3915	hgsc.bcm.edu	37	1	183111876	183111876	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:183111876A>G	ENST00000258341.4	+	28	5038	c.4781A>G	c.(4780-4782)aAg>aGg	p.K1594R	RP11-181K3.4_ENST00000457852.3_RNA	NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	1594	Domain II and I.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|endoderm development (GO:0007492)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|positive regulation of epithelial cell proliferation (GO:0050679)|protein complex assembly (GO:0006461)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)	p.K1594T(1)		NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(27)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	76						GACATCAGGAAGACCTTACCA	0.522																																																	1	Substitution - Missense(1)	ovary(1)	1											126.0	110.0	115.0					1																	183111876		2203	4300	6503	181378499	SO:0001583	missense	3915			J03202	CCDS1351.1	1q31	2013-03-01			ENSG00000135862	ENSG00000135862		"""Laminins"""	6492	protein-coding gene	gene with protein product		150290		LAMB2		3234037	Standard	NM_002293		Approved		uc001gpy.4	P11047	OTTHUMG00000035418	ENST00000258341.4:c.4781A>G	1.37:g.183111876A>G	ENSP00000258341:p.Lys1594Arg	Somatic		Capture	Illumina HiSeq	Phase_I	181378499	Q5VYE7	Missense_Mutation	SNP	ENST00000258341.4	37	CCDS1351.1	.	.	.	.	.	.	.	.	.	.	A	9.320	1.057726	0.19907	.	.	ENSG00000135862	ENST00000258341	T	0.30448	1.53	5.57	3.28	0.37604	.	0.159267	0.53938	N	0.000041	T	0.22627	0.0546	L	0.35723	1.085	0.39737	D	0.971694	B	0.14805	0.011	B	0.08055	0.003	T	0.05084	-1.0907	10	0.36615	T	0.2	.	9.517	0.39111	0.8577:0.0:0.1423:0.0	.	1594	P11047	LAMC1_HUMAN	R	1594	ENSP00000258341:K1594R	ENSP00000258341:K1594R	K	+	2	0	LAMC1	181378499	1.000000	0.71417	0.973000	0.42090	0.997000	0.91878	5.465000	0.66725	0.415000	0.25817	0.533000	0.62120	AAG		LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293	
KIF21B	23046	hgsc.bcm.edu	37	1	200972809	200972809	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:200972809T>C	ENST00000422435.2	-	8	1433	c.1117A>G	c.(1117-1119)Aag>Gag	p.K373E	KIF21B_ENST00000461742.2_Missense_Mutation_p.K373E|KIF21B_ENST00000332129.2_Missense_Mutation_p.K373E|KIF21B_ENST00000360529.5_Missense_Mutation_p.K373E	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	373					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						ACTACCACCTTGTTCTTGATG	0.542																																																	0			1											193.0	148.0	163.0					1																	200972809		2203	4300	6503	199239432	SO:0001583	missense	23046			BC031927	CCDS30965.1, CCDS58054.1, CCDS58055.1, CCDS58056.1	1q32.1	2013-01-10			ENSG00000116852	ENSG00000116852		"""Kinesins"", ""WD repeat domain containing"""	29442	protein-coding gene	gene with protein product		608322				9455484	Standard	NM_001252100		Approved	DKFZP434J212, KIAA0449	uc001gvs.2	O75037	OTTHUMG00000035787	ENST00000422435.2:c.1117A>G	1.37:g.200972809T>C	ENSP00000411831:p.Lys373Glu	Somatic		Capture	Illumina HiSeq	Phase_I	199239432	B2RP62|B7ZMI0|Q5T4J3	Missense_Mutation	SNP	ENST00000422435.2	37	CCDS58056.1	.	.	.	.	.	.	.	.	.	.	t	24.2	4.502713	0.85176	.	.	ENSG00000116852	ENST00000332129;ENST00000360529;ENST00000461742;ENST00000422435;ENST00000539858	T;T;T;T	0.73469	-0.75;-0.75;-0.75;-0.75	5.19	5.19	0.71726	Kinesin, motor domain (2);	0.000000	0.85682	D	0.000000	T	0.81964	0.4934	M	0.86178	2.8	0.58432	D	0.999996	D;D;P;D	0.56746	0.961;0.961;0.816;0.977	P;P;B;P	0.51974	0.489;0.489;0.188;0.686	D	0.85109	0.0962	10	0.87932	D	0	.	11.1258	0.48317	0.0:0.0:0.1544:0.8455	.	373;373;373;373	B7ZMI0;B2RP62;O75037;O75037-2	.;.;KI21B_HUMAN;.	E	373	ENSP00000328494:K373E;ENSP00000353724:K373E;ENSP00000433808:K373E;ENSP00000411831:K373E	ENSP00000328494:K373E	K	-	1	0	KIF21B	199239432	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.939000	0.63526	1.959000	0.56917	0.524000	0.50904	AAG		KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332	
RAB29	8934	hgsc.bcm.edu	37	1	205739922	205739922	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:205739922C>T	ENST00000367139.3	-	5	742	c.439G>A	c.(439-441)Ggt>Agt	p.G147S	RAB7L1_ENST00000414729.1_Missense_Mutation_p.G147S|RAB7L1_ENST00000437324.2_Missense_Mutation_p.G75S|RAB7L1_ENST00000446390.2_Missense_Mutation_p.G123S|RAB7L1_ENST00000468887.1_5'UTR|RAB7L1_ENST00000235932.4_Missense_Mutation_p.G147S	NM_003929.2	NP_003920.1	O14966	RAB7L_HUMAN		147					cell differentiation (GO:0030154)|Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|positive regulation of intracellular protein transport (GO:0090316)|protein transport (GO:0015031)|retrograde transport, plasma membrane to Golgi (GO:0035526)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|vacuole (GO:0005773)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|urinary_tract(1)	10	Breast(84;0.0799)		BRCA - Breast invasive adenocarcinoma(75;0.0194)			CCTGTGAAACCGTTCTCTTTA	0.428																																					Pancreas(25;658 872 27763 34889 38531)												0			1											160.0	129.0	139.0					1																	205739922		2203	4300	6503	204006545	SO:0001583	missense	8934																														ENST00000367139.3:c.439G>A	1.37:g.205739922C>T	ENSP00000356107:p.Gly147Ser	Somatic		Capture	Illumina HiSeq	Phase_I	204006545	B4E1K3|C9JE77	Missense_Mutation	SNP	ENST00000367139.3	37	CCDS1459.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.868480	0.91587	.	.	ENSG00000117280	ENST00000367139;ENST00000235932;ENST00000437324;ENST00000446390;ENST00000414729	D;D;T;D;D	0.81821	-1.54;-1.54;-0.74;-1.54;-1.54	5.27	5.27	0.74061	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.82655	0.5084	L	0.43554	1.36	0.49582	D	0.999801	P;D	0.60160	0.886;0.987	B;P	0.53593	0.195;0.73	D	0.84571	0.0655	10	0.72032	D	0.01	-10.8692	17.0021	0.86384	0.0:1.0:0.0:0.0	.	123;147	B4E1K3;O14966	.;RAB7L_HUMAN	S	147;147;75;123;147	ENSP00000356107:G147S;ENSP00000235932:G147S;ENSP00000416613:G75S;ENSP00000389899:G123S;ENSP00000402910:G147S	ENSP00000235932:G147S	G	-	1	0	RAB7L1	204006545	1.000000	0.71417	0.935000	0.37517	0.908000	0.53690	5.420000	0.66441	2.619000	0.88677	0.561000	0.74099	GGT		RAB7L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087732.1		
HHAT	55733	hgsc.bcm.edu	37	1	210577849	210577849	+	Silent	SNP	G	G	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:210577849G>A	ENST00000367010.1	+	6	737	c.510G>A	c.(508-510)caG>caA	p.Q170Q	HHAT_ENST00000391905.3_Silent_p.Q170Q|HHAT_ENST00000537898.1_Silent_p.Q105Q|HHAT_ENST00000261458.3_Silent_p.Q170Q|HHAT_ENST00000545781.1_Silent_p.Q107Q|HHAT_ENST00000541565.1_Intron|HHAT_ENST00000545154.1_Silent_p.Q171Q|HHAT_ENST00000413764.2_Silent_p.Q170Q|HHAT_ENST00000308852.6_Silent_p.Q125Q	NM_001170580.1	NP_001164051.1	Q5VTY9	HHAT_HUMAN	hedgehog acyltransferase	170					multicellular organismal development (GO:0007275)|protein palmitoylation (GO:0018345)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)|palmitoyltransferase activity (GO:0016409)			breast(3)|central_nervous_system(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	27				OV - Ovarian serous cystadenocarcinoma(81;0.0136)|all cancers(67;0.161)|KIRC - Kidney renal clear cell carcinoma(1967;0.215)		ACCTGCTGCAGTTCACGCTGA	0.542																																																	0			1											109.0	88.0	95.0					1																	210577849		2203	4300	6503	208644472	SO:0001819	synonymous_variant	55733			AK001586	CCDS1495.1, CCDS53471.1, CCDS53472.1, CCDS53473.1	1q32	2008-02-05			ENSG00000054392	ENSG00000054392			18270	protein-coding gene	gene with protein product		605743				11160356	Standard	NM_001170587		Approved	FLJ10724, MART-2, MART2, Skn, ski, rasp, sit, GUP2	uc009xcx.3	Q5VTY9	OTTHUMG00000036447	ENST00000367010.1:c.510G>A	1.37:g.210577849G>A		Somatic		Capture	Illumina HiSeq	Phase_I	208644472	B7Z4D5|B7Z5I1|B7Z868|B7ZA75|D3DT91|F5H444|Q17RZ7|Q4G0K3|Q5CZ95|Q5TGI2|Q9NVH9|Q9Y3N8	Silent	SNP	ENST00000367010.1	37	CCDS1495.1																																																																																				HHAT-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088662.1	NM_018194	
CHRM3	1131	hgsc.bcm.edu	37	1	240072213	240072213	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:240072213A>G	ENST00000255380.4	+	5	2241	c.1462A>G	c.(1462-1464)Aaa>Gaa	p.K488E		NM_000740.2	NP_000731.1	P20309	ACM3_HUMAN	cholinergic receptor, muscarinic 3	488					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|energy reserve metabolic process (GO:0006112)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|positive regulation of smooth muscle contraction (GO:0045987)|regulation of insulin secretion (GO:0050796)|regulation of vascular smooth muscle contraction (GO:0003056)|saliva secretion (GO:0046541)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|smooth muscle contraction (GO:0006939)	asymmetric synapse (GO:0032279)|axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|drug binding (GO:0008144)|G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)|receptor activity (GO:0004872)			breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(19)|ovary(4)|prostate(1)|skin(12)|upper_aerodigestive_tract(1)	51	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Brompheniramine(DB00835)|Cevimeline(DB00185)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxepin(DB01142)|Fesoterodine(DB06702)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Isopropamide(DB01625)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Mepenzolate(DB04843)|Methacholine(DB06709)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tramadol(DB00193)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	CAAGGAGAAGAAAGCGGCCCA	0.507																																																	0			1											135.0	129.0	131.0					1																	240072213		2203	4300	6503	238138836	SO:0001583	missense	1131			U29589	CCDS1616.1	1q43	2012-09-20			ENSG00000133019	ENSG00000133019		"""Cholinergic receptors"", ""GPCR / Class A : Cholinergic receptors, muscarinic"""	1952	protein-coding gene	gene with protein product	"""acetylcholine receptor, muscarinic 3"""	118494					Standard	XM_005273032		Approved		uc001hyp.3	P20309	OTTHUMG00000039649	ENST00000255380.4:c.1462A>G	1.37:g.240072213A>G	ENSP00000255380:p.Lys488Glu	Somatic		Capture	Illumina HiSeq	Phase_I	238138836	Q0VAJ8|Q4QRI3|Q5VXY2|Q9HB60	Missense_Mutation	SNP	ENST00000255380.4	37	CCDS1616.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.142363	0.77888	.	.	ENSG00000133019	ENST00000255380	T	0.42131	0.98	5.85	5.85	0.93711	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.66848	0.2831	M	0.86097	2.795	0.80722	D	1	D	0.59767	0.986	P	0.62014	0.897	T	0.73065	-0.4100	10	0.87932	D	0	-18.1655	16.2343	0.82363	1.0:0.0:0.0:0.0	.	488	P20309	ACM3_HUMAN	E	488	ENSP00000255380:K488E	ENSP00000255380:K488E	K	+	1	0	CHRM3	238138836	1.000000	0.71417	0.997000	0.53966	0.991000	0.79684	9.339000	0.96797	2.234000	0.73211	0.533000	0.62120	AAA		CHRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095644.2	NM_000740	
OSBPL5	114879	hgsc.bcm.edu	37	11	3143293	3143293	+	Silent	SNP	G	G	A	rs11828515	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr11:3143293G>A	ENST00000263650.7	-	5	495	c.336C>T	c.(334-336)cgC>cgT	p.R112R	OSBPL5_ENST00000542243.1_Intron|OSBPL5_ENST00000348039.5_Silent_p.R112R|OSBPL5_ENST00000389989.3_Silent_p.R112R|OSBPL5_ENST00000525498.1_Silent_p.R64R	NM_020896.3	NP_065947.1	Q9H0X9	OSBL5_HUMAN	oxysterol binding protein-like 5	112					cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|Golgi to plasma membrane transport (GO:0006893)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	cholesterol binding (GO:0015485)|oxysterol binding (GO:0008142)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	25		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)		GCCGTGTGGCGCGCTTCTTCT	0.682													G|||	18	0.00359425	0.0136	0.0	5008	,	,		15914	0.0		0.0	False		,,,				2504	0.0																0			11						G	,,	32,4348		0,32,2158	43.0	35.0	38.0		336,336,336	-8.3	0.0	11	dbSNP_120	38	0,8582		0,0,4291	no	coding-synonymous,coding-synonymous,coding-synonymous	OSBPL5	NM_001144063.1,NM_020896.3,NM_145638.2	,,	0,32,6449	AA,AG,GG		0.0,0.7306,0.2469	,,	112/812,112/880,112/812	3143293	32,12930	2190	4291	6481	3099869	SO:0001819	synonymous_variant	114879			AF392453	CCDS31343.1, CCDS31344.1	11p15.4	2013-01-10			ENSG00000021762	ENSG00000021762		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16392	protein-coding gene	gene with protein product		606733					Standard	NM_145638		Approved	KIAA1534, ORP5	uc001lxk.2	Q9H0X9	OTTHUMG00000011702	ENST00000263650.7:c.336C>T	11.37:g.3143293G>A		Somatic		Capture	Illumina HiSeq	Phase_I	3099869	A6NDP0|A6NJS8|Q54A90|Q8N596|Q9BZB0|Q9P1Z4	Silent	SNP	ENST00000263650.7	37	CCDS31344.1																																																																																				OSBPL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032332.2		
OR52B6	340980	hgsc.bcm.edu	37	11	5603051	5603051	+	Silent	SNP	G	G	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr11:5603051G>A	ENST00000345043.2	+	1	945	c.945G>A	c.(943-945)agG>agA	p.R315R	HBG2_ENST00000380259.2_Intron|AC015691.13_ENST00000394793.2_RNA	NM_001005162.2	NP_001005162.2	Q8NGF0	O52B6_HUMAN	olfactory receptor, family 52, subfamily B, member 6	315						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|lung(7)|ovary(1)|prostate(1)	12		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;3.56e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ATGGAGTGAGGACTAAGCCAA	0.438																																																	0			11											196.0	175.0	182.0					11																	5603051		1915	4130	6045	5559627	SO:0001819	synonymous_variant	340980			AB065858	CCDS41611.1	11p15.4	2012-08-09			ENSG00000187747	ENSG00000187747		"""GPCR / Class A : Olfactory receptors"""	15211	protein-coding gene	gene with protein product							Standard	NM_001005162		Approved		uc010qzi.2	Q8NGF0	OTTHUMG00000066906	ENST00000345043.2:c.945G>A	11.37:g.5603051G>A		Somatic		Capture	Illumina HiSeq	Phase_I	5559627	Q6IFI7	Silent	SNP	ENST00000345043.2	37	CCDS41611.1																																																																																				OR52B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143397.1	NM_001005162	
ABCC8	6833	hgsc.bcm.edu	37	11	17418522	17418522	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr11:17418522C>T	ENST00000389817.3	-	33	4128	c.4060G>A	c.(4060-4062)Gac>Aac	p.D1354N	ABCC8_ENST00000302539.4_Missense_Mutation_p.D1355N			Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 8	1354	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium ion transmembrane transporter activity (GO:0015079)|sulfonylurea receptor activity (GO:0008281)	p.D1354N(1)|p.D1354Y(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(38)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	67				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Chlorpropamide(DB00672)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Gliquidone(DB01251)|Glyburide(DB01016)|Glycodiazine(DB01382)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)|Tolbutamide(DB01124)	AGGGAGCTGTCGTAGCGCACG	0.632																																																	2	Substitution - Missense(2)	ovary(1)|lung(1)	11											130.0	104.0	113.0					11																	17418522		2200	4293	6493	17375098	SO:0001583	missense	6833			L78207	CCDS31437.1, CCDS73264.1	11p15.1	2014-09-17			ENSG00000006071	ENSG00000006071		"""ATP binding cassette transporters / subfamily C"""	59	protein-coding gene	gene with protein product	"""sulfonylurea receptor (hyperinsulinemia)"""	600509		SUR, HRINS		7920639, 7716548	Standard	NM_000352		Approved	HI, PHHI, SUR1, MRP8, ABC36, HHF1, TNDM2	uc001mnc.3	Q09428	OTTHUMG00000166316	ENST00000389817.3:c.4060G>A	11.37:g.17418522C>T	ENSP00000374467:p.Asp1354Asn	Somatic		Capture	Illumina HiSeq	Phase_I	17375098	A6NMX8|E3UYX6|O75948|Q16583	Missense_Mutation	SNP	ENST00000389817.3	37	CCDS31437.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.8|20.8	4.046357|4.046357	0.75846|0.75846	.|.	.|.	ENSG00000006071|ENSG00000006071	ENST00000389817;ENST00000302539|ENST00000528374	D;D|.	0.90504|.	-2.68;-2.68|.	4.83|4.83	4.83|4.83	0.62350|0.62350	ABC transporter-like (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.56202|0.56202	0.1969|0.1969	L|L	0.28014|0.28014	0.82|0.82	0.80722|0.80722	D|D	1|1	B|.	0.26318|.	0.146|.	B|.	0.17433|.	0.018|.	T|T	0.52403|0.52403	-0.8580|-0.8580	10|5	0.42905|.	T|.	0.14|.	.|.	18.2867|18.2867	0.90117|0.90117	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1354|.	Q09428|.	ABCC8_HUMAN|.	N|Q	1354;1355|181	ENSP00000374467:D1354N;ENSP00000303960:D1355N|.	ENSP00000303960:D1355N|.	D|R	-|-	1|2	0|0	ABCC8|ABCC8	17375098|17375098	1.000000|1.000000	0.71417|0.71417	0.984000|0.984000	0.44739|0.44739	0.924000|0.924000	0.55760|0.55760	5.983000|5.983000	0.70540|0.70540	2.386000|2.386000	0.81285|0.81285	0.555000|0.555000	0.69702|0.69702	GAC|CGA		ABCC8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389093.1	NM_000352	
MACROD1	28992	hgsc.bcm.edu	37	11	63884784	63884784	+	Intron	SNP	G	G	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr11:63884784G>A	ENST00000255681.6	-	3	584				RP11-21A7A.3_ENST00000543817.1_RNA|FLRT1_ENST00000246841.3_Missense_Mutation_p.V349M	NM_014067.3	NP_054786.2	Q9BQ69	MACD1_HUMAN	MACRO domain containing 1						cellular response to DNA damage stimulus (GO:0006974)|protein de-ADP-ribosylation (GO:0051725)|purine nucleoside metabolic process (GO:0042278)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	deacetylase activity (GO:0019213)|hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(1)|large_intestine(3)|lung(6)|skin(1)	11						ACGGGCGGCCGTGGTCAACGT	0.632																																																	0			11											51.0	51.0	51.0					11																	63884784		2201	4297	6498	63641360	SO:0001627	intron_variant	23769			AF202922	CCDS8056.1	11q13.1	2007-07-24	2007-06-11		ENSG00000133315	ENSG00000133315			29598	protein-coding gene	gene with protein product		610400				15691879	Standard	NM_014067		Approved	LRP16	uc001nyh.3	Q9BQ69	OTTHUMG00000167843	ENST00000255681.6:c.517+33926C>T	11.37:g.63884784G>A		Somatic		Capture	Illumina HiSeq	Phase_I	63641360	Q9UH96	Missense_Mutation	SNP	ENST00000255681.6	37	CCDS8056.1	.	.	.	.	.	.	.	.	.	.	G	15.42	2.827920	0.50845	.	.	ENSG00000126500	ENST00000246841	T	0.02498	4.27	4.84	4.84	0.62591	Cysteine-rich flanking region, C-terminal (1);	0.394868	0.24052	N	0.041987	T	0.08358	0.0208	M	0.64997	1.995	0.39604	D	0.969782	D	0.71674	0.998	P	0.51550	0.673	T	0.33497	-0.9866	10	0.33141	T	0.24	-25.1881	17.0921	0.86625	0.0:0.0:1.0:0.0	.	321	Q9NZU1	FLRT1_HUMAN	M	349	ENSP00000246841:V349M	ENSP00000246841:V349M	V	+	1	0	FLRT1	63641360	0.992000	0.36948	0.990000	0.47175	0.889000	0.51656	2.162000	0.42367	2.395000	0.81488	0.555000	0.69702	GTG		MACROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396570.1	NM_014067	
MEN1	4221	hgsc.bcm.edu	37	11	64571900	64571900	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr11:64571900G>A	ENST00000337652.1	-	10	2257	c.1754C>T	c.(1753-1755)aCg>aTg	p.T585M	MEN1_ENST00000394376.1_Missense_Mutation_p.T585M|MEN1_ENST00000478548.1_5'UTR|MAP4K2_ENST00000377350.3_5'Flank|MAP4K2_ENST00000468062.1_5'Flank|MEN1_ENST00000443283.1_Missense_Mutation_p.T585M|MEN1_ENST00000394374.2_Missense_Mutation_p.T585M|MEN1_ENST00000312049.6_Missense_Mutation_p.T580M|MEN1_ENST00000377321.1_Missense_Mutation_p.T545M|MEN1_ENST00000377313.1_Missense_Mutation_p.T585M|MAP4K2_ENST00000294066.2_5'Flank|MEN1_ENST00000377326.3_Missense_Mutation_p.T580M|MEN1_ENST00000377316.2_Missense_Mutation_p.T525M|MEN1_ENST00000315422.4_Missense_Mutation_p.T580M	NM_130803.2	NP_570715	O00255	MEN1_HUMAN	multiple endocrine neoplasia I	585					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA repair (GO:0006281)|embryonic skeletal system morphogenesis (GO:0048704)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|histone lysine methylation (GO:0034968)|leukocyte homeostasis (GO:0001776)|MAPK cascade (GO:0000165)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of JNK cascade (GO:0046329)|negative regulation of organ growth (GO:0046621)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|osteoblast fate commitment (GO:0002051)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell division (GO:0051781)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of histone methylation (GO:0031062)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of activin receptor signaling pathway (GO:0032925)|response to gamma radiation (GO:0010332)|response to UV (GO:0009411)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	chromatin (GO:0000785)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|four-way junction DNA binding (GO:0000400)|protein binding, bridging (GO:0030674)|protein N-terminus binding (GO:0047485)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|Y-form DNA binding (GO:0000403)	p.T580R(1)		NS(7)|adrenal_gland(5)|breast(2)|central_nervous_system(5)|endometrium(1)|gastrointestinal_tract_(site_indeterminate)(15)|large_intestine(2)|lung(21)|ovary(1)|pancreas(64)|parathyroid(181)|pituitary(7)|prostate(4)|retroperitoneum(1)|skin(1)|small_intestine(13)|soft_tissue(4)|stomach(1)|thymus(2)	337						CGACTGTGCCGTGAGTTGCAG	0.542			"""D, Mis, N, F, S"""		"""parathyroid tumors, Pancreatic neuroendocrine tumors"""	"""parathyroid adenoma, pituitary adenoma, pancreatic islet cell, carcinoid"""			Multiple Endocrine Neoplasia, type 1;Hyperparathyroidism, Familial Isolated																												Esophageal Squamous(1;83 158 15500 18603 18803 29295)		yes	Rec	yes	Multiple Endocrine Neoplasia Type 1	11	11q13	4221	multiple endocrine neoplasia type 1 gene		E	1	Substitution - Missense(1)	parathyroid(1)	11											240.0	215.0	223.0					11																	64571900		2201	4297	6498	64328476	SO:0001583	missense	4221	Familial Cancer Database	MEN1, Wermer disease;FIHP, FIHPT, HRPT1, Familial Isolated Primary Hyperparathyroidism	U93236	CCDS8083.1, CCDS31600.1	11q13	2014-09-17			ENSG00000133895	ENSG00000133895			7010	protein-coding gene	gene with protein product	"""menin"""	613733					Standard	NM_130799		Approved		uc001obn.3	O00255	OTTHUMG00000045366	ENST00000337652.1:c.1754C>T	11.37:g.64571900G>A	ENSP00000337088:p.Thr585Met	Somatic		Capture	Illumina HiSeq	Phase_I	64328476	A5HBC6|A5HBC7|A5HBC8|A5HBC9|A5HBD0|A5HBD1|A5HBD2|O00632|Q9BUF0|Q9BUK2	Missense_Mutation	SNP	ENST00000337652.1	37	CCDS8083.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.940959	0.73557	.	.	ENSG00000133895	ENST00000377316;ENST00000377321;ENST00000377326;ENST00000312049;ENST00000315422;ENST00000337652;ENST00000394376;ENST00000394374;ENST00000443283;ENST00000377313	D;D;D;D;D;D;D;D;D;D	0.99598	-6.26;-6.26;-6.26;-6.26;-6.26;-6.26;-6.26;-6.26;-6.26;-6.26	4.67	4.67	0.58626	.	0.111153	0.64402	D	0.000014	D	0.99477	0.9814	M	0.65975	2.015	0.58432	D	0.999995	D;P;D	0.89917	1.0;0.834;1.0	D;B;D	0.87578	0.996;0.337;0.998	D	0.98272	1.0504	10	0.87932	D	0	-10.9542	15.5063	0.75743	0.0:0.0:1.0:0.0	.	580;545;585	O00255-2;O00255-3;O00255	.;.;MEN1_HUMAN	M	525;545;580;580;580;585;585;585;585;585	ENSP00000366533:T525M;ENSP00000366538:T545M;ENSP00000366543:T580M;ENSP00000308975:T580M;ENSP00000323747:T580M;ENSP00000337088:T585M;ENSP00000377901:T585M;ENSP00000377899:T585M;ENSP00000396940:T585M;ENSP00000366530:T585M	ENSP00000308975:T580M	T	-	2	0	MEN1	64328476	1.000000	0.71417	0.997000	0.53966	0.975000	0.68041	8.325000	0.90007	2.327000	0.79052	0.555000	0.69702	ACG		MEN1-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000143881.1		
MEN1	4221	hgsc.bcm.edu	37	11	64574511	64574511	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr11:64574511C>T	ENST00000337652.1	-	6	1402	c.899G>A	c.(898-900)cGg>cAg	p.R300Q	MEN1_ENST00000394376.1_Missense_Mutation_p.R300Q|MEN1_ENST00000478548.1_5'Flank|MEN1_ENST00000443283.1_Missense_Mutation_p.R300Q|MEN1_ENST00000394374.2_Missense_Mutation_p.R300Q|MEN1_ENST00000312049.6_Missense_Mutation_p.R295Q|MEN1_ENST00000377321.1_Missense_Mutation_p.R260Q|MEN1_ENST00000377313.1_Missense_Mutation_p.R300Q|MEN1_ENST00000377326.3_Missense_Mutation_p.R295Q|MEN1_ENST00000377316.2_Missense_Mutation_p.R295Q|MEN1_ENST00000315422.4_Missense_Mutation_p.R295Q	NM_130803.2	NP_570715	O00255	MEN1_HUMAN	multiple endocrine neoplasia I	300	Interaction with FANCD2.				brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA repair (GO:0006281)|embryonic skeletal system morphogenesis (GO:0048704)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|histone lysine methylation (GO:0034968)|leukocyte homeostasis (GO:0001776)|MAPK cascade (GO:0000165)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of JNK cascade (GO:0046329)|negative regulation of organ growth (GO:0046621)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|osteoblast fate commitment (GO:0002051)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell division (GO:0051781)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of histone methylation (GO:0031062)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of activin receptor signaling pathway (GO:0032925)|response to gamma radiation (GO:0010332)|response to UV (GO:0009411)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	chromatin (GO:0000785)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|four-way junction DNA binding (GO:0000400)|protein binding, bridging (GO:0030674)|protein N-terminus binding (GO:0047485)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|Y-form DNA binding (GO:0000403)	p.R295L(1)		NS(7)|adrenal_gland(5)|breast(2)|central_nervous_system(5)|endometrium(1)|gastrointestinal_tract_(site_indeterminate)(15)|large_intestine(2)|lung(21)|ovary(1)|pancreas(64)|parathyroid(181)|pituitary(7)|prostate(4)|retroperitoneum(1)|skin(1)|small_intestine(13)|soft_tissue(4)|stomach(1)|thymus(2)	337						TGGGTCTGGCCGGCCAGGGGT	0.627			"""D, Mis, N, F, S"""		"""parathyroid tumors, Pancreatic neuroendocrine tumors"""	"""parathyroid adenoma, pituitary adenoma, pancreatic islet cell, carcinoid"""			Multiple Endocrine Neoplasia, type 1;Hyperparathyroidism, Familial Isolated																												Esophageal Squamous(1;83 158 15500 18603 18803 29295)		yes	Rec	yes	Multiple Endocrine Neoplasia Type 1	11	11q13	4221	multiple endocrine neoplasia type 1 gene		E	1	Substitution - Missense(1)	lung(1)	11											49.0	55.0	53.0					11																	64574511		2201	4297	6498	64331087	SO:0001583	missense	4221	Familial Cancer Database	MEN1, Wermer disease;FIHP, FIHPT, HRPT1, Familial Isolated Primary Hyperparathyroidism	U93236	CCDS8083.1, CCDS31600.1	11q13	2014-09-17			ENSG00000133895	ENSG00000133895			7010	protein-coding gene	gene with protein product	"""menin"""	613733					Standard	NM_130799		Approved		uc001obn.3	O00255	OTTHUMG00000045366	ENST00000337652.1:c.899G>A	11.37:g.64574511C>T	ENSP00000337088:p.Arg300Gln	Somatic		Capture	Illumina HiSeq	Phase_I	64331087	A5HBC6|A5HBC7|A5HBC8|A5HBC9|A5HBD0|A5HBD1|A5HBD2|O00632|Q9BUF0|Q9BUK2	Missense_Mutation	SNP	ENST00000337652.1	37	CCDS8083.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.482561	0.84747	.	.	ENSG00000133895	ENST00000377316;ENST00000377321;ENST00000377326;ENST00000312049;ENST00000315422;ENST00000337652;ENST00000394376;ENST00000394374;ENST00000443283;ENST00000377313;ENST00000440873	D;D;D;D;D;D;D;D;D;D;D	0.99369	-5.78;-5.78;-5.78;-5.78;-5.78;-5.78;-5.78;-5.78;-5.78;-5.78;-5.78	4.24	4.24	0.50183	.	0.072223	0.52532	D	0.000076	D	0.98305	0.9438	L	0.49126	1.545	0.37982	D	0.933627	P;P;P	0.50710	0.923;0.706;0.938	B;B;P	0.47162	0.405;0.124;0.54	D	0.99933	1.1335	10	0.72032	D	0.01	-27.2369	14.501	0.67722	0.0:1.0:0.0:0.0	.	295;260;300	O00255-2;O00255-3;O00255	.;.;MEN1_HUMAN	Q	295;260;295;295;295;300;300;300;300;300;295	ENSP00000366533:R295Q;ENSP00000366538:R260Q;ENSP00000366543:R295Q;ENSP00000308975:R295Q;ENSP00000323747:R295Q;ENSP00000337088:R300Q;ENSP00000377901:R300Q;ENSP00000377899:R300Q;ENSP00000396940:R300Q;ENSP00000366530:R300Q;ENSP00000413944:R295Q	ENSP00000308975:R295Q	R	-	2	0	MEN1	64331087	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.567000	0.60850	2.080000	0.62538	0.462000	0.41574	CGG		MEN1-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000143881.1		
MEN1	4221	hgsc.bcm.edu	37	11	64577457	64577457	+	Missense_Mutation	SNP	C	C	T	rs386134248		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr11:64577457C>T	ENST00000337652.1	-	2	628	c.125G>A	c.(124-126)gGc>gAc	p.G42D	MEN1_ENST00000394376.1_Missense_Mutation_p.G42D|MEN1_ENST00000443283.1_Missense_Mutation_p.G42D|MEN1_ENST00000394374.2_Missense_Mutation_p.G42D|MEN1_ENST00000312049.6_Missense_Mutation_p.G42D|MEN1_ENST00000377321.1_Missense_Mutation_p.G42D|MEN1_ENST00000377313.1_Missense_Mutation_p.G42D|MEN1_ENST00000377326.3_Missense_Mutation_p.G42D|MEN1_ENST00000377316.2_Missense_Mutation_p.G42D|MEN1_ENST00000315422.4_Missense_Mutation_p.G42D	NM_130803.2	NP_570715	O00255	MEN1_HUMAN	multiple endocrine neoplasia I	42			G -> D (in MEN1). {ECO:0000269|PubMed:12112656, ECO:0000269|PubMed:9463336}.		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA repair (GO:0006281)|embryonic skeletal system morphogenesis (GO:0048704)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|histone lysine methylation (GO:0034968)|leukocyte homeostasis (GO:0001776)|MAPK cascade (GO:0000165)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of JNK cascade (GO:0046329)|negative regulation of organ growth (GO:0046621)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|osteoblast fate commitment (GO:0002051)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell division (GO:0051781)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of histone methylation (GO:0031062)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of activin receptor signaling pathway (GO:0032925)|response to gamma radiation (GO:0010332)|response to UV (GO:0009411)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	chromatin (GO:0000785)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|four-way junction DNA binding (GO:0000400)|protein binding, bridging (GO:0030674)|protein N-terminus binding (GO:0047485)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|Y-form DNA binding (GO:0000403)	p.E30_F47>D(1)|p.L22_P59del(1)		NS(7)|adrenal_gland(5)|breast(2)|central_nervous_system(5)|endometrium(1)|gastrointestinal_tract_(site_indeterminate)(15)|large_intestine(2)|lung(21)|ovary(1)|pancreas(64)|parathyroid(181)|pituitary(7)|prostate(4)|retroperitoneum(1)|skin(1)|small_intestine(13)|soft_tissue(4)|stomach(1)|thymus(2)	337						CTCCACGAAGCCCAGCACCAA	0.672			"""D, Mis, N, F, S"""		"""parathyroid tumors, Pancreatic neuroendocrine tumors"""	"""parathyroid adenoma, pituitary adenoma, pancreatic islet cell, carcinoid"""			Multiple Endocrine Neoplasia, type 1;Hyperparathyroidism, Familial Isolated																												Esophageal Squamous(1;83 158 15500 18603 18803 29295)		yes	Rec	yes	Multiple Endocrine Neoplasia Type 1	11	11q13	4221	multiple endocrine neoplasia type 1 gene		E	2	Complex - deletion inframe(1)|Deletion - In frame(1)	parathyroid(2)	11	GRCh37	CM981250	MEN1	M							46.0	48.0	47.0					11																	64577457		2192	4292	6484	64334033	SO:0001583	missense	4221	Familial Cancer Database	MEN1, Wermer disease;FIHP, FIHPT, HRPT1, Familial Isolated Primary Hyperparathyroidism	U93236	CCDS8083.1, CCDS31600.1	11q13	2014-09-17			ENSG00000133895	ENSG00000133895			7010	protein-coding gene	gene with protein product	"""menin"""	613733					Standard	NM_130799		Approved		uc001obn.3	O00255	OTTHUMG00000045366	ENST00000337652.1:c.125G>A	11.37:g.64577457C>T	ENSP00000337088:p.Gly42Asp	Somatic		Capture	Illumina HiSeq	Phase_I	64334033	A5HBC6|A5HBC7|A5HBC8|A5HBC9|A5HBD0|A5HBD1|A5HBD2|O00632|Q9BUF0|Q9BUK2	Missense_Mutation	SNP	ENST00000337652.1	37	CCDS8083.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.857404	0.91433	.	.	ENSG00000133895	ENST00000377316;ENST00000377321;ENST00000377326;ENST00000312049;ENST00000315422;ENST00000337652;ENST00000394376;ENST00000394374;ENST00000443283;ENST00000377313;ENST00000440873;ENST00000450708;ENST00000413626;ENST00000429702;ENST00000424912	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.99773	-6.72;-6.72;-6.72;-6.72;-6.72;-6.72;-6.72;-6.72;-6.72;-6.72;-6.72;-6.72;-6.72;-6.72;-6.72	4.89	3.98	0.46160	.	0.000000	0.85682	D	0.000000	D	0.99603	0.9856	M	0.67397	2.05	0.58432	D	0.999999	D;B;D	0.89917	1.0;0.028;1.0	D;B;D	0.97110	1.0;0.016;1.0	D	0.98091	1.0409	10	0.87932	D	0	-30.7605	11.2371	0.48946	0.0:0.9096:0.0:0.0904	.	42;42;42	O00255-2;O00255-3;O00255	.;.;MEN1_HUMAN	D	42	ENSP00000366533:G42D;ENSP00000366538:G42D;ENSP00000366543:G42D;ENSP00000308975:G42D;ENSP00000323747:G42D;ENSP00000337088:G42D;ENSP00000377901:G42D;ENSP00000377899:G42D;ENSP00000396940:G42D;ENSP00000366530:G42D;ENSP00000413944:G42D;ENSP00000394933:G42D;ENSP00000411218:G42D;ENSP00000402752:G42D;ENSP00000388016:G42D	ENSP00000308975:G42D	G	-	2	0	MEN1	64334033	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	5.464000	0.66719	1.191000	0.43056	0.462000	0.41574	GGC		MEN1-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000143881.1		
EHBP1L1	254102	hgsc.bcm.edu	37	11	65349195	65349195	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr11:65349195C>T	ENST00000309295.4	+	9	1317	c.1052C>T	c.(1051-1053)aCa>aTa	p.T351I		NM_001099409.1	NP_001092879.1	Q8N3D4	EH1L1_HUMAN	EH domain binding protein 1-like 1	351						membrane (GO:0016020)				central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23						CAGGAAGGGACAGAAGCCCAT	0.602																																																	0			11											22.0	25.0	24.0					11																	65349195		1911	4104	6015	65105771	SO:0001583	missense	254102			AL834433	CCDS44649.1	11q13.1	2008-02-05			ENSG00000173442	ENSG00000173442			30682	protein-coding gene	gene with protein product							Standard	NM_001099409		Approved	DKFZp762C186, TANGERIN	uc001oeo.4	Q8N3D4	OTTHUMG00000166520	ENST00000309295.4:c.1052C>T	11.37:g.65349195C>T	ENSP00000312671:p.Thr351Ile	Somatic		Capture	Illumina HiSeq	Phase_I	65105771	Q8TB89|Q9H7M7	Missense_Mutation	SNP	ENST00000309295.4	37	CCDS44649.1	.	.	.	.	.	.	.	.	.	.	C	10.97	1.501541	0.26861	.	.	ENSG00000173442	ENST00000309295;ENST00000533237	T;T	0.81163	-0.23;-1.46	4.13	-0.573	0.11742	.	0.813010	0.10520	N	0.665133	T	0.78052	0.4223	L	0.36672	1.1	0.34121	D	0.664121	D	0.65815	0.995	P	0.56278	0.795	T	0.77778	-0.2460	10	0.87932	D	0	.	5.253	0.15532	0.0:0.4692:0.3132:0.2176	.	351	Q8N3D4	EH1L1_HUMAN	I	351	ENSP00000312671:T351I;ENSP00000431996:T351I	ENSP00000312671:T351I	T	+	2	0	EHBP1L1	65105771	0.151000	0.22747	0.976000	0.42696	0.238000	0.25445	0.494000	0.22467	0.301000	0.22738	-0.367000	0.07326	ACA		EHBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390145.1	XM_170658	
TYR	7299	hgsc.bcm.edu	37	11	88924500	88924500	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr11:88924500A>G	ENST00000263321.5	+	2	1452	c.950A>G	c.(949-951)gAt>gGt	p.D317G	TYR_ENST00000526139.1_3'UTR	NM_000372.4	NP_000363.1	P14679	TYRO_HUMAN	tyrosinase	317					cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process from tyrosine (GO:0006583)|thymus development (GO:0048538)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|Golgi-associated vesicle (GO:0005798)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|melanosome (GO:0042470)|perinuclear region of cytoplasm (GO:0048471)	copper ion binding (GO:0005507)|monophenol monooxygenase activity (GO:0004503)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.D317A(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.0033)			Azelaic Acid(DB00548)|Mimosine(DB01055)|Monobenzone(DB00600)	TCTTCAGCTGATGTAGAATTT	0.448																																																	1	Substitution - Missense(1)	ovary(1)	11											120.0	117.0	118.0					11																	88924500		2201	4299	6500	88564148	SO:0001583	missense	7299			M27160	CCDS8284.1	11q14.3	2013-09-27	2012-09-28		ENSG00000077498	ENSG00000077498	1.14.18.1		12442	protein-coding gene	gene with protein product	"""oculocutaneous albinism IA"""	606933					Standard	NM_000372		Approved	OCAIA, OCA1A, OCA1	uc001pcs.3	P14679	OTTHUMG00000167294	ENST00000263321.5:c.950A>G	11.37:g.88924500A>G	ENSP00000263321:p.Asp317Gly	Somatic		Capture	Illumina HiSeq	Phase_I	88564148	Q15675|Q15676|Q15680|Q8TAK4|Q9BYY0|Q9BZX1	Missense_Mutation	SNP	ENST00000263321.5	37	CCDS8284.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.635987	0.87760	.	.	ENSG00000077498	ENST00000263321	D	0.97480	-4.4	5.59	5.59	0.84812	Tyrosinase (1);Uncharacterised domain, di-copper centre (2);	0.197051	0.52532	D	0.000062	D	0.98485	0.9495	M	0.91249	3.19	0.58432	D	0.999999	D	0.56746	0.977	P	0.59703	0.862	D	0.99327	1.0908	9	.	.	.	.	15.7688	0.78149	1.0:0.0:0.0:0.0	.	317	P14679	TYRO_HUMAN	G	317	ENSP00000263321:D317G	.	D	+	2	0	TYR	88564148	1.000000	0.71417	0.969000	0.41365	0.970000	0.65996	8.771000	0.91751	2.134000	0.65973	0.533000	0.62120	GAT		TYR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394045.2	NM_000372	
KIAA1731	85459	hgsc.bcm.edu	37	11	93431000	93431000	+	Silent	SNP	G	G	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr11:93431000G>A	ENST00000325212.6	+	15	3084	c.2922G>A	c.(2920-2922)ttG>ttA	p.L974L	KIAA1731_ENST00000531700.1_Intron|KIAA1731_ENST00000411936.1_Silent_p.L974L|KIAA1731_ENST00000344196.4_5'UTR			Q9C0D2	K1731_HUMAN	KIAA1731	974						centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)	11		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				AGGAAGTATTGTATGTACATA	0.408																																																	0			11											71.0	66.0	68.0					11																	93431000		692	1591	2283	93070648	SO:0001819	synonymous_variant	85459			AB051518	CCDS44708.1	11q21	2014-03-11			ENSG00000166004	ENSG00000166004			29366	protein-coding gene	gene with protein product						20844083	Standard	NM_033395		Approved		uc009ywb.1	Q9C0D2	OTTHUMG00000167449	ENST00000325212.6:c.2922G>A	11.37:g.93431000G>A		Somatic		Capture	Illumina HiSeq	Phase_I	93070648	C9J5H9|C9JQY8|Q8N7L4|Q8N919|Q8N9B0|Q96LT8	Silent	SNP	ENST00000325212.6	37	CCDS44708.1																																																																																				KIAA1731-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000394640.1	NM_033395	
CNTN5	53942	hgsc.bcm.edu	37	11	100179135	100179135	+	Missense_Mutation	SNP	G	G	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr11:100179135G>T	ENST00000524871.1	+	21	2955	c.2665G>T	c.(2665-2667)Gtg>Ttg	p.V889L	CNTN5_ENST00000527185.1_Missense_Mutation_p.V889L|CNTN5_ENST00000528682.1_Missense_Mutation_p.V889L|CNTN5_ENST00000279463.3_Missense_Mutation_p.V889L|CNTN5_ENST00000418526.2_Missense_Mutation_p.V815L|CNTN5_ENST00000524560.1_3'UTR	NM_014361.3	NP_055176.1	O94779	CNTN5_HUMAN	contactin 5	889	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(12)|lung(38)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	81		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		AAGTGTGTCTGTGTCAGAGAT	0.383																																																	0			11											77.0	76.0	76.0					11																	100179135		1883	4115	5998	99684345	SO:0001583	missense	53942			AB013802	CCDS53696.1, CCDS53697.1, CCDS58168.1	11q22.1	2013-02-11			ENSG00000149972	ENSG00000149972		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2175	protein-coding gene	gene with protein product		607219					Standard	NM_014361		Approved	NB-2, hNB-2	uc021qpb.1	O94779	OTTHUMG00000167579	ENST00000524871.1:c.2665G>T	11.37:g.100179135G>T	ENSP00000435637:p.Val889Leu	Somatic		Capture	Illumina HiSeq	Phase_I	99684345	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	Missense_Mutation	SNP	ENST00000524871.1	37	CCDS53696.1	.	.	.	.	.	.	.	.	.	.	G	15.87	2.960201	0.53400	.	.	ENSG00000149972	ENST00000527185;ENST00000528682;ENST00000524871;ENST00000418526;ENST00000279463	T;T;T;T;T	0.56611	2.33;0.45;0.45;0.45;0.45	5.69	0.605	0.17553	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.446700	0.26251	N	0.025450	T	0.34395	0.0896	N	0.17082	0.46	0.33590	D	0.601012	B;B	0.30146	0.228;0.27	B;B	0.31812	0.058;0.136	T	0.40924	-0.9537	10	0.66056	D	0.02	.	9.9907	0.41870	0.331:0.0:0.669:0.0	.	815;889	O94779-2;O94779	.;CNTN5_HUMAN	L	889;889;889;815;889	ENSP00000433575:V889L;ENSP00000436185:V889L;ENSP00000435637:V889L;ENSP00000393229:V815L;ENSP00000279463:V889L	ENSP00000279463:V889L	V	+	1	0	CNTN5	99684345	1.000000	0.71417	0.987000	0.45799	0.994000	0.84299	1.557000	0.36299	-0.058000	0.13177	0.591000	0.81541	GTG		CNTN5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395148.2	NM_014361	
ATM	472	hgsc.bcm.edu	37	11	108117712	108117712	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr11:108117712G>A	ENST00000452508.2	+	9	1112	c.923G>A	c.(922-924)tGg>tAg	p.W308*	ATM_ENST00000278616.4_Nonsense_Mutation_p.W308*			Q13315	ATM_HUMAN	ATM serine/threonine kinase	308					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.W308*(1)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	TCAACAAAATGGAGAAGTATT	0.313			"""D, Mis, N, F, S"""		T-PLL	"""leukemia, lymphoma, medulloblastoma, glioma"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																													yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"""L, O"""	1	Substitution - Nonsense(1)	haematopoietic_and_lymphoid_tissue(1)	11											44.0	47.0	46.0					11																	108117712		2200	4294	6494	107622922	SO:0001587	stop_gained	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"""TEL1, telomere maintenance 1, homolog (S. cerevisiae)"""	607585	"""ataxia telangiectasia mutated (includes complementation groups A, C and D)"", ""ataxia telangiectasia mutated"""	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.923G>A	11.37:g.108117712G>A	ENSP00000388058:p.Trp308*	Somatic		Capture	Illumina HiSeq	Phase_I	107622922	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Nonsense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	G	40	8.432389	0.98808	.	.	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000452508	.	.	.	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.4005	0.94627	0.0:0.0:1.0:0.0	.	.	.	.	X	308	.	ENSP00000278616:W308X	W	+	2	0	ATM	107622922	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	9.254000	0.95512	2.591000	0.87537	0.655000	0.94253	TGG		ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051	
HIST1H4A	8359	hgsc.bcm.edu	37	6	26022177	26022177	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr6:26022177C>T	ENST00000359907.3	+	1	271	c.271C>T	c.(271-273)Ctt>Ttt	p.L91F		NM_003538.3	NP_003529.1	P62805	H4_HUMAN	histone cluster 1, H4a	91					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of megakaryocyte differentiation (GO:0045653)|nucleosome assembly (GO:0006334)|telomere maintenance (GO:0000723)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|histone demethylase activity (H4-K20 specific) (GO:0035575)|poly(A) RNA binding (GO:0044822)			large_intestine(1)|skin(1)	2						GGTCTACGCGCTTAAGCGCCA	0.557																																																	0			6											99.0	85.0	90.0					6																	26022177		2203	4300	6503	26130156	SO:0001583	missense	8359			X60481	CCDS4571.1	6p22.1	2011-01-27	2006-10-11	2003-03-07	ENSG00000196176	ENSG00000278637		"""Histones / Replication-dependent"""	4781	protein-coding gene	gene with protein product		602822	"""H4 histone family, member A"", ""histone 1, H4a"""	H4FA		9119399, 12408966	Standard	NM_003538		Approved		uc003nfq.3	P62805	OTTHUMG00000014419	ENST00000359907.3:c.271C>T	6.37:g.26022177C>T	ENSP00000352980:p.Leu91Phe	Somatic		Capture	Illumina HiSeq	Phase_I	26130156	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Missense_Mutation	SNP	ENST00000359907.3	37	CCDS4571.1	.	.	.	.	.	.	.	.	.	.	c	19.49	3.837513	0.71373	.	.	ENSG00000196176	ENST00000359907	T	0.70986	-0.53	3.97	3.97	0.46021	.	.	.	.	.	T	0.71500	0.3347	.	.	.	0.47778	D	0.99951	.	.	.	.	.	.	T	0.72001	-0.4422	5	.	.	.	.	15.9333	0.79683	0.0:1.0:0.0:0.0	.	.	.	.	F	91	ENSP00000352980:L91F	.	L	+	1	0	HIST1H4A	26130156	1.000000	0.71417	1.000000	0.80357	0.152000	0.21847	4.718000	0.61930	2.134000	0.65973	0.655000	0.94253	CTT		HIST1H4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040081.1	NM_003538	
MAS1L	116511	hgsc.bcm.edu	37	6	29454673	29454673	+	Missense_Mutation	SNP	G	G	A	rs566796111	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr6:29454673G>A	ENST00000377127.3	-	1	1065	c.1007C>T	c.(1006-1008)gCg>gTg	p.A336V		NM_052967.1	NP_443199.1	P35410	MAS1L_HUMAN	MAS1 proto-oncogene like, G protein-coupled receptor	336					G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.A336V(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(7)|pancreas(1)|prostate(2)|skin(2)	28						ATCTGCTAACGCCCGTTGGAG	0.493													G|||	2	0.000399361	0.0015	0.0	5008	,	,		17088	0.0		0.0	False		,,,				2504	0.0				NSCLC(153;755 1987 3859 11251 32945)												1	Substitution - Missense(1)	large_intestine(1)	6											137.0	138.0	138.0					6																	29454673		2203	4300	6503	29562652	SO:0001583	missense	116511			S78653	CCDS4661.1	6p22.1	2014-06-26	2014-06-26		ENSG00000204687	ENSG00000204687		"""GPCR / Class A : Orphans"""	13961	protein-coding gene	gene with protein product		607235	"""MAS1 oncogene-like"""				Standard	NM_052967		Approved	MAS-L, MRG, dJ994E9.2	uc011dlq.2	P35410	OTTHUMG00000031089	ENST00000377127.3:c.1007C>T	6.37:g.29454673G>A	ENSP00000366331:p.Ala336Val	Somatic		Capture	Illumina HiSeq	Phase_I	29562652	Q5SUN5	Missense_Mutation	SNP	ENST00000377127.3	37	CCDS4661.1	.	.	.	.	.	.	.	.	.	.	G	8.581	0.882339	0.17467	.	.	ENSG00000204687	ENST00000377127	T	0.36878	1.23	2.23	0.27	0.15635	.	.	.	.	.	T	0.10680	0.0261	L	0.45285	1.41	0.09310	N	1	B	0.27700	0.186	B	0.29942	0.109	T	0.33033	-0.9884	9	0.44086	T	0.13	.	2.6171	0.04907	0.2894:0.0:0.4883:0.2223	.	336	P35410	MAS1L_HUMAN	V	336	ENSP00000366331:A336V	ENSP00000366331:A336V	A	-	2	0	MAS1L	29562652	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.361000	0.07612	-0.075000	0.12798	-0.364000	0.07487	GCG		MAS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076126.2	NM_052967	
MICA	100507436	hgsc.bcm.edu	37	6	31379840	31379840	+	Missense_Mutation	SNP	G	G	T	rs41540613	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr6:31379840G>T	ENST00000449934.2	+	4	784	c.730G>T	c.(730-732)Gta>Tta	p.V244L	HCP5_ENST00000414046.2_RNA	NM_001177519.1	NP_001170990.1			MHC class I polypeptide-related sequence A											breast(1)|endometrium(3)|kidney(1)	5		Ovarian(999;0.0253)				TCAGGATGGGGTATCTTTGAG	0.592																																																	0			6											18.0	18.0	18.0					6																	31379840		692	1591	2283	31487819	SO:0001583	missense	4276			L14848	CCDS56412.1, CCDS75421.1	6p21.3	2013-01-11			ENSG00000204520	ENSG00000204520		"""Immunoglobulin superfamily / C1-set domain containing"""	7090	protein-coding gene	gene with protein product		600169				8022771	Standard	NM_000247		Approved	PERB11.1	uc003ntk.1	Q29983	OTTHUMG00000031073	ENST00000449934.2:c.730G>T	6.37:g.31379840G>T	ENSP00000413079:p.Val244Leu	Somatic		Capture	Illumina HiSeq	Phase_I	31487819		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1	.	.	.	.	.	.	.	.	.	.	g	8.834	0.940646	0.18281	.	.	ENSG00000204520	ENST00000376222;ENST00000364810;ENST00000399172;ENST00000449934;ENST00000421350	T;T	0.02944	4.1;4.1	2.52	-1.02	0.10135	.	2.098610	0.03122	U	0.163877	T	0.01061	0.0035	L	0.52364	1.645	0.09310	N	1	B;B	0.32382	0.368;0.036	B;B	0.35688	0.208;0.092	T	0.44967	-0.9293	10	0.34782	T	0.22	.	0.3146	0.00293	0.2776:0.2026:0.3136:0.2061	.	106;244	Q5SS58;Q96QC4	.;.	L	106;244;201;244;135	ENSP00000413079:V244L;ENSP00000402410:V135L	ENSP00000365394:V244L	V	+	1	0	MICA	31487819	0.070000	0.21116	0.000000	0.03702	0.013000	0.08279	0.375000	0.20518	-0.001000	0.14495	0.444000	0.29173	GTA		MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
LY6G6C	80740	hgsc.bcm.edu	37	6	31691923	31691923	+	5'Flank	SNP	C	C	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr6:31691923C>T	ENST00000375819.2	-	0	0				C6orf25_ENST00000375810.4_Silent_p.S138S|DDAH2_ENST00000480913.1_5'Flank|C6orf25_ENST00000375809.3_Silent_p.S138S|C6orf25_ENST00000375805.2_Intron|LY6G6C_ENST00000495859.1_5'Flank|C6orf25_ENST00000480039.1_Silent_p.S138S	NM_025261.2	NP_079537.1	O95867	LY66C_HUMAN	lymphocyte antigen 6 complex, locus G6C							anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				NS(1)|large_intestine(1)|lung(1)|skin(1)	4						CCCCAGGGTCCGTGTATCCCC	0.667																																																	0			6											39.0	28.0	32.0					6																	31691923		1509	2709	4218	31799902	SO:0001631	upstream_gene_variant	80739				CCDS4714.1	6p21	2008-08-29	2002-07-29	2002-08-01	ENSG00000204421	ENSG00000204421			13936	protein-coding gene	gene with protein product		610435	"""chromosome 6 open reading frame 24"""	C6orf24		10384126, 12079290	Standard	NM_025261		Approved	G6c, NG24	uc003nwh.3	O95867	OTTHUMG00000031251		6.37:g.31691923C>T	Exception_encountered	Somatic		Capture	Illumina HiSeq	Phase_I	31799902	Q5SRS8|Q8IY94	Silent	SNP	ENST00000375819.2	37	CCDS4714.1																																																																																				LY6G6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076530.2		
TFAP2D	83741	hgsc.bcm.edu	37	6	50682843	50682843	+	Silent	SNP	A	A	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr6:50682843A>G	ENST00000008391.3	+	2	282	c.54A>G	c.(52-54)ggA>ggG	p.G18G		NM_172238.3	NP_758438.2			transcription factor AP-2 delta (activating enhancer binding protein 2 delta)											NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(26)|ovary(6)|pancreas(1)|prostate(5)|stomach(1)	60	Lung NSC(77;0.0334)					GTCACGACGGATCAAACAGCT	0.527																																																	0			6											118.0	96.0	103.0					6																	50682843		2203	4300	6503	50790802	SO:0001819	synonymous_variant	83741			AY028376	CCDS4933.1	6p12.3	2008-02-05	2004-10-26	2004-10-27		ENSG00000008197			15581	protein-coding gene	gene with protein product		610161	"""transcription factor AP-2 beta (activating enhancer-binding protein 2 beta)-like 1"""	TFAP2BL1		11733187	Standard	NM_172238		Approved		uc003paf.3	Q7Z6R9		ENST00000008391.3:c.54A>G	6.37:g.50682843A>G		Somatic		Capture	Illumina HiSeq	Phase_I	50790802		Silent	SNP	ENST00000008391.3	37	CCDS4933.1																																																																																				TFAP2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040881.1	NM_172238	
PTPRK	5796	hgsc.bcm.edu	37	6	128297824	128297824	+	Missense_Mutation	SNP	A	A	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr6:128297824A>T	ENST00000368215.3	-	27	3943	c.3944T>A	c.(3943-3945)tTt>tAt	p.F1315Y	PTPRK_ENST00000368207.3_Missense_Mutation_p.F1348Y|PTPRK_ENST00000368210.3_Missense_Mutation_p.F1334Y|PTPRK_ENST00000368227.3_Missense_Mutation_p.F1333Y|PTPRK_ENST00000368213.5_Missense_Mutation_p.F1322Y|PTPRK_ENST00000532331.1_Missense_Mutation_p.F1338Y|PTPRK_ENST00000368226.4_Missense_Mutation_p.F1316Y			Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K	1315	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to reactive oxygen species (GO:0034614)|cellular response to UV (GO:0034644)|focal adhesion assembly (GO:0048041)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)		PTPRK/RSPO3(10)	autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(14)|lung(24)|ovary(3)|pancreas(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	72				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)		GCATATCCTAAAAATCCGGTT	0.423																																																	0			6											98.0	80.0	86.0					6																	128297824		2203	4300	6503	128339517	SO:0001583	missense	5796			L77886	CCDS5137.1, CCDS47473.1, CCDS75517.1	6q22.2-q22.3	2013-02-11			ENSG00000152894	ENSG00000152894		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9674	protein-coding gene	gene with protein product		602545				9047348, 8663237	Standard	NM_002844		Approved	R-PTP-kappa	uc010kfc.3	Q15262	OTTHUMG00000015536	ENST00000368215.3:c.3944T>A	6.37:g.128297824A>T	ENSP00000357198:p.Phe1315Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	128339517	B2RTQ8|B7ZMG0|Q14763|Q5TG10|Q5TG11	Missense_Mutation	SNP	ENST00000368215.3	37		.	.	.	.	.	.	.	.	.	.	A	31	5.084202	0.94100	.	.	ENSG00000152894	ENST00000368226;ENST00000368227;ENST00000532331;ENST00000368213;ENST00000368210;ENST00000368215;ENST00000368207	T;T;T;T;T;T;T	0.16196	2.36;2.36;2.36;2.36;2.36;2.36;2.36	5.56	5.56	0.83823	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.85682	D	0.000000	T	0.44265	0.1285	M	0.91972	3.26	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;0.991;0.989	D;D;D;D	0.91635	0.999;0.999;0.982;0.969	T	0.57659	-0.7773	10	0.87932	D	0	.	15.9985	0.80270	1.0:0.0:0.0:0.0	.	1338;1322;1315;1316	B7ZMG0;Q15262-3;Q15262;Q15262-2	.;.;PTPRK_HUMAN;.	Y	1316;1333;1338;1322;1334;1315;1348	ENSP00000357209:F1316Y;ENSP00000357210:F1333Y;ENSP00000432973:F1338Y;ENSP00000357196:F1322Y;ENSP00000357193:F1334Y;ENSP00000357198:F1315Y;ENSP00000357190:F1348Y	ENSP00000357190:F1348Y	F	-	2	0	PTPRK	128339517	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.287000	0.95975	2.237000	0.73441	0.533000	0.62120	TTT		PTPRK-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000042163.1		
SYNE1	23345	hgsc.bcm.edu	37	6	152712587	152712587	+	Missense_Mutation	SNP	C	C	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr6:152712587C>G	ENST00000367255.5	-	52	8430	c.7829G>C	c.(7828-7830)aGa>aCa	p.R2610T	SYNE1_ENST00000423061.1_Missense_Mutation_p.R2617T|SYNE1_ENST00000448038.1_Missense_Mutation_p.R2617T|SYNE1_ENST00000341594.5_Missense_Mutation_p.R2649T|SYNE1_ENST00000265368.4_Missense_Mutation_p.R2610T	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	2610					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TTTGGTCATTCTAAGTAGGTT	0.582										HNSCC(10;0.0054)																																							0			6											62.0	61.0	61.0					6																	152712587		2203	4300	6503	152754280	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.7829G>C	6.37:g.152712587C>G	ENSP00000356224:p.Arg2610Thr	Somatic		Capture	Illumina HiSeq	Phase_I	152754280	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	12.73	2.024271	0.35701	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.54479	0.66;0.64;0.57;0.64;0.77	5.91	4.11	0.48088	.	0.094910	0.44688	D	0.000422	T	0.19127	0.0459	L	0.29908	0.895	0.80722	D	1	P;P;P;P	0.43094	0.799;0.611;0.611;0.682	B;B;B;B	0.39531	0.205;0.159;0.159;0.302	T	0.03887	-1.0995	10	0.14252	T	0.57	.	5.9398	0.19186	0.0:0.7034:0.0:0.2966	.	2593;2610;2610;2617	B3W695;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	T	2610;2617;2610;2617;2649	ENSP00000356224:R2610T;ENSP00000396024:R2617T;ENSP00000265368:R2610T;ENSP00000390975:R2617T;ENSP00000341887:R2649T	ENSP00000265368:R2610T	R	-	2	0	SYNE1	152754280	0.996000	0.38824	0.333000	0.25482	0.926000	0.56050	2.959000	0.49153	2.793000	0.96121	0.655000	0.94253	AGA		SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
SYNE1	23345	hgsc.bcm.edu	37	6	152776694	152776694	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr6:152776694T>C	ENST00000367255.5	-	24	3360	c.2759A>G	c.(2758-2760)aAg>aGg	p.K920R	SYNE1_ENST00000423061.1_Missense_Mutation_p.K927R|SYNE1_ENST00000367253.4_Missense_Mutation_p.K920R|SYNE1_ENST00000495090.2_Missense_Mutation_p.K487R|SYNE1_ENST00000448038.1_Missense_Mutation_p.K927R|SYNE1_ENST00000413186.2_Missense_Mutation_p.K920R|SYNE1_ENST00000341594.5_Missense_Mutation_p.K986R|SYNE1_ENST00000367248.3_Missense_Mutation_p.K910R|SYNE1_ENST00000265368.4_Missense_Mutation_p.K920R	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	920					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TTCCACATGCTTCTTCCAATC	0.433										HNSCC(10;0.0054)																																							0			6											117.0	115.0	116.0					6																	152776694		2203	4300	6503	152818387	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.2759A>G	6.37:g.152776694T>C	ENSP00000356224:p.Lys920Arg	Somatic		Capture	Illumina HiSeq	Phase_I	152818387	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	T	16.24	3.068351	0.55539	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000367253;ENST00000367248;ENST00000413186;ENST00000495090	T;T;T;T;T;T;T;T;T	0.35236	1.32;1.32;1.32;1.32;1.39;1.32;1.32;1.32;1.32	5.48	5.48	0.80851	.	0.000000	0.64402	D	0.000015	T	0.37571	0.1008	L	0.52364	1.645	0.80722	D	1	D;B;B;B;D;B;P	0.69078	0.997;0.397;0.281;0.423;0.993;0.397;0.454	D;B;B;B;P;B;B	0.63957	0.92;0.093;0.103;0.138;0.876;0.093;0.137	T	0.13926	-1.0491	10	0.14656	T	0.56	.	15.5657	0.76290	0.0:0.0:0.0:1.0	.	903;920;487;910;920;920;927	B3W695;Q8NF91;F5H422;F5GXQ8;Q8NF91-6;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.;.;.;.	R	920;927;920;927;986;920;910;920;487	ENSP00000356224:K920R;ENSP00000396024:K927R;ENSP00000265368:K920R;ENSP00000390975:K927R;ENSP00000341887:K986R;ENSP00000356222:K920R;ENSP00000356217:K910R;ENSP00000414510:K920R;ENSP00000438508:K487R	ENSP00000265368:K920R	K	-	2	0	SYNE1	152818387	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	3.910000	0.56371	2.069000	0.61940	0.533000	0.62120	AAG		SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
TAGAP	117289	hgsc.bcm.edu	37	6	159457675	159457675	+	Missense_Mutation	SNP	G	G	C	rs201570448		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr6:159457675G>C	ENST00000367066.3	-	10	1711	c.1380C>G	c.(1378-1380)ttC>ttG	p.F460L	RP1-111C20.4_ENST00000607796.1_RNA|TAGAP_ENST00000326965.6_Missense_Mutation_p.F282L|RP1-111C20.4_ENST00000606466.1_RNA|RP1-111C20.4_ENST00000607391.1_RNA|RP1-111C20.4_ENST00000606470.1_RNA	NM_001278733.1|NM_054114.3	NP_001265662.1|NP_473455.2	Q8N103	TAGAP_HUMAN	T-cell activation RhoGTPase activating protein	460					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|autonomic_ganglia(1)|endometrium(3)|large_intestine(8)|lung(7)|ovary(2)|skin(1)	23		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.16e-16)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		AGCTGCTGGAGAAGGCTTTGA	0.572																																																	0			6											84.0	96.0	92.0					6																	159457675		2203	4300	6503	159377663	SO:0001583	missense	117289			AF385429	CCDS5261.1, CCDS5262.1, CCDS5263.1	6q25.3	2011-09-07	2008-03-25		ENSG00000164691	ENSG00000164691		"""Rho GTPase activating proteins"""	15669	protein-coding gene	gene with protein product		609667	"""T-cell activation GTPase activating protein"""			16375659, 18311140, 18356936	Standard	NM_152133		Approved	FLJ32631, IDDM21, ARHGAP47	uc003qrz.3	Q8N103	OTTHUMG00000015923	ENST00000367066.3:c.1380C>G	6.37:g.159457675G>C	ENSP00000356033:p.Phe460Leu	Somatic		Capture	Illumina HiSeq	Phase_I	159377663	Q2NKM8|Q8NI40|Q96KZ2|Q96QA2	Missense_Mutation	SNP	ENST00000367066.3	37	CCDS5261.1	.	.	.	.	.	.	.	.	.	.	G	6.603	0.479673	0.12581	.	.	ENSG00000164691	ENST00000367066;ENST00000326965;ENST00000539071	T;T	0.15603	2.41;2.67	6.05	4.23	0.50019	.	1.573710	0.02913	N	0.136931	T	0.04452	0.0122	L	0.35414	1.06	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.44081	-0.9351	10	0.07813	T	0.8	-0.69	7.4384	0.27169	0.1443:0.1703:0.6854:0.0	.	460	Q8N103	TAGAP_HUMAN	L	460;282;125	ENSP00000356033:F460L;ENSP00000322650:F282L	ENSP00000322650:F282L	F	-	3	2	TAGAP	159377663	0.891000	0.30450	0.039000	0.18376	0.853000	0.48598	0.660000	0.25009	0.807000	0.34208	0.650000	0.86243	TTC		TAGAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042890.1	NM_054114	
IGF2R	3482	hgsc.bcm.edu	37	6	160517551	160517551	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr6:160517551T>C	ENST00000356956.1	+	45	6884	c.6736T>C	c.(6736-6738)Ttc>Ctc	p.F2246L	IGF2R_ENST00000475584.1_3'UTR|RP11-288H12.3_ENST00000569097.1_RNA	NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	2246					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)			breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	CACCATCTTCTTCCACTGTGA	0.552																																																	0			6											263.0	206.0	226.0					6																	160517551		2203	4300	6503	160437541	SO:0001583	missense	3482			J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"""CD molecules"""	5467	protein-coding gene	gene with protein product	"""cation-independent mannose-6 phosphate receptor"""	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.6736T>C	6.37:g.160517551T>C	ENSP00000349437:p.Phe2246Leu	Somatic		Capture	Illumina HiSeq	Phase_I	160437541	Q7Z7G9|Q96PT5	Missense_Mutation	SNP	ENST00000356956.1	37	CCDS5273.1	.	.	.	.	.	.	.	.	.	.	T	33	5.255695	0.95336	.	.	ENSG00000197081	ENST00000356956	T	0.05996	3.36	5.69	5.69	0.88448	Mannose-6-phosphate receptor, binding (1);	0.000000	0.85682	D	0.000000	T	0.20373	0.0490	M	0.85710	2.77	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.01639	-1.1306	10	0.44086	T	0.13	-4.6091	15.9393	0.79743	0.0:0.0:0.0:1.0	.	2246	P11717	MPRI_HUMAN	L	2246	ENSP00000349437:F2246L	ENSP00000349437:F2246L	F	+	1	0	IGF2R	160437541	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.929000	0.70096	2.162000	0.67917	0.533000	0.62120	TTC		IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876	
ALOX15	246	hgsc.bcm.edu	37	17	4542791	4542791	+	Missense_Mutation	SNP	C	C	T	rs139214774		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr17:4542791C>T	ENST00000570836.1	-	3	367	c.271G>A	c.(271-273)Gag>Aag	p.E91K	ALOX15_ENST00000293761.3_Missense_Mutation_p.E91K|ALOX15_ENST00000574640.1_Missense_Mutation_p.E52K|ALOX15_ENST00000545513.1_Missense_Mutation_p.E113K			P16050	LOX15_HUMAN	arachidonate 15-lipoxygenase	91	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				apoptotic cell clearance (GO:0043277)|arachidonic acid metabolic process (GO:0019369)|bone mineralization (GO:0030282)|cellular response to calcium ion (GO:0071277)|cellular response to interleukin-13 (GO:0035963)|hepoxilin biosynthetic process (GO:0051122)|inflammatory response (GO:0006954)|leukotriene metabolic process (GO:0006691)|lipoxin A4 biosynthetic process (GO:2001303)|lipoxygenase pathway (GO:0019372)|negative regulation of adaptive immune response (GO:0002820)|ossification (GO:0001503)|phosphatidylethanolamine biosynthetic process (GO:0006646)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of engulfment of apoptotic cell (GO:1901074)|regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035358)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)|wound healing (GO:0042060)	cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|lipid particle (GO:0005811)|membrane (GO:0016020)|plasma membrane (GO:0005886)	arachidonate 12-lipoxygenase activity (GO:0004052)|arachidonate 15-lipoxygenase activity (GO:0050473)|eoxin A4 synthase activity (GO:0097260)|iron ion binding (GO:0005506)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(5)	20				READ - Rectum adenocarcinoma(115;0.0327)		AACCTGACCTCGTCCCCGGCT	0.652																																																	0			17						C	LYS/GLU	0,4406		0,0,2203	48.0	50.0	49.0		271	2.7	0.1	17	dbSNP_134	49	1,8599		0,1,4299	no	missense	ALOX15	NM_001140.3	56	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	91/663	4542791	1,13005	2203	4300	6503	4489540	SO:0001583	missense	246			M23892	CCDS11049.1	17p13.3	2010-09-24			ENSG00000161905	ENSG00000161905	1.13.11.33	"""Arachidonate lipoxygenases"""	433	protein-coding gene	gene with protein product		152392				1570320	Standard	NM_001140		Approved	15-LOX-1	uc002fyh.3	P16050	OTTHUMG00000090746	ENST00000570836.1:c.271G>A	17.37:g.4542791C>T	ENSP00000458832:p.Glu91Lys	Somatic		Capture	Illumina HiSeq	Phase_I	4489540	A8K2P4|B7ZA11|Q8N6R7|Q99657	Missense_Mutation	SNP	ENST00000570836.1	37	CCDS11049.1	.	.	.	.	.	.	.	.	.	.	C	7.363	0.625227	0.14257	0.0	1.16E-4	ENSG00000161905	ENST00000293761;ENST00000545513	T;T	0.62498	0.02;0.02	4.81	2.73	0.32206	Lipoxygenase, LH2 (4);Lipase/lipooxygenase, PLAT/LH2 (1);	0.593720	0.16110	N	0.229141	T	0.49779	0.1577	L	0.48362	1.52	0.09310	N	1	B;B;B	0.17667	0.023;0.007;0.016	B;B;B	0.13407	0.005;0.002;0.009	T	0.34179	-0.9839	10	0.25751	T	0.34	-19.0055	7.0033	0.24821	0.0:0.7282:0.1736:0.0981	.	113;52;91	F5H0G8;B7ZA11;P16050	.;.;LOX15_HUMAN	K	91;113	ENSP00000293761:E91K;ENSP00000439855:E113K	ENSP00000293761:E91K	E	-	1	0	ALOX15	4489540	0.167000	0.22975	0.119000	0.21687	0.136000	0.21042	1.951000	0.40333	0.407000	0.25591	0.561000	0.74099	GAG		ALOX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207487.2		
NLRP1	22861	hgsc.bcm.edu	37	17	5445208	5445208	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr17:5445208T>C	ENST00000572272.1	-	6	2667	c.2668A>G	c.(2668-2670)Aga>Gga	p.R890G	NLRP1_ENST00000269280.4_Missense_Mutation_p.R890G|NLRP1_ENST00000345221.3_Missense_Mutation_p.R890G|NLRP1_ENST00000262467.5_Missense_Mutation_p.R890G|NLRP1_ENST00000577119.1_Missense_Mutation_p.R890G|NLRP1_ENST00000354411.3_Missense_Mutation_p.R890G|NLRP1_ENST00000571307.1_5'UTR			Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1	890					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of inflammatory response (GO:0050727)|response to muramyl dipeptide (GO:0032495)	cytosol (GO:0005829)|intracellular (GO:0005622)|NLRP1 inflammasome complex (GO:0072558)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|enzyme binding (GO:0019899)|protein domain specific binding (GO:0019904)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(17)|liver(5)|lung(17)|ovary(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Colorectal(1115;3.48e-05)				CTCGGCTGTCTCAGTCTCTGG	0.587																																																	0			17											101.0	81.0	88.0					17																	5445208		2203	4300	6503	5385932	SO:0001583	missense	22861			AB023143	CCDS32537.1, CCDS42244.1, CCDS42245.1, CCDS42246.1, CCDS58508.1	17p13	2014-01-29	2006-12-08	2006-12-08	ENSG00000091592	ENSG00000091592		"""Nucleotide-binding domain and leucine rich repeat containing"""	14374	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 1"""	606636	"""NACHT, leucine rich repeat and PYD (pyrin domain) containing 1"", ""systemic lupus erythematosus, vitiligo-related 1"""	NALP1, SLEV1		8781126, 12563287, 17377159	Standard	NM_033006		Approved	KIAA0926, DKFZp586O1822, CARD7, NAC, CLR17.1, DEFCAP, VAMAS1	uc002gci.3	Q9C000		ENST00000572272.1:c.2668A>G	17.37:g.5445208T>C	ENSP00000460475:p.Arg890Gly	Somatic		Capture	Illumina HiSeq	Phase_I	5385932	E9PE50|I6L9D9|Q9BZZ8|Q9BZZ9|Q9H5Z7|Q9H5Z8|Q9HAV8|Q9UFT4|Q9Y2E0	Missense_Mutation	SNP	ENST00000572272.1	37	CCDS42246.1	.	.	.	.	.	.	.	.	.	.	T	10.02	1.234869	0.22626	.	.	ENSG00000091592	ENST00000544378;ENST00000262467;ENST00000269280;ENST00000354411;ENST00000345221;ENST00000537069	T;T;T;T;T	0.13778	2.56;2.56;2.56;2.56;2.56	2.01	2.01	0.26516	.	0.933482	0.08723	N	0.903207	T	0.14527	0.0351	M	0.64676	1.99	0.09310	N	1	B;B;B;B;B;B	0.31548	0.328;0.16;0.137;0.009;0.037;0.015	B;B;B;B;B;B	0.28011	0.085;0.056;0.075;0.006;0.014;0.008	T	0.24870	-1.0148	10	0.56958	D	0.05	.	6.0548	0.19804	0.0:0.0:0.0:1.0	.	156;890;890;890;890;890	F5H042;Q9C000-3;Q9C000-4;Q9C000;Q9C000-2;E9PE50	.;.;.;NALP1_HUMAN;.;.	G	890;890;890;890;890;156	ENSP00000442029:R890G;ENSP00000262467:R890G;ENSP00000269280:R890G;ENSP00000346390:R890G;ENSP00000324366:R890G	ENSP00000262467:R890G	R	-	1	2	NLRP1	5385932	0.008000	0.16893	0.014000	0.15608	0.019000	0.09904	0.346000	0.19997	1.211000	0.43351	0.454000	0.30748	AGA		NLRP1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439517.1	NM_033004	
ODF4	146852	hgsc.bcm.edu	37	17	8248732	8248732	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr17:8248732T>C	ENST00000328248.2	+	2	714	c.526T>C	c.(526-528)Tcc>Ccc	p.S176P	ODF4_ENST00000584943.1_Missense_Mutation_p.S61P	NM_153007.4	NP_694552.2	Q2M2E3	ODFP4_HUMAN	outer dense fiber of sperm tails 4	176					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|outer dense fiber (GO:0001520)		p.S176T(1)		endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|stomach(1)	8						AAGGAATGTATCCATCCCCAT	0.517																																																	1	Substitution - Missense(1)	ovary(1)	17											292.0	254.0	267.0					17																	8248732		2203	4300	6503	8189457	SO:0001583	missense	146852			AB081120	CCDS11140.1	17p13	2010-09-27			ENSG00000184650	ENSG00000184650			19056	protein-coding gene	gene with protein product	"""cancer/testis antigen 136"""	610097					Standard	NM_153007		Approved	OPPO1, CT136	uc002gle.1	Q2M2E3	OTTHUMG00000108190	ENST00000328248.2:c.526T>C	17.37:g.8248732T>C	ENSP00000331086:p.Ser176Pro	Somatic		Capture	Illumina HiSeq	Phase_I	8189457	Q8J021	Missense_Mutation	SNP	ENST00000328248.2	37	CCDS11140.1	.	.	.	.	.	.	.	.	.	.	T	1.687	-0.505050	0.04261	.	.	ENSG00000184650	ENST00000328248	T	0.28069	1.63	4.59	2.18	0.27775	.	0.000000	0.38663	N	0.001606	T	0.16599	0.0399	N	0.17082	0.46	0.09310	N	1	P	0.44816	0.844	B	0.42319	0.383	T	0.08391	-1.0724	10	0.62326	D	0.03	-8.8169	3.6185	0.08086	0.1916:0.1042:0.0:0.7042	.	176	Q2M2E3	ODFP4_HUMAN	P	176	ENSP00000331086:S176P	ENSP00000331086:S176P	S	+	1	0	ODF4	8189457	0.086000	0.21541	0.019000	0.16419	0.047000	0.14425	1.871000	0.39539	0.888000	0.36160	0.460000	0.39030	TCC		ODF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226996.1		
MYH4	4622	hgsc.bcm.edu	37	17	10351935	10351935	+	Splice_Site	SNP	G	G	A	rs545963911	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr17:10351935G>A	ENST00000255381.2	-	32	4641	c.4531C>T	c.(4531-4533)Cag>Tag	p.Q1511*	RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	1511					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)			NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						AGTGACTCACGTTGTAAGTTC	0.378													G|||	2	0.000399361	0.0008	0.0	5008	,	,		20564	0.0		0.0	False		,,,				2504	0.001																0			17											99.0	100.0	99.0					17																	10351935		2203	4300	6503	10292660	SO:0001630	splice_region_variant	4622				CCDS11154.1	17p13.1	2013-09-19	2006-09-29		ENSG00000264424	ENSG00000264424		"""Myosins / Myosin superfamily : Class II"""	7574	protein-coding gene	gene with protein product		160742	"""myosin, heavy polypeptide 4, skeletal muscle"""			8518795	Standard	NM_017533		Approved	MYH2B, MyHC-2B, MyHC-IIb	uc002gmn.3	Q9Y623	OTTHUMG00000130365	ENST00000255381.2:c.4531+1C>T	17.37:g.10351935G>A		Somatic		Capture	Illumina HiSeq	Phase_I	10292660		Nonsense_Mutation	SNP	ENST00000255381.2	37	CCDS11154.1	.	.	.	.	.	.	.	.	.	.	G	41	8.891088	0.98992	.	.	ENSG00000141048	ENST00000255381	.	.	.	5.34	5.34	0.76211	.	0.000000	0.35772	U	0.002987	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.3996	0.94623	0.0:0.0:1.0:0.0	.	.	.	.	X	1511	.	.	Q	-	1	0	MYH4	10292660	0.895000	0.30542	0.998000	0.56505	0.594000	0.36715	1.244000	0.32778	2.666000	0.90696	0.655000	0.94253	CAG		MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533	Nonsense_Mutation
DNAH9	1770	hgsc.bcm.edu	37	17	11872712	11872712	+	Silent	SNP	C	C	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr17:11872712C>T	ENST00000262442.4	+	69	13397	c.13329C>T	c.(13327-13329)cgC>cgT	p.R4443R	DNAH9_ENST00000396001.2_3'UTR|RP11-1096G20.5_ENST00000580270.1_RNA|DNAH9_ENST00000608377.1_Silent_p.R755R|DNAH9_ENST00000454412.2_Silent_p.R4367R	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	4443			R -> C (in dbSNP:rs9913494).		cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		AGGACTGCCGCAGTGTCTATT	0.517																																																	0			17											106.0	90.0	95.0					17																	11872712		2203	4300	6503	11813437	SO:0001819	synonymous_variant	1770			U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.13329C>T	17.37:g.11872712C>T		Somatic		Capture	Illumina HiSeq	Phase_I	11813437	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																				DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
ZNF286A	57335	hgsc.bcm.edu	37	17	15611544	15611544	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr17:15611544C>T	ENST00000464847.2	+	4	870	c.317C>T	c.(316-318)cCc>cTc	p.P106L	ZNF286A_ENST00000395893.2_Missense_Mutation_p.P106L|ZNF286A_ENST00000585171.1_3'UTR|ZNF286A_ENST00000413242.2_Missense_Mutation_p.P106L|ZNF286A_ENST00000421016.1_Missense_Mutation_p.P106L|ZNF286A_ENST00000472486.1_Missense_Mutation_p.P96L|ZNF286A_ENST00000593105.1_Missense_Mutation_p.P96L|ZNF286A_ENST00000395894.2_Missense_Mutation_p.P106L|ZNF286A_ENST00000583566.1_Missense_Mutation_p.P106L|ZNF286A_ENST00000581529.1_3'UTR|ZNF286A_ENST00000585194.1_Missense_Mutation_p.P106L|ZNF286A_ENST00000580259.1_3'UTR			Q9HBT8	Z286A_HUMAN	zinc finger protein 286A	106	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P106L(2)		central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(1115;0.0222)|BRCA - Breast invasive adenocarcinoma(8;0.0781)		AGAAAAGCCCCCAAAAGCAGC	0.403																																																	2	Substitution - Missense(2)	ovary(1)|central_nervous_system(1)	17											57.0	58.0	57.0					17																	15611544		2203	4300	6503	15552269	SO:0001583	missense	57335			AF217226	CCDS11172.1, CCDS73997.1	17p11.2	2013-02-14	2007-01-05	2007-01-05		ENSG00000187607		"""Zinc fingers, C2H2-type"", ""-"""	13501	protein-coding gene	gene with protein product			"""zinc finger protein 286"""	ZNF286		11347906	Standard	NM_020652		Approved	KIAA1874	uc010cot.3	Q9HBT8	OTTHUMG00000166448	ENST00000464847.2:c.317C>T	17.37:g.15611544C>T	ENSP00000464218:p.Pro106Leu	Somatic		Capture	Illumina HiSeq	Phase_I	15552269	B4DKF9|Q96JF3	Missense_Mutation	SNP	ENST00000464847.2	37	CCDS11172.1	.	.	.	.	.	.	.	.	.	.	c	11.26	1.587257	0.28268	.	.	ENSG00000187607	ENST00000421016;ENST00000412988;ENST00000395894;ENST00000395893	T;T;T;T	0.08282	3.47;3.11;5.43;5.59	4.85	3.84	0.44239	Krueppel-associated box (1);	30.442900	0.00744	N	0.001035	T	0.06280	0.0162	N	0.10685	0.025	0.09310	N	1	B	0.27498	0.18	B	0.21546	0.035	T	0.31696	-0.9934	10	0.27785	T	0.31	-0.0869	10.6557	0.45673	0.2079:0.7921:0.0:0.0	.	106	Q9HBT8	Z286A_HUMAN	L	106;96;106;106	ENSP00000397163:P106L;ENSP00000408168:P96L;ENSP00000379231:P106L;ENSP00000379230:P106L	ENSP00000435872:P106L	P	+	2	0	ZNF286A	15552269	0.000000	0.05858	0.003000	0.11579	0.188000	0.23474	0.417000	0.21214	1.321000	0.45227	0.563000	0.77884	CCC		ZNF286A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130696.4	NM_020652	
SPECC1	92521	hgsc.bcm.edu	37	17	20163524	20163524	+	Missense_Mutation	SNP	C	C	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr17:20163524C>G	ENST00000261503.5	+	12	2908	c.2857C>G	c.(2857-2859)Ctg>Gtg	p.L953V	AC004702.2_ENST00000580225.1_lincRNA|SPECC1_ENST00000395527.4_Missense_Mutation_p.L953V|SPECC1_ENST00000395530.2_Missense_Mutation_p.L872V|SPECC1_ENST00000536879.1_Missense_Mutation_p.L293V	NM_001033553.2	NP_001028725.1	Q5M775	CYTSB_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1	953					cell adhesion (GO:0007155)	nucleus (GO:0005634)				breast(1)|large_intestine(3)|ovary(4)	8				KIRC - Kidney renal clear cell carcinoma(2;0.166)|Kidney(2;0.196)		AAAAGACCCTCTGGCAGCCTT	0.443																																																	0			17											89.0	93.0	92.0					17																	20163524		2203	4300	6503	20104116	SO:0001583	missense	92521			AY816329, AB041533	CCDS32590.1, CCDS42280.1, CCDS42281.1, CCDS45628.1, CCDS58531.1	17p11.2	2012-11-19	2010-09-17	2010-09-17	ENSG00000128487	ENSG00000128487			30615	protein-coding gene	gene with protein product	"""sperm antigen HCMOGT 1"", ""cytokinesis and spindle organization B"", ""cytospin B"""	608793				15602574, 18763323, 15087372	Standard	NM_001033553		Approved	HCMOGT-1, FLJ36955, NSP, CYTSB	uc002gwq.3	Q5M775	OTTHUMG00000179808	ENST00000261503.5:c.2857C>G	17.37:g.20163524C>G	ENSP00000261503:p.Leu953Val	Somatic		Capture	Illumina HiSeq	Phase_I	20104116	B4DHH0|B7WNS8|Q5IBP1|Q5IBP2|Q5IBP3|Q5IBP4|Q5M772|Q5M773|Q5M774|Q86XT8|Q8N4U4|Q8WU84|Q9HCQ3	Missense_Mutation	SNP	ENST00000261503.5	37	CCDS32590.1	.	.	.	.	.	.	.	.	.	.	C	16.39	3.109202	0.56398	.	.	ENSG00000128487	ENST00000395530;ENST00000261503;ENST00000536879;ENST00000395527	T;D	0.95205	-0.35;-3.64	4.31	4.31	0.51392	.	0.000000	0.64402	D	0.000004	D	0.94915	0.8356	L	0.43152	1.355	0.51767	D	0.999931	D;D;D	0.89917	1.0;0.999;0.997	D;D;D	0.87578	0.998;0.997;0.965	D	0.94244	0.7487	10	0.87932	D	0	-11.4805	8.2976	0.31995	0.0:0.893:0.0:0.107	.	953;872;953	A8MV89;Q5M775-4;Q5M775	.;.;CYTSB_HUMAN	V	953;953;293;872	ENSP00000261503:L953V;ENSP00000438294:L293V	ENSP00000261503:L953V	L	+	1	2	SPECC1	20104116	0.051000	0.20477	0.999000	0.59377	0.994000	0.84299	0.320000	0.19540	2.399000	0.81585	0.655000	0.94253	CTG		SPECC1-018	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441206.1	NM_152904	
PCGF2	7703	hgsc.bcm.edu	37	17	36895858	36895858	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr17:36895858G>A	ENST00000580830.1	-	5	891	c.190C>T	c.(190-192)Cgg>Tgg	p.R64W	PCGF2_ENST00000579882.1_Missense_Mutation_p.R64W|PCGF2_ENST00000360797.2_Missense_Mutation_p.R64W|PCGF2_ENST00000578109.1_Missense_Mutation_p.R10W|PCGF2_ENST00000581345.1_Missense_Mutation_p.R64W|PCGF2_ENST00000585100.1_Missense_Mutation_p.R64W			P35227	PCGF2_HUMAN	polycomb group ring finger 2	64					anterior/posterior pattern specification (GO:0009952)|cellular response to hydrogen peroxide (GO:0070301)|embryonic skeletal system morphogenesis (GO:0048704)|histone acetylation (GO:0016573)|in utero embryonic development (GO:0001701)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R64W(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	10	Breast(7;9.07e-22)					AGCAGCGGCCGGGTTTTATGG	0.617																																																	1	Substitution - Missense(1)	central_nervous_system(1)	17											145.0	117.0	127.0					17																	36895858		2203	4300	6503	34149384	SO:0001583	missense	7703			D13969	CCDS32638.1	17q12	2013-01-09	2005-01-17	2005-01-19		ENSG00000277258		"""RING-type (C3HC4) zinc fingers"", ""Polycomb group ring fingers"""	12929	protein-coding gene	gene with protein product		600346	"""ring finger protein 110"""	ZNF144, RNF110		8325509	Standard	NM_007144		Approved	MEL-18	uc002hqp.1	P35227		ENST00000580830.1:c.190C>T	17.37:g.36895858G>A	ENSP00000461961:p.Arg64Trp	Somatic		Capture	Illumina HiSeq	Phase_I	34149384	A6NGD8	Missense_Mutation	SNP	ENST00000580830.1	37	CCDS32638.1	.	.	.	.	.	.	.	.	.	.	G	10.69	1.421315	0.25639	.	.	ENSG00000056661	ENST00000360797	T	0.43294	0.95	4.56	2.5	0.30297	Zinc finger, RING/FYVE/PHD-type (1);	0.070142	0.64402	D	0.000017	T	0.42449	0.1203	M	0.68952	2.095	0.40076	D	0.976072	D	0.62365	0.991	P	0.44860	0.462	T	0.42766	-0.9432	10	0.46703	T	0.11	-9.2425	11.0498	0.47880	0.0:0.0:0.6189:0.3811	.	64	P35227	PCGF2_HUMAN	W	64	ENSP00000354033:R64W	ENSP00000354033:R64W	R	-	1	2	PCGF2	34149384	0.009000	0.17119	0.520000	0.27837	0.916000	0.54674	0.548000	0.23314	0.478000	0.27488	0.491000	0.48974	CGG		PCGF2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442246.2	NM_007144	
GJC1	10052	hgsc.bcm.edu	37	17	42882687	42882687	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr17:42882687G>A	ENST00000426548.1	-	3	768	c.499C>T	c.(499-501)Cgg>Tgg	p.R167W	GJC1_ENST00000330514.4_Missense_Mutation_p.R167W|GJC1_ENST00000590758.1_Missense_Mutation_p.R167W|GJC1_ENST00000592524.1_Missense_Mutation_p.R167W	NM_001080383.1|NM_005497.3	NP_001073852.1|NP_005488.2	P36383	CXG1_HUMAN	gap junction protein, gamma 1, 45kDa	167					atrial cardiac muscle cell action potential (GO:0086014)|cardiac muscle tissue development (GO:0048738)|cell development (GO:0048468)|cell-cell junction assembly (GO:0007043)|gap junction assembly (GO:0016264)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vasculogenesis (GO:0001570)|visual perception (GO:0007601)	connexon complex (GO:0005922)|endoplasmic reticulum membrane (GO:0005789)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)	gap junction channel activity (GO:0005243)|ion channel activity (GO:0005216)			NS(1)|kidney(1)|large_intestine(5)|liver(1)|lung(10)|prostate(1)	19		Prostate(33;0.0959)				TCCCGAATCCGTCGTCGGCCA	0.463																																																	0			17											205.0	185.0	192.0					17																	42882687		2203	4300	6503	40238213	SO:0001583	missense	125111			U03493	CCDS11487.1	17q21.31	2008-02-04	2007-11-06	2007-11-06		ENSG00000182963		"""Ion channels / Gap junction proteins (connexins)"""	4280	protein-coding gene	gene with protein product	"""connexin 45"""	608655	"""gap junction protein, alpha 7, 45kDa"""	GJA7		7966354	Standard	NM_005497		Approved	CX45	uc002ihl.3	P36383		ENST00000426548.1:c.499C>T	17.37:g.42882687G>A	ENSP00000411528:p.Arg167Trp	Somatic		Capture	Illumina HiSeq	Phase_I	40238213	B3KW68|Q4VAY0	Missense_Mutation	SNP	ENST00000426548.1	37	CCDS11487.1	.	.	.	.	.	.	.	.	.	.	G	17.20	3.327755	0.60743	.	.	ENSG00000182963	ENST00000426548;ENST00000330514	D;D	0.98280	-4.84;-4.84	5.52	5.52	0.82312	.	0.060473	0.64402	D	0.000002	D	0.98782	0.9590	M	0.75615	2.305	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	D	0.99201	1.0873	10	0.40728	T	0.16	.	18.419	0.90582	0.0:0.0:1.0:0.0	.	167	P36383	CXG1_HUMAN	W	167	ENSP00000411528:R167W;ENSP00000333193:R167W	ENSP00000333193:R167W	R	-	1	2	GJC1	40238213	1.000000	0.71417	0.247000	0.24249	0.815000	0.46073	6.590000	0.74085	2.581000	0.87130	0.514000	0.50259	CGG		GJC1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448661.1	NM_005497	
ABCC3	8714	hgsc.bcm.edu	37	17	48735832	48735832	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr17:48735832C>T	ENST00000285238.8	+	6	729	c.649C>T	c.(649-651)Cgc>Tgc	p.R217C	ABCC3_ENST00000427699.1_Missense_Mutation_p.R217C	NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	217					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)	p.L215_F219delLSRLF(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33			BRCA - Breast invasive adenocarcinoma(22;3.05e-09)		Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Doxorubicin(DB00997)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indomethacin(DB00328)|Lamivudine(DB00709)|Leucovorin(DB00650)|Methotrexate(DB00563)|Metyrapone(DB01011)|Nifedipine(DB01115)|Omeprazole(DB00338)|Phenobarbital(DB01174)|Probenecid(DB01032)|Rifampicin(DB01045)|Sulfinpyrazone(DB01138)|Verapamil(DB00661)|Vincristine(DB00541)	CTTTCTCTCCCGCCTGTTTTT	0.582																																																	1	Deletion - In frame(1)	prostate(1)	17											128.0	118.0	121.0					17																	48735832		2203	4300	6503	46090831	SO:0001583	missense	8714			Y17151	CCDS32681.1, CCDS45739.1	17q21	2012-03-14			ENSG00000108846	ENSG00000108846		"""ATP binding cassette transporters / subfamily C"""	54	protein-coding gene	gene with protein product	"""canalicular multispecific organic anion transporter 2"""	604323				8894702, 9827529	Standard	NM_003786		Approved	MRP3, cMOAT2, EST90757, MLP2, MOAT-D	uc002isl.3	O15438	OTTHUMG00000162245	ENST00000285238.8:c.649C>T	17.37:g.48735832C>T	ENSP00000285238:p.Arg217Cys	Somatic		Capture	Illumina HiSeq	Phase_I	46090831	B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52	Missense_Mutation	SNP	ENST00000285238.8	37	CCDS32681.1	.	.	.	.	.	.	.	.	.	.	C	18.87	3.716134	0.68844	.	.	ENSG00000108846	ENST00000427699;ENST00000285238	D;D	0.93247	-3.19;-3.19	5.92	4.96	0.65561	.	0.158362	0.42964	D	0.000632	D	0.96849	0.8971	M	0.92691	3.335	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	P;D	0.72338	0.852;0.977	D	0.96712	0.9526	10	0.66056	D	0.02	-14.056	8.5005	0.33154	0.2579:0.6706:0.0:0.0715	.	217;217	O15438;O15438-5	MRP3_HUMAN;.	C	217	ENSP00000395160:R217C;ENSP00000285238:R217C	ENSP00000285238:R217C	R	+	1	0	ABCC3	46090831	0.028000	0.19301	1.000000	0.80357	0.985000	0.73830	1.110000	0.31147	1.515000	0.48885	0.561000	0.74099	CGC		ABCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368083.2	NM_020038	
SPAG9	9043	hgsc.bcm.edu	37	17	49048080	49048080	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr17:49048080C>T	ENST00000262013.7	-	29	4046	c.3838G>A	c.(3838-3840)Gac>Aac	p.D1280N	SPAG9_ENST00000510283.1_Missense_Mutation_p.D1136N|SPAG9_ENST00000505279.1_Missense_Mutation_p.D1270N|SPAG9_ENST00000357122.4_Missense_Mutation_p.D1266N	NM_001130528.2	NP_001124000.1	O60271	JIP4_HUMAN	sperm associated antigen 9	1280					activation of JUN kinase activity (GO:0007257)|muscle cell differentiation (GO:0042692)|negative regulation of protein homodimerization activity (GO:0090074)|positive regulation of cell migration (GO:0030335)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron differentiation (GO:0045666)|protein homooligomerization (GO:0051260)|retrograde transport, endosome to Golgi (GO:0042147)|spermatogenesis (GO:0007283)|striated muscle cell differentiation (GO:0051146)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)				NS(1)|breast(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)			ATTCGGAAGTCGATGTAGCCC	0.493																																																	0			17											126.0	102.0	110.0					17																	49048080		2203	4300	6503	46403079	SO:0001583	missense	9043			AB011088	CCDS11577.1, CCDS45740.1, CCDS58577.1, CCDS58578.1	17q21.33	2013-09-23			ENSG00000008294	ENSG00000008294			14524	protein-coding gene	gene with protein product	"""sperm surface protein"", ""JNK/SAPK-associated protein"", ""JNK interacting protein"", ""sperm specific protein"", ""c-Jun NH2-terminal kinase-associated leucine zipper protein"", ""Max-binding protein"", ""JNK-associated leucine-zipper protein"", ""HLC-4 protein"", ""lung cancer oncogene 4"", ""proliferation-inducing gene 6"", ""cancer/testis antigen 89"""	605430				9480848, 11106729	Standard	NM_003971		Approved	HSS, SYD1, KIAA0516, MGC14967, MGC74461, MGC117291, JLP, PHET, HLC4, PIG6, FLJ13450, FLJ14006, FLJ26141, FLJ34602, CT89	uc002itc.3	O60271	OTTHUMG00000162316	ENST00000262013.7:c.3838G>A	17.37:g.49048080C>T	ENSP00000262013:p.Asp1280Asn	Somatic		Capture	Illumina HiSeq	Phase_I	46403079	A6H8U5|A8MSX0|B4DHH2|O60905|Q3KQU8|Q3MKM7|Q86WC7|Q86WC8|Q8IZX7|Q96II0|Q9H811	Missense_Mutation	SNP	ENST00000262013.7	37	CCDS45740.1	.	.	.	.	.	.	.	.	.	.	C	18.02	3.531065	0.64972	.	.	ENSG00000008294	ENST00000262013;ENST00000376407;ENST00000357804;ENST00000510283;ENST00000505279;ENST00000357122;ENST00000535445	T;T;T;T	0.39056	1.13;1.1;1.14;1.14	6.17	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.65207	0.2669	M	0.70842	2.15	0.80722	D	1	D;D;D;D	0.89917	1.0;0.998;1.0;1.0	D;P;D;D	0.97110	0.964;0.886;1.0;1.0	T	0.69435	-0.5146	10	0.66056	D	0.02	-18.5972	17.0955	0.86634	0.1278:0.8722:0.0:0.0	.	1270;1280;1266;1136	O60271-2;O60271;O60271-4;E7ENU2	.;JIP4_HUMAN;.;.	N	1280;1037;1027;1136;1270;1266;878	ENSP00000262013:D1280N;ENSP00000423165:D1136N;ENSP00000426900:D1270N;ENSP00000349636:D1266N	ENSP00000262013:D1280N	D	-	1	0	SPAG9	46403079	1.000000	0.71417	0.953000	0.39169	0.026000	0.11368	7.333000	0.79214	1.615000	0.50252	-0.169000	0.13324	GAC		SPAG9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368543.2	NM_003971	
BAGE2	85319	hgsc.bcm.edu	37	21	11098733	11098733	+	RNA	SNP	G	G	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr21:11098733G>A	ENST00000470054.1	-	0	192							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2							extracellular region (GO:0005576)								Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		tgctccggccgccatcttact	0.632																																																	0			21											104.0	151.0	135.0					21																	11098733		2124	4261	6385	10120604			574			AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172			15723	protein-coding gene	gene with protein product	"""cancer/testis antigen family 2, member 2"""					12461691	Standard	NM_182482		Approved	CT2.2		Q86Y30	OTTHUMG00000074128		21.37:g.11098733G>A		Somatic		Capture	Illumina HiSeq	Phase_I	10120604	A8K925|Q08ER0	Missense_Mutation	SNP	ENST00000470054.1	37																																																																																					BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	NM_182482	
CCDC154	645811	hgsc.bcm.edu	37	16	1487952	1487952	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr16:1487952G>A	ENST00000389176.3	-	11	1349	c.1183C>T	c.(1183-1185)Cga>Tga	p.R395*	CCDC154_ENST00000409671.1_Nonsense_Mutation_p.R241*	NM_001143980.1	NP_001137452.1	A6NI56	CC154_HUMAN	coiled-coil domain containing 154	395						endosome (GO:0005768)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)	5						CTCTTCTCTCGGAGCTGCAGG	0.682																																																	0			16											17.0	20.0	19.0					16																	1487952		691	1589	2280	1427953	SO:0001587	stop_gained	645811					16p13.3	2012-12-13			ENSG00000197599	ENSG00000197599			34454	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 29"""	C16orf29			Standard	NM_001143980		Approved	LOC645811	uc010uve.2	A6NI56	OTTHUMG00000154097	ENST00000389176.3:c.1183C>T	16.37:g.1487952G>A	ENSP00000373828:p.Arg395*	Somatic		Capture	Illumina HiSeq	Phase_I	1427953	G9JV18	Nonsense_Mutation	SNP	ENST00000389176.3	37		.	.	.	.	.	.	.	.	.	.	G	35	5.450042	0.96205	.	.	ENSG00000197599	ENST00000409671;ENST00000389176	.	.	.	3.91	2.94	0.34122	.	1.289940	0.05728	N	0.599023	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.6168	0.28163	0.1195:0.0:0.8805:0.0	.	.	.	.	X	241;395	.	.	R	-	1	2	CCDC154	1427953	0.004000	0.15560	0.971000	0.41717	0.020000	0.10135	-0.159000	0.10056	0.855000	0.35359	0.561000	0.74099	CGA		CCDC154-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_001143980	
CREBBP	1387	hgsc.bcm.edu	37	16	3788618	3788618	+	Missense_Mutation	SNP	G	G	T	rs398124146		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr16:3788618G>T	ENST00000262367.5	-	26	5145	c.4336C>A	c.(4336-4338)Cgc>Agc	p.R1446S	CREBBP_ENST00000382070.3_Missense_Mutation_p.R1408S	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1446	Acetyl-CoA binding. {ECO:0000250|UniProtKB:Q09472}.|CBP/p300-type HAT. {ECO:0000255|PROSITE- ProRule:PRU01065}.|Cys/His-rich.				cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.R1446C(6)|p.R1446G(1)		NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		ACGGCTGTGCGGAGGCAACGT	0.413			"""T, N, F, Mis, O"""	"""MLL, MORF, RUNXBP2"""	"""ALL, AML, DLBCL, B-NHL """		Rubinstein-Taybi syndrome																																	Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	7	Substitution - Missense(7)	haematopoietic_and_lymphoid_tissue(4)|urinary_tract(1)|lung(1)|central_nervous_system(1)	16											75.0	68.0	71.0					16																	3788618		2197	4300	6497	3728619	SO:0001583	missense	1387			U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"""Chromatin-modifying enzymes / K-acetyltransferases"""	2348	protein-coding gene	gene with protein product		600140	"""Rubinstein-Taybi syndrome"""	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.4336C>A	16.37:g.3788618G>T	ENSP00000262367:p.Arg1446Ser	Somatic		Capture	Illumina HiSeq	Phase_I	3728619	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	37	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	g	17.58	3.424625	0.62733	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070;ENST00000323508	D;D	0.93763	-3.28;-3.28	5.28	4.29	0.51040	.	0.000000	0.64402	D	0.000004	D	0.97732	0.9256	H	0.96080	3.765	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98886	1.0771	10	0.72032	D	0.01	-29.6499	15.2916	0.73870	0.0:0.0:0.8588:0.1412	.	1476;1446	Q4LE28;Q92793	.;CBP_HUMAN	S	1446;1476;1408;35	ENSP00000262367:R1446S;ENSP00000371502:R1408S	ENSP00000262367:R1446S	R	-	1	0	CREBBP	3728619	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	4.937000	0.63513	1.303000	0.44873	0.561000	0.74099	CGC		CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380	
CIITA	4261	hgsc.bcm.edu	37	16	11001528	11001528	+	Missense_Mutation	SNP	G	G	A	rs548646642	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr16:11001528G>A	ENST00000324288.8	+	11	2312	c.2179G>A	c.(2179-2181)Gaa>Aaa	p.E727K	CIITA_ENST00000537380.1_Intron|CIITA_ENST00000381835.5_Intron	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	727					aging (GO:0007568)|cellular response to electrical stimulus (GO:0071257)|cellular response to exogenous dsRNA (GO:0071360)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to antibiotic (GO:0046677)|response to interferon-gamma (GO:0034341)|transcription, DNA-templated (GO:0006351)	cell surface (GO:0009986)|nucleoplasm (GO:0005654)|PML body (GO:0016605)	activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|GTP binding (GO:0005525)|kinase activity (GO:0016301)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transferase activity, transferring acyl groups (GO:0016746)			central_nervous_system(1)|large_intestine(7)|ovary(1)|skin(1)|stomach(2)	12						TCTGAGTGGCGAAATCAAGGA	0.622			T	"""FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"""	"""PMBL, Hodgkin Lymphona, """																																			Dom	yes		16	16p13	4261	"""class II, major histocompatibility complex, transactivator"""		L	0			16											60.0	65.0	64.0					16																	11001528		2197	4300	6497	10909029	SO:0001583	missense	4261			U18259	CCDS10544.1, CCDS66943.1, CCDS73826.1	16p13	2014-09-17	2005-08-12	2005-08-12	ENSG00000179583	ENSG00000179583		"""Nucleotide-binding domain and leucine rich repeat containing"""	7067	protein-coding gene	gene with protein product	"""NLR family, acid domain containing"", ""nucleotide-binding oligomerization domain, leucine rich repeat and acid domain containing"""	600005	"""MHC class II transactivator"""	MHC2TA		8402893	Standard	NM_000246		Approved	C2TA, NLRA	uc002dai.4	P33076	OTTHUMG00000129753	ENST00000324288.8:c.2179G>A	16.37:g.11001528G>A	ENSP00000316328:p.Glu727Lys	Somatic		Capture	Illumina HiSeq	Phase_I	10909029	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Missense_Mutation	SNP	ENST00000324288.8	37	CCDS10544.1	.	.	.	.	.	.	.	.	.	.	G	5.722	0.317775	0.10845	.	.	ENSG00000179583	ENST00000324288;ENST00000388910	T	0.73789	-0.78	5.47	4.48	0.54585	.	0.352334	0.24366	N	0.039142	T	0.71584	0.3357	L	0.56769	1.78	0.33576	D	0.599176	P;B;P;P	0.51351	0.535;0.019;0.878;0.944	B;B;B;B	0.43508	0.189;0.006;0.422;0.262	T	0.79235	-0.1887	10	0.39692	T	0.17	.	13.2692	0.60152	0.0:0.3048:0.6952:0.0	.	727;727;679;727	A0N0N9;P33076;F2Z2G8;Q96KL4	.;C2TA_HUMAN;.;.	K	727;679	ENSP00000316328:E727K	ENSP00000316328:E727K	E	+	1	0	CIITA	10909029	0.998000	0.40836	0.015000	0.15790	0.006000	0.05464	3.885000	0.56182	1.235000	0.43724	0.655000	0.94253	GAA		CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246	
TNRC6A	27327	hgsc.bcm.edu	37	16	24816116	24816116	+	Missense_Mutation	SNP	C	C	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr16:24816116C>G	ENST00000395799.3	+	13	4057	c.3928C>G	c.(3928-3930)Cag>Gag	p.Q1310E	TNRC6A_ENST00000315183.7_Intron|CTD-2515A14.1_ENST00000568895.1_RNA	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	1310	Sufficient for interaction with AGO1 and AGO4.				cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		ACTACCTAACCAGGCCCTTGG	0.443																																																	0			16											135.0	126.0	129.0					16																	24816116		2197	4300	6497	24723617	SO:0001583	missense	27327			U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"""Trinucleotide (CAG) repeat containing"""	11969	protein-coding gene	gene with protein product		610739	"""trinucleotide repeat containing 6"""	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.3928C>G	16.37:g.24816116C>G	ENSP00000379144:p.Gln1310Glu	Somatic		Capture	Illumina HiSeq	Phase_I	24723617	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Missense_Mutation	SNP	ENST00000395799.3	37	CCDS10624.2	.	.	.	.	.	.	.	.	.	.	C	15.46	2.840489	0.51057	.	.	ENSG00000090905	ENST00000395799	T	0.13307	2.6	5.82	5.82	0.92795	.	0.269312	0.32719	N	0.005737	T	0.30386	0.0763	L	0.50333	1.59	0.80722	D	1	P	0.49447	0.924	P	0.62298	0.9	T	0.00754	-1.1580	10	0.15066	T	0.55	-4.8507	20.0989	0.97860	0.0:1.0:0.0:0.0	.	1310	Q8NDV7	TNR6A_HUMAN	E	1310	ENSP00000379144:Q1310E	ENSP00000379144:Q1310E	Q	+	1	0	TNRC6A	24723617	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.368000	0.66133	2.764000	0.94973	0.650000	0.86243	CAG		TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847	
MMP2	4313	hgsc.bcm.edu	37	16	55518020	55518020	+	Missense_Mutation	SNP	G	G	A	rs368486758		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr16:55518020G>A	ENST00000219070.4	+	3	982	c.473G>A	c.(472-474)cGg>cAg	p.R158Q	MMP2_ENST00000437642.2_Missense_Mutation_p.R108Q|MMP2_ENST00000570308.1_Missense_Mutation_p.R82Q|MMP2_ENST00000543485.1_Missense_Mutation_p.R82Q	NM_004530.4	NP_004521.1	P08253	MMP2_HUMAN	matrix metallopeptidase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)	158	Collagenase-like 1.				angiogenesis (GO:0001525)|blood vessel maturation (GO:0001955)|bone trabecula formation (GO:0060346)|cellular protein metabolic process (GO:0044267)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|intramembranous ossification (GO:0001957)|positive regulation of innate immune response (GO:0045089)|proteolysis (GO:0006508)|response to hypoxia (GO:0001666)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|sarcomere (GO:0030017)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|liver(2)|lung(23)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	58		Renal(780;0.00183)|Breast(268;0.00354)|Hepatocellular(780;0.00826)|all_neural(199;0.0189)		UCEC - Uterine corpus endometrioid carcinoma (183;0.0185)|all cancers(182;7.16e-45)|Epithelial(162;5.26e-37)|GBM - Glioblastoma multiforme(240;9e-08)|Kidney(780;0.00227)|BRCA - Breast invasive adenocarcinoma(181;0.00786)	Captopril(DB01197)|Marimastat(DB00786)	ACCCCACTGCGGTTTTCTCGA	0.557																																																	0			16						G	GLN/ARG,GLN/ARG	1,4395	2.1+/-5.4	0,1,2197	150.0	121.0	131.0		323,473	2.7	0.7	16		131	0,8600		0,0,4300	no	missense,missense	MMP2	NM_001127891.1,NM_004530.4	43,43	0,1,6497	AA,AG,GG		0.0,0.0227,0.0077	benign,benign	108/611,158/661	55518020	1,12995	2198	4300	6498	54075521	SO:0001583	missense	4313				CCDS10752.1, CCDS45487.1	16q13-q21	2008-02-05	2005-08-08		ENSG00000087245	ENSG00000087245	3.4.24.24		7166	protein-coding gene	gene with protein product		120360	"""matrix metalloproteinase 2 (gelatinase A, 72kD gelatinase, 72kD type IV collagenase)"", ""matrix metalloproteinase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)"""	CLG4, CLG4A			Standard	NM_004530		Approved	TBE-1	uc002ehz.4	P08253	OTTHUMG00000133202	ENST00000219070.4:c.473G>A	16.37:g.55518020G>A	ENSP00000219070:p.Arg158Gln	Somatic		Capture	Illumina HiSeq	Phase_I	54075521	B2R6U1|B4DWH3|E9PE45|Q9UCJ8	Missense_Mutation	SNP	ENST00000219070.4	37	CCDS10752.1	.	.	.	.	.	.	.	.	.	.	G	10.70	1.424160	0.25639	2.27E-4	0.0	ENSG00000087245	ENST00000219070;ENST00000543485;ENST00000437642	T;T;T	0.21031	2.03;2.03;2.03	4.72	2.72	0.32119	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.431251	0.26635	N	0.023290	T	0.11707	0.0285	N	0.16602	0.42	0.09310	N	1	B;B	0.15719	0.003;0.014	B;B	0.08055	0.003;0.002	T	0.19063	-1.0317	10	0.42905	T	0.14	.	8.2601	0.31779	0.2443:0.0:0.7557:0.0	.	108;158	E9PE45;P08253	.;MMP2_HUMAN	Q	158;82;108	ENSP00000219070:R158Q;ENSP00000444143:R82Q;ENSP00000394237:R108Q	ENSP00000219070:R158Q	R	+	2	0	MMP2	54075521	0.000000	0.05858	0.721000	0.30653	0.984000	0.73092	0.383000	0.20651	1.122000	0.41944	0.455000	0.32223	CGG		MMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256913.3		
CDH8	1006	hgsc.bcm.edu	37	16	61687915	61687915	+	Missense_Mutation	SNP	C	C	T	rs146063486	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr16:61687915C>T	ENST00000577390.1	-	12	2951	c.1997G>A	c.(1996-1998)cGc>cAc	p.R666H	CDH8_ENST00000299345.6_Missense_Mutation_p.R666H|CDH8_ENST00000577730.1_Missense_Mutation_p.R666H	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	666					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|response to cold (GO:0009409)|synaptic transmission, glutamatergic (GO:0035249)	axon terminus (GO:0043679)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(22)|liver(2)|lung(49)|ovary(6)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(4)	112		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		ATCATCGTAGCGAATGATGTT	0.408													C|||	2	0.000399361	0.0	0.0	5008	,	,		17903	0.0		0.002	False		,,,				2504	0.0																0			16						C	HIS/ARG	6,4400	11.4+/-27.6	0,6,2197	120.0	112.0	115.0		1997	5.7	1.0	16	dbSNP_134	115	15,8585	10.5+/-38.8	0,15,4285	yes	missense	CDH8	NM_001796.4	29	0,21,6482	TT,TC,CC		0.1744,0.1362,0.1615	probably-damaging	666/800	61687915	21,12985	2203	4300	6503	60245416	SO:0001583	missense	1006			L34060	CCDS10802.1	16q22.1	2010-01-26			ENSG00000150394	ENSG00000150394		"""Cadherins / Major cadherins"""	1767	protein-coding gene	gene with protein product		603008				9615235, 2059658	Standard	NM_001796		Approved		uc002eog.2	P55286	OTTHUMG00000137493	ENST00000577390.1:c.1997G>A	16.37:g.61687915C>T	ENSP00000462701:p.Arg666His	Somatic		Capture	Illumina HiSeq	Phase_I	60245416	B3KWC1|Q14DC6|Q9ULB2	Missense_Mutation	SNP	ENST00000577390.1	37	CCDS10802.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	29.5	5.012465	0.93346	0.001362	0.001744	ENSG00000150394	ENST00000299345	T	0.76316	-1.01	5.7	5.7	0.88788	Cadherin, cytoplasmic domain (1);	0.105154	0.64402	D	0.000002	T	0.80929	0.4718	N	0.22421	0.69	0.80722	D	1	D	0.71674	0.998	D	0.66716	0.946	T	0.80236	-0.1466	10	0.38643	T	0.18	.	18.8311	0.92139	0.0:1.0:0.0:0.0	.	666	P55286	CADH8_HUMAN	H	666	ENSP00000299345:R666H	ENSP00000299345:R666H	R	-	2	0	CDH8	60245416	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.046000	0.71029	2.679000	0.91253	0.655000	0.94253	CGC		CDH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268754.3	NM_001796	
CDH1	999	hgsc.bcm.edu	37	16	68846134	68846134	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr16:68846134A>G	ENST00000261769.5	+	8	1296	c.1105A>G	c.(1105-1107)Aac>Gac	p.N369D	RP11-354M1.2_ENST00000563916.1_RNA|CDH1_ENST00000562836.1_3'UTR|CDH1_ENST00000422392.2_Missense_Mutation_p.N369D	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	369	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)	p.N369D(1)|p.S337_T379del(1)|p.?(1)		NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		CACTGACACCAACGATAATCC	0.463			"""Mis, N, F, S"""		"""lobular breast, gastric"""	gastric			Hereditary Diffuse Gastric Cancer																														yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"""cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"""		E	3	Substitution - Missense(1)|Unknown(1)|Deletion - In frame(1)	stomach(2)|breast(1)	16											182.0	139.0	154.0					16																	68846134		2198	4300	6498	67403635	SO:0001583	missense	51343	Familial Cancer Database	HDGC	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"""CD molecules"", ""Cadherins / Major cadherins"""	1748	protein-coding gene	gene with protein product	"""E-Cadherin"""	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.1105A>G	16.37:g.68846134A>G	ENSP00000261769:p.Asn369Asp	Somatic		Capture	Illumina HiSeq	Phase_I	67403635	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Missense_Mutation	SNP	ENST00000261769.5	37	CCDS10869.1	.	.	.	.	.	.	.	.	.	.	A	19.35	3.810509	0.70797	.	.	ENSG00000039068	ENST00000261769;ENST00000379120;ENST00000268794;ENST00000422392	T;T	0.75821	-0.97;-0.17	5.72	5.72	0.89469	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);	0.000000	0.53938	D	0.000041	D	0.89350	0.6690	M	0.92169	3.28	0.53005	D	0.999963	D;D	0.89917	0.997;1.0	D;D	0.91635	0.991;0.999	D	0.91857	0.5496	10	0.87932	D	0	.	15.6694	0.77262	1.0:0.0:0.0:0.0	.	369;369	Q9UII8;P12830	.;CADH1_HUMAN	D	369	ENSP00000261769:N369D;ENSP00000414946:N369D	ENSP00000261769:N369D	N	+	1	0	CDH1	67403635	1.000000	0.71417	0.928000	0.36995	0.058000	0.15608	7.112000	0.77086	2.190000	0.69967	0.454000	0.30748	AAC		CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268897.2	NM_004360	
MYOM1	8736	hgsc.bcm.edu	37	18	3188882	3188882	+	Missense_Mutation	SNP	C	C	T	rs200770047		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr18:3188882C>T	ENST00000356443.4	-	4	968	c.635G>A	c.(634-636)aGg>aAg	p.R212K	MYOM1_ENST00000400569.3_Missense_Mutation_p.R212K|MYOM1_ENST00000261606.7_Missense_Mutation_p.R212K|RP13-270P17.2_ENST00000580139.1_RNA	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	212	6 X 6 AA tandem repeats.				muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)	p.R212K(1)		NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						CGTGGACTGCCTGGATGCCGT	0.517																																																	1	Substitution - Missense(1)	endometrium(1)	18											260.0	242.0	248.0					18																	3188882		2044	4187	6231	3178882	SO:0001583	missense	8736			AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7613	protein-coding gene	gene with protein product	"""skelemin"""	603508	"""myomesin 1 (skelemin) (185kD)"", ""myomesin 1 (skelemin) 185kDa"", ""myomesin 1, 185kDa"""			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.635G>A	18.37:g.3188882C>T	ENSP00000348821:p.Arg212Lys	Somatic		Capture	Illumina HiSeq	Phase_I	3178882	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	37	CCDS45824.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	2.966	-0.213546	0.06140	.	.	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.45668	1.03;1.04;0.89	3.23	0.752	0.18398	.	0.084010	0.41097	N	0.000942	T	0.14830	0.0358	N	0.08118	0	0.09310	N	0.999995	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.28808	-1.0032	10	0.05351	T	0.99	.	4.9448	0.13984	0.0:0.2653:0.0:0.7347	.	212;212	P52179-2;P52179	.;MYOM1_HUMAN	K	212	ENSP00000348821:R212K;ENSP00000383413:R212K;ENSP00000261606:R212K	ENSP00000261606:R212K	R	-	2	0	MYOM1	3178882	0.789000	0.28775	0.018000	0.16275	0.000000	0.00434	1.455000	0.35190	0.165000	0.19558	-1.097000	0.02148	AGG		MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
MIB1	57534	hgsc.bcm.edu	37	18	19348680	19348680	+	Missense_Mutation	SNP	A	A	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr18:19348680A>T	ENST00000261537.6	+	3	762	c.498A>T	c.(496-498)gaA>gaT	p.E166D	MIB1_ENST00000578646.1_3'UTR	NM_020774.2	NP_065825.1	Q86YT6	MIB1_HUMAN	mindbomb E3 ubiquitin protein ligase 1	166	MIB/HERC2 2. {ECO:0000255|PROSITE- ProRule:PRU00749}.				blood vessel development (GO:0001568)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|negative regulation of neuron differentiation (GO:0045665)|neural tube formation (GO:0001841)|Notch signaling pathway (GO:0007219)|positive regulation of endocytosis (GO:0045807)|somitogenesis (GO:0001756)	centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(13)|ovary(5)	27			STAD - Stomach adenocarcinoma(5;0.212)			GGCAGTGGGAAGATCAAGATG	0.418																																																	0			18											83.0	80.0	81.0					18																	19348680		2203	4300	6503	17602678	SO:0001583	missense	57534			AB037744	CCDS11871.1	18q11.2	2014-09-17	2012-02-23		ENSG00000101752	ENSG00000101752		"""Zinc fingers, ZZ-type"", ""Ankyrin repeat domain containing"""	21086	protein-coding gene	gene with protein product		608677	"""mindbomb homolog 1 (Drosophila)"""				Standard	NM_020774		Approved	DIP-1, MIB, KIAA1323, ZZANK2, ZZZ6	uc002ktq.3	Q86YT6	OTTHUMG00000131753	ENST00000261537.6:c.498A>T	18.37:g.19348680A>T	ENSP00000261537:p.Glu166Asp	Somatic		Capture	Illumina HiSeq	Phase_I	17602678	B0YJ38|Q2TB37|Q68D01|Q6YI51|Q8NBY0|Q8TCB5|Q8TCL7|Q9P2M3	Missense_Mutation	SNP	ENST00000261537.6	37	CCDS11871.1	.	.	.	.	.	.	.	.	.	.	A	18.13	3.556376	0.65425	.	.	ENSG00000101752	ENST00000261537	T	0.37235	1.21	5.0	3.83	0.44106	Mib-herc2 (2);	0.000000	0.85682	D	0.000000	T	0.42200	0.1192	L	0.33189	0.99	0.54753	D	0.999982	P	0.40032	0.699	P	0.58928	0.848	T	0.13308	-1.0514	10	0.17832	T	0.49	-19.7346	10.7948	0.46453	0.924:0.0:0.076:0.0	.	166	Q86YT6	MIB1_HUMAN	D	166	ENSP00000261537:E166D	ENSP00000261537:E166D	E	+	3	2	MIB1	17602678	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.876000	0.63079	1.870000	0.54199	0.533000	0.62120	GAA		MIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254675.1	NM_020774	
SMAD4	4089	hgsc.bcm.edu	37	18	48575112	48575112	+	Silent	SNP	T	T	C			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr18:48575112T>C	ENST00000342988.3	+	3	844	c.306T>C	c.(304-306)ccT>ccC	p.P102P	SMAD4_ENST00000588745.1_Silent_p.P102P|RP11-729L2.2_ENST00000590722.2_3'UTR|SMAD4_ENST00000452201.2_Silent_p.P102P|SMAD4_ENST00000398417.2_Silent_p.P102P	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	102	MH1. {ECO:0000255|PROSITE- ProRule:PRU00438}.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(4)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		GGAGGTGGCCTGATCTTCACA	0.388																																																	40	Whole gene deletion(36)|Unknown(4)	pancreas(26)|large_intestine(3)|stomach(3)|breast(3)|lung(2)|upper_aerodigestive_tract(1)|oesophagus(1)|NS(1)	18											161.0	147.0	152.0					18																	48575112		2203	4300	6503	46829110	SO:0001819	synonymous_variant	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"""SMADs"""	6770	protein-coding gene	gene with protein product		600993	"""MAD, mothers against decapentaplegic homolog 4 (Drosophila)"", ""SMAD, mothers against DPP homolog 4 (Drosophila)"""	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.306T>C	18.37:g.48575112T>C		Somatic		Capture	Illumina HiSeq	Phase_I	46829110	A8K405	Silent	SNP	ENST00000342988.3	37	CCDS11950.1																																																																																				SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359	
SMAD4	4089	hgsc.bcm.edu	37	18	48591809	48591809	+	Silent	SNP	T	T	C			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr18:48591809T>C	ENST00000342988.3	+	9	1510	c.972T>C	c.(970-972)tgT>tgC	p.C324C	SMAD4_ENST00000588745.1_Silent_p.C228C|SMAD4_ENST00000398417.2_Silent_p.C324C	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	324	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(2)|p.W323fs*11(1)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		AGTATTGGTGTTCCATTGCTT	0.413																																																	39	Whole gene deletion(36)|Unknown(2)|Deletion - Frameshift(1)	pancreas(26)|large_intestine(3)|breast(3)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|small_intestine(1)|oesophagus(1)	18											248.0	214.0	225.0					18																	48591809		2203	4300	6503	46845807	SO:0001819	synonymous_variant	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"""SMADs"""	6770	protein-coding gene	gene with protein product		600993	"""MAD, mothers against decapentaplegic homolog 4 (Drosophila)"", ""SMAD, mothers against DPP homolog 4 (Drosophila)"""	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.972T>C	18.37:g.48591809T>C		Somatic		Capture	Illumina HiSeq	Phase_I	46845807	A8K405	Silent	SNP	ENST00000342988.3	37	CCDS11950.1																																																																																				SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359	
ALPK2	115701	hgsc.bcm.edu	37	18	56204708	56204708	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr18:56204708T>C	ENST00000361673.3	-	5	2924	c.2711A>G	c.(2710-2712)gAa>gGa	p.E904G	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	904						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						TGTGGCACCTTCACTAGCTGT	0.512																																																	0			18											78.0	78.0	78.0					18																	56204708		2203	4300	6503	54355688	SO:0001583	missense	115701			AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.2711A>G	18.37:g.56204708T>C	ENSP00000354991:p.Glu904Gly	Somatic		Capture	Illumina HiSeq	Phase_I	54355688	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	37	CCDS11966.2	.	.	.	.	.	.	.	.	.	.	T	12.43	1.935262	0.34189	.	.	ENSG00000198796	ENST00000361673	T	0.48522	0.81	5.43	1.84	0.25277	.	0.414085	0.22635	N	0.057527	T	0.34513	0.0900	L	0.41824	1.3	0.09310	N	1	B;B	0.23735	0.09;0.014	B;B	0.26310	0.068;0.008	T	0.20240	-1.0281	10	0.38643	T	0.18	-1.5835	6.3066	0.21141	0.0:0.2867:0.0:0.7133	.	904;904	Q86TB3-2;Q86TB3	.;ALPK2_HUMAN	G	904	ENSP00000354991:E904G	ENSP00000354991:E904G	E	-	2	0	ALPK2	54355688	0.000000	0.05858	0.000000	0.03702	0.109000	0.19521	0.276000	0.18716	0.384000	0.24942	0.482000	0.46254	GAA		ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
DSEL	92126	hgsc.bcm.edu	37	18	65178966	65178966	+	Missense_Mutation	SNP	T	T	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr18:65178966T>A	ENST00000310045.7	-	2	4383	c.2910A>T	c.(2908-2910)aaA>aaT	p.K970N	CTD-2541J13.2_ENST00000583493.1_RNA|CTD-2541J13.2_ENST00000581951.1_RNA	NM_032160.2	NP_115536.1	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	960					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	isomerase activity (GO:0016853)|sulfotransferase activity (GO:0008146)			NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(25)|lung(23)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)				TCCTTTTAAATTTTCTTTTTT	0.378																																																	0			18											43.0	50.0	47.0					18																	65178966		2183	4286	6469	63329946	SO:0001583	missense	92126			AF480435	CCDS11995.1	18q22.1	2007-01-29	2007-01-29	2007-01-29	ENSG00000171451	ENSG00000171451			18144	protein-coding gene	gene with protein product		611125	"""chromosome 18 open reading frame 4"""	C18orf4		16505484	Standard	NM_032160		Approved	NCAG1, FLJ11477	uc002lke.1	Q8IZU8	OTTHUMG00000132804	ENST00000310045.7:c.2910A>T	18.37:g.65178966T>A	ENSP00000310565:p.Lys970Asn	Somatic		Capture	Illumina HiSeq	Phase_I	63329946	Q17RH1|Q6P5Z3	Missense_Mutation	SNP	ENST00000310045.7	37	CCDS11995.1	.	.	.	.	.	.	.	.	.	.	T	9.044	0.990304	0.18966	.	.	ENSG00000171451	ENST00000310045;ENST00000397964	D	0.81996	-1.56	5.17	2.81	0.32909	Sulfotransferase domain (1);	0.081233	0.46758	U	0.000274	T	0.79907	0.4527	L	0.40543	1.245	0.19300	N	0.99997	P	0.42078	0.77	P	0.48598	0.583	T	0.71397	-0.4605	10	0.72032	D	0.01	-21.7788	8.2308	0.31597	0.0:0.2936:0.0:0.7064	.	960	Q8IZU8	DSEL_HUMAN	N	970;960	ENSP00000310565:K970N	ENSP00000310565:K970N	K	-	3	2	DSEL	63329946	0.098000	0.21812	0.693000	0.30195	0.407000	0.30961	0.391000	0.20784	0.806000	0.34183	0.460000	0.39030	AAA		DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	NM_032160	
CCDC102B	79839	hgsc.bcm.edu	37	18	66678184	66678184	+	Missense_Mutation	SNP	T	T	C	rs567681416		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr18:66678184T>C	ENST00000360242.5	+	7	1394	c.1277T>C	c.(1276-1278)cTt>cCt	p.L426P	CCDC102B_ENST00000319445.6_Missense_Mutation_p.L426P|CCDC102B_ENST00000584156.1_Missense_Mutation_p.L426P	NM_024781.2	NP_079057	Q68D86	C102B_HUMAN	coiled-coil domain containing 102B	426										breast(2)|endometrium(3)|large_intestine(5)|lung(19)|ovary(1)|skin(5)|stomach(1)	36		Esophageal squamous(42;0.0559)|Colorectal(73;0.0604)				TTACTGAACCTTCAACATGCC	0.323																																																	0			18											62.0	60.0	61.0					18																	66678184		2203	4300	6503	64829164	SO:0001583	missense	79839			AK027247	CCDS11996.2	18q22.1	2007-11-14	2006-04-10	2006-04-10	ENSG00000150636	ENSG00000150636			26295	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 14"", ""aminoacylase 1-like"""	C18orf14, ACY1L		14702039	Standard	NM_001093729		Approved	FLJ23594, HsT1731, AN	uc002lkk.2	Q68D86	OTTHUMG00000132808	ENST00000360242.5:c.1277T>C	18.37:g.66678184T>C	ENSP00000353377:p.Leu426Pro	Somatic		Capture	Illumina HiSeq	Phase_I	64829164	Q7Z467|Q8NDK7|Q9H5C1	Missense_Mutation	SNP	ENST00000360242.5	37	CCDS11996.2	.	.	.	.	.	.	.	.	.	.	T	9.106	1.005407	0.19199	.	.	ENSG00000150636	ENST00000319445;ENST00000360242	T;T	0.22539	1.95;1.95	5.4	4.21	0.49690	.	0.466449	0.18234	N	0.147474	T	0.38719	0.1051	M	0.67397	2.05	0.80722	D	1	D	0.89917	1.0	D	0.68943	0.961	T	0.06197	-1.0840	10	0.31617	T	0.26	-3.7455	8.4266	0.32733	0.174:0.0:0.0:0.826	.	426	Q68D86	C102B_HUMAN	P	426	ENSP00000316237:L426P;ENSP00000353377:L426P	ENSP00000316237:L426P	L	+	2	0	CCDC102B	64829164	0.980000	0.34600	0.178000	0.23040	0.822000	0.46500	2.526000	0.45607	0.844000	0.35094	0.528000	0.53228	CTT		CCDC102B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256225.2	NM_024781	
NGLY1	55768	hgsc.bcm.edu	37	3	25761660	25761660	+	Missense_Mutation	SNP	C	C	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr3:25761660C>A	ENST00000280700.5	-	11	1794	c.1634G>T	c.(1633-1635)gGa>gTa	p.G545V	NGLY1_ENST00000417874.2_Missense_Mutation_p.G503V|NGLY1_ENST00000422724.2_3'UTR|NGLY1_ENST00000396649.3_Intron|NGLY1_ENST00000467224.1_5'UTR|NGLY1_ENST00000428257.1_Missense_Mutation_p.G527V	NM_018297.3	NP_060767.2	Q96IV0	NGLY1_HUMAN	N-glycanase 1	545	PAW. {ECO:0000255|PROSITE- ProRule:PRU00731}.				glycoprotein catabolic process (GO:0006516)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity (GO:0000224)			breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(2)|skin(1)	18						AAAAGATGATCCTTCCTTTCG	0.358																																																	0			3											70.0	68.0	68.0					3																	25761660		2203	4300	6503	25736664	SO:0001583	missense	55768			AF250924	CCDS33719.1, CCDS46777.1, CCDS46778.1, CCDS46779.1	3p23	2006-08-30			ENSG00000151092	ENSG00000151092			17646	protein-coding gene	gene with protein product		610661					Standard	NM_018297		Approved	FLJ11005, PNG1	uc003cdl.3	Q96IV0	OTTHUMG00000155600	ENST00000280700.5:c.1634G>T	3.37:g.25761660C>A	ENSP00000280700:p.Gly545Val	Somatic		Capture	Illumina HiSeq	Phase_I	25736664	B4DJE9|Q59FB1|Q6PJD8|Q9BVR8|Q9NR70	Missense_Mutation	SNP	ENST00000280700.5	37	CCDS33719.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.615578	0.87359	.	.	ENSG00000151092	ENST00000428257;ENST00000280700;ENST00000308710;ENST00000417874	T;T;T;T	0.35236	1.32;1.32;1.32;1.32	5.79	5.79	0.91817	Peptide N glycanase, PAW domain (3);Galactose-binding domain-like (1);	0.044965	0.85682	D	0.000000	T	0.66499	0.2795	M	0.83223	2.63	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.69661	-0.5085	10	0.87932	D	0	-25.1316	20.0402	0.97587	0.0:1.0:0.0:0.0	.	503;527;545	B4DJE9;Q96IV0-2;Q96IV0	.;.;NGLY1_HUMAN	V	527;545;524;503	ENSP00000387430:G527V;ENSP00000280700:G545V;ENSP00000307980:G524V;ENSP00000389888:G503V	ENSP00000280700:G545V	G	-	2	0	NGLY1	25736664	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	4.696000	0.61774	2.750000	0.94351	0.563000	0.77884	GGA		NGLY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340832.2		
TRANK1	9881	hgsc.bcm.edu	37	3	36871126	36871126	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr3:36871126T>C	ENST00000429976.2	-	22	8853	c.8606A>G	c.(8605-8607)aAc>aGc	p.N2869S	TRANK1_ENST00000428977.2_Missense_Mutation_p.N2319S|TRANK1_ENST00000301807.6_Missense_Mutation_p.N2319S	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	2869							ATP binding (GO:0005524)|hydrolase activity (GO:0016787)			NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(20)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	73						GATCAGAATGTTGACCAGCCG	0.483																																																	0			3											92.0	94.0	93.0					3																	36871126		2075	4208	6283	36846130	SO:0001583	missense	0			AK096678	CCDS46789.1, CCDS46789.2	3p22.2	2013-01-11			ENSG00000168016	ENSG00000168016		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29011	protein-coding gene	gene with protein product	"""lupus brain antigen 1"", ""KIAA0342"""					9205841	Standard	NM_014831		Approved	LBA1, KIAA0342	uc003cgj.3	O15050	OTTHUMG00000155848	ENST00000429976.2:c.8606A>G	3.37:g.36871126T>C	ENSP00000416168:p.Asn2869Ser	Somatic		Capture	Illumina HiSeq	Phase_I	36846130	Q8N8K0	Missense_Mutation	SNP	ENST00000429976.2	37	CCDS46789.2	.	.	.	.	.	.	.	.	.	.	T	11.00	1.510046	0.27036	.	.	ENSG00000168016	ENST00000428977;ENST00000429976;ENST00000301807	T;T;T	0.30448	1.53;1.95;1.53	5.17	0.0217	0.14130	.	0.807151	0.10197	U	0.703837	T	0.18130	0.0435	L	0.27053	0.805	0.09310	N	1	B	0.23937	0.094	B	0.19666	0.026	T	0.24728	-1.0152	10	0.51188	T	0.08	.	3.7329	0.08500	0.1537:0.2583:0.0:0.588	.	2869	O15050	TRNK1_HUMAN	S	2319;2869;2319	ENSP00000416826:N2319S;ENSP00000416168:N2869S;ENSP00000301807:N2319S	ENSP00000301807:N2319S	N	-	2	0	TRANK1	36846130	0.000000	0.05858	0.000000	0.03702	0.802000	0.45316	-0.264000	0.08658	0.057000	0.16193	0.459000	0.35465	AAC		TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831	
GRM2	2912	hgsc.bcm.edu	37	3	51746730	51746730	+	Missense_Mutation	SNP	G	G	A	rs147501226		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr3:51746730G>A	ENST00000395052.3	+	3	926	c.692G>A	c.(691-693)cGc>cAc	p.R231H	GRM2_ENST00000442933.2_Missense_Mutation_p.R231H|GRM2_ENST00000475478.1_Intron	NM_000839.3	NP_000830.2	Q14416	GRM2_HUMAN	glutamate receptor, metabotropic 2	231					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|glutamate secretion (GO:0014047)|negative regulation of adenylate cyclase activity (GO:0007194)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	calcium channel regulator activity (GO:0005246)|G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group II metabotropic glutamate receptor activity (GO:0001641)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(1)|lung(11)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		GCTCGTGCCCGCAACATCTGT	0.622													G|||	1	0.000199681	0.0	0.0	5008	,	,		15266	0.0		0.0	False		,,,				2504	0.001																0			3											57.0	54.0	55.0					3																	51746730		2203	4300	6503	51721770	SO:0001583	missense	2912			L35318	CCDS2834.1	3p21.2	2013-09-20			ENSG00000164082	ENSG00000164082		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4594	protein-coding gene	gene with protein product		604099				7620613	Standard	NM_000839		Approved	GPRC1B, mGlu2, MGLUR2	uc010hlv.3	Q14416	OTTHUMG00000156902	ENST00000395052.3:c.692G>A	3.37:g.51746730G>A	ENSP00000378492:p.Arg231His	Somatic		Capture	Illumina HiSeq	Phase_I	51721770	B0M0K7|Q14CU5|Q52MC6|Q9H3N6	Missense_Mutation	SNP	ENST00000395052.3	37	CCDS2834.1	.	.	.	.	.	.	.	.	.	.	G	13.27	2.187530	0.38609	.	.	ENSG00000164082	ENST00000395052;ENST00000442933	D;D	0.84800	-1.9;-1.9	5.25	3.42	0.39159	Extracellular ligand-binding receptor (1);	0.094462	0.40064	N	0.001188	T	0.80204	0.4580	L	0.59436	1.845	0.80722	D	1	B	0.26602	0.154	B	0.27170	0.077	T	0.73833	-0.3858	10	0.21540	T	0.41	.	10.0298	0.42094	0.0718:0.0:0.7893:0.1388	.	231	Q14416	GRM2_HUMAN	H	231	ENSP00000378492:R231H;ENSP00000408906:R231H	ENSP00000296479:R231H	R	+	2	0	GRM2	51721770	1.000000	0.71417	1.000000	0.80357	0.336000	0.28762	8.022000	0.88759	1.356000	0.45884	-0.175000	0.13238	CGC		GRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346542.1		
DZIP3	9666	hgsc.bcm.edu	37	3	108330154	108330154	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr3:108330154A>G	ENST00000361582.3	+	4	466	c.236A>G	c.(235-237)gAt>gGt	p.D79G	DZIP3_ENST00000463306.1_Missense_Mutation_p.D79G	NM_014648.3	NP_055463.1	Q86Y13	DZIP3_HUMAN	DAZ interacting zinc finger protein 3	79					protein polyubiquitination (GO:0000209)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|phosphatase binding (GO:0019902)|poly(A) RNA binding (GO:0044822)|polyubiquitin binding (GO:0031593)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(21)|ovary(1)|pancreas(1)|prostate(5)|skin(1)	45						TTACAAGAAGATTTTTCCTTC	0.328																																																	0			3											71.0	74.0	73.0					3																	108330154		2203	4300	6503	109812844	SO:0001583	missense	9666			AF279370	CCDS2952.1	3q13.13	2013-05-22	2013-05-22		ENSG00000198919	ENSG00000198919		"""RING-type (C3HC4) zinc fingers"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	30938	protein-coding gene	gene with protein product	"""human RNA-binding ubiquitin ligase of 138 kDa"", ""protein phosphatase 1, regulatory subunit 66"""	608672	"""DAZ interacting protein 3, zinc finger"""			9734811, 12538761	Standard	NM_014648		Approved	hRUL138, PPP1R66	uc003dxd.3	Q86Y13	OTTHUMG00000159232	ENST00000361582.3:c.236A>G	3.37:g.108330154A>G	ENSP00000355028:p.Asp79Gly	Somatic		Capture	Illumina HiSeq	Phase_I	109812844	B3KN01|O75162|Q6P3R9|Q6PH82|Q86Y14|Q86Y15|Q86Y16|Q8IWI0|Q96RS9	Missense_Mutation	SNP	ENST00000361582.3	37	CCDS2952.1	.	.	.	.	.	.	.	.	.	.	A	14.37	2.516279	0.44763	.	.	ENSG00000198919	ENST00000393969;ENST00000361582;ENST00000479138;ENST00000463306	T;T	0.19250	2.16;2.16	5.02	3.86	0.44501	.	0.336984	0.25851	N	0.027897	T	0.14141	0.0342	L	0.27053	0.805	0.31401	N	0.676648	B	0.16603	0.018	B	0.14023	0.01	T	0.05084	-1.0907	10	0.72032	D	0.01	-10.4218	8.1869	0.31343	0.7788:0.2212:0.0:0.0	.	79	Q86Y13	DZIP3_HUMAN	G	79	ENSP00000355028:D79G;ENSP00000419981:D79G	ENSP00000355028:D79G	D	+	2	0	DZIP3	109812844	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.532000	0.36029	2.101000	0.63845	0.528000	0.53228	GAT		DZIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353968.1	NM_014648	
GATA2	2624	hgsc.bcm.edu	37	3	128205664	128205664	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr3:128205664A>G	ENST00000341105.2	-	2	542	c.211T>C	c.(211-213)Tcc>Ccc	p.S71P	RP11-475N22.4_ENST00000464242.1_RNA|GATA2_ENST00000430265.2_Missense_Mutation_p.S71P|RP11-475N22.4_ENST00000468377.1_RNA|RP11-475N22.4_ENST00000473958.1_RNA|GATA2_ENST00000487848.1_Missense_Mutation_p.S71P	NM_032638.4	NP_116027.2	P23769	GATA2_HUMAN	GATA binding protein 2	71					blood coagulation (GO:0007596)|cell differentiation in hindbrain (GO:0021533)|cell fate determination (GO:0001709)|cell maturation (GO:0048469)|central nervous system neuron development (GO:0021954)|commitment of neuronal cell to specific neuron type in forebrain (GO:0021902)|definitive hemopoiesis (GO:0060216)|embryonic placenta development (GO:0001892)|eosinophil fate commitment (GO:0035854)|GABAergic neuron differentiation (GO:0097154)|homeostasis of number of cells within a tissue (GO:0048873)|inner ear morphogenesis (GO:0042472)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fat cell proliferation (GO:0070345)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phagocytosis (GO:0006909)|pituitary gland development (GO:0021983)|positive regulation of angiogenesis (GO:0045766)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of phagocytosis (GO:0050766)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of forebrain neuron differentiation (GO:2000977)|regulation of histone acetylation (GO:0035065)|semicircular canal development (GO:0060872)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)|urogenital system development (GO:0001655)|ventral spinal cord interneuron differentiation (GO:0021514)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	C2H2 zinc finger domain binding (GO:0070742)|chromatin binding (GO:0003682)|enhancer sequence-specific DNA binding (GO:0001158)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(58)|kidney(2)|large_intestine(3)|lung(9)|prostate(3)|skin(1)|urinary_tract(1)	79				GBM - Glioblastoma multiforme(114;0.173)		GGGCTGTAGGAGACGCGCGCC	0.692			Mis		AML(CML blast transformation)																																			Dom	yes		3	3q21.3	2624	GATA binding protein 2		L	0			3											30.0	30.0	30.0					3																	128205664		2201	4298	6499	129688354	SO:0001583	missense	2624			AF169253	CCDS3049.1, CCDS46903.1	3q21	2014-09-17	2001-11-28		ENSG00000179348	ENSG00000179348		"""GATA zinc finger domain containing"""	4171	protein-coding gene	gene with protein product		137295	"""GATA-binding protein 2"""			1714909	Standard	NM_032638		Approved	NFE1B	uc003eko.2	P23769	OTTHUMG00000159689	ENST00000341105.2:c.211T>C	3.37:g.128205664A>G	ENSP00000345681:p.Ser71Pro	Somatic		Capture	Illumina HiSeq	Phase_I	129688354	D3DNB3|Q53YE0|Q96BH0|Q96BH8|Q9BUJ6	Missense_Mutation	SNP	ENST00000341105.2	37	CCDS3049.1	.	.	.	.	.	.	.	.	.	.	A	14.41	2.528384	0.44969	.	.	ENSG00000179348	ENST00000341105;ENST00000430265;ENST00000487848;ENST00000492608	D;D;D	0.97232	-4.3;-4.3;-4.3	4.74	4.74	0.60224	.	0.094180	0.46758	D	0.000270	D	0.96340	0.8806	M	0.70275	2.135	0.48830	D	0.999715	P;B	0.46220	0.874;0.0	P;B	0.44990	0.466;0.003	D	0.95498	0.8575	10	0.35671	T	0.21	-15.1408	14.2339	0.65911	1.0:0.0:0.0:0.0	.	71;71	P23769-2;P23769	.;GATA2_HUMAN	P	71	ENSP00000345681:S71P;ENSP00000400259:S71P;ENSP00000417074:S71P	ENSP00000345681:S71P	S	-	1	0	GATA2	129688354	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	2.849000	0.48286	1.756000	0.51951	0.260000	0.18958	TCC		GATA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356925.1	NM_032638	
COL6A6	131873	hgsc.bcm.edu	37	3	130300560	130300560	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr3:130300560A>G	ENST00000358511.6	+	8	3734	c.3703A>G	c.(3703-3705)Act>Gct	p.T1235A	COL6A6_ENST00000453409.2_Missense_Mutation_p.T1235A	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	1235	Nonhelical region.|VWFA 7. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						GGGCACAGAGACTCAGGTCAG	0.448																																																	0			3											98.0	96.0	97.0					3																	130300560		2018	4175	6193	131783250	SO:0001583	missense	131873			AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"""Collagens"""	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.3703A>G	3.37:g.130300560A>G	ENSP00000351310:p.Thr1235Ala	Somatic		Capture	Illumina HiSeq	Phase_I	131783250	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	37	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	A	14.88	2.666675	0.47677	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	T;T	0.38887	1.11;1.11	6.06	6.06	0.98353	von Willebrand factor, type A (2);	.	.	.	.	T	0.32556	0.0833	N	0.24115	0.695	0.28237	N	0.925854	P	0.52463	0.953	P	0.47603	0.551	T	0.07233	-1.0783	9	0.08179	T	0.78	.	11.5702	0.50829	0.8509:0.1491:0.0:0.0	.	1235	A6NMZ7	CO6A6_HUMAN	A	1235	ENSP00000351310:T1235A;ENSP00000399236:T1235A	ENSP00000351310:T1235A	T	+	1	0	COL6A6	131783250	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.558000	0.45879	2.324000	0.78689	0.533000	0.62120	ACT		COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608	
ZIC1	7545	hgsc.bcm.edu	37	3	147128637	147128637	+	Missense_Mutation	SNP	C	C	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr3:147128637C>G	ENST00000282928.4	+	1	1467	c.738C>G	c.(736-738)ttC>ttG	p.F246L		NM_003412.3	NP_003403.2	Q15915	ZIC1_HUMAN	Zic family member 1	246					adult walking behavior (GO:0007628)|brain development (GO:0007420)|cell differentiation (GO:0030154)|inner ear morphogenesis (GO:0042472)|pattern specification process (GO:0007389)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of smoothened signaling pathway (GO:0008589)|spinal cord development (GO:0021510)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(4)|cervix(1)|endometrium(2)|large_intestine(8)|lung(38)|ovary(1)|prostate(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	63						ACAAAACTTTCAGCACCATGC	0.572																																																	0			3											93.0	86.0	89.0					3																	147128637		2203	4300	6503	148611327	SO:0001583	missense	7545			D76435	CCDS3136.1	3q24	2013-01-08	2011-05-19		ENSG00000152977	ENSG00000152977		"""Zinc fingers, C2H2-type"""	12872	protein-coding gene	gene with protein product		600470	"""Zic family member 1 (odd-paired Drosophila homolog)"", ""Zic family member 1 (odd-paired homolog, Drosophila)"""			8542595	Standard	NM_003412		Approved	ZIC, ZNF201	uc003ewe.3	Q15915	OTTHUMG00000159456	ENST00000282928.4:c.738C>G	3.37:g.147128637C>G	ENSP00000282928:p.Phe246Leu	Somatic		Capture	Illumina HiSeq	Phase_I	148611327	Q2M3N1	Missense_Mutation	SNP	ENST00000282928.4	37	CCDS3136.1	.	.	.	.	.	.	.	.	.	.	C	15.68	2.905112	0.52333	.	.	ENSG00000152977	ENST00000282928	T	0.49432	0.78	3.86	2.96	0.34315	Zinc finger, C2H2-like (1);	0.000000	0.85682	D	0.000000	T	0.72293	0.3442	M	0.89840	3.065	0.58432	D	0.999999	P	0.41710	0.76	P	0.60286	0.872	T	0.76410	-0.2969	10	0.87932	D	0	.	14.6385	0.68706	0.0:0.918:0.0:0.082	.	246	Q15915	ZIC1_HUMAN	L	246	ENSP00000282928:F246L	ENSP00000282928:F246L	F	+	3	2	ZIC1	148611327	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	1.334000	0.33827	0.237000	0.21200	-1.134000	0.01955	TTC		ZIC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355497.1	NM_003412	
DHX36	170506	hgsc.bcm.edu	37	3	154032850	154032850	+	Silent	SNP	C	C	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr3:154032850C>T	ENST00000496811.1	-	3	668	c.588G>A	c.(586-588)cgG>cgA	p.R196R	DHX36_ENST00000329463.5_Silent_p.R196R|DHX36_ENST00000544526.1_Silent_p.R196R|DHX36_ENST00000308361.6_Silent_p.R196R	NM_020865.2	NP_065916.2	Q9H2U1	DHX36_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 36	196					ATP catabolic process (GO:0006200)|innate immune response (GO:0045087)|ossification (GO:0001503)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RNA secondary structure unwinding (GO:0010501)|transcription, DNA-templated (GO:0006351)	chromosome, telomeric region (GO:0000781)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|core promoter binding (GO:0001047)|DNA-dependent ATPase activity (GO:0008094)|double-stranded RNA binding (GO:0003725)|G-quadruplex DNA binding (GO:0051880)|G-quadruplex RNA binding (GO:0002151)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|transcription regulatory region DNA binding (GO:0044212)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(11)|prostate(2)|skin(1)|urinary_tract(1)	35			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			TTTCAATATACCGAAGGTCAT	0.308																																																	0			3											31.0	34.0	33.0					3																	154032850		2192	4286	6478	155515544	SO:0001819	synonymous_variant	170506			AF217190	CCDS3171.1, CCDS54657.1	3q25.2	2012-09-20	2003-06-13	2003-06-20	ENSG00000174953	ENSG00000174953		"""DEAH-boxes"""	14410	protein-coding gene	gene with protein product		612767	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 36"""	DDX36			Standard	NM_020865		Approved	MLEL1, KIAA1488	uc003ezy.4	Q9H2U1	OTTHUMG00000159109	ENST00000496811.1:c.588G>A	3.37:g.154032850C>T		Somatic		Capture	Illumina HiSeq	Phase_I	155515544	B2RB00|Q70JU3|Q8IYE5|Q9P240	Silent	SNP	ENST00000496811.1	37	CCDS3171.1																																																																																				DHX36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353349.1	NM_020865	
PIK3CA	5290	hgsc.bcm.edu	37	3	178951995	178951995	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr3:178951995A>G	ENST00000263967.3	+	21	3207	c.3050A>G	c.(3049-3051)gAt>gGt	p.D1017G	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1017	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.D1017V(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	CAATCTTTTGATGACATTGCA	0.393		57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)			Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	1	Substitution - Missense(1)	lung(1)	3											107.0	95.0	98.0					3																	178951995		1879	4117	5996	180434689	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3050A>G	3.37:g.178951995A>G	ENSP00000263967:p.Asp1017Gly	Somatic		Capture	Illumina HiSeq	Phase_I	180434689	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	19.82	3.897876	0.72639	.	.	ENSG00000121879	ENST00000263967	T	0.80824	-1.42	6.07	6.07	0.98685	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	T	0.82098	0.4963	L	0.35288	1.05	0.80722	D	1	D	0.65815	0.995	P	0.56700	0.804	T	0.82131	-0.0609	10	0.42905	T	0.14	-22.9512	16.635	0.85050	1.0:0.0:0.0:0.0	.	1017	P42336	PK3CA_HUMAN	G	1017	ENSP00000263967:D1017G	ENSP00000263967:D1017G	D	+	2	0	PIK3CA	180434689	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.798000	0.91888	2.330000	0.79161	0.477000	0.44152	GAT		PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2		
FBXO45	200933	hgsc.bcm.edu	37	3	196311032	196311032	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr3:196311032A>G	ENST00000311630.6	+	3	1001	c.704A>G	c.(703-705)gAc>gGc	p.D235G	FBXO45_ENST00000440469.1_Missense_Mutation_p.D56G	NM_001105573.1	NP_001099043.1	P0C2W1	FBSP1_HUMAN	F-box protein 45	235	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				anterior commissure morphogenesis (GO:0021960)|cellular response to DNA damage stimulus (GO:0006974)|cerebral cortex radially oriented cell migration (GO:0021799)|cerebral cortex tangential migration (GO:0021800)|corticospinal tract morphogenesis (GO:0021957)|neuron migration (GO:0001764)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|synapse assembly involved in innervation (GO:0060386)	cell junction (GO:0030054)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)				cervix(1)|kidney(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	7	all_cancers(143;8.88e-09)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;2.75e-23)|all cancers(36;2.47e-21)|OV - Ovarian serous cystadenocarcinoma(49;2.32e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00314)		GTCATCTTGGACATGGAAGAT	0.408																																																	0			3											135.0	129.0	131.0					3																	196311032		1838	4087	5925	197795429	SO:0001583	missense	200933			AK025697	CCDS46985.1	3q29	2008-02-05			ENSG00000174013	ENSG00000174013		"""F-boxes /  ""other"""""	29148	protein-coding gene	gene with protein product		609112					Standard	NM_001105573		Approved	Fbx45	uc010iai.3	P0C2W1	OTTHUMG00000155571	ENST00000311630.6:c.704A>G	3.37:g.196311032A>G	ENSP00000310332:p.Asp235Gly	Somatic		Capture	Illumina HiSeq	Phase_I	197795429	A6NF90|D3DXB5	Missense_Mutation	SNP	ENST00000311630.6	37	CCDS46985.1	.	.	.	.	.	.	.	.	.	.	A	19.93	3.918358	0.73098	.	.	ENSG00000174013	ENST00000440469;ENST00000311630	D;D	0.82526	-1.62;-1.62	4.97	4.97	0.65823	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.85682	D	0.000000	D	0.93350	0.7880	H	0.94925	3.6	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95098	0.8228	10	0.87932	D	0	-16.4144	15.0971	0.72244	1.0:0.0:0.0:0.0	.	235	P0C2W1	FBSP1_HUMAN	G	56;235	ENSP00000389868:D56G;ENSP00000310332:D235G	ENSP00000310332:D235G	D	+	2	0	FBXO45	197795429	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.500000	0.90498	2.212000	0.71576	0.460000	0.39030	GAC		FBXO45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340687.2		
CACNA1C	775	hgsc.bcm.edu	37	12	2788865	2788865	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr12:2788865G>A	ENST00000347598.4	+	44	5491	c.5491G>A	c.(5491-5493)Ggc>Agc	p.G1831S	CACNA1C_ENST00000406454.3_Missense_Mutation_p.G1783S|CACNA1C_ENST00000399621.1_Missense_Mutation_p.G1802S|CACNA1C_ENST00000335762.5_Missense_Mutation_p.G1808S|CACNA1C-AS1_ENST00000501371.1_RNA|CACNA1C_ENST00000399601.1_Missense_Mutation_p.G1783S|CACNA1C_ENST00000399641.1_Missense_Mutation_p.G1783S|CACNA1C_ENST00000399597.1_Missense_Mutation_p.G1783S|CACNA1C_ENST00000399637.1_Missense_Mutation_p.G1802S|CACNA1C_ENST00000399606.1_Missense_Mutation_p.G1803S|CACNA1C_ENST00000399591.1_Missense_Mutation_p.G1791S|CACNA1C_ENST00000399655.1_Missense_Mutation_p.G1783S|CACNA1C_ENST00000402845.3_Missense_Mutation_p.G1802S|CACNA1C_ENST00000399595.1_Missense_Mutation_p.G1791S|CACNA1C_ENST00000327702.7_Missense_Mutation_p.G1783S|CACNA1C_ENST00000399634.1_Missense_Mutation_p.G1783S|CACNA1C_ENST00000344100.3_Missense_Mutation_p.G1824S|CACNA1C_ENST00000399603.1_Missense_Mutation_p.G1783S|CACNA1C_ENST00000399629.1_Missense_Mutation_p.G1800S|CACNA1C_ENST00000399617.1_Missense_Mutation_p.G1783S|CACNA1C_ENST00000399644.1_Missense_Mutation_p.G1783S|CACNA1C_ENST00000399649.1_Missense_Mutation_p.G1789S|CACNA1C_ENST00000399638.1_Missense_Mutation_p.G1811S	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	1831					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	TCGCCCCGCCGGCTACCCCAG	0.677																																																	0			12											41.0	49.0	46.0					12																	2788865		2054	4198	6252	2659126	SO:0001583	missense	775			AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.5491G>A	12.37:g.2788865G>A	ENSP00000266376:p.Gly1831Ser	Somatic		Capture	Illumina HiSeq	Phase_I	2659126	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Missense_Mutation	SNP	ENST00000347598.4	37	CCDS44788.1	.	.	.	.	.	.	.	.	.	.	G	5.139	0.211285	0.09757	.	.	ENSG00000151067	ENST00000335762;ENST00000399655;ENST00000399644;ENST00000399638;ENST00000399597;ENST00000399621;ENST00000399637;ENST00000399591;ENST00000399641;ENST00000347598;ENST00000399606;ENST00000399601;ENST00000344100;ENST00000399629;ENST00000327702;ENST00000399649;ENST00000402845;ENST00000399603;ENST00000399634;ENST00000399617;ENST00000406454;ENST00000399595;ENST00000322367	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.95949	-3.8;-3.79;-3.79;-3.8;-3.79;-3.81;-3.7;-3.75;-3.79;-3.73;-3.72;-3.79;-3.85;-3.72;-3.63;-3.85;-3.8;-3.79;-3.78;-3.73;-3.78;-3.86	5.06	3.19	0.36642	.	2.241760	0.01598	N	0.021892	D	0.92051	0.7481	L	0.41573	1.285	0.26335	N	0.977457	B;P;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.50710	0.003;0.938;0.0;0.004;0.005;0.004;0.003;0.008;0.001;0.003;0.004;0.0;0.003;0.012;0.001;0.003;0.003;0.001;0.004;0.003;0.001;0.004;0.004;0.0;0.001	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.43225	0.002;0.412;0.001;0.003;0.01;0.005;0.002;0.01;0.001;0.002;0.006;0.001;0.003;0.01;0.001;0.004;0.003;0.005;0.006;0.004;0.001;0.007;0.007;0.001;0.002	T	0.82649	-0.0353	10	0.15952	T	0.53	.	3.0471	0.06157	0.1067:0.3219:0.4061:0.1652	.	474;1824;1780;1831;1783;1802;1783;1800;1811;1783;1803;1783;1743;1831;1783;1783;1783;1791;1789;1791;1772;1802;1802;1783;1783	B7Z7Z5;Q13936-14;Q13936-35;Q13936;Q13936-33;Q13936-13;Q13936-22;Q13936-32;Q13936-31;Q13936-21;Q13936-30;Q13936-23;Q13936-28;Q13936-11;E9PDJ1;E9PDJ0;F5GY28;Q13936-25;Q13936-15;Q13936-29;Q13936-19;Q13936-24;Q13936-27;Q13936-20;Q13936-12	.;.;.;CAC1C_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	S	1808;1783;1783;1811;1783;1802;1802;1791;1783;1831;1803;1783;1824;1800;1783;1789;1802;1783;1783;1783;1783;1791;1613	ENSP00000336982:G1808S;ENSP00000382563:G1783S;ENSP00000382552:G1783S;ENSP00000382547:G1811S;ENSP00000382506:G1783S;ENSP00000382530:G1802S;ENSP00000382546:G1802S;ENSP00000382500:G1791S;ENSP00000382549:G1783S;ENSP00000266376:G1831S;ENSP00000382515:G1803S;ENSP00000382510:G1783S;ENSP00000341092:G1824S;ENSP00000382537:G1800S;ENSP00000329877:G1783S;ENSP00000382557:G1789S;ENSP00000385724:G1802S;ENSP00000382512:G1783S;ENSP00000382542:G1783S;ENSP00000382526:G1783S;ENSP00000385896:G1783S;ENSP00000382504:G1791S	ENSP00000323129:G1613S	G	+	1	0	CACNA1C	2659126	0.981000	0.34729	0.048000	0.18961	0.022000	0.10575	2.143000	0.42187	0.506000	0.28125	0.305000	0.20034	GGC		CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719	
ENO2	2026	hgsc.bcm.edu	37	12	7028820	7028820	+	Missense_Mutation	SNP	G	G	A	rs151259229		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr12:7028820G>A	ENST00000535366.1	+	7	1384	c.758G>A	c.(757-759)cGt>cAt	p.R253H	ENO2_ENST00000545045.2_Missense_Mutation_p.R134H|ENO2_ENST00000541477.1_Missense_Mutation_p.R253H|ENO2_ENST00000229277.1_Missense_Mutation_p.R253H|ENO2_ENST00000538763.1_Missense_Mutation_p.R210H|ENO2_ENST00000544774.1_Missense_Mutation_p.R210H			P09104	ENOG_HUMAN	enolase 2 (gamma, neuronal)	253					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|perikaryon (GO:0043204)|phosphopyruvate hydratase complex (GO:0000015)|photoreceptor inner segment (GO:0001917)|plasma membrane (GO:0005886)	magnesium ion binding (GO:0000287)|phosphopyruvate hydratase activity (GO:0004634)			endometrium(3)|large_intestine(2)|lung(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10						GAGTTTTATCGTGATGGCAAA	0.527													g|||	1	0.000199681	0.0008	0.0	5008	,	,		-128	0.0		0.0	False		,,,				2504	0.0																0			12							HIS/ARG	0,4406		0,0,2203	168.0	134.0	145.0		758	5.2	1.0	12	dbSNP_134	145	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ENO2	NM_001975.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	253/435	7028820	1,13005	2203	4300	6503	6899081	SO:0001583	missense	2026			M22349	CCDS8570.1	12p13	2012-10-02				ENSG00000111674	4.2.1.11		3353	protein-coding gene	gene with protein product		131360					Standard	NM_001975		Approved		uc001qru.1	P09104		ENST00000535366.1:c.758G>A	12.37:g.7028820G>A	ENSP00000437402:p.Arg253His	Somatic		Capture	Illumina HiSeq	Phase_I	6899081	B7Z2X9|Q96J33	Missense_Mutation	SNP	ENST00000535366.1	37	CCDS8570.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	g	18.57	3.652762	0.67472	0.0	1.16E-4	ENSG00000111674	ENST00000541477;ENST00000229277;ENST00000538763;ENST00000544774;ENST00000535366;ENST00000545045	T;T;T;T;T;T	0.21734	1.99;1.99;1.99;1.99;1.99;1.99	5.23	5.23	0.72850	Enolase, C-terminal (1);	0.152089	0.64402	D	0.000010	T	0.31199	0.0789	M	0.73319	2.225	0.80722	D	1	B;B	0.23128	0.08;0.031	B;B	0.27715	0.082;0.013	T	0.13548	-1.0505	10	0.72032	D	0.01	-9.7732	18.8056	0.92035	0.0:0.0:1.0:0.0	.	210;253	B7Z2X9;P09104	.;ENOG_HUMAN	H	253;253;210;210;253;134	ENSP00000438873:R253H;ENSP00000229277:R253H;ENSP00000441490:R210H;ENSP00000446195:R210H;ENSP00000437402:R253H;ENSP00000438062:R134H	ENSP00000229277:R253H	R	+	2	0	ENO2	6899081	1.000000	0.71417	0.993000	0.49108	0.975000	0.68041	3.953000	0.56699	2.447000	0.82792	0.543000	0.68304	CGT		ENO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401786.1		
KRAS	3845	hgsc.bcm.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	A	rs121913529		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr12:25398284C>A	ENST00000256078.4	-	2	98	c.35G>T	c.(34-36)gGt>gTt	p.G12V	KRAS_ENST00000556131.1_Missense_Mutation_p.G12V|KRAS_ENST00000311936.3_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"""pancreatic, colorectal, lung, thyroid, AML, others"""				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)			Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"""L, E, M, O"""	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	12											91.0	81.0	85.0					12																	25398284		2203	4300	6503	25289551	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"""v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog"", ""v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"""	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>T	12.37:g.25398284C>A	ENSP00000256078:p.Gly12Val	Somatic		Capture	Illumina HiSeq	Phase_I	25289551	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.808637	0.90707	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90373	0.6987	M	0.90650	3.135	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.72625	0.969;0.978	D	0.91773	0.5429	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	V	12	ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V	ENSP00000256078:G12V	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360	
HOXC8	3224	hgsc.bcm.edu	37	12	54404943	54404943	+	Silent	SNP	C	C	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr12:54404943C>G	ENST00000040584.4	+	2	744	c.507C>G	c.(505-507)ctC>ctG	p.L169L	RP11-834C11.12_ENST00000513209.1_Intron	NM_022658.3	NP_073149.1	P31273	HXC8_HUMAN	homeobox C8	169					anterior/posterior pattern specification (GO:0009952)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|skin(3)	8						AGGAGTTTCTCTTTAATCCTT	0.498																																					GBM(197;701 2226 7002 18822 41696)												0			12											88.0	84.0	85.0					12																	54404943		2203	4300	6503	52691210	SO:0001819	synonymous_variant	3224			X99680	CCDS8870.1	12q13.13	2011-06-20	2005-12-22			ENSG00000037965		"""Homeoboxes / ANTP class : HOXL subclass"""	5129	protein-coding gene	gene with protein product		142970	"""homeo box C8"""	HOX3, HOX3A		1973146, 1358459	Standard	NM_022658		Approved		uc001ser.3	P31273		ENST00000040584.4:c.507C>G	12.37:g.54404943C>G		Somatic		Capture	Illumina HiSeq	Phase_I	52691210	A8K4J4|O15221|O15362	Silent	SNP	ENST00000040584.4	37	CCDS8870.1																																																																																				HOXC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358957.2		
YEATS4	8089	hgsc.bcm.edu	37	12	69753758	69753758	+	Missense_Mutation	SNP	C	C	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr12:69753758C>G	ENST00000247843.2	+	1	276	c.6C>G	c.(4-6)ttC>ttG	p.F2L	YEATS4_ENST00000548020.1_Missense_Mutation_p.F2L	NM_006530.2	NP_006521.1	O95619	YETS4_HUMAN	YEATS domain containing 4	2					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic nuclear division (GO:0007067)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|protein C-terminus binding (GO:0008022)|sequence-specific DNA binding transcription factor activity (GO:0003700)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(1)	5	all_epithelial(5;9.25e-35)|Breast(13;9.83e-07)|Esophageal squamous(21;0.187)		Epithelial(6;6.89e-18)|BRCA - Breast invasive adenocarcinoma(5;3.14e-09)|Lung(24;9.68e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|OV - Ovarian serous cystadenocarcinoma(12;0.00691)|STAD - Stomach adenocarcinoma(21;0.0151)|LUSC - Lung squamous cell carcinoma(43;0.24)|Kidney(9;0.241)			ACAATATGTTCAAGAGAATGG	0.687																																																	0			12											29.0	33.0	32.0					12																	69753758		2203	4300	6503	68040025	SO:0001583	missense	8089			AJ245746	CCDS8990.1, CCDS73495.1	12q13-q15	2008-02-05				ENSG00000127337			24859	protein-coding gene	gene with protein product		602116				9302258, 11903063	Standard	XM_005269163		Approved	NuBI-1, GAS41, YAF9	uc001sux.3	O95619	OTTHUMG00000169358	ENST00000247843.2:c.6C>G	12.37:g.69753758C>G	ENSP00000247843:p.Phe2Leu	Somatic		Capture	Illumina HiSeq	Phase_I	68040025	Q9NQD0	Missense_Mutation	SNP	ENST00000247843.2	37	CCDS8990.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.574102	0.86542	.	.	ENSG00000127337	ENST00000247843;ENST00000548020;ENST00000552955	.	.	.	5.31	5.31	0.75309	.	0.044747	0.85682	D	0.000000	T	0.39226	0.1070	N	0.08118	0	0.80722	D	1	B	0.14438	0.01	B	0.14023	0.01	T	0.21895	-1.0232	8	.	.	.	-6.3934	19.1698	0.93572	0.0:1.0:0.0:0.0	.	2	O95619	YETS4_HUMAN	L	2	.	.	F	+	3	2	YEATS4	68040025	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.965000	0.49200	2.761000	0.94854	0.563000	0.77884	TTC		YEATS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403663.1	NM_006530	
BEST3	144453	hgsc.bcm.edu	37	12	70091550	70091550	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr12:70091550G>A	ENST00000330891.5	-	2	255	c.29C>T	c.(28-30)gCa>gTa	p.A10V	BEST3_ENST00000266661.4_Intron|BEST3_ENST00000476098.1_Intron|BEST3_ENST00000533674.1_Intron|BEST3_ENST00000393365.1_5'UTR|BEST3_ENST00000331471.4_Missense_Mutation_p.A10V|BEST3_ENST00000551160.1_Intron|BEST3_ENST00000553096.1_Intron	NM_001282613.1|NM_032735.2	NP_001269542.1|NP_116124.2	Q8N1M1	BEST3_HUMAN	bestrophin 3	10					negative regulation of ion transport (GO:0043271)	chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			cervix(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(2)	12	Breast(13;2.31e-06)|Esophageal squamous(21;0.187)		Lung(24;0.000278)|OV - Ovarian serous cystadenocarcinoma(12;0.0019)|STAD - Stomach adenocarcinoma(21;0.00694)			AGTTGCATTTGCTACTTTACT	0.343																																																	0			12											110.0	107.0	108.0					12																	70091550		1828	4089	5917	68377817	SO:0001583	missense	144453			AF440758	CCDS8992.2, CCDS41810.1, CCDS61192.1, CCDS61193.1, CCDS73496.1	12q14.2-q15	2012-09-26	2006-10-18	2006-10-18	ENSG00000127325	ENSG00000127325		"""Ion channels / Chloride channels : Calcium activated : Bestrophins"""	17105	protein-coding gene	gene with protein product		607337	"""vitelliform macular dystrophy 2-like 3"""	VMD2L3		12032738	Standard	NM_032735		Approved	MGC40411, MGC13168	uc001svg.3	Q8N1M1	OTTHUMG00000149919	ENST00000330891.5:c.29C>T	12.37:g.70091550G>A	ENSP00000332413:p.Ala10Val	Somatic		Capture	Illumina HiSeq	Phase_I	68377817	B5MDI8|F8VVZ2|Q53YQ7|Q8N356|Q8NFT9|Q9BR80	Missense_Mutation	SNP	ENST00000330891.5	37	CCDS8992.2	.	.	.	.	.	.	.	.	.	.	G	35	5.495272	0.96355	.	.	ENSG00000127325	ENST00000331471;ENST00000330891;ENST00000548658	D;D;D	0.98732	-5.1;-5.1;-5.1	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	D	0.99447	0.9804	H	0.94964	3.605	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.982	D	0.98604	1.0660	10	0.87932	D	0	-18.1199	20.1535	0.98095	0.0:0.0:1.0:0.0	.	10;10	Q8N1M1;Q8N1M1-1	BEST3_HUMAN;.	V	10	ENSP00000329064:A10V;ENSP00000332413:A10V;ENSP00000446575:A10V	ENSP00000332413:A10V	A	-	2	0	BEST3	68377817	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.764000	0.94973	0.650000	0.86243	GCA		BEST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313908.2	NM_152439	
ATP2B1	490	hgsc.bcm.edu	37	12	89997555	89997555	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr12:89997555T>C	ENST00000428670.3	-	17	3238	c.2782A>G	c.(2782-2784)Atg>Gtg	p.M928V	ATP2B1_ENST00000393164.2_Missense_Mutation_p.M671V|ATP2B1_ENST00000261173.2_Missense_Mutation_p.M928V|ATP2B1_ENST00000359142.3_Missense_Mutation_p.M928V|ATP2B1_ENST00000348959.3_Missense_Mutation_p.M928V			P20020	AT2B1_HUMAN	ATPase, Ca++ transporting, plasma membrane 1	928					blood coagulation (GO:0007596)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	45						TTCTTCATCATTGTACGTGAG	0.413																																																	0			12											132.0	122.0	126.0					12																	89997555		2203	4300	6503	88521686	SO:0001583	missense	490			J04027	CCDS9035.1, CCDS41817.1	12q21.33	2010-04-20			ENSG00000070961	ENSG00000070961	3.6.3.8	"""ATPases / P-type"""	814	protein-coding gene	gene with protein product	"""plasma membrane calcium-transporting ATPase 1"""	108731				1674727	Standard	NM_001682		Approved	PMCA1	uc001tbh.3	P20020		ENST00000428670.3:c.2782A>G	12.37:g.89997555T>C	ENSP00000392043:p.Met928Val	Somatic		Capture	Illumina HiSeq	Phase_I	88521686	Q12992|Q12993|Q13819|Q13820|Q13821|Q16504|Q93082	Missense_Mutation	SNP	ENST00000428670.3	37	CCDS9035.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.395123	0.83011	.	.	ENSG00000070961	ENST00000261173;ENST00000348959;ENST00000359142;ENST00000428670;ENST00000393164	D;D;D;D;D	0.96587	-4.06;-4.06;-4.06;-4.06;-4.06	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	D	0.98185	0.9400	M	0.88512	2.96	0.80722	D	1	P;D;D	0.69078	0.917;0.968;0.997	D;P;D	0.64042	0.915;0.8;0.921	D	0.99129	1.0852	10	0.87932	D	0	-27.3567	16.3634	0.83296	0.0:0.0:0.0:1.0	.	928;928;928	P20020-3;P20020-2;P20020-6	.;.;.	V	928;928;928;928;671	ENSP00000261173:M928V;ENSP00000343599:M928V;ENSP00000352054:M928V;ENSP00000392043:M928V;ENSP00000376869:M671V	ENSP00000261173:M928V	M	-	1	0	ATP2B1	88521686	1.000000	0.71417	0.993000	0.49108	0.998000	0.95712	7.997000	0.88414	2.324000	0.78689	0.533000	0.62120	ATG		ATP2B1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406653.1	NM_001682	
LUM	4060	hgsc.bcm.edu	37	12	91502182	91502182	+	Missense_Mutation	SNP	C	C	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr12:91502182C>G	ENST00000266718.4	-	2	1029	c.575G>C	c.(574-576)aGc>aCc	p.S192T	LUM_ENST00000548071.1_Intron	NM_002345.3	NP_002336.1	P51884	LUM_HUMAN	lumican	192					carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to growth factor (GO:0070848)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrillar collagen trimer (GO:0005583)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	24						CTGATTGAAGCTCAAGTCAAG	0.433																																																	0			12											138.0	134.0	135.0					12																	91502182		2203	4300	6503	90026313	SO:0001583	missense	4060			BT006707	CCDS9038.1	12q21.33	2014-06-13			ENSG00000139329			"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	6724	protein-coding gene	gene with protein product	"""lumican proteoglycan"""	600616		LDC		7558030	Standard	NM_002345		Approved	SLRR2D	uc001tbm.3	P51884	OTTHUMG00000170074	ENST00000266718.4:c.575G>C	12.37:g.91502182C>G	ENSP00000266718:p.Ser192Thr	Somatic		Capture	Illumina HiSeq	Phase_I	90026313	B2R6R5|Q96QM7	Missense_Mutation	SNP	ENST00000266718.4	37	CCDS9038.1	.	.	.	.	.	.	.	.	.	.	C	18.97	3.735252	0.69189	.	.	ENSG00000139329	ENST00000266718	T	0.61627	0.09	5.6	4.68	0.58851	.	0.000000	0.85682	D	0.000000	T	0.68595	0.3018	L	0.60012	1.86	0.58432	D	0.999997	D	0.54601	0.967	P	0.58391	0.838	T	0.69636	-0.5092	10	0.45353	T	0.12	-10.3664	15.6021	0.76634	0.1386:0.8614:0.0:0.0	.	192	P51884	LUM_HUMAN	T	192	ENSP00000266718:S192T	ENSP00000266718:S192T	S	-	2	0	LUM	90026313	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.487000	0.81328	1.311000	0.45024	0.557000	0.71058	AGC		LUM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407150.2	NM_002345	
CHST11	50515	hgsc.bcm.edu	37	12	105151178	105151178	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr12:105151178G>A	ENST00000303694.5	+	3	1095	c.656G>A	c.(655-657)cGc>cAc	p.R219H	CHST11_ENST00000549260.1_Missense_Mutation_p.R214H	NM_018413.5	NP_060883.1	Q9NPF2	CHSTB_HUMAN	carbohydrate (chondroitin 4) sulfotransferase 11	219					carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondrocyte development (GO:0002063)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|developmental growth (GO:0048589)|embryonic digit morphogenesis (GO:0042733)|embryonic viscerocranium morphogenesis (GO:0048703)|glycosaminoglycan metabolic process (GO:0030203)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|polysaccharide localization (GO:0033037)|post-anal tail morphogenesis (GO:0036342)|post-embryonic development (GO:0009791)|regulation of cell proliferation (GO:0042127)|respiratory gaseous exchange (GO:0007585)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	chondroitin 4-sulfotransferase activity (GO:0047756)|N-acetylgalactosamine 4-O-sulfotransferase activity (GO:0001537)|N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity (GO:0050659)			breast(2)|endometrium(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|skin(1)	18						ATCATCAAACGCCAGCGGAAG	0.582																																																	0			12											121.0	104.0	110.0					12																	105151178		2203	4300	6503	103675308	SO:0001583	missense	50515			AB042326	CCDS9099.1, CCDS55878.1	12q23.3	2008-02-05				ENSG00000171310	2.8.2.5	"""Sulfotransferases, membrane-bound"""	17422	protein-coding gene	gene with protein product		610128				10781601	Standard	NM_018413		Approved	C4ST1, C4St-1, C4ST, HSA269537	uc001tkz.3	Q9NPF2	OTTHUMG00000169803	ENST00000303694.5:c.656G>A	12.37:g.105151178G>A	ENSP00000305725:p.Arg219His	Somatic		Capture	Illumina HiSeq	Phase_I	103675308	A8K4F8|Q9NXY6|Q9NY36	Missense_Mutation	SNP	ENST00000303694.5	37	CCDS9099.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.976433	0.92982	.	.	ENSG00000171310	ENST00000549260;ENST00000303694	T;T	0.75154	-0.91;-0.91	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	D	0.86698	0.5995	M	0.77486	2.375	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.977;0.995	D	0.86448	0.1771	10	0.46703	T	0.11	-29.1637	19.2155	0.93776	0.0:0.0:1.0:0.0	.	214;219	Q9NPF2-2;Q9NPF2	.;CHSTB_HUMAN	H	214;219	ENSP00000450004:R214H;ENSP00000305725:R219H	ENSP00000305725:R219H	R	+	2	0	CHST11	103675308	1.000000	0.71417	0.956000	0.39512	0.978000	0.69477	8.004000	0.88535	2.553000	0.86117	0.655000	0.94253	CGC		CHST11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000405960.2	NM_018413	
CORO1C	23603	hgsc.bcm.edu	37	12	109046145	109046145	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr12:109046145C>T	ENST00000261401.3	-	8	1076	c.904G>A	c.(904-906)Gtc>Atc	p.V302I	CORO1C_ENST00000549384.1_Intron|CORO1C_ENST00000420959.2_Missense_Mutation_p.V355I|CORO1C_ENST00000549772.1_Missense_Mutation_p.V308I|CORO1C_ENST00000421578.2_Missense_Mutation_p.V197I|CORO1C_ENST00000541050.1_Missense_Mutation_p.V302I	NM_001105237.2|NM_001276471.1|NM_014325.2	NP_001098707.1|NP_001263400.1|NP_055140.1	Q9ULV4	COR1C_HUMAN	coronin, actin binding protein, 1C	302					actin cytoskeleton organization (GO:0030036)|phagocytosis (GO:0006909)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(12)|skin(4)	24						AGGTAGTGGACGTACGGGGAT	0.468																																																	0			12											201.0	178.0	186.0					12																	109046145		2203	4300	6503	107570274	SO:0001583	missense	23603			BC002342	CCDS9120.1, CCDS61236.1	12q24.1	2013-01-10	2001-11-28			ENSG00000110880		"""Coronins"", ""WD repeat domain containing"""	2254	protein-coding gene	gene with protein product		605269	"""coronin, actin-binding protein, 1C"""			9778037, 10461187	Standard	NM_014325		Approved	coronin-3, HCRNN4	uc009zva.4	Q9ULV4		ENST00000261401.3:c.904G>A	12.37:g.109046145C>T	ENSP00000261401:p.Val302Ile	Somatic		Capture	Illumina HiSeq	Phase_I	107570274	A7MAP0|A7MAP1|B3KU12|Q9NSK5	Missense_Mutation	SNP	ENST00000261401.3	37	CCDS9120.1	.	.	.	.	.	.	.	.	.	.	C	18.52	3.641882	0.67244	.	.	ENSG00000110880	ENST00000261401;ENST00000541050;ENST00000421578;ENST00000549772;ENST00000420959	T;T;T;T;T	0.29397	1.57;1.57;1.57;1.57;1.57	5.8	5.8	0.92144	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);Domain of unknown function DUF1900 (1);	0.228765	0.43747	D	0.000540	T	0.29389	0.0732	L	0.31065	0.9	0.80722	D	1	B;B;B	0.24483	0.052;0.104;0.052	B;B;B	0.29716	0.047;0.106;0.032	T	0.03453	-1.1035	10	0.30078	T	0.28	-17.0323	20.0716	0.97726	0.0:1.0:0.0:0.0	.	265;355;302	B4DMH3;A7MAP1;Q9ULV4	.;.;COR1C_HUMAN	I	302;302;197;308;355	ENSP00000261401:V302I;ENSP00000438341:V302I;ENSP00000415554:V197I;ENSP00000447534:V308I;ENSP00000394496:V355I	ENSP00000261401:V302I	V	-	1	0	CORO1C	107570274	1.000000	0.71417	0.994000	0.49952	0.989000	0.77384	6.042000	0.70996	2.741000	0.93983	0.585000	0.79938	GTC		CORO1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403802.1	NM_014325	
EPB42	2038	hgsc.bcm.edu	37	15	43499591	43499591	+	Missense_Mutation	SNP	G	G	A	rs115972761	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr15:43499591G>A	ENST00000441366.2	-	9	1349	c.1124C>T	c.(1123-1125)aCg>aTg	p.T375M	EPB42_ENST00000563128.1_5'Flank|EPB42_ENST00000540029.1_Missense_Mutation_p.T297M|EPB42_ENST00000300215.3_Missense_Mutation_p.T405M	NM_000119.2|NM_001114134.1	NP_000110.2|NP_001107606.1	P16452	EPB42_HUMAN	erythrocyte membrane protein band 4.2	375					cell morphogenesis (GO:0000902)|erythrocyte maturation (GO:0043249)|hemoglobin metabolic process (GO:0020027)|iron ion homeostasis (GO:0055072)|peptide cross-linking (GO:0018149)|regulation of cell shape (GO:0008360)|spleen development (GO:0048536)	cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)|structural constituent of cytoskeleton (GO:0005200)			endometrium(3)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20		all_cancers(109;1.37e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.7e-07)		CAGCCCCAGCGTCCCCTCCTT	0.582													G|||	2	0.000399361	0.0015	0.0	5008	,	,		15600	0.0		0.0	False		,,,				2504	0.0																0			15											66.0	53.0	58.0					15																	43499591		2203	4299	6502	41286883	SO:0001583	missense	2038			M60298	CCDS10093.1, CCDS45249.1	15q15-q21	2013-05-02			ENSG00000166947	ENSG00000166947		"""Transglutaminases"""	3381	protein-coding gene	gene with protein product	"""Erythrocyte surface protein band 4.2"""	177070				1284644	Standard	NM_000119		Approved	PA, MGC116735, MGC116737	uc001zrb.4	P16452	OTTHUMG00000130701	ENST00000441366.2:c.1124C>T	15.37:g.43499591G>A	ENSP00000396616:p.Thr375Met	Somatic		Capture	Illumina HiSeq	Phase_I	41286883	Q4KKX0|Q4VB97	Missense_Mutation	SNP	ENST00000441366.2	37	CCDS45249.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	7.005	0.555666	0.13436	.	.	ENSG00000166947	ENST00000300215;ENST00000540029;ENST00000441366	T;T;T	0.51071	0.72;0.72;0.72	6.02	-12.0	0.00017	.	1.311570	0.04307	N	0.348294	T	0.28333	0.0700	L	0.51422	1.61	0.09310	N	1	B;B;B;B	0.27823	0.029;0.068;0.19;0.068	B;B;B;B	0.16289	0.005;0.006;0.015;0.006	T	0.08330	-1.0727	10	0.38643	T	0.18	4.7421	1.2729	0.02025	0.4301:0.1641:0.1298:0.276	.	297;375;405;375	F5H563;B7Z4C3;P16452-2;P16452	.;.;.;EPB42_HUMAN	M	405;297;375	ENSP00000300215:T405M;ENSP00000444699:T297M;ENSP00000396616:T375M	ENSP00000300215:T405M	T	-	2	0	EPB42	41286883	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-1.186000	0.03070	-2.622000	0.00439	-0.769000	0.03391	ACG		EPB42-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432219.1	NM_000119	
UNC13C	440279	hgsc.bcm.edu	37	15	54557568	54557568	+	Missense_Mutation	SNP	G	G	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr15:54557568G>T	ENST00000260323.11	+	9	3692	c.3692G>T	c.(3691-3693)gGt>gTt	p.G1231V	UNC13C_ENST00000545554.1_Missense_Mutation_p.G1231V|UNC13C_ENST00000537900.1_Missense_Mutation_p.G1229V	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	1231	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		TCTGCACAGGGTCTACAGGCA	0.303																																																	0			15											51.0	46.0	48.0					15																	54557568		1806	4059	5865	52344860	SO:0001583	missense	440279			AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.3692G>T	15.37:g.54557568G>T	ENSP00000260323:p.Gly1231Val	Somatic		Capture	Illumina HiSeq	Phase_I	52344860	Q0P613|Q8ND48|Q96NP3	Missense_Mutation	SNP	ENST00000260323.11	37	CCDS45264.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.092843	0.76756	.	.	ENSG00000137766	ENST00000260323;ENST00000545554;ENST00000537900	T;T;T	0.73575	-0.76;-0.76;-0.76	5.04	5.04	0.67666	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.050091	0.85682	D	0.000000	D	0.87811	0.6271	M	0.86097	2.795	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.89771	0.3954	10	0.87932	D	0	.	17.722	0.88355	0.0:0.0:1.0:0.0	.	1231;1231	F5H090;Q8NB66	.;UN13C_HUMAN	V	1231;1231;1229	ENSP00000260323:G1231V;ENSP00000438156:G1231V;ENSP00000442569:G1229V	ENSP00000260323:G1231V	G	+	2	0	UNC13C	52344860	1.000000	0.71417	1.000000	0.80357	0.891000	0.51852	9.794000	0.99096	2.487000	0.83934	0.591000	0.81541	GGT		UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166	
MYZAP	100820829	hgsc.bcm.edu	37	15	57910378	57910378	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr15:57910378A>G	ENST00000267853.5	+	3	404	c.310A>G	c.(310-312)Atc>Gtc	p.I104V	GCOM1_ENST00000380569.2_Missense_Mutation_p.I104V|GCOM1_ENST00000396180.1_Missense_Mutation_p.I104V|GCOM1_ENST00000380560.2_Missense_Mutation_p.I104V|GCOM1_ENST00000380561.2_Missense_Mutation_p.I104V|GCOM1_ENST00000574161.1_Missense_Mutation_p.I104V|GCOM1_ENST00000587652.1_Missense_Mutation_p.I104V|MYZAP_ENST00000380565.4_Missense_Mutation_p.I104V|GCOM1_ENST00000572390.1_Missense_Mutation_p.I104V|POLR2M_ENST00000380563.2_5'UTR|GCOM1_ENST00000380568.3_Missense_Mutation_p.I104V			P0CAP1	MYZAP_HUMAN	myocardial zonula adherens protein	104					intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|I band (GO:0031674)											GATGAACTACATCAAAGATGT	0.413																																																	0			15											166.0	149.0	155.0					15																	57910378		2192	4292	6484	55697670	SO:0001583	missense	145781			FJ970029		15q21.3	2012-10-05			ENSG00000263155	ENSG00000263155			43444	protein-coding gene	gene with protein product	"""myocardium-enriched zonula adherens protein"""	614071				20093627, 21992629, 22160502	Standard	NM_001018100		Approved	MYOZAP, Gup, Gup1, GCOM1		P0CAP1	OTTHUMG00000132453	ENST00000267853.5:c.310A>G	15.37:g.57910378A>G	ENSP00000267853:p.Ile104Val	Somatic		Capture	Illumina HiSeq	Phase_I	55697670	D2E9U7|Q6EER8|Q6EES2|Q6EEV3|Q6EF00|Q6EF01|Q6EF02|Q6EF46|Q6EFN8|Q6EM48|Q6K046|Q6K050|Q6K051|Q6ZQZ3|Q8NC58|Q8NCF3|Q96DI5|Q96JB7|Q96NF5	Missense_Mutation	SNP	ENST00000267853.5	37	CCDS10162.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.956280	0.73902	.	.	ENSG00000137878	ENST00000380569;ENST00000380561;ENST00000396180;ENST00000380560;ENST00000267853;ENST00000380565;ENST00000380568	T;T;T;T;T;T;T	0.36340	1.26;1.42;1.47;1.64;1.26;1.26;1.26	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.55242	0.1908	M	0.63843	1.955	0.80722	D	1	D;D;D;D	0.71674	0.997;0.997;0.997;0.998	D;D;D;D	0.81914	0.99;0.99;0.99;0.995	T	0.48758	-0.9007	10	0.15066	T	0.55	-21.5521	15.8048	0.78491	1.0:0.0:0.0:0.0	.	104;104;104;104	P0CAP1-2;P0CAP1-11;P0CAP1-4;P0CAP1	.;.;.;GCOM1_HUMAN	V	104	ENSP00000369943:I104V;ENSP00000369935:I104V;ENSP00000379483:I104V;ENSP00000369933:I104V;ENSP00000267853:I104V;ENSP00000369939:I104V;ENSP00000369942:I104V	ENSP00000267853:I104V	I	+	1	0	GCOM1	55697670	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	7.025000	0.76449	2.371000	0.80710	0.533000	0.62120	ATC		MYZAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255716.2	NM_001018100	
MYO9A	4649	hgsc.bcm.edu	37	15	72260362	72260362	+	Missense_Mutation	SNP	A	A	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr15:72260362A>T	ENST00000356056.5	-	13	2421	c.1949T>A	c.(1948-1950)aTa>aAa	p.I650K	MYO9A_ENST00000444904.1_Missense_Mutation_p.I631K|MYO9A_ENST00000424560.1_Missense_Mutation_p.I650K|MYO9A_ENST00000566885.1_Missense_Mutation_p.I245K|MYO9A_ENST00000563542.1_5'UTR|MYO9A_ENST00000564571.1_Missense_Mutation_p.I650K	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	650	Myosin motor.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)			NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						ATAATGTTTTATAATGAAAGC	0.383																																																	0			15											126.0	124.0	125.0					15																	72260362		2199	4297	6496	70047416	SO:0001583	missense	4649			AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933		"""Myosins / Myosin superfamily : Class IX"""	7608	protein-coding gene	gene with protein product		604875				10409426	Standard	NM_006901		Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000356056.5:c.1949T>A	15.37:g.72260362A>T	ENSP00000348349:p.Ile650Lys	Somatic		Capture	Illumina HiSeq	Phase_I	70047416	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	ENST00000356056.5	37	CCDS10239.1	.	.	.	.	.	.	.	.	.	.	A	27.0	4.787098	0.90367	.	.	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904;ENST00000261864;ENST00000446448	T;T;T	0.78364	-1.17;-1.17;-1.17	5.13	5.13	0.70059	Myosin head, motor domain (2);	.	.	.	.	D	0.92107	0.7498	H	0.97240	3.965	0.80722	D	1	D;D;D;D	0.76494	0.999;0.995;0.995;0.998	D;D;D;D	0.79108	0.982;0.929;0.929;0.992	D	0.94786	0.7958	9	0.87932	D	0	.	14.9176	0.70810	1.0:0.0:0.0:0.0	.	631;650;631;650	B2RTY4-2;B2RTY4-3;B7WP69;B2RTY4	.;.;.;MYO9A_HUMAN	K	650;650;631;631;650	ENSP00000348349:I650K;ENSP00000399162:I650K;ENSP00000398250:I631K	ENSP00000261864:I631K	I	-	2	0	MYO9A	70047416	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.231000	0.95317	1.917000	0.55516	0.455000	0.32223	ATA		MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901	
ISLR	3671	hgsc.bcm.edu	37	15	74467645	74467645	+	Missense_Mutation	SNP	G	G	A	rs149796219		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr15:74467645G>A	ENST00000249842.3	+	2	803	c.446G>A	c.(445-447)cGc>cAc	p.R149H	RP11-665J16.1_ENST00000561647.1_RNA|ISLR_ENST00000395118.1_Missense_Mutation_p.R149H	NM_005545.3	NP_005536.1	O14498	ISLR_HUMAN	immunoglobulin superfamily containing leucine-rich repeat	149					cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)		p.R149H(1)		central_nervous_system(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)	20						CGTGCTCTGCGCTCGCTGCAA	0.622																																																	1	Substitution - Missense(1)	large_intestine(1)	15						G	HIS/ARG,HIS/ARG	0,4396		0,0,2198	73.0	72.0	72.0		446,446	3.1	0.9	15	dbSNP_134	72	1,8593	1.2+/-3.3	0,1,4296	no	missense,missense	ISLR	NM_005545.3,NM_201526.1	29,29	0,1,6494	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	149/429,149/429	74467645	1,12989	2198	4297	6495	72254698	SO:0001583	missense	3671			AB003184	CCDS10260.1	15q23-q24	2013-01-11			ENSG00000129009	ENSG00000129009		"""Immunoglobulin superfamily / I-set domain containing"""	6133	protein-coding gene	gene with protein product		602059				9325048	Standard	NM_005545		Approved	HsT17563	uc002axh.1	O14498	OTTHUMG00000137623	ENST00000249842.3:c.446G>A	15.37:g.74467645G>A	ENSP00000249842:p.Arg149His	Somatic		Capture	Illumina HiSeq	Phase_I	72254698		Missense_Mutation	SNP	ENST00000249842.3	37	CCDS10260.1	.	.	.	.	.	.	.	.	.	.	G	15.61	2.885881	0.51908	0.0	1.16E-4	ENSG00000129009	ENST00000249842;ENST00000395118	T;T	0.58506	0.33;0.33	4.05	3.11	0.35812	.	0.125517	0.28431	U	0.015369	T	0.61999	0.2392	L	0.39898	1.24	0.43579	D	0.995915	D	0.89917	1.0	D	0.67231	0.95	T	0.60342	-0.7282	10	0.56958	D	0.05	.	7.4589	0.27283	0.0911:0.1698:0.739:0.0	.	149	O14498	ISLR_HUMAN	H	149	ENSP00000249842:R149H;ENSP00000378550:R149H	ENSP00000249842:R149H	R	+	2	0	ISLR	72254698	1.000000	0.71417	0.880000	0.34516	0.312000	0.27988	4.800000	0.62524	0.672000	0.31204	0.313000	0.20887	CGC		ISLR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269044.1	NM_005545	
AP3B2	8120	hgsc.bcm.edu	37	15	83346498	83346498	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr15:83346498G>A	ENST00000261722.3	-	12	1510	c.1303C>T	c.(1303-1305)Cgc>Tgc	p.R435C	AP3B2_ENST00000535348.1_Missense_Mutation_p.R403C|AP3B2_ENST00000535359.1_Missense_Mutation_p.R435C|RP11-752G15.3_ENST00000560650.1_RNA	NM_004644.3	NP_004635.2	Q13367	AP3B2_HUMAN	adaptor-related protein complex 3, beta 2 subunit	435					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|intracellular protein transport (GO:0006886)|post-Golgi vesicle-mediated transport (GO:0006892)	AP-3 adaptor complex (GO:0030123)|COPI-coated vesicle (GO:0030137)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transporter activity (GO:0005215)			breast(4)|endometrium(1)|kidney(1)|large_intestine(4)|lung(21)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(2)	41			BRCA - Breast invasive adenocarcinoma(143;0.229)			GTTGCACAGCGTCCAATGGCC	0.537																																																	0			15											47.0	50.0	49.0					15																	83346498		2115	4232	6347	81143553	SO:0001583	missense	8120			U37673	CCDS45331.1, CCDS61736.1, CCDS61737.1	15q	2008-07-07			ENSG00000103723	ENSG00000103723			567	protein-coding gene	gene with protein product		602166				7671305, 1851215	Standard	NM_004644		Approved	NAPTB	uc010uoh.2	Q13367	OTTHUMG00000168009	ENST00000261722.3:c.1303C>T	15.37:g.83346498G>A	ENSP00000261722:p.Arg435Cys	Somatic		Capture	Illumina HiSeq	Phase_I	81143553	A4Z4T7|B7ZKR7|B7ZKS0|O14808|Q52LY8	Silent	SNP	ENST00000261722.3	37	CCDS45331.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.083481	0.76642	.	.	ENSG00000103723	ENST00000261722;ENST00000535348;ENST00000535359	T;T;T	0.28454	1.61;1.61;1.61	4.98	1.62	0.23740	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.097447	0.64402	D	0.000006	T	0.62648	0.2445	H	0.96175	3.78	0.80722	D	1	B;D;D	0.89917	0.018;1.0;1.0	B;D;D	0.91635	0.016;0.999;0.993	T	0.66945	-0.5795	10	0.87932	D	0	-12.5333	8.099	0.30846	0.1646:0.0:0.7018:0.1336	.	403;435;435	B7ZKR7;B7ZKS0;Q13367	.;.;AP3B2_HUMAN	C	435;403;435	ENSP00000261722:R435C;ENSP00000438721:R403C;ENSP00000440984:R435C	ENSP00000261722:R435C	R	-	1	0	AP3B2	81143553	1.000000	0.71417	0.964000	0.40570	0.998000	0.95712	5.441000	0.66569	0.602000	0.29896	0.655000	0.94253	CGC		AP3B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397463.1		
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84566668	84566668	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr15:84566668G>A	ENST00000286744.5	+	14	1750	c.1526G>A	c.(1525-1527)cGc>cAc	p.R509H	ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.R509H	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	509	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.					proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			ATTAACCACCGCGGAGAGCAT	0.458																																																	0			15											148.0	122.0	131.0					15																	84566668		2203	4300	6503	82357672	SO:0001583	missense	57188			AF237652	CCDS10326.1, CCDS73773.1	15q25.2	2013-01-29			ENSG00000156218	ENSG00000156218		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14633	protein-coding gene	gene with protein product		609199				9628581, 10574462	Standard	NM_207517		Approved	KIAA1233, punctin-2	uc002bjz.4	P82987	OTTHUMG00000147363	ENST00000286744.5:c.1526G>A	15.37:g.84566668G>A	ENSP00000286744:p.Arg509His	Somatic		Capture	Illumina HiSeq	Phase_I	82357672	A1A566|A1A567|Q9ULI7	Missense_Mutation	SNP	ENST00000286744.5	37	CCDS10326.1	.	.	.	.	.	.	.	.	.	.	G	11.14	1.552246	0.27739	.	.	ENSG00000156218	ENST00000286744	T	0.61040	0.14	5.24	-5.95	0.02241	.	0.351880	0.29087	N	0.013189	T	0.36413	0.0966	L	0.38953	1.18	0.09310	N	1	B;B	0.19073	0.033;0.005	B;B	0.22152	0.038;0.007	T	0.11131	-1.0600	10	0.45353	T	0.12	.	5.3902	0.16240	0.3496:0.0:0.3829:0.2675	.	509;509	P82987-2;P82987	.;ATL3_HUMAN	H	509	ENSP00000286744:R509H	ENSP00000286744:R509H	R	+	2	0	ADAMTSL3	82357672	0.047000	0.20315	0.000000	0.03702	0.395000	0.30598	0.726000	0.25984	-1.036000	0.03287	-0.880000	0.02959	CGC		ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517	
ISG20	3669	hgsc.bcm.edu	37	15	89195465	89195465	+	Missense_Mutation	SNP	G	G	A	rs549880749		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr15:89195465G>A	ENST00000306072.5	+	3	711	c.353G>A	c.(352-354)cGt>cAt	p.R118H	ISG20_ENST00000560746.1_3'UTR|ISG20_ENST00000560741.1_Missense_Mutation_p.R118H	NM_002201.4	NP_002192.2	Q96AZ6	ISG20_HUMAN	interferon stimulated exonuclease gene 20kDa	118					cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|DNA catabolic process, exonucleolytic (GO:0000738)|negative regulation of viral genome replication (GO:0045071)|response to virus (GO:0009615)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)|type I interferon signaling pathway (GO:0060337)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	3'-5'-exoribonuclease activity (GO:0000175)|exonuclease activity (GO:0004527)|exoribonuclease II activity (GO:0008859)|metal ion binding (GO:0046872)|single-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008310)|U1 snRNA binding (GO:0030619)|U2 snRNA binding (GO:0030620)|U3 snoRNA binding (GO:0034511)			large_intestine(1)|lung(3)|prostate(1)	5	Lung NSC(78;0.0554)|all_lung(78;0.103)		BRCA - Breast invasive adenocarcinoma(143;0.12)			CTGTTGTGGCGTGAGGCCAAG	0.592																																																	0			15											162.0	133.0	143.0					15																	89195465		2200	4299	6499	86996469	SO:0001583	missense	3669			X89773	CCDS10345.1	15q26	2006-02-22	2002-08-29		ENSG00000172183	ENSG00000172183			6130	protein-coding gene	gene with protein product		604533	"""interferon stimulated gene (20kD)"""			9235947, 9605874	Standard	NM_002201		Approved	HEM45, CD25	uc002bmv.1	Q96AZ6	OTTHUMG00000148679	ENST00000306072.5:c.353G>A	15.37:g.89195465G>A	ENSP00000306565:p.Arg118His	Somatic		Capture	Illumina HiSeq	Phase_I	86996469	O00441|O00586	Missense_Mutation	SNP	ENST00000306072.5	37	CCDS10345.1	.	.	.	.	.	.	.	.	.	.	G	4.007	-0.001342	0.07819	.	.	ENSG00000172183	ENST00000306072;ENST00000546338	T	0.24908	1.83	4.58	-4.59	0.03400	Exonuclease (1);Exonuclease, RNase T/DNA polymerase III (1);Ribonuclease H-like (1);	0.771688	0.12177	N	0.492459	T	0.17916	0.0430	L	0.39245	1.2	0.09310	N	1	B	0.15473	0.013	B	0.09377	0.004	T	0.18681	-1.0329	10	0.33940	T	0.23	-9.4457	11.8782	0.52560	0.8125:0.0:0.1875:0.0	.	118	Q96AZ6	ISG20_HUMAN	H	118;126	ENSP00000306565:R118H	ENSP00000306565:R118H	R	+	2	0	ISG20	86996469	0.000000	0.05858	0.001000	0.08648	0.186000	0.23388	-1.156000	0.03160	-0.847000	0.04168	-0.339000	0.08088	CGT		ISG20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309069.2	NM_002201	
FRMPD4	9758	hgsc.bcm.edu	37	X	12734761	12734761	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chrX:12734761C>T	ENST00000380682.1	+	15	2689	c.2183C>T	c.(2182-2184)gCg>gTg	p.A728V		NM_014728.3	NP_055543.2	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	728					positive regulation of synapse structural plasticity (GO:0051835)	cytoskeleton (GO:0005856)|dendritic spine (GO:0043197)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.A728V(1)		breast(1)|central_nervous_system(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)	22						TTCCAGGCCGCGGAGGGGATC	0.547																																																	1	Substitution - Missense(1)	ovary(1)	X											106.0	108.0	107.0					X																	12734761		2203	4300	6503	12644682	SO:0001583	missense	9758			AB002314	CCDS35201.1	Xp22.31	2006-02-09	2006-02-09	2006-02-09	ENSG00000169933	ENSG00000169933			29007	protein-coding gene	gene with protein product		300838	"""PDZ domain containing 10"""	PDZK10, PDZD10		9205841	Standard	NM_014728		Approved	KIAA0316	uc004cuz.2	Q14CM0	OTTHUMG00000021138	ENST00000380682.1:c.2183C>T	X.37:g.12734761C>T	ENSP00000370057:p.Ala728Val	Somatic		Capture	Illumina HiSeq	Phase_I	12644682	A8K0X9|O15032	Missense_Mutation	SNP	ENST00000380682.1	37	CCDS35201.1	.	.	.	.	.	.	.	.	.	.	C	13.29	2.192817	0.38707	.	.	ENSG00000169933	ENST00000380682;ENST00000429478;ENST00000304087	T	0.27104	1.69	5.71	5.71	0.89125	.	0.304412	0.35870	N	0.002934	T	0.28234	0.0697	M	0.63428	1.95	0.09310	N	1	B;B	0.31459	0.324;0.324	B;B	0.23852	0.049;0.049	T	0.16394	-1.0404	10	0.22706	T	0.39	.	18.8648	0.92287	0.0:1.0:0.0:0.0	.	720;728	B7ZLE1;Q14CM0	.;FRPD4_HUMAN	V	728;719;717	ENSP00000370057:A728V	ENSP00000304583:A717V	A	+	2	0	FRMPD4	12644682	0.519000	0.26242	0.005000	0.12908	0.097000	0.18754	5.634000	0.67833	2.402000	0.81655	0.600000	0.82982	GCG		FRMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055771.1	XM_045712	
TLR8	51311	hgsc.bcm.edu	37	X	12937316	12937316	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chrX:12937316C>T	ENST00000218032.6	+	2	244	c.157C>T	c.(157-159)Cga>Tga	p.R53*	TLR8_ENST00000311912.5_Nonsense_Mutation_p.R71*	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	53					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)	p.R71*(1)		breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	CAGCAATCGTCGACTACAGGA	0.413																																																	1	Substitution - Nonsense(1)	large_intestine(1)	X											100.0	91.0	94.0					X																	12937316		2203	4300	6503	12847237	SO:0001587	stop_gained	51311			AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"""CD molecules"""	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.157C>T	X.37:g.12937316C>T	ENSP00000218032:p.Arg53*	Somatic		Capture	Illumina HiSeq	Phase_I	12847237	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Nonsense_Mutation	SNP	ENST00000218032.6	37	CCDS14152.1	.	.	.	.	.	.	.	.	.	.	C	16.41	3.116415	0.56505	.	.	ENSG00000101916	ENST00000218032;ENST00000311912	.	.	.	5.17	3.37	0.38596	.	0.824012	0.09906	N	0.740514	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.859	0.41103	0.0:0.7852:0.1368:0.078	.	.	.	.	X	53;71	.	ENSP00000218032:R53X	R	+	1	2	TLR8	12847237	0.032000	0.19561	0.000000	0.03702	0.160000	0.22226	2.131000	0.42074	0.410000	0.25675	0.523000	0.50628	CGA		TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055784.2	NM_016610	
TLR8	51311	hgsc.bcm.edu	37	X	12938669	12938669	+	Missense_Mutation	SNP	C	C	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chrX:12938669C>A	ENST00000218032.6	+	2	1597	c.1510C>A	c.(1510-1512)Ctt>Att	p.L504I	TLR8_ENST00000311912.5_Missense_Mutation_p.L522I	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	504					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	ATTTGAAAATCTTCCTGACAT	0.373																																																	0			X											47.0	45.0	45.0					X																	12938669		2203	4300	6503	12848590	SO:0001583	missense	51311			AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"""CD molecules"""	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.1510C>A	X.37:g.12938669C>A	ENSP00000218032:p.Leu504Ile	Somatic		Capture	Illumina HiSeq	Phase_I	12848590	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Missense_Mutation	SNP	ENST00000218032.6	37	CCDS14152.1	.	.	.	.	.	.	.	.	.	.	C	2.979	-0.210730	0.06140	.	.	ENSG00000101916	ENST00000218032;ENST00000311912	D;D	0.82526	-1.62;-1.62	5.97	3.56	0.40772	.	0.184908	0.26099	N	0.026349	T	0.76919	0.4055	M	0.66939	2.045	0.09310	N	1	B;B	0.31581	0.329;0.329	B;B	0.27887	0.084;0.084	T	0.70839	-0.4763	10	0.72032	D	0.01	.	4.8411	0.13491	0.1348:0.2705:0.0:0.5947	.	504;522	Q9NR97;D1CS70	TLR8_HUMAN;.	I	504;522	ENSP00000218032:L504I;ENSP00000312082:L522I	ENSP00000218032:L504I	L	+	1	0	TLR8	12848590	0.009000	0.17119	0.019000	0.16419	0.136000	0.21042	0.348000	0.20031	0.877000	0.35895	-0.340000	0.08031	CTT		TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055784.2	NM_016610	
MAP7D2	256714	hgsc.bcm.edu	37	X	20033383	20033383	+	Missense_Mutation	SNP	C	C	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chrX:20033383C>G	ENST00000379651.3	-	11	1602	c.1584G>C	c.(1582-1584)caG>caC	p.Q528H	MAP7D2_ENST00000452324.3_Missense_Mutation_p.Q476H|MAP7D2_ENST00000443379.3_Missense_Mutation_p.Q483H|MAP7D2_ENST00000543767.1_Missense_Mutation_p.Q413H|MIR23C_ENST00000579846.1_RNA|MAP7D2_ENST00000379643.5_Missense_Mutation_p.Q569H	NM_152780.3	NP_689993.2	Q96T17	MA7D2_HUMAN	MAP7 domain containing 2	528					microtubule cytoskeleton organization (GO:0000226)	microtubule (GO:0005874)				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(13)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	37						GCAGCATAATCTGTTCTCTCT	0.458																																																	0			X											196.0	148.0	164.0					X																	20033383		2203	4300	6503	19943304	SO:0001583	missense	256714			BC089400	CCDS14195.1, CCDS55384.1, CCDS55385.1, CCDS55386.1	Xp22.12	2008-02-05			ENSG00000184368	ENSG00000184368			25899	protein-coding gene	gene with protein product						12477932	Standard	NM_152780		Approved	FLJ14503	uc010nfo.2	Q96T17	OTTHUMG00000021228	ENST00000379651.3:c.1584G>C	X.37:g.20033383C>G	ENSP00000368972:p.Gln528His	Somatic		Capture	Illumina HiSeq	Phase_I	19943304	B7Z2J8|B7Z3S7|B9EGC7|C9JMA4|C9JYW0|Q5EBN1|Q5JPS7|Q6PIC7|Q8N792	Missense_Mutation	SNP	ENST00000379651.3	37	CCDS14195.1	.	.	.	.	.	.	.	.	.	.	C	15.59	2.878461	0.51801	.	.	ENSG00000184368	ENST00000379651;ENST00000379643;ENST00000543767;ENST00000443379;ENST00000544957;ENST00000452324	T;T;T;T;T	0.24908	1.83;1.83;1.83;1.83;1.83	5.6	2.34	0.29019	.	0.000000	0.64402	D	0.000003	T	0.45175	0.1329	M	0.78637	2.42	0.39036	D	0.960034	D;D;D;D;D	0.89917	0.999;0.999;0.999;1.0;0.996	D;D;D;D;D	0.81914	0.986;0.976;0.976;0.995;0.968	T	0.41520	-0.9504	10	0.66056	D	0.02	-14.5599	5.7878	0.18343	0.0:0.5608:0.1606:0.2787	.	483;476;569;528;413	B7Z3S7;C9JYW0;Q96T17-2;Q96T17;F5GYC2	.;.;.;MA7D2_HUMAN;.	H	528;569;413;483;211;476	ENSP00000368972:Q528H;ENSP00000368964:Q569H;ENSP00000440691:Q413H;ENSP00000388239:Q483H;ENSP00000413301:Q476H	ENSP00000368964:Q569H	Q	-	3	2	MAP7D2	19943304	0.362000	0.24980	1.000000	0.80357	0.714000	0.41099	-0.375000	0.07475	0.512000	0.28257	0.508000	0.49915	CAG		MAP7D2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056001.1	NM_152780	
FAM47C	442444	hgsc.bcm.edu	37	X	37026939	37026939	+	Silent	SNP	G	G	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chrX:37026939G>A	ENST00000358047.3	+	1	508	c.456G>A	c.(454-456)ccG>ccA	p.P152P		NM_001013736.2	NP_001013758.1	Q5HY64	FA47C_HUMAN	family with sequence similarity 47, member C	152										breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	120						TACTGAAACCGCTGGACCCTG	0.557																																																	0			X											64.0	56.0	59.0					X																	37026939		2202	4300	6502	36936860	SO:0001819	synonymous_variant	442444			AK125992	CCDS35227.1	Xp21.1	2006-07-04			ENSG00000198173	ENSG00000198173			25301	protein-coding gene	gene with protein product							Standard	NM_001013736		Approved		uc004ddl.2	Q5HY64	OTTHUMG00000024025	ENST00000358047.3:c.456G>A	X.37:g.37026939G>A		Somatic		Capture	Illumina HiSeq	Phase_I	36936860	Q6ZU46	Silent	SNP	ENST00000358047.3	37	CCDS35227.1																																																																																				FAM47C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060508.1	NM_001013736	
WNK3	65267	hgsc.bcm.edu	37	X	54334413	54334413	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chrX:54334413G>A	ENST00000375159.2	-	4	1030	c.1031C>T	c.(1030-1032)tCg>tTg	p.S344L	WNK3_ENST00000375169.3_Missense_Mutation_p.S344L|WNK3_ENST00000354646.2_Missense_Mutation_p.S344L			Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3	344	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of ion transmembrane transporter activity (GO:0032414)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of rubidium ion transmembrane transporter activity (GO:2000688)|positive regulation of rubidium ion transport (GO:2000682)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(24)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80						AGGATACTCCGATGTGGCCAT	0.388																																																	0			X											170.0	147.0	155.0					X																	54334413		2203	4300	6503	54351138	SO:0001583	missense	65267			AJ409088	CCDS14357.1, CCDS35302.1	Xp11.22	2008-05-14	2005-01-19	2005-01-22	ENSG00000196632	ENSG00000196632			14543	protein-coding gene	gene with protein product		300358	"""protein kinase, lysine deficient 3"""	PRKWNK3			Standard	NM_020922		Approved		uc004dtc.2	Q9BYP7	OTTHUMG00000021626	ENST00000375159.2:c.1031C>T	X.37:g.54334413G>A	ENSP00000364301:p.Ser344Leu	Somatic		Capture	Illumina HiSeq	Phase_I	54351138	B1AKG2|Q5JRC1|Q6JP76|Q8TCX6|Q9HCK6	Missense_Mutation	SNP	ENST00000375159.2	37	CCDS14357.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.941565	0.73557	.	.	ENSG00000196632	ENST00000375169;ENST00000354646;ENST00000375159	T;T;T	0.23552	1.9;1.9;1.9	5.38	5.38	0.77491	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.48767	D	0.000175	T	0.24122	0.0584	N	0.02181	-0.65	0.47511	D	0.999446	P;D	0.61080	0.934;0.989	P;P	0.61397	0.731;0.888	T	0.51787	-0.8661	10	0.56958	D	0.05	-5.7368	17.083	0.86603	0.0:0.0:1.0:0.0	.	344;344	Q9BYP7-3;Q9BYP7	.;WNK3_HUMAN	L	344	ENSP00000364312:S344L;ENSP00000346667:S344L;ENSP00000364301:S344L	ENSP00000346667:S344L	S	-	2	0	WNK3	54351138	1.000000	0.71417	0.898000	0.35279	0.333000	0.28666	9.757000	0.98924	2.386000	0.81285	0.544000	0.68410	TCG		WNK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056799.2	NM_020922	
UPF3B	65109	hgsc.bcm.edu	37	X	118971919	118971919	+	Missense_Mutation	SNP	C	C	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chrX:118971919C>A	ENST00000276201.2	-	10	1172	c.1103G>T	c.(1102-1104)cGg>cTg	p.R368L	UPF3B_ENST00000345865.2_Missense_Mutation_p.R355L|UPF3B_ENST00000478840.1_5'Flank	NM_080632.2	NP_542199.1	Q9BZI7	REN3B_HUMAN	UPF3 regulator of nonsense transcripts homolog B (yeast)	368	Sufficient for association with EJC core.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(12)|ovary(2)|prostate(1)	30						TTCTTCTTGCCGCTTCAGCCT	0.473																																																	0			X											148.0	126.0	134.0					X																	118971919		2203	4300	6503	118855947	SO:0001583	missense	65109			AF318576	CCDS14587.1, CCDS14588.1	Xq25-q26	2014-01-31			ENSG00000125351	ENSG00000125351			20439	protein-coding gene	gene with protein product		300298	"""mental retardation, X-linked 62"""	MRX62		11113196, 11163187, 19238151	Standard	NM_023010		Approved	RENT3B, UPF3X, HUPF3B	uc004erz.2	Q9BZI7	OTTHUMG00000022282	ENST00000276201.2:c.1103G>T	X.37:g.118971919C>A	ENSP00000276201:p.Arg368Leu	Somatic		Capture	Illumina HiSeq	Phase_I	118855947	D3DWI3|D3DWI4|Q0VAK8|Q9H1J0	Missense_Mutation	SNP	ENST00000276201.2	37	CCDS14588.1	.	.	.	.	.	.	.	.	.	.	C	14.26	2.480885	0.44044	.	.	ENSG00000125351	ENST00000276201;ENST00000345865	T;T	0.79454	-1.19;-1.27	5.59	5.59	0.84812	.	0.215397	0.47852	D	0.000211	T	0.76392	0.3981	M	0.63843	1.955	0.53005	D	0.999968	P;P	0.51933	0.949;0.914	P;P	0.48114	0.567;0.448	T	0.72798	-0.4184	10	0.13853	T	0.58	.	11.1005	0.48170	0.0:0.9145:0.0:0.0855	.	355;368	Q9BZI7-2;Q9BZI7	.;REN3B_HUMAN	L	368;355	ENSP00000276201:R368L;ENSP00000245418:R355L	ENSP00000276201:R368L	R	-	2	0	UPF3B	118855947	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	2.688000	0.46984	2.360000	0.80028	0.526000	0.51066	CGG		UPF3B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058068.1		
TENM1	10178	hgsc.bcm.edu	37	X	123517987	123517987	+	Missense_Mutation	SNP	G	G	A	rs372260419		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chrX:123517987G>A	ENST00000371130.3	-	29	6836	c.6773C>T	c.(6772-6774)gCg>gTg	p.A2258V	STAG2_ENST00000469481.1_Intron|TENM1_ENST00000422452.2_Missense_Mutation_p.A2265V	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	2258					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.A2260V(1)									GGACTTACTCGCGACACGTCG	0.458																																																	1	Substitution - Missense(1)	ovary(1)	X						G	VAL/ALA,VAL/ALA,VAL/ALA	1,3834		0,1,1631,571	99.0	95.0	96.0		6794,6791,6773	5.7	1.0	X		96	0,6728		0,0,2428,1872	no	missense,missense,missense	ODZ1	NM_001163278.1,NM_001163279.1,NM_014253.3	64,64,64	0,1,4059,2443	AA,AG,GG,G		0.0,0.0261,0.0095	possibly-damaging,possibly-damaging,possibly-damaging	2265/2733,2264/2732,2258/2726	123517987	1,10562	2203	4300	6503	123345668	SO:0001583	missense	10178			AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"""tenascin M"", ""odz, odd Oz/ten-m homolog 1 (Drosophila)"""	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.6773C>T	X.37:g.123517987G>A	ENSP00000360171:p.Ala2258Val	Somatic		Capture	Illumina HiSeq	Phase_I	123345668	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	37	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.249756	0.80024	2.61E-4	0.0	ENSG00000009694	ENST00000371130;ENST00000422452	D;D	0.86769	-2.17;-2.13	5.66	5.66	0.87406	.	0.051235	0.85682	D	0.000000	D	0.91489	0.7313	L	0.53561	1.675	0.80722	D	1	D;D;D	0.89917	1.0;0.998;0.997	D;P;P	0.63793	0.918;0.692;0.647	D	0.91220	0.5006	10	0.48119	T	0.1	.	18.6847	0.91559	0.0:0.0:1.0:0.0	.	2264;2265;2258	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	V	2258;2265	ENSP00000360171:A2258V;ENSP00000403954:A2265V	ENSP00000360171:A2258V	A	-	2	0	ODZ1	123345668	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.022000	0.88759	2.356000	0.79943	0.600000	0.82982	GCG		TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253	
GPR112	139378	hgsc.bcm.edu	37	X	135430849	135430849	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chrX:135430849A>G	ENST00000394143.1	+	6	5275	c.4984A>G	c.(4984-4986)Acc>Gcc	p.T1662A	GPR112_ENST00000412101.1_Missense_Mutation_p.T1457A|GPR112_ENST00000287534.4_Missense_Mutation_p.T1599A|GPR112_ENST00000394141.1_Missense_Mutation_p.T1457A|GPR112_ENST00000370652.1_Missense_Mutation_p.T1662A	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	1662					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					CGTTCCCACCACCATTATGGC	0.478																																																	0			X											153.0	153.0	153.0					X																	135430849		2203	4300	6503	135258515	SO:0001583	missense	139378			AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.4984A>G	X.37:g.135430849A>G	ENSP00000377699:p.Thr1662Ala	Somatic		Capture	Illumina HiSeq	Phase_I	135258515	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	37	CCDS35409.1	.	.	.	.	.	.	.	.	.	.	a	17.27	3.346207	0.61073	.	.	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.37915	1.21;1.21;1.17;1.28;1.17	3.39	-5.38	0.02673	.	.	.	.	.	T	0.23926	0.0579	L	0.32530	0.975	0.09310	N	1	P;P;P	0.49783	0.928;0.597;0.646	P;B;B	0.46975	0.533;0.242;0.162	T	0.16041	-1.0416	9	0.62326	D	0.03	.	0.8592	0.01189	0.2145:0.3331:0.122:0.3304	.	1599;1457;1662	Q8IZF6-2;Q8IZF6-3;Q8IZF6	.;.;GP112_HUMAN	A	1662;1662;1457;1599;1457	ENSP00000377699:T1662A;ENSP00000359686:T1662A;ENSP00000416526:T1457A;ENSP00000287534:T1599A;ENSP00000377697:T1457A	ENSP00000287534:T1599A	T	+	1	0	GPR112	135258515	0.000000	0.05858	0.000000	0.03702	0.611000	0.37282	0.220000	0.17660	-0.631000	0.05560	0.347000	0.21830	ACC		GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1		
FGF13	2258	hgsc.bcm.edu	37	X	137717737	137717737	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chrX:137717737C>T	ENST00000315930.6	-	4	1143	c.482G>A	c.(481-483)cGt>cAt	p.R161H	FGF13_ENST00000370603.3_Missense_Mutation_p.R171H|FGF13_ENST00000541469.1_Missense_Mutation_p.R115H|FGF13_ENST00000441825.2_Missense_Mutation_p.R142H|FGF13_ENST00000305414.4_Missense_Mutation_p.R108H	NM_004114.3	NP_004105.1	Q92913	FGF13_HUMAN	fibroblast growth factor 13	161	Mediates interaction with sodium channels.				cell-cell signaling (GO:0007267)|cerebral cortex cell migration (GO:0021795)|establishment of neuroblast polarity (GO:0045200)|hippocampus development (GO:0021766)|learning (GO:0007612)|MAPK cascade (GO:0000165)|memory (GO:0007613)|microtubule polymerization (GO:0046785)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of microtubule depolymerization (GO:0007026)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|positive regulation of protein kinase activity (GO:0045860)|protein localization to plasma membrane (GO:0072659)|signal transduction (GO:0007165)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular region (GO:0005576)|filopodium (GO:0030175)|growth cone (GO:0030426)|intercalated disc (GO:0014704)|microtubule (GO:0005874)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-tubulin binding (GO:0048487)|growth factor activity (GO:0008083)|ion channel binding (GO:0044325)|microtubule binding (GO:0008017)|protein kinase activator activity (GO:0030295)|sodium channel regulator activity (GO:0017080)			breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)	24	Acute lymphoblastic leukemia(192;0.000127)					CTGCTGCTGACGGTATATCAT	0.398																																																	0			X											153.0	128.0	136.0					X																	137717737		2203	4300	6503	137545403	SO:0001583	missense	2258			BC034340	CCDS14664.1, CCDS14665.1, CCDS55511.1	Xq26.3	2008-02-05			ENSG00000129682	ENSG00000129682			3670	protein-coding gene	gene with protein product	"""fibroblast growth factor homologous factor 2"""	300070				8790420	Standard	NM_033642		Approved	FHF2, FGF2	uc011mwj.2	Q92913	OTTHUMG00000022532	ENST00000315930.6:c.482G>A	X.37:g.137717737C>T	ENSP00000322390:p.Arg161His	Somatic		Capture	Illumina HiSeq	Phase_I	137545403	B1AK18|B7Z4M7|B7Z8N0|D3DWH4|O95830|Q9NZH9|Q9NZI0	Missense_Mutation	SNP	ENST00000315930.6	37	CCDS14665.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.995021	0.93167	.	.	ENSG00000129682	ENST00000315930;ENST00000305414;ENST00000441825;ENST00000370603;ENST00000541469;ENST00000436198;ENST00000455663	T;T;T;T;T;T;T	0.68181	-0.31;-0.31;-0.31;-0.31;-0.31;-0.31;-0.31	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.82495	0.5049	M	0.75150	2.29	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.79108	0.977;0.987;0.96;0.992	D	0.83631	0.0145	10	0.87932	D	0	.	18.5888	0.91200	0.0:1.0:0.0:0.0	.	115;171;108;161	B7Z8N0;B7Z4M7;Q92913-2;Q92913	.;.;.;FGF13_HUMAN	H	161;108;142;171;115;171;177	ENSP00000322390:R161H;ENSP00000303391:R108H;ENSP00000409276:R142H;ENSP00000359635:R171H;ENSP00000437903:R115H;ENSP00000396198:R171H;ENSP00000406916:R177H	ENSP00000303391:R108H	R	-	2	0	FGF13	137545403	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.487000	0.81328	2.618000	0.88619	0.600000	0.82982	CGT		FGF13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058534.2	NM_004114	
FMR1	2332	hgsc.bcm.edu	37	X	147011728	147011728	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chrX:147011728A>G	ENST00000370475.4	+	7	723	c.595A>G	c.(595-597)Ata>Gta	p.I199V	FMR1_ENST00000370470.1_Missense_Mutation_p.I199V|FMR1_ENST00000370477.1_Missense_Mutation_p.I199V|FMR1_ENST00000370471.3_Missense_Mutation_p.I199V|FMR1_ENST00000334557.6_Missense_Mutation_p.I199V|FMR1_ENST00000218200.8_Missense_Mutation_p.I199V|FMR1_ENST00000440235.2_5'UTR|FMR1_ENST00000439526.2_Missense_Mutation_p.I199V	NM_002024.5	NP_002015.1	Q06787	FMR1_HUMAN	fragile X mental retardation 1	199					central nervous system development (GO:0007417)|mRNA transport (GO:0051028)|negative regulation of translational initiation (GO:0045947)	cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|membrane (GO:0016020)|mRNA cap binding complex (GO:0005845)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|synapse (GO:0045202)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	35	Acute lymphoblastic leukemia(192;6.56e-05)					GTTGTCTCTGATAATGAGAAA	0.413									Fragile X syndrome																																								0			X											137.0	114.0	122.0					X																	147011728		2203	4300	6503	146819420	SO:0001583	missense	2477	Familial Cancer Database	Martin-Bell syndrome, FRAXA syndrome	X69962	CCDS14682.1, CCDS55518.1, CCDS55519.1, CCDS76039.1	Xq27.3	2014-09-17			ENSG00000102081	ENSG00000102081			3775	protein-coding gene	gene with protein product		309550	"""premature ovarian failure 1"""	POF1, POF		1572655	Standard	NM_002024		Approved	FMRP, FRAXA, MGC87458	uc010nst.3	Q06787	OTTHUMG00000022606	ENST00000370475.4:c.595A>G	X.37:g.147011728A>G	ENSP00000359506:p.Ile199Val	Somatic		Capture	Illumina HiSeq	Phase_I	146819420	A6NNH4|D3DWT0|D3DWT1|D3DWT2|G8JL90|Q16578|Q5PQZ6|Q99054	Missense_Mutation	SNP	ENST00000370475.4	37	CCDS14682.1	.	.	.	.	.	.	.	.	.	.	A	13.70	2.314123	0.40996	.	.	ENSG00000102081	ENST00000218200;ENST00000370471;ENST00000370477;ENST00000370475;ENST00000334557;ENST00000439526;ENST00000370470	T;T;T;T;T;T;T	0.55588	1.28;0.51;1.28;1.28;1.58;1.29;1.3	5.06	5.06	0.68205	.	0.097230	0.85682	D	0.000000	T	0.42944	0.1225	L	0.36672	1.1	0.80722	D	1	B;B;B;B;B	0.31009	0.002;0.155;0.06;0.303;0.166	B;B;B;B;B	0.29353	0.007;0.065;0.031;0.076;0.101	T	0.36866	-0.9730	10	0.40728	T	0.16	-32.2746	13.1966	0.59743	1.0:0.0:0.0:0.0	.	199;199;115;199;199	Q8IXW7;Q06787;Q59GC1;Q06787-8;G3V0J0	.;FMR1_HUMAN;.;.;.	V	199	ENSP00000218200:I199V;ENSP00000359502:I199V;ENSP00000359508:I199V;ENSP00000359506:I199V;ENSP00000355115:I199V;ENSP00000395923:I199V;ENSP00000359501:I199V	ENSP00000218200:I199V	I	+	1	0	FMR1	146819420	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.095000	0.76952	1.778000	0.52293	0.486000	0.48141	ATA		FMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058655.1	NM_002024	
PASD1	139135	hgsc.bcm.edu	37	X	150842517	150842517	+	Silent	SNP	A	A	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chrX:150842517A>G	ENST00000370357.4	+	15	2279	c.2034A>G	c.(2032-2034)tcA>tcG	p.S678S		NM_173493.2	NP_775764.2	Q8IV76	PASD1_HUMAN	PAS domain containing 1	678						nucleus (GO:0005634)	signal transducer activity (GO:0004871)	p.S678S(1)		breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(3)|liver(1)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	48	Acute lymphoblastic leukemia(192;6.56e-05)					CTTCAGACTCAACCATAAGCA	0.498																																																	1	Substitution - coding silent(1)	ovary(1)	X											128.0	115.0	119.0					X																	150842517		2203	4300	6503	150593173	SO:0001819	synonymous_variant	139135			AY270020	CCDS35431.1	Xq28	2009-08-06			ENSG00000166049	ENSG00000166049			20686	protein-coding gene	gene with protein product	"""cancer/testis antigen 63"""					15122589, 15162151	Standard	NM_173493		Approved	CT63	uc004fev.4	Q8IV76	OTTHUMG00000024169	ENST00000370357.4:c.2034A>G	X.37:g.150842517A>G		Somatic		Capture	Illumina HiSeq	Phase_I	150593173	Q3MNE0|Q69HD7|Q8N7X9	Silent	SNP	ENST00000370357.4	37	CCDS35431.1																																																																																				PASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060879.2	NM_173493	
POLN	353497	hgsc.bcm.edu	37	4	2209942	2209942	+	Silent	SNP	A	A	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr4:2209942A>G	ENST00000511885.2	-	5	839	c.486T>C	c.(484-486)aaT>aaC	p.N162N	POLN_ENST00000382865.1_Silent_p.N162N|POLN_ENST00000515357.1_5'UTR			Q7Z5Q5	DPOLN_HUMAN	polymerase (DNA directed) nu	162					double-strand break repair via homologous recombination (GO:0000724)|interstrand cross-link repair (GO:0036297)|translesion synthesis (GO:0019985)	nucleus (GO:0005634)	cyclin binding (GO:0030332)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)			kidney(6)|large_intestine(5)|liver(1)|lung(8)|ovary(2)|skin(4)|urinary_tract(2)	28			OV - Ovarian serous cystadenocarcinoma(23;0.0955)			CTGACAAATTATTATATGTAA	0.313								DNA polymerases (catalytic subunits)																																									0			4											66.0	66.0	66.0					4																	2209942		2203	4300	6503	2179740	SO:0001819	synonymous_variant	353497			AF044578	CCDS3360.1	4p16.3	2012-05-18			ENSG00000130997	ENSG00000130997		"""DNA polymerases"""	18870	protein-coding gene	gene with protein product		610887				12794064	Standard	NM_181808		Approved		uc003ger.2	Q7Z5Q5	OTTHUMG00000090081	ENST00000511885.2:c.486T>C	4.37:g.2209942A>G		Somatic		Capture	Illumina HiSeq	Phase_I	2179740	A2A336|B4E158|Q4TTW4|Q6ZNF4	Silent	SNP	ENST00000511885.2	37	CCDS3360.1																																																																																				POLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000205684.2	NM_181808	
GUF1	60558	hgsc.bcm.edu	37	4	44685325	44685325	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr4:44685325A>G	ENST00000281543.5	+	6	853	c.659A>G	c.(658-660)gAa>gGa	p.E220G	GUF1_ENST00000506793.1_3'UTR	NM_021927.2	NP_068746.2			GUF1 GTPase homolog (S. cerevisiae)											breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	19						CCAAGTGATGAATGTATTAAG	0.299																																																	0			4											60.0	65.0	63.0					4																	44685325		2202	4294	6496	44380082	SO:0001583	missense	60558				CCDS3468.1	4p13	2006-02-16			ENSG00000151806	ENSG00000151806			25799	protein-coding gene	gene with protein product						8553703	Standard	NM_021927		Approved	FLJ13220	uc003gww.4	Q8N442	OTTHUMG00000128608	ENST00000281543.5:c.659A>G	4.37:g.44685325A>G	ENSP00000281543:p.Glu220Gly	Somatic		Capture	Illumina HiSeq	Phase_I	44380082		Missense_Mutation	SNP	ENST00000281543.5	37	CCDS3468.1	.	.	.	.	.	.	.	.	.	.	A	22.9	4.355053	0.82243	.	.	ENSG00000151806	ENST00000281543	T	0.76186	-1.0	5.18	5.18	0.71444	Small GTP-binding protein domain (1);Protein synthesis factor, GTP-binding (1);	0.155195	0.56097	D	0.000026	T	0.80717	0.4676	M	0.66506	2.035	0.80722	D	1	D	0.52996	0.957	P	0.54431	0.752	T	0.82236	-0.0557	10	0.52906	T	0.07	-22.1232	14.222	0.65833	1.0:0.0:0.0:0.0	.	220	Q8N442	GUF1_HUMAN	G	220	ENSP00000281543:E220G	ENSP00000281543:E220G	E	+	2	0	GUF1	44380082	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	8.782000	0.91809	1.952000	0.56665	0.455000	0.32223	GAA		GUF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250469.3	NM_021927	
KIT	3815	hgsc.bcm.edu	37	4	55593649	55593649	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr4:55593649A>G	ENST00000288135.5	+	11	1812	c.1715A>G	c.(1714-1716)gAc>gGc	p.D572G		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	572					actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.Y570_L576del(9)|p.V560_L576del(4)|p.Y553_T574>S(3)|p.V555_P573del(3)|p.I563_L576del(2)|p.Q556_L576del(2)|p.W557_P573>S(2)|p.N564_Y578del(2)|p.W557_Q575del(2)|p.N564_L576del(2)|p.I571_L576del(2)|p.Y568_T574del(2)|p.Y568_L576>CV(1)|p.I563_D572del(1)|p.N564_T574del(1)|p.K558_Q575del(1)|p.V569_D572del(1)|p.V569_L576del(1)|p.M552_T574>TESA(1)|p.571_572>GE(1)|p.Q556_T574del(1)|p.Q556_D572>PS(1)|p.E561_P577del(1)|p.I571_N587del(1)|p.Q556_D572del(1)|p.N564_P573>T(1)|p.V569_L576>G(1)|p.K558_L576>NV(1)|p.V559_P573>A(1)|p.V569_Q575del(1)|p.N564_P577del(1)|p.V559_L576del(1)|p.K558_D572del(1)|p.Q556_D572>H(1)|p.N567_L576>E(1)|p.M552_D572del(1)|p.E562_P573del(1)|p.D572A(1)|p.Q556_P573del(1)|p.E554_D572del(1)|p.N567_P573del(1)|p.Y570_L576delYIDPTQL(1)|p.N564_P573>TS(1)		NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	GTTTACATAGACCCAACACAA	0.408		1	"""Mis, O"""		"""GIST, AML, TGCT, mastocytosis, mucosal melanoma"""	"""GIST, epithelioma"""	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																														yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"""L, M, O, E"""	66	Deletion - In frame(49)|Complex - deletion inframe(15)|Substitution - Missense(1)|Complex - insertion inframe(1)	soft_tissue(60)|skin(3)|haematopoietic_and_lymphoid_tissue(2)|testis(1)	4											77.0	77.0	77.0					4																	55593649		2203	4300	6503	55288406	SO:0001583	missense	3815	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6342	protein-coding gene	gene with protein product		164920	"""piebald trait"""	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.1715A>G	4.37:g.55593649A>G	ENSP00000288135:p.Asp572Gly	Somatic		Capture	Illumina HiSeq	Phase_I	55288406	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	37	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	A	25.3	4.629174	0.87560	.	.	ENSG00000157404	ENST00000288135;ENST00000412167	D;D	0.97404	-4.37;-4.37	6.06	6.06	0.98353	Protein kinase-like domain (1);	0.000000	0.64402	D	0.000003	D	0.98579	0.9525	M	0.88105	2.93	0.80722	D	1	D;D;D	0.64830	0.976;0.994;0.99	P;D;D	0.68039	0.477;0.955;0.93	D	0.99544	1.0964	10	0.87932	D	0	.	16.6003	0.84812	1.0:0.0:0.0:0.0	.	79;568;572	D5MAV8;P10721-2;P10721	.;.;KIT_HUMAN	G	572;568	ENSP00000288135:D572G;ENSP00000390987:D568G	ENSP00000288135:D572G	D	+	2	0	KIT	55288406	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	9.150000	0.94667	2.319000	0.78375	0.533000	0.62120	GAC		KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1		
AASDH	132949	hgsc.bcm.edu	37	4	57221472	57221472	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr4:57221472C>T	ENST00000205214.6	-	6	1159	c.979G>A	c.(979-981)Gtt>Att	p.V327I	AASDH_ENST00000510762.1_5'UTR|AASDH_ENST00000451613.1_Missense_Mutation_p.V327I|AASDH_ENST00000502617.1_Missense_Mutation_p.V327I|AASDH_ENST00000434343.2_5'UTR|AASDH_ENST00000513376.1_Missense_Mutation_p.V227I|AASDH_ENST00000602986.1_Missense_Mutation_p.V174I	NM_181806.2	NP_861522.2	Q4L235	ACSF4_HUMAN	aminoadipate-semialdehyde dehydrogenase	327					fatty acid metabolic process (GO:0006631)		acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)			endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	40	Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.0017)				CTTCTGAGAACTGTCAATGAT	0.403																																																	0			4											130.0	120.0	123.0					4																	57221472		2203	4300	6503	56916229	SO:0001583	missense	132949			AF516672	CCDS3504.1, CCDS68705.1, CCDS68706.1, CCDS75126.1, CCDS75127.1	4q12	2010-12-14			ENSG00000157426	ENSG00000157426	1.2.1.31	"""Acyl-CoA synthetase family"""	23993	protein-coding gene	gene with protein product	"""acyl-CoA synthetase family member 4"""	614365				15865210, 12712191, 17762044	Standard	XM_005265721		Approved	NRPS998, LYS2, ACSF4	uc003hbn.3	Q4L235	OTTHUMG00000128841	ENST00000205214.6:c.979G>A	4.37:g.57221472C>T	ENSP00000205214:p.Val327Ile	Somatic		Capture	Illumina HiSeq	Phase_I	56916229	A5D8V3|A5PL22|Q63HK2|Q63HR7|Q6IPP8|Q6TFZ6|Q7Z5Y3|Q96BW4|Q9P064	Missense_Mutation	SNP	ENST00000205214.6	37	CCDS3504.1	.	.	.	.	.	.	.	.	.	.	C	5.624	0.299750	0.10622	.	.	ENSG00000157426	ENST00000205214;ENST00000513376;ENST00000451613;ENST00000503808;ENST00000502617	T;T;T;T	0.41758	0.99;0.99;0.99;0.99	5.68	2.99	0.34606	AMP-dependent synthetase/ligase (1);	0.470851	0.24158	N	0.041019	T	0.31979	0.0814	L	0.43554	1.36	0.09310	N	1	B;B;B;B	0.25719	0.132;0.11;0.11;0.016	B;B;B;B	0.25614	0.026;0.037;0.037;0.062	T	0.18777	-1.0326	10	0.39692	T	0.17	-2.6129	7.7383	0.28827	0.0:0.6636:0.1271:0.2094	.	174;327;327;327	E9PH98;Q4L235-4;Q4L235-3;Q4L235	.;.;.;ACSF4_HUMAN	I	327;227;327;174;327	ENSP00000205214:V327I;ENSP00000423760:V227I;ENSP00000409656:V327I;ENSP00000421171:V327I	ENSP00000205214:V327I	V	-	1	0	AASDH	56916229	0.107000	0.21998	0.134000	0.22075	0.074000	0.17049	0.757000	0.26433	0.736000	0.32559	0.650000	0.86243	GTT		AASDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250780.1	NM_181806	
GPRIN3	285513	hgsc.bcm.edu	37	4	90170717	90170717	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr4:90170717T>C	ENST00000609438.1	-	2	1063	c.545A>G	c.(544-546)aAa>aGa	p.K182R	GPRIN3_ENST00000333209.4_Missense_Mutation_p.K182R	NM_198281.2	NP_938022.2	Q6ZVF9	GRIN3_HUMAN	GPRIN family member 3	182										breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(5)|prostate(2)|skin(1)	36		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;5.67e-05)		CACCTGATCTTTGCTGCTACT	0.512																																																	0			4											132.0	123.0	126.0					4																	90170717		2203	4300	6503	90389740	SO:0001583	missense	285513			AK124616	CCDS34030.1	4q22.1	2006-08-24				ENSG00000185477			27733	protein-coding gene	gene with protein product		611241				15488195	Standard	NM_198281		Approved	GRIN3, FLJ42625	uc003hsm.1	Q6ZVF9		ENST00000609438.1:c.545A>G	4.37:g.90170717T>C	ENSP00000476603:p.Lys182Arg	Somatic		Capture	Illumina HiSeq	Phase_I	90389740	Q8IVE4	Missense_Mutation	SNP	ENST00000609438.1	37	CCDS34030.1	.	.	.	.	.	.	.	.	.	.	T	14.63	2.593311	0.46214	.	.	ENSG00000185477	ENST00000333209	T	0.11169	2.8	5.05	5.05	0.67936	.	0.690951	0.11930	N	0.515804	T	0.11024	0.0269	L	0.27053	0.805	0.09310	N	1	P	0.36909	0.573	B	0.39217	0.294	T	0.24261	-1.0165	10	0.40728	T	0.16	-1.6179	13.8113	0.63266	0.0:0.0:0.0:1.0	.	182	Q6ZVF9	GRIN3_HUMAN	R	182	ENSP00000328672:K182R	ENSP00000328672:K182R	K	-	2	0	GPRIN3	90389740	0.001000	0.12720	0.200000	0.23457	0.142000	0.21351	0.988000	0.29616	2.242000	0.73789	0.528000	0.53228	AAA		GPRIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363540.2	NM_198281	
ALPK1	80216	hgsc.bcm.edu	37	4	113351613	113351613	+	Missense_Mutation	SNP	G	G	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr4:113351613G>T	ENST00000458497.1	+	11	1189	c.910G>T	c.(910-912)Ggc>Tgc	p.G304C	ALPK1_ENST00000177648.9_Missense_Mutation_p.G304C|ALPK1_ENST00000504176.2_Missense_Mutation_p.G226C	NM_001102406.1|NM_025144.3	NP_001095876.1|NP_079420.3	Q96QP1	ALPK1_HUMAN	alpha-kinase 1	304							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(20)|ovary(6)|prostate(2)|urinary_tract(1)	53		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)		GAATATCCGTGGCACGTGTTT	0.388																																																	0			4											62.0	64.0	63.0					4																	113351613		2203	4300	6503	113571062	SO:0001583	missense	80216			AY044164	CCDS3697.1, CCDS58923.1	4q26	2008-02-05			ENSG00000073331	ENSG00000073331			20917	protein-coding gene	gene with protein product	"""lymphocyte alpha-kinase"""	607347				10021370, 10819331	Standard	NM_025144		Approved	Lak, FLJ22670, KIAA1527	uc003ian.4	Q96QP1	OTTHUMG00000132911	ENST00000458497.1:c.910G>T	4.37:g.113351613G>T	ENSP00000398048:p.Gly304Cys	Somatic		Capture	Illumina HiSeq	Phase_I	113571062	B4E3G1|F5H138|Q68CI9|Q6P9F9|Q6ZNK4|Q9P201	Missense_Mutation	SNP	ENST00000458497.1	37	CCDS3697.1	.	.	.	.	.	.	.	.	.	.	G	19.17	3.774904	0.70107	.	.	ENSG00000073331	ENST00000458497;ENST00000177648;ENST00000504176	T;T;T	0.56776	0.44;0.44;0.44	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.75384	0.3842	M	0.77820	2.39	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.77381	-0.2609	10	0.87932	D	0	-22.5725	19.8968	0.96969	0.0:0.0:1.0:0.0	.	226;226;304	F5H138;B4E3G1;Q96QP1	.;.;ALPK1_HUMAN	C	304;304;226	ENSP00000398048:G304C;ENSP00000177648:G304C;ENSP00000426044:G226C	ENSP00000177648:G304C	G	+	1	0	ALPK1	113571062	1.000000	0.71417	0.995000	0.50966	0.387000	0.30353	9.361000	0.97122	2.691000	0.91804	0.655000	0.94253	GGC		ALPK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256421.2	NM_025144	
METTL14	57721	hgsc.bcm.edu	37	4	119631268	119631268	+	Missense_Mutation	SNP	A	A	C			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr4:119631268A>C	ENST00000388822.5	+	11	1349	c.1182A>C	c.(1180-1182)agA>agC	p.R394S	METTL14_ENST00000506780.1_Missense_Mutation_p.R356S			Q9HCE5	MET14_HUMAN	methyltransferase like 14	394					mRNA destabilization (GO:0061157)|mRNA methylation (GO:0080009)|stem cell maintenance (GO:0019827)	MIS complex (GO:0036396)|nucleus (GO:0005634)	mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity (GO:0016422)|RNA binding (GO:0003723)			endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|stomach(1)	16						AAATTGAGAGACTTCGACCAA	0.478																																																	0			4											84.0	85.0	85.0					4																	119631268		2203	4300	6503	119850716	SO:0001583	missense	57721			AB046847	CCDS34053.1	4q26	2009-02-24			ENSG00000145388	ENSG00000145388			29330	protein-coding gene	gene with protein product						10997877	Standard	NM_020961		Approved	KIAA1627	uc003icf.3	Q9HCE5	OTTHUMG00000161167	ENST00000388822.5:c.1182A>C	4.37:g.119631268A>C	ENSP00000373474:p.Arg394Ser	Somatic		Capture	Illumina HiSeq	Phase_I	119850716	A6NIG1|Q969V2	Missense_Mutation	SNP	ENST00000388822.5	37	CCDS34053.1	.	.	.	.	.	.	.	.	.	.	A	9.804	1.181391	0.21787	.	.	ENSG00000145388	ENST00000388822;ENST00000506780	.	.	.	5.62	1.88	0.25563	.	0.000000	0.85682	D	0.000000	T	0.32010	0.0815	L	0.32530	0.975	0.58432	D	0.999995	B;B	0.28880	0.205;0.226	B;B	0.19148	0.013;0.024	T	0.08848	-1.0702	9	0.08381	T	0.77	-0.6427	9.1099	0.36720	0.6824:0.0:0.3176:0.0	.	356;394	D6RBL4;Q9HCE5	.;MTL14_HUMAN	S	394;356	.	ENSP00000373474:R394S	R	+	3	2	METTL14	119850716	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.519000	0.35888	0.387000	0.25024	0.528000	0.53228	AGA		METTL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364034.3	NM_020961	
DCLK2	166614	hgsc.bcm.edu	37	4	151160899	151160899	+	Silent	SNP	T	T	C			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr4:151160899T>C	ENST00000296550.7	+	11	2326	c.1572T>C	c.(1570-1572)tgT>tgC	p.C524C	DCLK2_ENST00000302176.8_Silent_p.C541C|DCLK2_ENST00000506325.1_Silent_p.C523C	NM_001040260.3	NP_001035350.2	Q8N568	DCLK2_HUMAN	doublecortin-like kinase 2	524	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.C524W(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(1)	26	all_hematologic(180;0.151)					TTCAGGTGTGTGAATATCCTG	0.428																																					GBM(195;186 2215 13375 16801 37459)												1	Substitution - Missense(1)	ovary(1)	4											129.0	131.0	130.0					4																	151160899		2203	4300	6503	151380349	SO:0001819	synonymous_variant	166614			BC032726	CCDS34076.1, CCDS47142.1, CCDS47142.2	4q31.3	2008-02-05	2007-04-02	2007-04-02	ENSG00000170390	ENSG00000170390			19002	protein-coding gene	gene with protein product		613166	"""doublecortin and CaM kinase-like 2"""	DCAMKL2		12477932	Standard	NM_001040260		Approved	MGC45428, DCDC3, DCDC3B, DCK2	uc003ilo.4	Q8N568	OTTHUMG00000161444	ENST00000296550.7:c.1572T>C	4.37:g.151160899T>C		Somatic		Capture	Illumina HiSeq	Phase_I	151380349	C9J5Q9|Q59GC8|Q8N399	Silent	SNP	ENST00000296550.7	37	CCDS34076.1																																																																																				DCLK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364952.1	NM_001040260	
FBXW7	55294	hgsc.bcm.edu	37	4	153245398	153245398	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr4:153245398T>C	ENST00000281708.4	-	11	3022	c.1793A>G	c.(1792-1794)aAt>aGt	p.N598S	FBXW7_ENST00000603841.1_Missense_Mutation_p.N598S|FBXW7_ENST00000603548.1_Missense_Mutation_p.N598S|FBXW7_ENST00000263981.5_Missense_Mutation_p.N518S|FBXW7_ENST00000296555.5_Missense_Mutation_p.N480S|FBXW7_ENST00000393956.3_Missense_Mutation_p.N422S	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	598					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				AGAATCTGCATTCCCAGAGAC	0.388			"""Mis, N, D, F"""		"""colorectal, endometrial, T-ALL"""																																			Rec	yes		4	4q31.3	55294	"""F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"""		"""E, L"""	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	4											130.0	119.0	123.0					4																	153245398		2203	4300	6503	153464848	SO:0001583	missense	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	16712	protein-coding gene	gene with protein product	"""archipelago homolog (Drosophila)"""	606278	"""F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"", ""F-box and WD repeat domain containing 7"""			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1793A>G	4.37:g.153245398T>C	ENSP00000281708:p.Asn598Ser	Somatic		Capture	Illumina HiSeq	Phase_I	153464848	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.033104	0.75504	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	T;T;T;T	0.35236	1.32;1.32;1.32;1.32	5.45	5.45	0.79879	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.21022	0.0506	N	0.00069	-2.28	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.998;1.0;0.997;0.997	T	0.67722	-0.5597	10	0.35671	T	0.21	-27.2537	15.5099	0.75772	0.0:0.0:0.0:1.0	.	422;598;480;518	B7Z2C8;Q969H0;Q969H0-4;Q969H0-2	.;FBXW7_HUMAN;.;.	S	598;480;518;422	ENSP00000281708:N598S;ENSP00000296555:N480S;ENSP00000263981:N518S;ENSP00000377528:N422S	ENSP00000263981:N518S	N	-	2	0	FBXW7	153464848	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.040000	0.89188	2.060000	0.61445	0.533000	0.62120	AAT		FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1		
FBXW7	55294	hgsc.bcm.edu	37	4	153249460	153249460	+	Missense_Mutation	SNP	C	C	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr4:153249460C>A	ENST00000281708.4	-	9	2547	c.1318G>T	c.(1318-1320)Gat>Tat	p.D440Y	FBXW7_ENST00000603841.1_Missense_Mutation_p.D440Y|FBXW7_ENST00000603548.1_Missense_Mutation_p.D440Y|FBXW7_ENST00000263981.5_Missense_Mutation_p.D360Y|FBXW7_ENST00000296555.5_Missense_Mutation_p.D322Y|FBXW7_ENST00000393956.3_Missense_Mutation_p.D264Y	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	440					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.?(1)|p.D440N(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				AGTGTCCGATCTGTAGATCCA	0.408			"""Mis, N, D, F"""		"""colorectal, endometrial, T-ALL"""																																			Rec	yes		4	4q31.3	55294	"""F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"""		"""E, L"""	2	Substitution - Missense(1)|Unknown(1)	haematopoietic_and_lymphoid_tissue(1)|stomach(1)	4											310.0	262.0	278.0					4																	153249460		2203	4300	6503	153468910	SO:0001583	missense	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	16712	protein-coding gene	gene with protein product	"""archipelago homolog (Drosophila)"""	606278	"""F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"", ""F-box and WD repeat domain containing 7"""			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1318G>T	4.37:g.153249460C>A	ENSP00000281708:p.Asp440Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	153468910	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.574255	0.86542	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	D;D;D;D	0.89415	-2.51;-2.51;-2.51;-2.51	5.9	5.9	0.94986	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.97682	0.9240	H	0.99783	4.775	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;0.999;0.999	D	0.98877	1.0768	10	0.87932	D	0	-22.1701	20.2787	0.98501	0.0:1.0:0.0:0.0	.	264;440;322;360	B7Z2C8;Q969H0;Q969H0-4;Q969H0-2	.;FBXW7_HUMAN;.;.	Y	440;322;360;264	ENSP00000281708:D440Y;ENSP00000296555:D322Y;ENSP00000263981:D360Y;ENSP00000377528:D264Y	ENSP00000263981:D360Y	D	-	1	0	FBXW7	153468910	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.818000	0.86416	2.798000	0.96311	0.650000	0.86243	GAT		FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1		
FBXO8	26269	hgsc.bcm.edu	37	4	175158655	175158655	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr4:175158655G>A	ENST00000393674.2	-	6	1730	c.868C>T	c.(868-870)Cga>Tga	p.R290*	FBXO8_ENST00000503293.1_Nonsense_Mutation_p.R249*	NM_012180.2	NP_036312.2	Q9NRD0	FBX8_HUMAN	F-box protein 8	290					actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell junction (GO:0030054)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			breast(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(2)|prostate(1)|urinary_tract(1)	14		Prostate(90;0.00201)|Melanoma(52;0.012)|Renal(120;0.0183)|all_neural(102;0.0887)|all_hematologic(60;0.107)		all cancers(43;7.29e-18)|Epithelial(43;1.85e-15)|OV - Ovarian serous cystadenocarcinoma(60;5.62e-09)|GBM - Glioblastoma multiforme(59;0.00115)|STAD - Stomach adenocarcinoma(60;0.00299)|LUSC - Lung squamous cell carcinoma(193;0.1)		CGGGTATTTCGAATAAATTCC	0.388																																																	0			4											90.0	91.0	91.0					4																	175158655		2203	4300	6503	175395230	SO:0001587	stop_gained	26269			AF174596	CCDS3820.1	4q34.1	2008-02-05	2004-06-15			ENSG00000164117		"""F-boxes /  ""other"""""	13587	protein-coding gene	gene with protein product		605649	"""F-box only protein 8"""			10531035, 10531037	Standard	NM_012180		Approved	FBX8, FBS	uc003itp.3	Q9NRD0		ENST00000393674.2:c.868C>T	4.37:g.175158655G>A	ENSP00000377280:p.Arg290*	Somatic		Capture	Illumina HiSeq	Phase_I	175395230	B2RB40|D3DP41|G5E9Z0|Q6UWN4|Q8IWE1|Q9NRP5|Q9UKC4	Nonsense_Mutation	SNP	ENST00000393674.2	37	CCDS3820.1	.	.	.	.	.	.	.	.	.	.	G	43	10.161063	0.99350	.	.	ENSG00000164117	ENST00000393674;ENST00000503293;ENST00000296517	.	.	.	5.72	4.87	0.63330	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.7393	0.62838	0.0:0.0:0.7197:0.2803	.	.	.	.	X	290;249;203	.	ENSP00000296517:R203X	R	-	1	2	FBXO8	175395230	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.300000	0.59079	1.394000	0.46624	0.655000	0.94253	CGA		FBXO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362085.2	NM_012180	
ADAM29	11086	hgsc.bcm.edu	37	4	175896768	175896768	+	Missense_Mutation	SNP	C	C	T	rs544557652		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr4:175896768C>T	ENST00000359240.3	+	5	762	c.92C>T	c.(91-93)cCg>cTg	p.P31L	RP13-577H12.2_ENST00000507525.1_RNA|ADAM29_ENST00000514159.1_Missense_Mutation_p.P31L|ADAM29_ENST00000404450.4_Missense_Mutation_p.P31L|ADAM29_ENST00000445694.1_Missense_Mutation_p.P31L	NM_001278125.1|NM_014269.4	NP_001265054.1|NP_055084.3	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29	31			P -> L (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.P31L(2)		NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(25)|ovary(3)|pancreas(1)|prostate(7)|skin(24)|urinary_tract(2)	93		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		CACAGCCCTCCGGATGTGGTG	0.517																																					Ovarian(140;1727 1835 21805 25838 41440)												2	Substitution - Missense(2)	large_intestine(1)|kidney(1)	4											82.0	81.0	81.0					4																	175896768		2203	4300	6503	176133343	SO:0001583	missense	11086			AF171929	CCDS3823.1	4q34.1	2012-05-16	2005-08-18		ENSG00000168594	ENSG00000168594		"""ADAM metallopeptidase domain containing"""	207	protein-coding gene	gene with protein product	"""cancer/testis antigen 73"""	604778	"""a disintegrin and metalloproteinase domain 29"""			10644455	Standard	NM_014269		Approved	svph1, CT73	uc031shw.1	Q9UKF5	OTTHUMG00000160764	ENST00000359240.3:c.92C>T	4.37:g.175896768C>T	ENSP00000352177:p.Pro31Leu	Somatic		Capture	Illumina HiSeq	Phase_I	176133343	Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	Missense_Mutation	SNP	ENST00000359240.3	37	CCDS3823.1	.	.	.	.	.	.	.	.	.	.	C	7.389	0.630296	0.14257	.	.	ENSG00000168594	ENST00000359240;ENST00000445694;ENST00000502940;ENST00000502305;ENST00000404450;ENST00000514159	T;T;T;D;T;T	0.81579	4.66;4.66;0.9;-1.51;4.66;4.66	4.36	1.46	0.22682	.	.	.	.	.	D	0.85124	0.5625	M	0.71206	2.165	0.09310	N	1	D	0.89917	1.0	D	0.76575	0.988	T	0.71580	-0.4550	8	.	.	.	.	2.5819	0.04820	0.1935:0.5128:0.1878:0.1059	.	31	Q9UKF5	ADA29_HUMAN	L	31	ENSP00000352177:P31L;ENSP00000414544:P31L;ENSP00000427674:P31L;ENSP00000422537:P31L;ENSP00000384229:P31L;ENSP00000423517:P31L	.	P	+	2	0	ADAM29	176133343	0.003000	0.15002	0.098000	0.21074	0.004000	0.04260	0.096000	0.15147	0.156000	0.19299	0.637000	0.83480	CCG		ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding			
KCNS3	3790	hgsc.bcm.edu	37	2	18113666	18113666	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr2:18113666A>G	ENST00000403915.1	+	3	1842	c.1391A>G	c.(1390-1392)gAt>gGt	p.D464G	KCNS3_ENST00000465292.1_Intron|KCNS3_ENST00000304101.4_Missense_Mutation_p.D464G	NM_001282428.1	NP_001269357.1	Q9BQ31	KCNS3_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 3	464					energy reserve metabolic process (GO:0006112)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel regulator activity (GO:0015459)			endometrium(5)|kidney(1)|large_intestine(7)|lung(11)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					GTGGTGAGCGATCCTGACTCC	0.453																																																	0			2											123.0	112.0	116.0					2																	18113666		2203	4300	6503	17977147	SO:0001583	missense	3790			AF043472	CCDS1692.1	2p24	2011-07-05			ENSG00000170745	ENSG00000170745		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6302	protein-coding gene	gene with protein product		603888				10484328, 16382104	Standard	NM_002252		Approved	Kv9.3	uc002rcw.3	Q9BQ31	OTTHUMG00000044150	ENST00000403915.1:c.1391A>G	2.37:g.18113666A>G	ENSP00000385968:p.Asp464Gly	Somatic		Capture	Illumina HiSeq	Phase_I	17977147	D6W520|O43651|Q4ZFY1|Q96B56	Missense_Mutation	SNP	ENST00000403915.1	37	CCDS1692.1	.	.	.	.	.	.	.	.	.	.	A	10.70	1.425329	0.25639	.	.	ENSG00000170745	ENST00000403915;ENST00000304101	D;D	0.97209	-4.29;-4.29	6.07	6.07	0.98685	.	0.658090	0.16144	N	0.227590	D	0.92740	0.7692	N	0.22421	0.69	0.46279	D	0.998965	B	0.02656	0.0	B	0.01281	0.0	D	0.88473	0.3063	10	0.21540	T	0.41	.	10.8883	0.46981	0.9305:0.0:0.0695:0.0	.	464	Q9BQ31	KCNS3_HUMAN	G	464	ENSP00000385968:D464G;ENSP00000305824:D464G	ENSP00000305824:D464G	D	+	2	0	KCNS3	17977147	0.843000	0.29541	0.408000	0.26446	0.981000	0.71138	2.481000	0.45215	2.326000	0.78906	0.533000	0.62120	GAT		KCNS3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323808.1	NM_002252	
SULT6B1	391365	hgsc.bcm.edu	37	2	37398688	37398688	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr2:37398688A>G	ENST00000535679.1	-	6	669	c.670T>C	c.(670-672)Ttt>Ctt	p.F224L	SULT6B1_ENST00000407963.1_Missense_Mutation_p.F186L|SULT6B1_ENST00000260637.3_Missense_Mutation_p.F186L|SULT6B1_ENST00000379149.2_Missense_Mutation_p.F120L			Q6IMI4	ST6B1_HUMAN	sulfotransferase family, cytosolic, 6B, member 1	224						cytoplasm (GO:0005737)	sulfotransferase activity (GO:0008146)	p.F186I(1)		NS(1)|breast(1)|central_nervous_system(1)|large_intestine(3)|lung(5)|ovary(1)	12		all_hematologic(82;0.248)				CCAGTTAGAAAGAATCCCAAG	0.428																																																	1	Substitution - Missense(1)	central_nervous_system(1)	2											113.0	112.0	112.0					2																	37398688		2203	4300	6503	37252192	SO:0001583	missense	391365			AY289770, AY289774	CCDS33182.1	2p22.2	2007-07-26			ENSG00000138068	ENSG00000138068		"""Sulfotransferases, cytosolic"""	33433	protein-coding gene	gene with protein product						14676822	Standard	XM_005264307		Approved		uc002rpu.3	Q6IMI4	OTTHUMG00000152160	ENST00000535679.1:c.670T>C	2.37:g.37398688A>G	ENSP00000444081:p.Phe224Leu	Somatic		Capture	Illumina HiSeq	Phase_I	37252192	B2RTS7	Missense_Mutation	SNP	ENST00000535679.1	37		.	.	.	.	.	.	.	.	.	.	A	11.20	1.569186	0.28003	.	.	ENSG00000138068	ENST00000535679;ENST00000379149;ENST00000260637;ENST00000407963	T;T;T;T	0.11063	2.81;2.81;2.81;2.81	4.87	4.87	0.63330	Sulfotransferase domain (1);	0.462043	0.24518	N	0.037832	T	0.06554	0.0168	N	0.14661	0.345	0.24110	N	0.995844	B	0.11235	0.004	B	0.08055	0.003	T	0.25363	-1.0134	10	0.39692	T	0.17	.	8.6963	0.34298	0.9105:0.0:0.0895:0.0	.	224	Q6IMI4	ST6B1_HUMAN	L	224;120;186;186	ENSP00000444081:F224L;ENSP00000368444:F120L;ENSP00000260637:F186L;ENSP00000384950:F186L	ENSP00000260637:F186L	F	-	1	0	SULT6B1	37252192	1.000000	0.71417	0.972000	0.41901	0.217000	0.24651	2.353000	0.44089	2.041000	0.60428	0.482000	0.46254	TTT		SULT6B1-203	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001032377	
REG3A	5068	hgsc.bcm.edu	37	2	79384717	79384717	+	Silent	SNP	C	C	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr2:79384717C>T	ENST00000409839.3	-	5	477	c.441G>A	c.(439-441)gcG>gcA	p.A147A	AC011754.1_ENST00000415201.1_RNA|REG3A_ENST00000305165.2_Silent_p.A147A|REG3A_ENST00000393878.1_Silent_p.A147A	NM_002580.2|NM_138937.2	NP_002571.1|NP_620354.1	Q06141	REG3A_HUMAN	regenerating islet-derived 3 alpha	147	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				acute-phase response (GO:0006953)|cell proliferation (GO:0008283)|heterophilic cell-cell adhesion (GO:0007157)|multicellular organismal development (GO:0007275)|negative regulation of keratinocyte differentiation (GO:0045617)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of wound healing (GO:0090303)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)			breast(2)|large_intestine(4)|lung(41)|prostate(2)|skin(1)	50						TCGACAGGCTCGCACAGTGGC	0.527																																																	0			2											103.0	104.0	104.0					2																	79384717		2203	4300	6503	79238225	SO:0001819	synonymous_variant	5068			S51768	CCDS1965.1	2p12	2008-02-05	2005-02-11	2005-02-11	ENSG00000172016	ENSG00000172016			8601	protein-coding gene	gene with protein product		167805	"""pancreatitis-associated protein"""	PAP		8188210	Standard	NM_002580		Approved	HIP, REG-III, REG3, PBCGF, PAP1	uc002sof.2	Q06141	OTTHUMG00000130017	ENST00000409839.3:c.441G>A	2.37:g.79384717C>T		Somatic		Capture	Illumina HiSeq	Phase_I	79238225		Silent	SNP	ENST00000409839.3	37	CCDS1965.1																																																																																				REG3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252290.2	NM_002580	
MAP4K4	9448	hgsc.bcm.edu	37	2	102456283	102456283	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr2:102456283C>T	ENST00000347699.4	+	10	776	c.776C>T	c.(775-777)tCg>tTg	p.S259L	MAP4K4_ENST00000302217.5_Intron|MAP4K4_ENST00000350878.4_Missense_Mutation_p.S239L|MAP4K4_ENST00000350198.4_Missense_Mutation_p.S259L|MAP4K4_ENST00000413150.2_Missense_Mutation_p.S259L|MAP4K4_ENST00000456652.1_Intron|MAP4K4_ENST00000324219.4_Missense_Mutation_p.S259L|MAP4K4_ENST00000425019.1_Missense_Mutation_p.S259L	NM_001242559.1|NM_145687.3	NP_001229488.1|NP_663720.1	O95819	M4K4_HUMAN	mitogen-activated protein kinase kinase kinase kinase 4	259	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of JNK cascade (GO:0046328)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.S259L(1)		breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						TCTTACAGGTCGAAGAAGTTT	0.378																																																	1	Substitution - Missense(1)	lung(1)	2											68.0	57.0	60.0					2																	102456283		1822	4082	5904	101822715	SO:0001583	missense	9448			AF096300	CCDS56130.1, CCDS74546.1	2q11.2-q12	2011-06-09			ENSG00000071054	ENSG00000071054		"""Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"""	6866	protein-coding gene	gene with protein product	"""HPK/GCK-like kinase"", ""hepatocyte progenitor kinase-like/germinal center kinase-like kinase"""	604666				9890973, 9734811, 9135144	Standard	NM_004834		Approved	HGK, NIK, FLH21957	uc002tbf.3	O95819	OTTHUMG00000155394	ENST00000347699.4:c.776C>T	2.37:g.102456283C>T	ENSP00000314363:p.Ser259Leu	Somatic		Capture	Illumina HiSeq	Phase_I	101822715	O75172|Q9NST7	Missense_Mutation	SNP	ENST00000347699.4	37	CCDS56130.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.499809	0.85176	.	.	ENSG00000071054	ENST00000425019;ENST00000324219;ENST00000350198;ENST00000413150;ENST00000347699;ENST00000417294;ENST00000350878	T;T;T;T;T;T;T	0.33438	1.41;1.41;1.41;1.41;1.41;1.41;2.09	5.71	5.71	0.89125	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.68201	0.2975	M	0.93939	3.475	0.80722	D	1	D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;0.982;0.993;1.0;0.978;0.989	D;D;D;D;D;B;B;D;B;B	0.79108	0.992;0.991;0.988;0.969;0.963;0.289;0.376;0.97;0.191;0.384	T	0.76650	-0.2881	10	0.87932	D	0	.	19.8484	0.96730	0.0:1.0:0.0:0.0	.	239;259;259;239;259;259;259;259;259;259	B7Z388;B7Z3V5;E7ENQ1;E7ESS2;O95819-4;O95819;E7EN19;G3XAA2;O95819-2;G5E948	.;.;.;.;.;M4K4_HUMAN;.;.;.;.	L	259;259;259;259;259;221;239	ENSP00000392830:S259L;ENSP00000313644:S259L;ENSP00000281111:S259L;ENSP00000389752:S259L;ENSP00000314363:S259L;ENSP00000409720:S221L;ENSP00000343658:S239L	ENSP00000313644:S259L	S	+	2	0	MAP4K4	101822715	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.776000	0.85560	2.684000	0.91462	0.655000	0.94253	TCG		MAP4K4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339839.1	NM_004834	
LRP1B	53353	hgsc.bcm.edu	37	2	141625386	141625386	+	Nonsense_Mutation	SNP	G	G	C			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr2:141625386G>C	ENST00000389484.3	-	27	5323	c.4352C>G	c.(4351-4353)tCa>tGa	p.S1451*		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1451					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		ATAGAGGGCTGAATAAATAGC	0.383										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)												0			2											73.0	77.0	76.0					2																	141625386		2202	4300	6502	141341856	SO:0001587	stop_gained	53353			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.4352C>G	2.37:g.141625386G>C	ENSP00000374135:p.Ser1451*	Somatic		Capture	Illumina HiSeq	Phase_I	141341856	Q8WY29|Q8WY30|Q8WY31	Nonsense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	G	51	18.016610	0.99897	.	.	ENSG00000168702	ENST00000389484;ENST00000544579;ENST00000434794	.	.	.	5.64	5.64	0.86602	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	.	19.6932	0.96010	0.0:0.0:1.0:0.0	.	.	.	.	X	1451;1389;596	.	ENSP00000374135:S1451X	S	-	2	0	LRP1B	141341856	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.744000	0.98853	2.664000	0.90586	0.655000	0.94253	TCA		LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
LRP2	4036	hgsc.bcm.edu	37	2	170026297	170026297	+	Silent	SNP	C	C	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr2:170026297C>T	ENST00000263816.3	-	60	11697	c.11412G>A	c.(11410-11412)caG>caA	p.Q3804Q		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	3804	LDL-receptor class A 33. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""""""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"""	CACTTGTACACTGAAAATATT	0.438																																																	0			2											151.0	125.0	134.0					2																	170026297		2203	4300	6503	169734543	SO:0001819	synonymous_variant	4036				CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"""Low density lipoprotein receptors"""	6694	protein-coding gene	gene with protein product	"""megalin"""	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.11412G>A	2.37:g.170026297C>T		Somatic		Capture	Illumina HiSeq	Phase_I	169734543	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1																																																																																				LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
LRP2	4036	hgsc.bcm.edu	37	2	170147488	170147488	+	Silent	SNP	A	A	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr2:170147488A>G	ENST00000263816.3	-	8	1074	c.789T>C	c.(787-789)gtT>gtC	p.V263V	LRP2_ENST00000443831.1_Silent_p.V263V	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	263					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""""""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"""	AACATTTATGAACATCATGAG	0.463																																																	0			2											111.0	109.0	109.0					2																	170147488		2203	4300	6503	169855734	SO:0001819	synonymous_variant	4036				CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"""Low density lipoprotein receptors"""	6694	protein-coding gene	gene with protein product	"""megalin"""	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.789T>C	2.37:g.170147488A>G		Somatic		Capture	Illumina HiSeq	Phase_I	169855734	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1																																																																																				LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
ZAK	51776	hgsc.bcm.edu	37	2	174034552	174034552	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr2:174034552T>C	ENST00000375213.3	+	3	257	c.179T>C	c.(178-180)cTc>cCc	p.L60P	MLTK_ENST00000431503.2_5'UTR|MLTK_ENST00000539448.1_Missense_Mutation_p.L60P|MLTK_ENST00000409176.2_Missense_Mutation_p.L60P|MLK7-AS1_ENST00000422703.1_RNA|MLK7-AS1_ENST00000419609.1_RNA|MLTK_ENST00000480606.1_3'UTR|MLTK_ENST00000338983.3_Missense_Mutation_p.L60P	NM_016653.2	NP_057737.2	Q9NYL2	MLTK_HUMAN		60	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell death (GO:0008219)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|DNA damage checkpoint (GO:0000077)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|response to radiation (GO:0009314)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)										CTCAGTGTCCTCAGTCACAGA	0.333																																																	0			2											139.0	134.0	136.0					2																	174034552		2203	4300	6503	173742798	SO:0001583	missense	51776																														ENST00000375213.3:c.179T>C	2.37:g.174034552T>C	ENSP00000364361:p.Leu60Pro	Somatic		Capture	Illumina HiSeq	Phase_I	173742798	B3KPG2|Q53SX1|Q580W8|Q59GY5|Q86YW8|Q9HCC4|Q9HCC5|Q9HDD2|Q9NYE9	Missense_Mutation	SNP	ENST00000375213.3	37	CCDS42777.1	.	.	.	.	.	.	.	.	.	.	T	19.37	3.814709	0.70912	.	.	ENSG00000091436	ENST00000539448;ENST00000409176;ENST00000338983;ENST00000375213;ENST00000422149	D;D;D;D;D	0.92149	-2.98;-2.98;-2.98;-2.98;-2.98	5.67	5.67	0.87782	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.96962	0.9008	M	0.92459	3.31	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.998;1.0;0.999;0.991	D	0.97896	1.0300	10	0.87932	D	0	.	15.5783	0.76410	0.0:0.0:0.0:1.0	.	60;60;60;60	Q9NYL2-2;Q9NYL2;D4Q8H0;Q9NYL2-3	.;MLTK_HUMAN;.;.	P	60	ENSP00000439414:L60P;ENSP00000387259:L60P;ENSP00000340257:L60P;ENSP00000364361:L60P;ENSP00000411923:L60P	ENSP00000340257:L60P	L	+	2	0	AC013461.1	173742798	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.334000	0.79224	2.152000	0.67230	0.455000	0.32223	CTC		MLTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255401.1		
TTN	7273	hgsc.bcm.edu	37	2	179585116	179585116	+	Missense_Mutation	SNP	G	G	C			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr2:179585116G>C	ENST00000591111.1	-	78	22646	c.22422C>G	c.(22420-22422)ttC>ttG	p.F7474L	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.F7791L|TTN_ENST00000460472.2_Intron|TTN_ENST00000342175.6_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.F6547L|TTN_ENST00000359218.5_Intron			Q8WZ42	TITIN_HUMAN	titin	13029					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ACAAACCTTTGAACTTGACAG	0.413																																																	0			2											139.0	131.0	133.0					2																	179585116		1900	4121	6021	179293361	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.22422C>G	2.37:g.179585116G>C	ENSP00000465570:p.Phe7474Leu	Somatic		Capture	Illumina HiSeq	Phase_I	179293361	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	12.58	1.979761	0.34942	.	.	ENSG00000155657	ENST00000342992	T	0.39406	1.08	5.91	5.03	0.67393	Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.20577	0.0495	N	0.02539	-0.55	0.80722	D	1	B	0.12013	0.005	B	0.12837	0.008	T	0.06338	-1.0832	9	0.87932	D	0	.	11.0129	0.47673	0.1414:0.0:0.8586:0.0	.	7474	Q8WZ42	TITIN_HUMAN	L	6547	ENSP00000343764:F6547L	ENSP00000343764:F6547L	F	-	3	2	TTN	179293361	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.055000	0.49916	1.498000	0.48600	0.650000	0.86243	TTC		TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
HECW2	57520	hgsc.bcm.edu	37	2	197298107	197298107	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr2:197298107C>T	ENST00000260983.3	-	2	223	c.41G>A	c.(40-42)cGt>cAt	p.R14H		NM_020760.1	NP_065811.1	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	14					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(24)|lung(45)|ovary(5)|pancreas(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	113						GGGATTTCGACGCCTCACAAA	0.557																																																	0			2											70.0	63.0	65.0					2																	197298107		2203	4300	6503	197006352	SO:0001583	missense	57520			AL390186	CCDS33354.1	2q32.3	2004-12-13			ENSG00000138411	ENSG00000138411			29853	protein-coding gene	gene with protein product						10718198, 12890487	Standard	NM_020760		Approved	KIAA1301, NEDL2	uc002utm.1	Q9P2P5	OTTHUMG00000154435	ENST00000260983.3:c.41G>A	2.37:g.197298107C>T	ENSP00000260983:p.Arg14His	Somatic		Capture	Illumina HiSeq	Phase_I	197006352	B8ZZB4|Q17RT5|Q68DF8|Q9NPS9	Missense_Mutation	SNP	ENST00000260983.3	37	CCDS33354.1	.	.	.	.	.	.	.	.	.	.	C	31	5.066800	0.93898	.	.	ENSG00000138411	ENST00000260983;ENST00000452031;ENST00000427457	T	0.58797	0.31	5.27	5.27	0.74061	.	0.067263	0.64402	D	0.000013	T	0.75391	0.3843	M	0.69823	2.125	0.54753	D	0.999988	D	0.89917	1.0	D	0.78314	0.991	T	0.72629	-0.4235	10	0.35671	T	0.21	.	19.0714	0.93138	0.0:1.0:0.0:0.0	.	14	Q9P2P5	HECW2_HUMAN	H	14	ENSP00000260983:R14H	ENSP00000260983:R14H	R	-	2	0	HECW2	197006352	1.000000	0.71417	0.997000	0.53966	0.931000	0.56810	7.127000	0.77210	2.736000	0.93811	0.561000	0.74099	CGT		HECW2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335199.3	NM_020760	
ABCA12	26154	hgsc.bcm.edu	37	2	215807721	215807721	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr2:215807721A>G	ENST00000272895.7	-	50	7583	c.7364T>C	c.(7363-7365)cTc>cCc	p.L2455P	AC072062.1_ENST00000607412.1_RNA|ABCA12_ENST00000389661.4_Missense_Mutation_p.L2137P	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	2455	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		CCTGGTACAGAGAGCTTCACA	0.383																																					Ovarian(66;664 1488 5121 34295)												0			2											123.0	105.0	111.0					2																	215807721		2203	4300	6503	215515966	SO:0001583	missense	26154			AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"""ATP binding cassette transporters / subfamily A"""	14637	protein-coding gene	gene with protein product		607800	"""ichthyosis congenita II, lamellar ichthyosis B"""	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.7364T>C	2.37:g.215807721A>G	ENSP00000272895:p.Leu2455Pro	Somatic		Capture	Illumina HiSeq	Phase_I	215515966	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	37	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.528545	0.85706	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	D;D	0.98028	-4.67;-4.67	5.65	5.65	0.86999	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.000000	0.56097	D	0.000033	D	0.99230	0.9732	H	0.97564	4.03	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.98908	1.0779	10	0.87932	D	0	.	15.827	0.78718	1.0:0.0:0.0:0.0	.	2455;2137	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	P	2455;2137	ENSP00000272895:L2455P;ENSP00000374312:L2137P	ENSP00000272895:L2455P	L	-	2	0	ABCA12	215515966	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.971000	0.93419	2.276000	0.75962	0.528000	0.53228	CTC		ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076	
SPATA6L	55064	hgsc.bcm.edu	37	9	4661998	4661998	+	Silent	SNP	A	A	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr9:4661998A>G	ENST00000454239.2	-	3	323	c.78T>C	c.(76-78)gaT>gaC	p.D26D	SPATA6L_ENST00000223517.5_5'UTR|SPATA6L_ENST00000381895.5_5'UTR|PPAPDC2_ENST00000381883.2_5'Flank|SPATA6L_ENST00000381890.5_Silent_p.D26D|SPATA6L_ENST00000475086.1_Silent_p.D26D			Q8N4H0	SPA6L_HUMAN	spermatogenesis associated 6-like	26																	CGAGGTACACATCTTGTTTGC	0.433											OREG0019084	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					0			9											84.0	78.0	80.0					9																	4661998		1882	4113	5995	4651998	SO:0001819	synonymous_variant	55064			AK000920	CCDS43785.1, CCDS43785.2	9p24.2	2012-03-15	2012-03-15	2012-03-15	ENSG00000106686	ENSG00000106686			25472	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 68"""	C9orf68			Standard	NM_001039395		Approved	FLJ10058	uc011llz.2	Q8N4H0	OTTHUMG00000019469	ENST00000454239.2:c.78T>C	9.37:g.4661998A>G		Somatic	620	Capture	Illumina HiSeq	Phase_I	4651998	B4DIY4|Q5JVJ5|Q8IY90	Silent	SNP	ENST00000454239.2	37																																																																																					SPATA6L-202	KNOWN	basic	protein_coding	protein_coding		NM_017985	
TLN1	7094	hgsc.bcm.edu	37	9	35703799	35703799	+	Silent	SNP	A	A	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr9:35703799A>G	ENST00000314888.9	-	47	6683	c.6330T>C	c.(6328-6330)gcT>gcC	p.A2110A	TLN1_ENST00000464379.1_5'UTR|TLN1_ENST00000540444.1_Silent_p.A2004A	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	2110					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			GCTGCCACACAGCAGGGTCAT	0.493																																																	0			9											96.0	89.0	91.0					9																	35703799		2203	4300	6503	35693799	SO:0001819	synonymous_variant	7094			AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.6330T>C	9.37:g.35703799A>G		Somatic		Capture	Illumina HiSeq	Phase_I	35693799	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Silent	SNP	ENST00000314888.9	37	CCDS35009.1																																																																																				TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289	
TNFSF8	944	hgsc.bcm.edu	37	9	117666272	117666272	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr9:117666272T>C	ENST00000223795.2	-	4	757	c.644A>G	c.(643-645)gAt>gGt	p.D215G	TNFSF8_ENST00000474301.1_Intron	NM_001244.3	NP_001235.1	P32971	TNFL8_HUMAN	tumor necrosis factor (ligand) superfamily, member 8	215					apoptotic process (GO:0006915)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|defense response to Gram-positive bacterium (GO:0050830)|immune response (GO:0006955)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	receptor binding (GO:0005102)			endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|skin(3)|urinary_tract(1)	12						GGTGCTTGTATCTATGTACTG	0.418																																																	0			9											248.0	226.0	233.0					9																	117666272		2203	4300	6503	116706093	SO:0001583	missense	944			L09753	CCDS6810.1, CCDS75884.1	9q33	2008-02-05			ENSG00000106952	ENSG00000106952		"""Tumor necrosis factor (ligand) superfamily"", ""CD molecules"""	11938	protein-coding gene	gene with protein product		603875		CD30LG		8391931, 9349718	Standard	NM_001244		Approved	CD153	uc004bji.2	P32971	OTTHUMG00000021025	ENST00000223795.2:c.644A>G	9.37:g.117666272T>C	ENSP00000223795:p.Asp215Gly	Somatic		Capture	Illumina HiSeq	Phase_I	116706093	O43404	Missense_Mutation	SNP	ENST00000223795.2	37	CCDS6810.1	.	.	.	.	.	.	.	.	.	.	T	14.15	2.448623	0.43531	.	.	ENSG00000106952	ENST00000223795	D	0.95272	-3.66	5.78	5.78	0.91487	Tumour necrosis factor (3);Tumour necrosis factor-like (2);	0.104923	0.46442	D	0.000281	D	0.94112	0.8112	L	0.27053	0.805	0.38783	D	0.95481	D	0.63046	0.992	P	0.61477	0.889	D	0.95188	0.8305	10	0.56958	D	0.05	-13.2654	13.6253	0.62161	0.0:0.0:0.0:1.0	.	215	P32971	TNFL8_HUMAN	G	215	ENSP00000223795:D215G	ENSP00000223795:D215G	D	-	2	0	TNFSF8	116706093	1.000000	0.71417	1.000000	0.80357	0.111000	0.19643	4.057000	0.57455	2.203000	0.70933	0.533000	0.62120	GAT		TNFSF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055464.1		
TOR1A	1861	hgsc.bcm.edu	37	9	132576475	132576475	+	Missense_Mutation	SNP	C	C	T	rs17849354		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr9:132576475C>T	ENST00000351698.4	-	5	823	c.775G>A	c.(775-777)Gac>Aac	p.D259N		NM_000113.2	NP_000104.1	O14656	TOR1A_HUMAN	torsin family 1, member A (torsin A)	259	Interaction with KLC1.			D -> H (in Ref. 3; AAP35577 and 5; AAH00674). {ECO:0000305}.	ATP catabolic process (GO:0006200)|cell adhesion (GO:0007155)|chaperone mediated protein folding requiring cofactor (GO:0051085)|chaperone-mediated protein folding (GO:0061077)|chaperone-mediated protein transport (GO:0072321)|ER-associated misfolded protein catabolic process (GO:0071712)|intermediate filament cytoskeleton organization (GO:0045104)|neuron projection development (GO:0031175)|nuclear envelope organization (GO:0006998)|nuclear membrane organization (GO:0071763)|organelle organization (GO:0006996)|positive regulation of synaptic vesicle endocytosis (GO:1900244)|protein deneddylation (GO:0000338)|protein homooligomerization (GO:0051260)|protein localization to nucleus (GO:0034504)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of protein localization to cell surface (GO:2000008)|response to oxidative stress (GO:0006979)|synaptic vesicle transport (GO:0048489)|wound healing, spreading of cells (GO:0044319)	cell junction (GO:0030054)|cytoplasmic vesicle membrane (GO:0030659)|cytoskeleton (GO:0005856)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|extrinsic component of endoplasmic reticulum membrane (GO:0042406)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|secretory granule (GO:0030141)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cytoskeletal protein binding (GO:0008092)|kinesin binding (GO:0019894)|unfolded protein binding (GO:0051082)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(5)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	20		Ovarian(14;0.00556)				AGGTTCCGGTCAATTAAGCTG	0.493																																																	0			9											93.0	89.0	90.0					9																	132576475		2203	4300	6503	131616296	SO:0001583	missense	1861			AF007871	CCDS6930.1	9q32-q34	2008-07-21	2004-11-24	2004-11-26	ENSG00000136827	ENSG00000136827			3098	protein-coding gene	gene with protein product		605204	"""dystonia 1, torsion (autosomal dominant; torsin A)"""	DYT1		10644435	Standard	NM_000113		Approved	DQ2	uc004byl.3	O14656	OTTHUMG00000020794	ENST00000351698.4:c.775G>A	9.37:g.132576475C>T	ENSP00000345719:p.Asp259Asn	Somatic		Capture	Illumina HiSeq	Phase_I	131616296	B2RB58|Q53Y64|Q96CA0	Missense_Mutation	SNP	ENST00000351698.4	37	CCDS6930.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.634665	0.87660	.	.	ENSG00000136827	ENST00000427355;ENST00000351698	T	0.29655	1.56	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	T	0.51907	0.1702	M	0.73753	2.245	0.58432	D	0.999999	D	0.59357	0.985	P	0.57468	0.821	T	0.56908	-0.7901	10	0.59425	D	0.04	-11.0018	17.2642	0.87081	0.0:1.0:0.0:0.0	.	259	O14656	TOR1A_HUMAN	N	228;259	ENSP00000345719:D259N	ENSP00000345719:D259N	D	-	1	0	TOR1A	131616296	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	5.690000	0.68241	2.297000	0.77311	0.561000	0.74099	GAC		TOR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054611.1	NM_000113	
NUP214	8021	hgsc.bcm.edu	37	9	134098264	134098264	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr9:134098264G>A	ENST00000359428.5	+	32	5993	c.5849G>A	c.(5848-5850)gGa>gAa	p.G1950E	NUP214_ENST00000483497.2_Missense_Mutation_p.G776E|NUP214_ENST00000451030.1_Missense_Mutation_p.G1951E|NUP214_ENST00000411637.2_Missense_Mutation_p.G1940E			P35658	NU214_HUMAN	nucleoporin 214kDa	1950	11 X 3 AA approximate repeats.|11 X 5 AA approximate repeats.|18 X 4 AA approximate repeats.|Pro/Ser/Thr-rich.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)			NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		TTCAGCTCTGGAGGAGGAAGT	0.443			T	"""DEK, SET, ABL1"""	"""AML, T-ALL"""																																Pancreas(4;24 48 25510 30394 32571)			Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	0			9											120.0	111.0	114.0					9																	134098264		2203	4300	6503	133088085	SO:0001583	missense	8021			X64228	CCDS6940.1	9q34	2008-07-21	2002-08-29		ENSG00000126883	ENSG00000126883			8064	protein-coding gene	gene with protein product	"""nuclear pore complex protein Nup214"", ""CAN protein, putative oncogene"""	114350	"""nucleoporin 214kD (CAIN)"""			8108440, 2370860	Standard	NM_005085		Approved	CAIN, CAN, D9S46E, N214	uc004cag.3	P35658	OTTHUMG00000020816	ENST00000359428.5:c.5849G>A	9.37:g.134098264G>A	ENSP00000352400:p.Gly1950Glu	Somatic		Capture	Illumina HiSeq	Phase_I	133088085	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Missense_Mutation	SNP	ENST00000359428.5	37	CCDS6940.1	.	.	.	.	.	.	.	.	.	.	G	31	5.070750	0.93950	.	.	ENSG00000126883	ENST00000359428;ENST00000411637;ENST00000451030;ENST00000541375;ENST00000540899;ENST00000438605;ENST00000483497	T;T;T;T	0.69435	0.1;0.12;0.11;-0.4	5.71	5.71	0.89125	.	0.000000	0.40554	N	0.001076	T	0.67429	0.2892	N	0.08118	0	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	T	0.72265	-0.4344	10	0.45353	T	0.12	-12.9455	16.9975	0.86372	0.0:0.0:1.0:0.0	.	776;1544;1940;1950	B7ZAV2;Q5JUP9;P35658-4;P35658	.;.;.;NU214_HUMAN	E	1950;1940;1951;1929;1544;1379;776	ENSP00000352400:G1950E;ENSP00000396576:G1940E;ENSP00000405014:G1951E;ENSP00000436793:G776E	ENSP00000352400:G1950E	G	+	2	0	NUP214	133088085	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.060000	0.93907	2.700000	0.92200	0.655000	0.94253	GGA		NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085	
LRCH1	23143	hgsc.bcm.edu	37	13	47260086	47260086	+	Silent	SNP	A	A	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr13:47260086A>G	ENST00000389798.3	+	5	929	c.732A>G	c.(730-732)aaA>aaG	p.K244K	LRCH1_ENST00000311191.6_Silent_p.K244K|LRCH1_ENST00000389797.3_Silent_p.K244K	NM_015116.2	NP_055931	Q9Y2L9	LRCH1_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 1	244										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26		all_lung(13;5.61e-07)|Lung NSC(96;0.000117)|Breast(56;0.000141)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000123)		CCTGCAACAAAGTGCTCGTGA	0.368																																																	0			13											61.0	56.0	58.0					13																	47260086		2203	4300	6503	46158087	SO:0001819	synonymous_variant	23143			AB023233	CCDS31972.1, CCDS53865.1, CCDS53866.1	13q14.11	2008-02-05	2004-05-27	2004-05-28	ENSG00000136141	ENSG00000136141			20309	protein-coding gene	gene with protein product		610368	"""calponin homology (CH) domain containing 1"""	CHDC1		10231032	Standard	NM_015116		Approved	KIAA1016	uc001vbk.3	Q9Y2L9	OTTHUMG00000016877	ENST00000389798.3:c.732A>G	13.37:g.47260086A>G		Somatic		Capture	Illumina HiSeq	Phase_I	46158087	B7ZLL5|F8W6F0|Q17R43|Q2KHR1|Q5TBU9|Q7Z5F6|Q7Z5F7	Silent	SNP	ENST00000389798.3	37	CCDS31972.1																																																																																				LRCH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044824.2	NM_015116	
HTR2A	3356	hgsc.bcm.edu	37	13	47466659	47466659	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr13:47466659G>A	ENST00000378688.4	-	2	610	c.479C>T	c.(478-480)aCg>aTg	p.T160M	HTR2A_ENST00000543956.1_Missense_Mutation_p.T76M|HTR2A_ENST00000542664.1_Missense_Mutation_p.T160M			P28223	5HT2A_HUMAN	5-hydroxytryptamine (serotonin) receptor 2A, G protein-coupled	160	Agonist binding. {ECO:0000250}.				activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|artery smooth muscle contraction (GO:0014824)|behavioral response to cocaine (GO:0048148)|cell death (GO:0008219)|cellular calcium ion homeostasis (GO:0006874)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|memory (GO:0007613)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phospholipase C-activating serotonin receptor signaling pathway (GO:0007208)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of glycolytic process (GO:0045821)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|positive regulation of vasoconstriction (GO:0045907)|protein localization to cytoskeleton (GO:0044380)|regulation of behavior (GO:0050795)|regulation of dopamine secretion (GO:0014059)|regulation of hormone secretion (GO:0046883)|release of sequestered calcium ion into cytosol (GO:0051209)|response to drug (GO:0042493)|serotonin receptor signaling pathway (GO:0007210)|sleep (GO:0030431)|synaptic transmission (GO:0007268)|temperature homeostasis (GO:0001659)|urinary bladder smooth muscle contraction (GO:0014832)	cell body fiber (GO:0070852)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding (GO:0071886)|drug binding (GO:0008144)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|liver(1)|lung(10)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36		all_lung(13;7.2e-10)|Lung NSC(96;3.77e-07)|Breast(56;2.06e-05)|Prostate(109;0.00116)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|Myeloproliferative disorder(33;0.0333)		GBM - Glioblastoma multiforme(144;4.67e-05)|COAD - Colon adenocarcinoma(199;0.224)	Acepromazine(DB01614)|Amisulpride(DB06288)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinitapride(DB08810)|Cisapride(DB00604)|Clomipramine(DB01242)|Clozapine(DB00363)|Cyclobenzaprine(DB00924)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Donepezil(DB00843)|Doxepin(DB01142)|Epinastine(DB00751)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Flupentixol(DB00875)|Fluspirilene(DB04842)|Haloperidol(DB00502)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Mesoridazine(DB00933)|Methotrimeprazine(DB01403)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Molindone(DB01618)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paliperidone(DB01267)|Paroxetine(DB00715)|Pergolide(DB01186)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Sertindole(DB06144)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Thiothixene(DB01623)|Trazodone(DB00656)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246)	GATGGAGGCCGTGGAGAAGAG	0.572																																																	0			13											187.0	178.0	181.0					13																	47466659		2203	4300	6503	46364660	SO:0001583	missense	3356			X57830	CCDS9405.1, CCDS53867.1	13q14-q21	2012-08-08	2012-02-03		ENSG00000102468	ENSG00000102468		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5293	protein-coding gene	gene with protein product		182135	"""5-hydroxytryptamine (serotonin) receptor 2A"""	HTR2		8035173	Standard	NM_000621		Approved	5-HT2A	uc010acr.4	P28223	OTTHUMG00000016881	ENST00000378688.4:c.479C>T	13.37:g.47466659G>A	ENSP00000367959:p.Thr160Met	Somatic		Capture	Illumina HiSeq	Phase_I	46364660	B2RAC5|B4DZ79|F5GWE8|Q5T8C0	Missense_Mutation	SNP	ENST00000378688.4	37	CCDS9405.1	.	.	.	.	.	.	.	.	.	.	G	34	5.291601	0.95546	.	.	ENSG00000102468	ENST00000378688;ENST00000543956;ENST00000542664	T;T;T	0.74421	2.43;-0.84;2.43	6.16	6.16	0.99307	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.91925	0.7443	H	0.97240	3.965	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.93711	0.7024	10	0.87932	D	0	.	19.848	0.96722	0.0:0.0:1.0:0.0	.	76;160	F5GWE8;P28223	.;5HT2A_HUMAN	M	160;76;160	ENSP00000367959:T160M;ENSP00000441861:T76M;ENSP00000437737:T160M	ENSP00000367959:T160M	T	-	2	0	HTR2A	46364660	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.860000	0.99555	2.937000	0.99478	0.650000	0.86243	ACG		HTR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044835.3	NM_000621	
RB1	5925	hgsc.bcm.edu	37	13	49027203	49027203	+	Silent	SNP	T	T	C	rs145310579	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr13:49027203T>C	ENST00000267163.4	+	18	1908	c.1770T>C	c.(1768-1770)tgT>tgC	p.C590C		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	590	Pocket; binds T and E1A.|Spacer.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(10)|p.C590C(1)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	AATCTGCTTGTCCTCTTAATC	0.328		6	"""D, Mis, N, F, S"""		"""retinoblastoma, sarcoma, breast, small cell lung"""	"""retinoblastoma, sarcoma, breast, small cell lung"""			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			T|||	2	0.000399361	0.0	0.0014	5008	,	,		19059	0.0		0.001	False		,,,				2504	0.0						yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"""L, E, M, O"""	26	Whole gene deletion(15)|Unknown(10)|Substitution - coding silent(1)	bone(10)|haematopoietic_and_lymphoid_tissue(4)|breast(4)|adrenal_gland(1)|eye(1)|soft_tissue(1)|central_nervous_system(1)|endometrium(1)|urinary_tract(1)|lung(1)|liver(1)	13						T		0,4406		0,0,2203	121.0	113.0	116.0		1770	3.4	1.0	13	dbSNP_134	116	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	RB1	NM_000321.2		0,3,6500	CC,CT,TT		0.0349,0.0,0.0231		590/929	49027203	3,13003	2203	4300	6503	47925204	SO:0001819	synonymous_variant	5925	Familial Cancer Database		M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"""Endogenous ligands"""	9884	protein-coding gene	gene with protein product	"""prepro-retinoblastoma-associated protein"", ""protein phosphatase 1, regulatory subunit 130"""	614041	"""osteosarcoma"""	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.1770T>C	13.37:g.49027203T>C		Somatic		Capture	Illumina HiSeq	Phase_I	47925204	A8K5E3|P78499|Q5VW46|Q8IZL4	Silent	SNP	ENST00000267163.4	37	CCDS31973.1																																																																																				RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1		
KPNA3	3839	hgsc.bcm.edu	37	13	50307151	50307151	+	Missense_Mutation	SNP	C	C	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr13:50307151C>G	ENST00000261667.3	-	3	560	c.146G>C	c.(145-147)aGa>aCa	p.R49T		NM_002267.3	NP_002258.2	O00505	IMA4_HUMAN	karyopherin alpha 3 (importin alpha 4)	49	IBB. {ECO:0000255|PROSITE- ProRule:PRU00561}.				cytokine-mediated signaling pathway (GO:0019221)|NLS-bearing protein import into nucleus (GO:0006607)|protein complex assembly (GO:0006461)|viral entry into host cell (GO:0046718)|viral penetration into host nucleus (GO:0075732)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)	nuclear localization sequence binding (GO:0008139)|protein transporter activity (GO:0008565)			cervix(1)|endometrium(3)|large_intestine(4)|liver(1)|lung(5)|ovary(1)|skin(1)|stomach(1)|urinary_tract(4)	21		Lung NSC(96;2.46e-05)|Breast(56;9.7e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;1.42e-09)		GGGAACATTTCTCTTTTTCAA	0.284																																																	0			13											122.0	123.0	122.0					13																	50307151		2202	4295	6497	49205152	SO:0001583	missense	3839			D89618	CCDS9421.1	13q14.3	2013-02-14			ENSG00000102753	ENSG00000102753		"""Importins"", ""Armadillo repeat containing"""	6396	protein-coding gene	gene with protein product		601892				9154134, 9435235	Standard	NM_002267		Approved	SRP1gamma, SRP4, hSRP1, IPOA4	uc001vdj.2	O00505	OTTHUMG00000016922	ENST00000261667.3:c.146G>C	13.37:g.50307151C>G	ENSP00000261667:p.Arg49Thr	Somatic		Capture	Illumina HiSeq	Phase_I	49205152	O00191|O43195|Q5JVM9|Q96AA7	Missense_Mutation	SNP	ENST00000261667.3	37	CCDS9421.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.354162	0.82243	.	.	ENSG00000102753	ENST00000261667	T	0.78126	-1.15	5.77	5.77	0.91146	Importin-alpha, importin-beta-binding domain (2);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.91744	0.7389	M	0.94101	3.495	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93135	0.6536	10	0.87932	D	0	-12.7609	19.9795	0.97321	0.0:1.0:0.0:0.0	.	49	O00505	IMA3_HUMAN	T	49	ENSP00000261667:R49T	ENSP00000261667:R49T	R	-	2	0	KPNA3	49205152	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.738000	0.68613	2.720000	0.93068	0.650000	0.86243	AGA		KPNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044939.2	NM_002267	
CARKD	55739	hgsc.bcm.edu	37	13	111277575	111277575	+	Silent	SNP	C	C	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr13:111277575C>T	ENST00000309957.2	+	4	350	c.336C>T	c.(334-336)gcC>gcT	p.A112A	CARKD_ENST00000458711.2_Intron|CARKD_ENST00000397191.4_Intron|CARKD_ENST00000470164.2_Intron|CARKD_ENST00000424185.2_Intron	NM_001242881.1|NM_018210.3	NP_001229810.1|NP_060680.2			carbohydrate kinase domain containing											NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)	15						CCAGTGCGGCCGCACCTGTGA	0.627																																																	0			13											83.0	69.0	74.0					13																	111277575		2203	4300	6503	110075576	SO:0001819	synonymous_variant	55739			AF151071	CCDS9513.1, CCDS55903.1	13q34	2008-12-19			ENSG00000213995	ENSG00000213995			25576	protein-coding gene	gene with protein product		615910					Standard	NM_018210		Approved	LP3298, FLJ10769	uc001vrc.3	Q8IW45	OTTHUMG00000017345	ENST00000309957.2:c.336C>T	13.37:g.111277575C>T		Somatic		Capture	Illumina HiSeq	Phase_I	110075576		Silent	SNP	ENST00000309957.2	37	CCDS9513.1																																																																																				CARKD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045764.1	NM_018210	
GTPBP4	23560	hgsc.bcm.edu	37	10	1042096	1042096	+	Missense_Mutation	SNP	G	G	A	rs374244248		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr10:1042096G>A	ENST00000360803.4	+	4	456	c.374G>A	c.(373-375)cGc>cAc	p.R125H	GTPBP4_ENST00000491635.1_3'UTR|GTPBP4_ENST00000545048.1_Missense_Mutation_p.R78H|GTPBP4_ENST00000538293.1_Missense_Mutation_p.R9H	NM_012341.2	NP_036473.2	Q9BZE4	NOG1_HUMAN	GTP binding protein 4	125					GTP catabolic process (GO:0006184)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of collagen binding (GO:0033342)|negative regulation of DNA replication (GO:0008156)|negative regulation of protein ubiquitination (GO:0031397)|osteoblast differentiation (GO:0001649)|protein stabilization (GO:0050821)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|ribosome biogenesis (GO:0042254)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)|skin(1)	21		all_epithelial(10;0.107)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.0814)	Epithelial(11;0.0513)|all cancers(11;0.135)|OV - Ovarian serous cystadenocarcinoma(14;0.173)		TCTCTCTACCGCTGCAAACAG	0.433																																																	0			10							HIS/ARG	0,4406		0,0,2203	77.0	59.0	65.0		374	5.5	1.0	10		65	1,8599	1.2+/-3.3	0,1,4299	no	missense	GTPBP4	NM_012341.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	125/635	1042096	1,13005	2203	4300	6503	1032096	SO:0001583	missense	23560			AK001548	CCDS31132.1	10p15-p14	2007-07-27			ENSG00000107937	ENSG00000107937			21535	protein-coding gene	gene with protein product	"""G protein-binding protein CRFG"", "" GTP-binding protein"""					11316846	Standard	NM_012341		Approved	CRFG, NGB, FLJ10690, FLJ10686, NOG1	uc001ift.3	Q9BZE4	OTTHUMG00000017538	ENST00000360803.4:c.374G>A	10.37:g.1042096G>A	ENSP00000354040:p.Arg125His	Somatic		Capture	Illumina HiSeq	Phase_I	1032096	B3KMC5|B4DY13|B7Z7A3|O95446|Q5T3R8|Q9NVJ8	Missense_Mutation	SNP	ENST00000360803.4	37	CCDS31132.1	.	.	.	.	.	.	.	.	.	.	g	29.2	4.989192	0.93106	0.0	1.16E-4	ENSG00000107937	ENST00000360803;ENST00000538293;ENST00000360059;ENST00000545048	T;T;T;T	0.40756	2.53;1.02;2.53;2.53	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.75170	0.3813	M	0.93763	3.455	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.81938	-0.0704	10	0.87932	D	0	-1.384	19.4919	0.95054	0.0:0.0:1.0:0.0	.	125	Q9BZE4	NOG1_HUMAN	H	125;9;78;78	ENSP00000354040:R125H;ENSP00000444277:R9H;ENSP00000353168:R78H;ENSP00000445473:R78H	ENSP00000353168:R78H	R	+	2	0	GTPBP4	1032096	1.000000	0.71417	1.000000	0.80357	0.637000	0.38172	9.595000	0.98260	2.615000	0.88500	0.550000	0.68814	CGC		GTPBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046412.1	NM_012341	
UCMA	221044	hgsc.bcm.edu	37	10	13276241	13276241	+	Silent	SNP	G	G	A	rs187657704	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr10:13276241G>A	ENST00000378681.3	-	1	90	c.18C>T	c.(16-18)gcC>gcT	p.A6A	UCMA_ENST00000463405.2_Silent_p.A6A	NM_145314.1	NP_660357.2	Q8WVF2	UCMA_HUMAN	upper zone of growth plate and cartilage matrix associated	6					negative regulation of osteoblast differentiation (GO:0045668)	aggresome (GO:0016235)|extracellular space (GO:0005615)|perinuclear region of cytoplasm (GO:0048471)|proteinaceous extracellular matrix (GO:0005578)				breast(2)|endometrium(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)	9						ACAGCAGGACGGCCTGTCTCC	0.582													G|||	2	0.000399361	0.0	0.0	5008	,	,		15154	0.001		0.001	False		,,,				2504	0.0																0			10											77.0	59.0	65.0					10																	13276241		2203	4300	6503	13316247	SO:0001819	synonymous_variant	221044			BC018068	CCDS31147.1	10p13	2009-03-25	2009-03-25	2009-03-25	ENSG00000165623	ENSG00000165623			25205	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 49"""	C10orf49		12477932	Standard	NM_145314		Approved		uc001imd.3	Q8WVF2	OTTHUMG00000017692	ENST00000378681.3:c.18C>T	10.37:g.13276241G>A		Somatic		Capture	Illumina HiSeq	Phase_I	13316247		Silent	SNP	ENST00000378681.3	37	CCDS31147.1																																																																																				UCMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046843.2	NM_145314	
CHAT	1103	hgsc.bcm.edu	37	10	50835688	50835688	+	Missense_Mutation	SNP	G	G	A	rs200176236		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr10:50835688G>A	ENST00000337653.2	+	7	1121	c.968G>A	c.(967-969)cGt>cAt	p.R323H	CHAT_ENST00000339797.1_Missense_Mutation_p.R205H|CHAT_ENST00000395562.2_Missense_Mutation_p.R241H|CHAT_ENST00000455728.2_Missense_Mutation_p.R205H|CHAT_ENST00000351556.3_Missense_Mutation_p.R205H|CHAT_ENST00000395559.2_Missense_Mutation_p.R205H	NM_001142929.1|NM_020549.4	NP_001136401.1|NP_065574	P28329	CLAT_HUMAN	choline O-acetyltransferase	323					adult walking behavior (GO:0007628)|dendrite development (GO:0016358)|establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|rhythmic behavior (GO:0007622)|rhythmic excitation (GO:0043179)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	choline O-acetyltransferase activity (GO:0004102)	p.R323H(2)		central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(11)|lung(34)|prostate(3)|urinary_tract(1)	56		all_neural(218;0.107)		GBM - Glioblastoma multiforme(2;0.000585)	Choline(DB00122)|Nicotine(DB00184)	AATTTCCGCCGTCTCAGTGAG	0.512																																																	2	Substitution - Missense(2)	prostate(1)|central_nervous_system(1)	10											216.0	182.0	194.0					10																	50835688		2203	4300	6503	50505694	SO:0001583	missense	10044			AF305907	CCDS7232.1, CCDS7233.1, CCDS44389.1	10q11.2	2010-05-11	2010-05-11		ENSG00000070748	ENSG00000070748	2.3.1.6		1912	protein-coding gene	gene with protein product		118490	"""choline acetyltransferase"""			1840566	Standard	NM_020984		Approved		uc001jhz.2	P28329	OTTHUMG00000018198	ENST00000337653.2:c.968G>A	10.37:g.50835688G>A	ENSP00000337103:p.Arg323His	Somatic		Capture	Illumina HiSeq	Phase_I	50505694	A2BDF4|A2BDF5|Q16488|Q9BQ23|Q9BQ35|Q9BQE1	Missense_Mutation	SNP	ENST00000337653.2	37	CCDS7232.1	.	.	.	.	.	.	.	.	.	.	G	34	5.387473	0.95988	.	.	ENSG00000070748	ENST00000339797;ENST00000351556;ENST00000395559;ENST00000337653;ENST00000395562;ENST00000455728	T;T;T;T;T;T	0.80738	-1.41;-1.41;-1.41;-1.41;-1.41;-1.41	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	D	0.88952	0.6577	M	0.69248	2.105	0.80722	D	1	D;D	0.89917	0.986;1.0	B;D	0.72338	0.37;0.977	D	0.87755	0.2594	10	0.44086	T	0.13	-10.1192	19.6873	0.95984	0.0:0.0:1.0:0.0	.	205;323	F8W8I2;P28329	.;CLAT_HUMAN	H	205;205;205;323;241;205	ENSP00000343486:R205H;ENSP00000345878:R205H;ENSP00000378926:R205H;ENSP00000337103:R323H;ENSP00000378929:R241H;ENSP00000390521:R205H	ENSP00000337103:R323H	R	+	2	0	CHAT	50505694	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.628000	0.83189	2.647000	0.89833	0.579000	0.79373	CGT		CHAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047997.1	NM_020549	
PTEN	5728	hgsc.bcm.edu	37	10	89624271	89624271	+	Silent	SNP	A	A	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr10:89624271A>G	ENST00000371953.3	+	1	1402	c.45A>G	c.(43-45)agA>agG	p.R15R	KLLN_ENST00000445946.3_5'Flank	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	15	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.		R -> S (in glioma). {ECO:0000269|PubMed:9090379}.		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.?(13)|p.R15S(3)|p.R15fs*23(1)|p.R14fs*26(1)|p.R15fs*28(1)|p.Y16fs*27(1)|p.R15fs*9(1)|p.N12fs*6(1)|p.R14_D22del(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)		ACAAAAGGAGATATCAAGAGG	0.478		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"""	60	Whole gene deletion(37)|Unknown(13)|Deletion - Frameshift(4)|Substitution - Missense(3)|Insertion - Frameshift(2)|Deletion - In frame(1)	central_nervous_system(14)|prostate(14)|skin(7)|lung(6)|endometrium(3)|ovary(3)|breast(3)|haematopoietic_and_lymphoid_tissue(2)|bone(2)|biliary_tract(1)|stomach(1)|soft_tissue(1)|large_intestine(1)|urinary_tract(1)|kidney(1)	10											186.0	177.0	180.0					10																	89624271		2203	4300	6503	89614251	SO:0001819	synonymous_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.45A>G	10.37:g.89624271A>G		Somatic		Capture	Illumina HiSeq	Phase_I	89614251	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Silent	SNP	ENST00000371953.3	37	CCDS31238.1																																																																																				PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314	
MKI67	4288	hgsc.bcm.edu	37	10	129903302	129903302	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr10:129903302T>C	ENST00000368654.3	-	13	7177	c.6802A>G	c.(6802-6804)Aca>Gca	p.T2268A	MKI67_ENST00000368653.3_Missense_Mutation_p.T1908A	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	2268	16 X 122 AA approximate repeats.				cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				GGTTTGGGTGTGTCCATAGCT	0.473																																																	0			10											301.0	273.0	282.0					10																	129903302		2203	4300	6503	129793292	SO:0001583	missense	4288			X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 105"""	176741	"""antigen identified by monoclonal antibody Ki-67"""			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.6802A>G	10.37:g.129903302T>C	ENSP00000357643:p.Thr2268Ala	Somatic		Capture	Illumina HiSeq	Phase_I	129793292	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	T	12.82	2.053516	0.36181	.	.	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.03065	4.06;4.06	2.91	0.477	0.16784	.	0.419884	0.17486	N	0.172501	T	0.06325	0.0163	M	0.63843	1.955	0.09310	N	1	P;D;D	0.55800	0.762;0.961;0.973	B;P;P	0.56163	0.348;0.793;0.754	T	0.22977	-1.0201	10	0.08599	T	0.76	.	2.4224	0.04451	0.3502:0.0:0.21:0.4398	.	2267;1908;2268	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	A	2268;1908;2267	ENSP00000357643:T2268A;ENSP00000357642:T1908A	ENSP00000357642:T1908A	T	-	1	0	MKI67	129793292	0.000000	0.05858	0.002000	0.10522	0.005000	0.04900	-1.759000	0.01808	0.301000	0.22738	0.533000	0.62120	ACA		MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
RIOK2	55781	hgsc.bcm.edu	37	5	96507042	96507042	+	Missense_Mutation	SNP	A	A	G	rs147608663		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr5:96507042A>G	ENST00000283109.3	-	6	715	c.647T>C	c.(646-648)aTt>aCt	p.I216T	RIOK2_ENST00000508447.1_Missense_Mutation_p.I216T|CTD-2215E18.1_ENST00000509481.1_Intron	NM_018343.2	NP_060813.2	Q9BVS4	RIOK2_HUMAN	RIO kinase 2	216			I -> T (in a renal clear cell carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.				ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.I216T(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(9)|pancreas(1)|prostate(1)|urinary_tract(2)	23		all_cancers(142;0.000125)|all_epithelial(76;8.48e-07)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0676)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0657)		AAGTTTGACAATTAGTTCCAT	0.338																																																	1	Substitution - Missense(1)	kidney(1)	5						A	THR/ILE,THR/ILE	3,4403	6.2+/-15.9	0,3,2200	106.0	98.0	101.0		647,647	5.1	1.0	5	dbSNP_134	101	0,8600		0,0,4300	no	missense,missense	RIOK2	NM_001159749.1,NM_018343.2	89,89	0,3,6500	GG,GA,AA		0.0,0.0681,0.0231	probably-damaging,probably-damaging	216/475,216/553	96507042	3,13003	2203	4300	6503	96532798	SO:0001583	missense	55781			AK002021	CCDS4089.1, CCDS54884.1	5q14	2012-12-10	2012-12-10		ENSG00000058729	ENSG00000058729			18999	protein-coding gene	gene with protein product			"""RIO kinase 2 (yeast)"""				Standard	NM_018343		Approved	FLJ11159	uc003kmz.3	Q9BVS4	OTTHUMG00000128723	ENST00000283109.3:c.647T>C	5.37:g.96507042A>G	ENSP00000283109:p.Ile216Thr	Somatic		Capture	Illumina HiSeq	Phase_I	96532798	D6RDI3|Q9NUT0	Missense_Mutation	SNP	ENST00000283109.3	37	CCDS4089.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.148761	0.78001	6.81E-4	0.0	ENSG00000058729	ENST00000283109;ENST00000508447	T;T	0.08984	3.03;3.03	5.06	5.06	0.68205	Protein kinase-like domain (1);RIO-like kinase (1);	0.000000	0.85682	D	0.000000	T	0.37019	0.0988	M	0.91612	3.225	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.992	T	0.48127	-0.9062	10	0.87932	D	0	-0.2874	14.4605	0.67445	1.0:0.0:0.0:0.0	.	216;216	D6RDI3;Q9BVS4	.;RIOK2_HUMAN	T	216	ENSP00000283109:I216T;ENSP00000420932:I216T	ENSP00000283109:I216T	I	-	2	0	RIOK2	96532798	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	8.586000	0.90806	1.900000	0.55004	0.482000	0.46254	ATT		RIOK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250628.1	NM_018343	
APC	324	hgsc.bcm.edu	37	5	112128143	112128143	+	Splice_Site	SNP	C	C	T	rs62619935		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr5:112128143C>T	ENST00000457016.1	+	7	1026	c.646C>T	c.(646-648)Cga>Tga	p.R216*	APC_ENST00000257430.4_Splice_Site_p.R216*|APC_ENST00000508376.2_Splice_Site_p.R216*			P25054	APC_HUMAN	adenomatous polyposis coli	216	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R216*(12)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TTTATTTTAGCGAAGAATAGC	0.323		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)		yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	12	Substitution - Nonsense(12)	large_intestine(12)	5	GRCh37	CM992133	APC	M	rs62619935						52.0	51.0	51.0					5																	112128143		2202	4300	6502	112156042	SO:0001630	splice_region_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.646-1C>T	5.37:g.112128143C>T		Somatic		Capture	Illumina HiSeq	Phase_I	112156042	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	39	7.466758	0.98302	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.19	2.99	0.34606	.	0.630262	0.16042	N	0.232387	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-5.2274	1.7088	0.02888	0.2899:0.3634:0.2259:0.1208	rs62619935	.	.	.	X	216	.	.	R	+	1	2	APC	112156042	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	0.662000	0.25038	1.304000	0.44892	-0.158000	0.13435	CGA		APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	Nonsense_Mutation
APC	324	hgsc.bcm.edu	37	5	112170692	112170692	+	Silent	SNP	A	A	G			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr5:112170692A>G	ENST00000457016.1	+	15	2168	c.1788A>G	c.(1786-1788)tcA>tcG	p.S596S	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Silent_p.S596S|APC_ENST00000508376.2_Silent_p.S596S			P25054	APC_HUMAN	adenomatous polyposis coli	596	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GGAATTTGTCAGCACATTGCA	0.393		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)		yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	1	Unknown(1)	skin(1)	5											197.0	162.0	174.0					5																	112170692		2202	4300	6502	112198591	SO:0001819	synonymous_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.1788A>G	5.37:g.112170692A>G		Somatic		Capture	Illumina HiSeq	Phase_I	112198591	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																				APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
FNIP1	96459	hgsc.bcm.edu	37	5	131042147	131042147	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr5:131042147G>A	ENST00000510461.1	-	9	966	c.871C>T	c.(871-873)Cgc>Tgc	p.R291C	FNIP1_ENST00000307968.7_Missense_Mutation_p.R263C|FNIP1_ENST00000307954.8_Missense_Mutation_p.R246C|CTC-432M15.3_ENST00000514667.1_Intron|FNIP1_ENST00000511848.1_Missense_Mutation_p.R291C	NM_133372.2	NP_588613	Q8TF40	FNIP1_HUMAN	folliculin interacting protein 1	291					cellular response to starvation (GO:0009267)|immature B cell differentiation (GO:0002327)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell apoptotic process (GO:0002904)|positive regulation of GTPase activity (GO:0043547)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein phosphorylation (GO:0001934)|regulation of pro-B cell differentiation (GO:2000973)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(11)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34		all_cancers(142;0.00347)|Lung NSC(810;0.106)|all_lung(232;0.123)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0665)		GTTTGGCTGCGTCGCCAACGT	0.443																																																	0			5											100.0	94.0	96.0					5																	131042147		2203	4300	6503	131070046	SO:0001583	missense	96459			DQ145719	CCDS34226.1, CCDS34227.1	5q23.3	2014-01-28				ENSG00000217128			29418	protein-coding gene	gene with protein product		610594				11853319, 17028174	Standard	NM_001008738		Approved	KIAA1961		Q8TF40		ENST00000510461.1:c.871C>T	5.37:g.131042147G>A	ENSP00000421985:p.Arg291Cys	Somatic		Capture	Illumina HiSeq	Phase_I	131070046	D6RJH5|Q86T47|Q9BUT0	Missense_Mutation	SNP	ENST00000510461.1	37	CCDS34227.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.924336	0.92319	.	.	ENSG00000217128	ENST00000307968;ENST00000307954;ENST00000544351;ENST00000510461;ENST00000511848	T;T;T;T	0.41400	2.01;1.8;1.72;1.0	5.6	4.7	0.59300	.	.	.	.	.	T	0.67785	0.2930	M	0.82517	2.595	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.997;0.998;0.999	T	0.74544	-0.3630	9	0.87932	D	0	-5.6888	15.9298	0.79651	0.0:0.0:0.8638:0.1361	.	291;291;263;291	A8K8V8;Q8TF40-2;Q8TF40-3;Q8TF40	.;.;.;FNIP1_HUMAN	C	263;246;51;291;291	ENSP00000309266:R263C;ENSP00000310453:R246C;ENSP00000421985:R291C;ENSP00000425619:R291C	ENSP00000310453:R246C	R	-	1	0	FNIP1	131070046	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.910000	0.87451	1.434000	0.47414	0.591000	0.81541	CGC		FNIP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370077.1	NM_133372	
PCDHA1	56147	hgsc.bcm.edu	37	5	140167966	140167966	+	Silent	SNP	C	C	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr5:140167966C>T	ENST00000504120.2	+	1	2091	c.2091C>T	c.(2089-2091)aaC>aaT	p.N697N	PCDHA1_ENST00000378133.3_Silent_p.N697N|PCDHA1_ENST00000394633.3_Intron	NM_018900.2	NP_061723.1	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1	697					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(34)|prostate(3)|skin(4)|upper_aerodigestive_tract(5)|urinary_tract(3)	70			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGATGTCAACGTGTACCTGA	0.667																																																	0			5											56.0	55.0	55.0					5																	140167966		2203	4299	6502	140148150	SO:0001819	synonymous_variant	56147			AF152479	CCDS54912.1, CCDS54913.1	5q31	2010-11-26				ENSG00000204970		"""Cadherins / Protocadherins : Clustered"""	8663	other	complex locus constituent	"""KIAA0345-like 13"""	606307				10380929	Standard	NM_018900		Approved			Q9Y5I3		ENST00000504120.2:c.2091C>T	5.37:g.140167966C>T		Somatic		Capture	Illumina HiSeq	Phase_I	140148150	O75288|Q9NRT7	Silent	SNP	ENST00000504120.2	37	CCDS54913.1																																																																																				PCDHA1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389127.1	NM_018900	
PCDHA3	56145	hgsc.bcm.edu	37	5	140182445	140182445	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr5:140182445G>A	ENST00000522353.2	+	1	1663	c.1663G>A	c.(1663-1665)Gtg>Atg	p.V555M	PCDHA3_ENST00000532566.2_Missense_Mutation_p.V555M|PCDHA2_ENST00000520672.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	555	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(16)|kidney(3)|large_intestine(19)|lung(36)|ovary(7)|prostate(8)|skin(3)|stomach(1)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCAGGTGTTCGTGCTGGACGA	0.692																																																	0			5											93.0	93.0	93.0					5																	140182445		2203	4298	6501	140162629	SO:0001583	missense	56145			AF152481	CCDS54915.1	5q31	2010-11-26				ENSG00000255408		"""Cadherins / Protocadherins : Clustered"""	8669	other	complex locus constituent	"""KIAA0345-like 11"""	606309				10380929	Standard	NM_018906		Approved	PCDH-ALPHA3		Q9Y5H8		ENST00000522353.2:c.1663G>A	5.37:g.140182445G>A	ENSP00000429808:p.Val555Met	Somatic		Capture	Illumina HiSeq	Phase_I	140162629	O75286	Missense_Mutation	SNP	ENST00000522353.2	37	CCDS54915.1	.	.	.	.	.	.	.	.	.	.	g	15.47	2.841798	0.51057	.	.	ENSG00000255408	ENST00000522353;ENST00000532566	T;T	0.68181	-0.31;-0.31	4.5	4.5	0.54988	Cadherin (5);Cadherin conserved site (1);Cadherin-like (1);	0.000000	0.37623	U	0.002008	D	0.83202	0.5203	M	0.89904	3.07	0.27208	N	0.959983	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.992	T	0.77292	-0.2642	10	0.87932	D	0	.	11.1965	0.48715	0.0859:0.0:0.9141:0.0	.	555;555	Q9Y5H8-2;Q9Y5H8	.;PCDA3_HUMAN	M	555	ENSP00000429808:V555M;ENSP00000434086:V555M	ENSP00000429808:V555M	V	+	1	0	PCDHA3	140162629	0.980000	0.34600	1.000000	0.80357	0.696000	0.40369	2.784000	0.47774	2.237000	0.73441	0.306000	0.20318	GTG		PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906	
TP53	7157	hgsc.bcm.edu	37	17	7579591	7579591	+	Splice_Site	SNP	C	C	T			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr17:7579591C>T	ENST00000269305.4	-	4	286		c.e4-1		TP53_ENST00000359597.4_Splice_Site|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Splice_Site|TP53_ENST00000445888.2_Splice_Site|TP53_ENST00000420246.2_Splice_Site|TP53_ENST00000455263.2_Splice_Site	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53						apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|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)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.?(8)|p.0?(8)|p.L35fs*10(3)|p.S33fs*10(1)|p.P13fs*18(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GCAAGGGGGACTGTAGATGGG	0.592		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)		yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	21	Unknown(11)|Whole gene deletion(8)|Insertion - Frameshift(1)|Deletion - Frameshift(1)	bone(4)|large_intestine(3)|central_nervous_system(3)|lung(3)|pancreas(3)|upper_aerodigestive_tract(2)|stomach(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)	17	GRCh37	CS971912	TP53	S							141.0	137.0	138.0					17																	7579591		2203	4300	6503	7520316	SO:0001630	splice_region_variant	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.97-1G>A	17.37:g.7579591C>T		Somatic		Capture	Illumina HiSeq	Phase_I	7520316	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Splice_Site	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	6.702	0.498192	0.12762	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000508793;ENST00000503591	.	.	.	2.49	2.49	0.30216	.	.	.	.	.	.	.	.	.	.	.	0.40380	D	0.979434	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.6143	0.33822	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TP53	7520316	0.879000	0.30193	0.021000	0.16686	0.027000	0.11550	1.937000	0.40193	1.730000	0.51580	0.561000	0.74099	.		TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	Intron
NUAK2	81788	hgsc.bcm.edu	37	1	205277835	205277838	+	Frame_Shift_Del	DEL	CACG	CACG	-	rs116063043		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	CACG	CACG					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:205277835_205277838delCACG	ENST00000367157.3	-	3	501_504	c.375_378delCGTG	c.(373-378)atcgtgfs	p.IV127fs		NM_030952.1	NP_112214.1			NUAK family, SNF1-like kinase, 2											breast(3)|kidney(3)|large_intestine(4)|lung(4)|ovary(3)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23	Breast(84;0.186)		BRCA - Breast invasive adenocarcinoma(75;0.117)			CCATGACGATCACGATCTTGCTGC	0.593																																																	0			1																																								203544461	SO:0001589	frameshift_variant	81788			AK074830	CCDS1453.1	1q32.1	2008-02-05			ENSG00000163545	ENSG00000163545			29558	protein-coding gene	gene with protein product	"""SNF1/AMP activated protein kinase"""	608131				11230166	Standard	NM_030952		Approved	SNARK, FLJ90349	uc001hce.3	Q9H093	OTTHUMG00000037196	ENST00000367157.3:c.375_378delCGTG	1.37:g.205277835_205277838delCACG	ENSP00000356125:p.Ile127fs	Somatic		Capture	Illumina HiSeq	Phase_I	203544458		Frame_Shift_Del	DEL	ENST00000367157.3	37	CCDS1453.1																																																																																				NUAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090390.1	NM_030952	
TGOLN2	10618	hgsc.bcm.edu	37	2	85554536	85554577	+	In_Frame_Del	DEL	CTTTTTGGGTCTTTGCCTCCGCACCCGACTTGTTGGAGCTGT	CTTTTTGGGTCTTTGCCTCCGCACCCGACTTGTTGGAGCTGT	-	rs1044964|rs1044965		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	CTTTTTGGGTCTTTGCCTCCGCACCCGACTTGTTGGAGCTGT	CTTTTTGGGTCTTTGCCTCCGCACCCGACTTGTTGGAGCTGT					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr2:85554536_85554577delCTTTTTGGGTCTTTGCCTCCGCACCCGACTTGTTGGAGCTGT	ENST00000409232.3	-	2	339_380	c.278_319delACAGCTCCAACAAGTCGGGTGCGGAGGCAAAGACCCAAAAAG	c.(277-321)gacagctccaacaagtcgggtgcggaggcaaagacccaaaaaggc>ggc	p.DSSNKSGAEAKTQK93del	TGOLN2_ENST00000377386.3_In_Frame_Del_p.DSSNKSGAEAKTQK93del|TGOLN2_ENST00000282120.2_Intron|TGOLN2_ENST00000444342.2_In_Frame_Del_p.DSSNKSGAEAKTQK93del|TGOLN2_ENST00000398263.2_In_Frame_Del_p.DSSNKSGAEAKTQK93del|TGOLN2_ENST00000409015.1_In_Frame_Del_p.DSSNKSGAEAKTQK93del			O43493	TGON2_HUMAN	trans-golgi network protein 2	93	14 X 14 AA tandem repeats.					Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|transport vesicle (GO:0030133)											CTAGTGCTGCCTTTTTGGGTCTTTGCCTCCGCACCCGACTTGTTGGAGCTGTCTTTTTGGGT	0.570																																																	0			2																																								85408088	SO:0001651	inframe_deletion	10618			AF027515	CCDS46351.1, CCDS56126.1, CCDS56127.1	2p11.2	2012-06-25			ENSG00000152291	ENSG00000152291			15450	protein-coding gene	gene with protein product	"""trans-Golgi network protein (46, 48, 51kD isoforms)"""	603062				9422759, 21994457	Standard	NM_001206840		Approved	TGN51, TGN46, TGN48, TGN38, TTGN2	uc021vjw.1	O43493	OTTHUMG00000153017	ENST00000409232.3:c.278_319delACAGCTCCAACAAGTCGGGTGCGGAGGCAAAGACCCAAAAAG	2.37:g.85554536_85554577delCTTTTTGGGTCTTTGCCTCCGCACCCGACTTGTTGGAGCTGT	ENSP00000386443:p.Asp93_Lys106del	Somatic		Capture	Illumina HiSeq	Phase_I	85408047	B2R686|B8ZZ88|D6W5K3|F8WBK2|O15282|O43492|O43499|O43500|O43501|Q53G68|Q53GV2|Q6MZV1|Q6ZTM7|Q8N6T8|Q92760|Q96QL2	In_Frame_Del	DEL	ENST00000409232.3	37	CCDS56126.1																																																																																				TGOLN2-006	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000329045.2	NM_006464	
ZNF717	100131827	hgsc.bcm.edu	37	3	75787042	75787043	+	Frame_Shift_Ins	INS	-	-	AAAT	rs78806516|rs369928577	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr3:75787042_75787043insAAAT	ENST00000478296.1	-	4	1857_1858	c.1581_1582insATTT	c.(1579-1584)ttcctafs	p.L528fs	ZNF717_ENST00000422325.1_Frame_Shift_Ins_p.L578fs|ZNF717_ENST00000491507.1_Intron|ZNF717_ENST00000477374.1_Intron|MIR4273_ENST00000582824.1_RNA|ZNF717_ENST00000400845.3_Frame_Shift_Ins_p.L571fs			Q9BY31	ZN717_HUMAN	zinc finger protein 717	571					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						TGTATAGTTAGGAATGACTTAC	0.366																																																	0			3																																								75869733	SO:0001589	frameshift_variant	100131827			AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124		"""Zinc fingers, C2H2-type"", ""-"""	29448	protein-coding gene	gene with protein product			"""zinc finger protein 838"""	ZNF838			Standard	NM_001128223		Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.1581_1582insATTT	3.37:g.75787042_75787043insAAAT	ENSP00000419377:p.Leu528fs	Somatic		Capture	Illumina HiSeq	Phase_I	75869732		Frame_Shift_Ins	INS	ENST00000478296.1	37																																																																																					ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000352764.2	NM_001128223	
ZNF717	100131827	hgsc.bcm.edu	37	3	75787044	75787045	+	In_Frame_Ins	INS	-	-	CTT	rs373780316		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr3:75787044_75787045insCTT	ENST00000478296.1	-	4	1855_1856	c.1579_1580insAAG	c.(1579-1581)ttc>tAAGtc	p.527_527F>*V	ZNF717_ENST00000422325.1_In_Frame_Ins_p.577_577F>*V|ZNF717_ENST00000491507.1_Intron|ZNF717_ENST00000477374.1_Intron|MIR4273_ENST00000582824.1_RNA|ZNF717_ENST00000400845.3_In_Frame_Ins_p.570_570F>*V			Q9BY31	ZN717_HUMAN	zinc finger protein 717	570					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						TATAGTTAGGAATGACTTACAG	0.361																																																	0			3																																								75869735	SO:0001652	inframe_insertion	100131827			AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124		"""Zinc fingers, C2H2-type"", ""-"""	29448	protein-coding gene	gene with protein product			"""zinc finger protein 838"""	ZNF838			Standard	NM_001128223		Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.1579_1580insAAG	3.37:g.75787044_75787045insCTT	ENSP00000419377:p.Phe527delins*Val	Somatic		Capture	Illumina HiSeq	Phase_I	75869734		In_Frame_Del	INS	ENST00000478296.1	37																																																																																					ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000352764.2	NM_001128223	
MUC4	4585	hgsc.bcm.edu	37	3	195506271	195506318	+	In_Frame_Del	DEL	ACCTGTGGATAATGAGGAAGCATTGGTGACAGGAAGAGGGGTGGTGTC	ACCTGTGGATAATGAGGAAGCATTGGTGACAGGAAGAGGGGTGGTGTC	-	rs199896027|rs201839412|rs192584273|rs62282465|rs199596856|rs62282466|rs77023345|rs551098007|rs563580319|rs201564403|rs201191776|rs200161977|rs377584277|rs202208985|rs200602926|rs201679145	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	ACCTGTGGATAATGAGGAAGCATTGGTGACAGGAAGAGGGGTGGTGTC	ACCTGTGGATAATGAGGAAGCATTGGTGACAGGAAGAGGGGTGGTGTC					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr3:195506271_195506318delACCTGTGGATAATGAGGAAGCATTGGTGACAGGAAGAGGGGTGGTGTC	ENST00000463781.3	-	2	12592_12639	c.12133_12180delGACACCACCCCTCTTCCTGTCACCAATGCTTCCTCATTATCCACAGGT	c.(12133-12180)gacaccacccctcttcctgtcaccaatgcttcctcattatccacaggtdel	p.DTTPLPVTNASSLSTG4045del	MUC4_ENST00000475231.1_In_Frame_Del_p.DTTPLPVTNASSLSTG4045del|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.P4050T(3)|p.T4046A(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGGTGGCGTGACCTGTGGATAATGAGGAAGCATTGGTGACAGGAAGAGGGGTGGTGTCACCTGTGGAT	0.589																																																	5	Substitution - Missense(5)	kidney(3)|haematopoietic_and_lymphoid_tissue(2)	3							,,	213,2197		69,75,1061					,,		0.0			23	808,3672		295,218,1727	no	intron,coding,intron	MUC4	NM_138297.4,NM_018406.6,NM_004532.5	,,	364,293,2788	A1A1,A1R,RR		18.0357,8.8382,14.8186	,,	,,		1021,5869				196991097	SO:0001651	inframe_deletion	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12133_12180delGACACCACCCCTCTTCCTGTCACCAATGCTTCCTCATTATCCACAGGT	3.37:g.195506271_195506318delACCTGTGGATAATGAGGAAGCATTGGTGACAGGAAGAGGGGTGGTGTC	ENSP00000417498:p.Asp4045_Gly4060del	Somatic		Capture	Illumina HiSeq	Phase_I	196991050	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	In_Frame_Del	DEL	ENST00000463781.3	37	CCDS54700.1																																																																																				MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MUC4	4585	hgsc.bcm.edu	37	3	195506713	195506760	+	In_Frame_Del	DEL	GCTGAGGAAGTGTCGGTGACAGGAAGAGGGGTGGCGTGACGTGTGGAT	GCTGAGGAAGTGTCGGTGACAGGAAGAGGGGTGGCGTGACGTGTGGAT	-	rs62282473|rs550221890|rs62282471|rs200597845|rs201121891|rs9882363|rs192522651|rs62282470|rs554841787|rs201914190|rs200055147|rs181895767|rs374267078|rs199635197|rs201530419|rs200381819|rs201961213	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	GCTGAGGAAGTGTCGGTGACAGGAAGAGGGGTGGCGTGACGTGTGGAT	GCTGAGGAAGTGTCGGTGACAGGAAGAGGGGTGGCGTGACGTGTGGAT					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr3:195506713_195506760delGCTGAGGAAGTGTCGGTGACAGGAAGAGGGGTGGCGTGACGTGTGGAT	ENST00000463781.3	-	2	12150_12197	c.11691_11738delATCCACACGTCACGCCACCCCTCTTCCTGTCACCGACACTTCCTCAGC	c.(11689-11739)gcatccacacgtcacgccacccctcttcctgtcaccgacacttcctcagct>gct	p.3897_3913ASTRHATPLPVTDTSSA>A	MUC4_ENST00000475231.1_In_Frame_Del_p.3897_3913ASTRHATPLPVTDTSSA>A|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.A3902V(2)|p.P3904S(2)|p.A3902T(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ATCTGTGGAAGCTGAGGAAGTGTCGGTGACAGGAAGAGGGGTGGCGTGACGTGTGGATGCTGAGGAAG	0.593																																																	5	Substitution - Missense(5)	kidney(2)|skin(2)|endometrium(1)	3							,,	327,1561		144,39,761					,,		0.0			8	1397,2107		610,177,965	no	intron,coding,intron	MUC4	NM_138297.4,NM_018406.6,NM_004532.5	,,	754,216,1726	A1A1,A1R,RR		39.8687,17.3199,31.9733	,,	,,		1724,3668				196991539	SO:0001651	inframe_deletion	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11691_11738delATCCACACGTCACGCCACCCCTCTTCCTGTCACCGACACTTCCTCAGC	3.37:g.195506713_195506760delGCTGAGGAAGTGTCGGTGACAGGAAGAGGGGTGGCGTGACGTGTGGAT	ENSP00000417498:p.Ala3897_Ser3912del	Somatic		Capture	Illumina HiSeq	Phase_I	196991492	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	In_Frame_Del	DEL	ENST00000463781.3	37	CCDS54700.1																																																																																				MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MUC4	4585	hgsc.bcm.edu	37	3	195515367	195515414	+	In_Frame_Del	DEL	GGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT	GGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT	-	rs369312980|rs547775645|rs201510137|rs200193644|rs531942134|rs13060431|rs200400545|rs71180964|rs199583597|rs55868431|rs55803325|rs550428312|rs199702053|rs13065584	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	GGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT	GGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr3:195515367_195515414delGGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT	ENST00000463781.3	-	2	3496_3543	c.3037_3084delAGCCCTTCCTCAGTATCCACAGGTCACACCACCCCTCTTCCTGTCACC	c.(3037-3084)agcccttcctcagtatccacaggtcacaccacccctcttcctgtcaccdel	p.SPSSVSTGHTTPLPVT1013del	MUC4_ENST00000475231.1_In_Frame_Del_p.SPSSVSTGHTTPLPVT1013del|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	448	Repeat.|Ser-rich.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.S1013_T1028delSPSSVSTGHTTPLPVT(4)|p.S1013G(2)|p.T1022A(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGGAAGTGTCGGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCTGGTGACAGGA	0.573																																																	8	Substitution - Missense(4)|Deletion - In frame(4)	stomach(6)|prostate(2)	3																																								196999809	SO:0001651	inframe_deletion	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.3037_3084delAGCCCTTCCTCAGTATCCACAGGTCACACCACCCCTCTTCCTGTCACC	3.37:g.195515367_195515414delGGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT	ENSP00000417498:p.Ser1013_Thr1028del	Somatic		Capture	Illumina HiSeq	Phase_I	196999762	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	In_Frame_Del	DEL	ENST00000463781.3	37	CCDS54700.1																																																																																				MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
FAT1	2195	hgsc.bcm.edu	37	4	187540871	187540871	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr4:187540871delA	ENST00000441802.2	-	10	7078	c.6869delT	c.(6868-6870)gtgfs	p.V2290fs		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2290	Cadherin 21. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						AGACAGGGTCACCGCATAAGA	0.453										HNSCC(5;0.00058)																											Colon(197;1040 2055 4143 4984 49344)												0			4											94.0	97.0	96.0					4																	187540871		1991	4160	6151	187777865	SO:0001589	frameshift_variant	2195			X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.6869delT	4.37:g.187540871delA	ENSP00000406229:p.Val2290fs	Somatic		Capture	Illumina HiSeq	Phase_I	187777865		Frame_Shift_Del	DEL	ENST00000441802.2	37	CCDS47177.1																																																																																				FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
TAS2R3	50831	hgsc.bcm.edu	37	7	141464569	141464571	+	In_Frame_Del	DEL	TCT	TCT	-			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	TCT	TCT					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr7:141464569_141464571delTCT	ENST00000247879.2	+	1	673_675	c.611_613delTCT	c.(610-615)atcttc>atc	p.F205del	SSBP1_ENST00000465582.1_Intron	NM_016943.2	NP_058639.1	Q9NYW6	TA2R3_HUMAN	taste receptor, type 2, member 3	205					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|sensory perception of taste (GO:0050909)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)	14	Melanoma(164;0.0171)					TCTTTGCTCATCTTCTCCCTGGG	0.512																																																	0			7																																								141111040	SO:0001651	inframe_deletion	50831			AF227130	CCDS5867.1	7q31.3-q32	2012-08-22			ENSG00000127362	ENSG00000127362		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14910	protein-coding gene	gene with protein product		604868					Standard	NM_016943		Approved	T2R3	uc003vwp.1	Q9NYW6	OTTHUMG00000157637	ENST00000247879.2:c.611_613delTCT	7.37:g.141464572_141464574delTCT	ENSP00000247879:p.Phe205del	Somatic		Capture	Illumina HiSeq	Phase_I	141111038	A4D1U2|Q645W2|Q75MV6	In_Frame_Del	DEL	ENST00000247879.2	37	CCDS5867.1																																																																																				TAS2R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349288.1		
RP1L1	94137	hgsc.bcm.edu	37	8	10467671	10467673	+	In_Frame_Del	DEL	CTC	CTC	-	rs200084961|rs374739066		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	CTC	CTC					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr8:10467671_10467673delCTC	ENST00000382483.3	-	4	4158_4160	c.3935_3937delGAG	c.(3934-3939)ggagaa>gaa	p.G1312del		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1328	8 X 16 AA approximate tandem repeats of T-E-E-G-L-Q-E-E-G-V-Q-L-E-E-T-K.				cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		tgcagcccttctccttctgttcc	0.488																																																	0			8																																								10505083	SO:0001651	inframe_deletion	94137			AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.3935_3937delGAG	8.37:g.10467671_10467673delCTC	ENSP00000371923:p.Gly1312del	Somatic		Capture	Illumina HiSeq	Phase_I	10505081	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	In_Frame_Del	DEL	ENST00000382483.3	37	CCDS43708.1																																																																																				RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
RP1L1	94137	hgsc.bcm.edu	37	8	10467681	10467686	+	In_Frame_Del	DEL	TCCTTC	TCCTTC	-	rs386722181		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	TCCTTC	TCCTTC					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr8:10467681_10467686delTCCTTC	ENST00000382483.3	-	4	4145_4150	c.3922_3927delGAAGGA	c.(3922-3927)gaaggadel	p.EG1308del		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1326	8 X 16 AA approximate tandem repeats of T-E-E-G-L-Q-E-E-G-V-Q-L-E-E-T-K.				cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		ctccttctgttccttcttTAGTTTCC	0.485																																																	0			8								43,79,3686		3,0,37,3,73,1788						-0.4	0.0			135	362,29,7561		4,0,354,0,29,3589	no	codingComplex	RP1L1	NM_178857.5		7,0,391,3,102,5377	A1A1,A1A2,A1R,A2A2,A2R,RR		4.917,3.2038,4.3622				405,108,11247				10505096	SO:0001651	inframe_deletion	94137			AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.3922_3927delGAAGGA	8.37:g.10467681_10467686delTCCTTC	ENSP00000371923:p.Glu1308_Gly1309del	Somatic		Capture	Illumina HiSeq	Phase_I	10505091	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	In_Frame_Del	DEL	ENST00000382483.3	37	CCDS43708.1																																																																																				RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
RUNX1T1	862	hgsc.bcm.edu	37	8	93026961	93026963	+	In_Frame_Del	DEL	GAA	GAA	-			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	GAA	GAA					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr8:93026961_93026963delGAA	ENST00000523629.1	-	4	766_768	c.312_314delTTC	c.(310-315)tcttcc>tcc	p.104_105SS>S	RUNX1T1_ENST00000422361.2_In_Frame_Del_p.67_68SS>S|RUNX1T1_ENST00000396218.1_In_Frame_Del_p.77_78SS>S|RUNX1T1_ENST00000518844.1_In_Frame_Del_p.77_78SS>S|RUNX1T1_ENST00000521553.1_In_Frame_Del_p.67_68SS>S|RUNX1T1_ENST00000360348.2_In_Frame_Del_p.67_68SS>S|RUNX1T1_ENST00000265814.3_In_Frame_Del_p.104_105SS>S|RUNX1T1_ENST00000436581.2_In_Frame_Del_p.115_116SS>S|RUNX1T1_ENST00000522163.1_5'Flank|RUNX1T1_ENST00000520724.1_In_Frame_Del_p.67_68SS>S	NM_001198626.1|NM_001198630.1|NM_001198633.1|NM_175634.2	NP_001185555.1|NP_001185559.1|NP_001185562.1|NP_783552.1	Q06455	MTG8_HUMAN	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	104	Poly-Ser.				fat cell differentiation (GO:0045444)|generation of precursor metabolites and energy (GO:0006091)|regulation of DNA binding (GO:0051101)|transcription, DNA-templated (GO:0006351)	nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(54)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	86			BRCA - Breast invasive adenocarcinoma(11;0.0141)			AGAGGAGGAGGAAGAAGAGGAAG	0.542																																																	0			8																																								93096139	SO:0001651	inframe_deletion	862			D43638	CCDS6256.1, CCDS6257.1, CCDS47891.1, CCDS56544.1, CCDS75766.1, CCDS75767.1	8q22	2007-01-29	2005-01-20	2005-01-22	ENSG00000079102	ENSG00000079102		"""Zinc fingers, MYND-type"""	1535	protein-coding gene	gene with protein product		133435	"""core-binding factor, runt domain, alpha subunit 2; translocated to, 1; cyclin D-related"""	AML1T1, CBFA2T1		1391946, 9790752	Standard	NM_004349		Approved	CDR, ETO, MTG8, ZMYND2	uc011lgi.2	Q06455	OTTHUMG00000164066	ENST00000523629.1:c.312_314delTTC	8.37:g.93026964_93026966delGAA	ENSP00000428543:p.Ser108del	Somatic		Capture	Illumina HiSeq	Phase_I	93096137	B7Z4P4|E7EPN4|O14784|Q06456|Q14873|Q16239|Q16346|Q16347|Q6IBL1|Q6NXH1|Q7Z4J5|Q92479|Q9BRZ0	In_Frame_Del	DEL	ENST00000523629.1	37	CCDS6256.1																																																																																				RUNX1T1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377045.3	NM_004349, NM_175635	
CEL	1056	hgsc.bcm.edu	37	9	135947002	135947034	+	In_Frame_Del	DEL	CCCACGGGTGACTCCGAGACCGCCCCCGTGCCG	CCCACGGGTGACTCCGAGACCGCCCCCGTGCCG	-	rs368091098|rs374263839|rs530591081|rs201411101|rs75294797	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	CCCACGGGTGACTCCGAGACCGCCCCCGTGCCG	CCCACGGGTGACTCCGAGACCGCCCCCGTGCCG					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr9:135947002_135947034delCCCACGGGTGACTCCGAGACCGCCCCCGTGCCG	ENST00000372080.4	+	11	2138_2170	c.2122_2154delCCCACGGGTGACTCCGAGACCGCCCCCGTGCCG	c.(2122-2154)cccacgggtgactccgagaccgcccccgtgccgdel	p.PTGDSETAPVP708del	CEL_ENST00000351304.7_In_Frame_Del_p.PTGDSETAPVP639del	NM_001807.3	NP_001798.2	P19835	CEL_HUMAN	carboxyl ester lipase	705	17 X 11 AA tandem repeats, glycodomain, O-linked (mucin type).				cholesterol catabolic process (GO:0006707)|fatty acid catabolic process (GO:0009062)|intestinal cholesterol absorption (GO:0030299)|intestinal lipid catabolic process (GO:0044258)|lipid digestion (GO:0044241)|lipid metabolic process (GO:0006629)|pancreatic juice secretion (GO:0030157)|protein esterification (GO:0018350)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	acylglycerol lipase activity (GO:0047372)|catalytic activity (GO:0003824)|heparin binding (GO:0008201)|hydrolase activity (GO:0016787)|sterol esterase activity (GO:0004771)|triglyceride lipase activity (GO:0004806)	p.P718T(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(9)|pancreas(2)|skin(1)	20				OV - Ovarian serous cystadenocarcinoma(145;1.03e-40)|Epithelial(140;3.58e-37)|GBM - Glioblastoma multiforme(294;0.00164)|READ - Rectum adenocarcinoma(205;0.196)		CCCCGTGACCCCCACGGGTGACTCCGAGACCGCCCCCGTGCCGCCCACGGGTG	0.777																																																	1	Substitution - Missense(1)	lung(1)	9																																								134936855	SO:0001651	inframe_deletion	1056			M54994	CCDS43896.1	9q34.3	2013-03-13	2013-03-13		ENSG00000170835	ENSG00000170835	3.1.1.3, 3.1.1.13		1848	protein-coding gene	gene with protein product	"""bile salt-stimulated lipase"""	114840				1676983	Standard	NM_001807		Approved	BSSL, MODY8	uc010naa.2	P19835	OTTHUMG00000020855	ENST00000372080.4:c.2122_2154delCCCACGGGTGACTCCGAGACCGCCCCCGTGCCG	9.37:g.135947002_135947034delCCCACGGGTGACTCCGAGACCGCCCCCGTGCCG	ENSP00000361151:p.Pro708_Pro718del	Somatic		Capture	Illumina HiSeq	Phase_I	134936823	Q16398|Q5T7U7|Q9UCH1|Q9UP41	In_Frame_Del	DEL	ENST00000372080.4	37	CCDS43896.1																																																																																				CEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054823.1		
OR6C76	390326	hgsc.bcm.edu	37	12	55820959	55820959	+	Frame_Shift_Del	DEL	A	A	-	rs397719965|rs57387180		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr12:55820959delA	ENST00000328314.3	+	1	922	c.922delA	c.(922-924)aaafs	p.K311fs		NM_001005183.1	NP_001005183.1	A6NM76	O6C76_HUMAN	olfactory receptor, family 6, subfamily C, member 76	311						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|large_intestine(3)|lung(4)|prostate(1)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						GATTTCCCACAAAAAAAAAAA	0.338																																																	0			12											19.0	20.0	19.0					12																	55820959		2110	4120	6230	54107226	SO:0001589	frameshift_variant	390326				CCDS31823.1	12q13.2	2013-09-23			ENSG00000185821	ENSG00000185821		"""GPCR / Class A : Olfactory receptors"""	31305	protein-coding gene	gene with protein product							Standard	NM_001005183		Approved		uc010spm.2	A6NM76	OTTHUMG00000169956	ENST00000328314.3:c.922delA	12.37:g.55820959delA	ENSP00000328402:p.Lys311fs	Somatic		Capture	Illumina HiSeq	Phase_I	54107226		Frame_Shift_Del	DEL	ENST00000328314.3	37	CCDS31823.1																																																																																				OR6C76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406675.1	NM_001005183	
LRRIQ1	84125	hgsc.bcm.edu	37	12	85638646	85638646	+	Frame_Shift_Del	DEL	A	A	-	rs5799725|rs398102301	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr12:85638646delA	ENST00000393217.2	+	27	5157	c.5096delA	c.(5095-5097)gaafs	p.E1699fs	LRRIQ1_ENST00000528777.3_3'UTR	NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	1699										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|liver(1)|lung(28)|ovary(5)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	83				GBM - Glioblastoma multiforme(134;0.212)		GTGAACAGAGAAAAAAAAAAT	0.388													|||unknown(HR)	991	0.197883	0.0893	0.2522	5008	,	,		15671	0.1776		0.2753	False		,,,				2504	0.2474																0			12											79.0	61.0	67.0					12																	85638646		1828	4079	5907	84162777	SO:0001589	frameshift_variant	84125			AK022365	CCDS41816.1	12q21	2008-02-05			ENSG00000133640	ENSG00000133640			25708	protein-coding gene	gene with protein product						11347906	Standard	NM_001079910		Approved	FLJ12303, KIAA1801	uc001tac.3	Q96JM4	OTTHUMG00000166185	ENST00000393217.2:c.5096delA	12.37:g.85638646delA	ENSP00000376910:p.Glu1699fs	Somatic		Capture	Illumina HiSeq	Phase_I	84162777	Q567P4|Q9BS17|Q9HA36	Frame_Shift_Del	DEL	ENST00000393217.2	37	CCDS41816.1																																																																																				LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165	
ORAI1	84876	hgsc.bcm.edu	37	12	122064774	122064779	+	In_Frame_Del	DEL	CCGCCA	CCGCCA	-	rs141919534|rs531278468		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	CCGCCA	CCGCCA					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr12:122064774_122064779delCCGCCA	ENST00000330079.7	+	1	320_325	c.127_132delCCGCCA	c.(127-132)ccgccadel	p.PP47del		NM_032790.3	NP_116179	Q96D31	CRCM1_HUMAN	ORAI calcium release-activated calcium modulator 1	0	Pro-rich.				blood coagulation (GO:0007596)|immune system process (GO:0002376)|positive regulation of calcium ion transport (GO:0051928)|regulation of calcium ion transport (GO:0051924)|store-operated calcium entry (GO:0002115)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|protein complex (GO:0043234)	identical protein binding (GO:0042802)|store-operated calcium channel activity (GO:0015279)	p.P43_P44delPP(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)	11	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000415)|Epithelial(86;0.00148)		cccgggggccccgccaccgccaccgc	0.748														5007	0.9998	1.0	1.0	5008	,	,		5795	1.0		1.0	False		,,,				2504	0.999																1	Deletion - In frame(1)	breast(1)	12																																								120549162	SO:0001651	inframe_deletion	84876			AK027372		12q24.31	2014-09-17	2007-08-14	2007-08-14	ENSG00000182500	ENSG00000276045		"""ORAI calcium release-activated calcium modulators"""	25896	protein-coding gene	gene with protein product	"""calcium release-activated calcium modulator 1"""	610277	"""transmembrane protein 142A"""	TMEM142A		16582901	Standard	NM_032790		Approved	FLJ14466, CRACM1	uc021rff.1	Q96D31		ENST00000330079.7:c.127_132delCCGCCA	12.37:g.122064780_122064785delCCGCCA	ENSP00000328216:p.Pro47_Pro48del	Somatic		Capture	Illumina HiSeq	Phase_I	120549157	Q3MHV3|Q6DHX2|Q96BP7|Q96K71	In_Frame_Del	DEL	ENST00000330079.7	37	CCDS41851.1																																																																																				ORAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402151.1	NM_032790	
WDR66	144406	hgsc.bcm.edu	37	12	122359397	122359398	+	In_Frame_Ins	INS	-	-	GAGGAGGAGGAGAAA	rs142042908|rs386767074|rs58098972|rs142971083|rs377641095|rs71082910		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr12:122359397_122359398insGAGGAGGAGGAGAAA	ENST00000288912.4	+	2	1040_1041	c.186_187insGAGGAGGAGGAGAAA	c.(187-189)gag>GAGGAGGAGGAGAAAgag	p.63_63E>EEEEKE	WDR66_ENST00000397454.2_In_Frame_Ins_p.63_63E>EEEEKE	NM_144668.5	NP_653269.3	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	63	Glu-rich.						calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(13)|ovary(2)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	all_neural(191;0.0496)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248)		aggaggaaggggaggaggaggg	0.465																																					Esophageal Squamous(85;849 1794 49757 52143)												0			12																																								120843781	SO:0001652	inframe_insertion	144406			AL833930	CCDS41853.1, CCDS53840.1	12q24.31	2014-07-31			ENSG00000158023	ENSG00000158023		"""WD repeat domain containing"""	28506	protein-coding gene	gene with protein product						17967944	Standard	NM_001178003		Approved	MGC33630, CaM-IP4	uc009zxk.3	Q8TBY9	OTTHUMG00000168948	Exception_encountered	12.37:g.122359397_122359398insGAGGAGGAGGAGAAA	Exception_encountered	Somatic		Capture	Illumina HiSeq	Phase_I	120843780	C9J1W2|Q8IYA3|Q8N898|Q8NDE7	In_Frame_Ins	INS	ENST00000288912.4	37	CCDS41853.1																																																																																				WDR66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401700.1	NM_144668	
GPHN	10243	hgsc.bcm.edu	37	14	67525469	67525470	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr14:67525469_67525470insC	ENST00000315266.5	+	10	2132_2133	c.1011_1012insC	c.(1012-1014)ccgfs	p.P338fs	GPHN_ENST00000478722.1_Frame_Shift_Ins_p.P371fs|GPHN_ENST00000459628.1_Frame_Shift_Ins_p.P353fs|GPHN_ENST00000543237.1_Frame_Shift_Ins_p.P384fs|GPHN_ENST00000305960.9_Frame_Shift_Ins_p.P307fs|GPHN_ENST00000544752.2_3'UTR	NM_001024218.1	NP_001019389.1	Q9NQX3	GEPH_HUMAN	gephyrin	338	MPT adenylyltransferase.				establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycine receptor clustering (GO:0072579)|Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|molybdopterin cofactor biosynthetic process (GO:0032324)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|inhibitory synapse (GO:0060077)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|molybdopterin adenylyltransferase activity (GO:0061598)|molybdopterin molybdotransferase activity (GO:0061599)|transferase activity (GO:0016740)			large_intestine(8)|liver(1)|ovary(2)|stomach(1)	12		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)		TGGAGATGACTCCGGTGCTTGG	0.406			T	MLL	AL																																			Dom	yes		14	14q24	10243	gephyrin (GPH)		L	0			14																																								66595223	SO:0001589	frameshift_variant	10243			AB037806	CCDS9777.1, CCDS32103.1	14q23.3	2008-04-22			ENSG00000171723	ENSG00000171723			15465	protein-coding gene	gene with protein product		603930				1319186, 10325225, 18403029	Standard	XM_005267250		Approved	KIAA1385	uc001xix.3	Q9NQX3	OTTHUMG00000029785	ENST00000315266.5:c.1013dupC	14.37:g.67525471_67525471dupC	ENSP00000312771:p.Pro338fs	Somatic		Capture	Illumina HiSeq	Phase_I	66595222	Q9H4E9|Q9P2G2	Frame_Shift_Ins	INS	ENST00000315266.5	37	CCDS32103.1																																																																																				GPHN-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000074299.2	NM_020806	
SULT1A4	445329	hgsc.bcm.edu	37	16	29466211	29466211	+	5'Flank	DEL	A	A	-			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr16:29466211delA	ENST00000395400.3	+	0	0				SLX1B-SULT1A4_ENST00000564950.1_RNA|RP11-345J4.5_ENST00000565417.1_5'Flank|SLX1B_ENST00000351581.4_Frame_Shift_Del_p.K51fs|SNX29P2_ENST00000398878.3_lincRNA|SLX1B_ENST00000330181.5_Frame_Shift_Del_p.K51fs|BOLA2_ENST00000330978.3_5'UTR|SULT1A4_ENST00000344620.6_5'Flank			P0DMN0	ST1A4_HUMAN	sulfotransferase family, cytosolic, 1A, phenol-preferring, member 4						catecholamine metabolic process (GO:0006584)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)	aryl sulfotransferase activity (GO:0004062)										TGGGGGCCGCAAAAAAGGCGG	0.697																																																	0			16																																								29373712	SO:0001631	upstream_gene_variant	0			L34160	CCDS32427.1	16p11.2	2013-05-10			ENSG00000213648	ENSG00000213648	2.8.2.1	"""Sulfotransferases, cytosolic"""	30004	protein-coding gene	gene with protein product		615819				15358107, 15752422	Standard	NM_001017390		Approved		uc002dxk.3	P0DMN0	OTTHUMG00000170468		16.37:g.29466211delA	Exception_encountered	Somatic		Capture	Illumina HiSeq	Phase_I	29373712	B4DNV0|O95603|P50224|Q1ET66|Q6ZWJ5	Frame_Shift_Del	DEL	ENST00000395400.3	37	CCDS32427.1																																																																																				SULT1A4-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_001017389	
RLTPR	146206	hgsc.bcm.edu	37	16	67681232	67681234	+	In_Frame_Del	DEL	ATG	ATG	-	rs201801777		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	ATG	ATG					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr16:67681232_67681234delATG	ENST00000334583.6	+	10	1046_1048	c.718_720delATG	c.(718-720)atgdel	p.M241del	RLTPR_ENST00000545661.1_In_Frame_Del_p.M241del	NM_001013838.1	NP_001013860.1	Q6F5E8	LR16C_HUMAN	RGD motif, leucine rich repeats, tropomodulin domain and proline-rich containing	241					cell migration (GO:0016477)|establishment of protein localization (GO:0045184)|homeostasis of number of cells (GO:0048872)|maintenance of cell polarity (GO:0030011)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interferon-gamma secretion (GO:1902715)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|F-actin capping protein complex (GO:0008290)|immunological synapse (GO:0001772)|membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(4)|kidney(1)|lung(9)|urinary_tract(2)	18		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232)		GATTCTGCACATGATGAGTCAGT	0.645																																																	0			16																																								66238735	SO:0001651	inframe_deletion	146206			AB113647	CCDS45513.1	16q22.1	2010-09-10				ENSG00000159753			27089	protein-coding gene	gene with protein product	"""RGD, leucine-rich repeat, tropomodulin and proline-rich containing protein"", ""leucine rich repeat containing 16C"""	610859				15588584, 19846667	Standard	XM_005255807		Approved	LRRC16C, CARMIL2	uc002etn.3	Q6F5E8		ENST00000334583.6:c.718_720delATG	16.37:g.67681235_67681237delATG	ENSP00000334958:p.Met241del	Somatic		Capture	Illumina HiSeq	Phase_I	66238733	B8X2Z3	In_Frame_Del	DEL	ENST00000334583.6	37	CCDS45513.1																																																																																				RLTPR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467858.1	NM_001013838	
LGALS9B	284194	hgsc.bcm.edu	37	17	20370782	20370783	+	Start_Codon_Ins	INS	-	-	TC	rs10687699|rs554373055|rs372509656	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr17:20370782_20370783insTC	ENST00000423676.3	-	0	64_65				LGALS9B_ENST00000324290.5_Start_Codon_Ins			Q3B8N2	LEG9B_HUMAN	lectin, galactoside-binding, soluble, 9B								carbohydrate binding (GO:0030246)	p.M1fs*12(1)		central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|skin(1)|upper_aerodigestive_tract(2)	10						GCTGAAGGCCATCTCCACCGCC	0.584														831	0.165935	0.2504	0.1326	5008	,	,		9041	0.127		0.1481	False		,,,				2504	0.1339																1	Insertion - Frameshift(1)	central_nervous_system(1)	17								372,1470		152,68,701						2.5	0.7		dbSNP_130	3	715,5069		234,247,2411	no	frameshift	LGALS9B	NM_001042685.1		386,315,3112	A1A1,A1R,RR		12.3617,20.1954,14.2539				1087,6539				20311375	SO:0001582	initiator_codon_variant	284194				CCDS42283.1	17p11.2	2011-08-04			ENSG00000170298	ENSG00000170298		"""Lectins, galactoside-binding"""	24842	protein-coding gene	gene with protein product						11997339	Standard	NM_001042685		Approved		uc002gwz.1	Q3B8N2	OTTHUMG00000130730	ENST00000423676.3:c.0_1dupGA	17.37:g.20370785_20370786dupTC		Somatic		Capture	Illumina HiSeq	Phase_I	20311374	A6NLF8|A8K2J8	Frame_Shift_Ins	INS	ENST00000423676.3	37																																																																																					LGALS9B-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000253230.2	NM_001042685	
KRTAP4-1	85285	hgsc.bcm.edu	37	17	39340796	39340852	+	In_Frame_Del	DEL	CGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG	CGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG	-	rs483929|rs543483191|rs79048996|rs1985673|rs2320229|rs483893|rs572749|rs543006020|rs71155126|rs554407371|rs2320230	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	CGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG	CGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr17:39340796_39340852delCGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG	ENST00000398472.1	-	1	742_798	c.255_311delCCCACTCTGCTGTCAGACCACCTGCCACCCCAGCTGTGGTATGTCCAGCTGCTGCCG	c.(253-312)cgcccactctgctgtcagaccacctgccaccccagctgtggtatgtccagctgctgccgt>cgt	p.85_104RPLCCQTTCHPSCGMSSCCR>R				Q9BYQ7	KRA41_HUMAN	keratin associated protein 4-1	85	18 X 5 AA repeats of C-C-[GRQC]-[SPT]- [VSTL].		Missing (in allele KAP4.10). {ECO:0000269|PubMed:15955084}.			keratin filament (GO:0045095)		p.H90_C108delHPSCGMSSCCRPLCCQTTC(2)|p.H94_C112delHPSCGMSSCCRPLCCQTTC(2)		kidney(1)|large_intestine(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	5		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			ACAGAGTGGACGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGGCGGCAGCAGC	0.646																																																	4	Deletion - In frame(4)	upper_aerodigestive_tract(2)|prostate(2)	17																																								36594378	SO:0001651	inframe_deletion	85285			AC006070		17q21.2	2013-06-25			ENSG00000198443	ENSG00000198443		"""Keratin associated proteins"""	18907	protein-coding gene	gene with protein product			"""keratin associated protein 4-10"""	KRTAP4-10		11279113	Standard	NM_033060		Approved	KAP4.1, KAP4.10	uc002hwe.4	Q9BYQ7	OTTHUMG00000132081	ENST00000398472.1:c.255_311delCCCACTCTGCTGTCAGACCACCTGCCACCCCAGCTGTGGTATGTCCAGCTGCTGCCG	17.37:g.39340796_39340852delCGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG	ENSP00000381489:p.Arg85_Cys103del	Somatic		Capture	Illumina HiSeq	Phase_I	36594322	A8MWS7|Q3SYF2	Frame_Shift_Del	DEL	ENST00000398472.1	37																																																																																					KRTAP4-1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255108.1	NM_033060	
GNRH2	2797	hgsc.bcm.edu	37	20	3026345	3026346	+	Frame_Shift_Ins	INS	-	-	GCCCC	rs544846287|rs67749149|rs16996832|rs377041343	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr20:3026345_3026346insGCCCC	ENST00000245983.2	+	4	377_378	c.326_327insGCCCC	c.(325-330)gagcccfs	p.-111fs	GNRH2_ENST00000359100.2_Frame_Shift_Ins_p.-104fs|GNRH2_ENST00000359987.1_Frame_Shift_Ins_p.-103fs|GNRH2_ENST00000380346.2_Frame_Shift_Ins_p.-103fs|MRPS26_ENST00000380325.3_5'Flank|GNRH2_ENST00000380347.2_Frame_Shift_Ins_p.-104fs	NM_001501.1	NP_001492.1	O43555	GON2_HUMAN	gonadotropin-releasing hormone 2						multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			ovary(1)|upper_aerodigestive_tract(1)	2						GCAGCCCGAGAGCCCCGCCCCG	0.634														729	0.145567	0.0295	0.1571	5008	,	,		10164	0.2391		0.1014	False		,,,				2504	0.2434																0			20																																								2974346	SO:0001589	frameshift_variant	2797			AF036329	CCDS13040.1, CCDS13041.1, CCDS13042.1	20p13	2013-02-26			ENSG00000125787	ENSG00000125787		"""Endogenous ligands"""	4420	protein-coding gene	gene with protein product		602352				9419371, 12447356	Standard	NM_178331		Approved		uc002whr.1	O43555	OTTHUMG00000031723	ENST00000245983.2:c.337_341dupGCCCC	20.37:g.3026351_3026355dupGCCCC	ENSP00000245983:p.Arg111fs	Somatic		Capture	Illumina HiSeq	Phase_I	2974345	Q14C68|Q14C69|Q9BYN9|Q9BYP0	Frame_Shift_Ins	INS	ENST00000245983.2	37	CCDS13040.1																																																																																				GNRH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077694.2	NM_001501	
RALY	22913	hgsc.bcm.edu	37	20	32664864	32664865	+	In_Frame_Ins	INS	-	-	CAG	rs10649600|rs57852506	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr20:32664864_32664865insCAG	ENST00000246194.3	+	8	1191_1192	c.689_690insCAG	c.(688-693)gccggc>gcCAGcggc	p.230_231AG>ASG	RALY_ENST00000375114.3_In_Frame_Ins_p.214_215AG>ASG	NM_016732.2	NP_057951.1	Q9UKM9	RALY_HUMAN	RALY heterogeneous nuclear ribonucleoprotein	230	Epitope (recognized by BKRF1 antibodies).|Poly-Gly.			A -> AS (in Ref. 2; AAC28898). {ECO:0000305}.	mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			kidney(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12						GGAggtggcgccggcggcggcg	0.658																																																	0			20																																								32128526	SO:0001652	inframe_insertion	22913			AF148457	CCDS13229.1, CCDS13230.1	20q11.21-q11.23	2013-08-06	2013-08-06		ENSG00000125970	ENSG00000125970		"""RNA binding motif (RRM) containing"""	15921	protein-coding gene	gene with protein product		614663	"""RNA-binding protein (autoantigenic, hnRNP-associated with lethal yellow)"", ""RNA binding protein, autoantigenic (hnRNP-associated with lethal yellow homolog (mouse))"""			10500250, 23614458	Standard	NM_016732		Approved	P542, HNRPCL2	uc002xab.3	Q9UKM9	OTTHUMG00000032283	Exception_encountered	20.37:g.32664864_32664865insCAG	ENSP00000246194:p.Ala230_Gly231insSer	Somatic		Capture	Illumina HiSeq	Phase_I	32128525	Q14621|Q2M365|Q5QPL8|Q9BQX6|Q9UJE3	In_Frame_Ins	INS	ENST00000246194.3	37	CCDS13230.1																																																																																				RALY-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078753.1		
KRTAP10-7	386675	hgsc.bcm.edu	37	21	46020656	46020670	+	In_Frame_Del	DEL	CTGCTGCGCCCCCAG	CTGCTGCGCCCCCAG	-	rs36208679|rs60739860|rs373191083		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	CTGCTGCGCCCCCAG	CTGCTGCGCCCCCAG					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr21:46020656_46020670delCTGCTGCGCCCCCAG	ENST00000380102.2	+	1	160_174	c.135_149delCTGCTGCGCCCCCAG	c.(133-150)ccctgctgcgcccccagc>ccc	p.CCAPS46del	TSPEAR_ENST00000323084.4_Intron	NM_198689.2	NP_941962.1	P60409	KR107_HUMAN	keratin associated protein 10-7	46	30 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)		p.S50_P54delSCCAP(1)		breast(1)|large_intestine(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	8						GCGAGCCCCCCTGCTGCGCCCCCAGCTGCTGCGCC	0.698																																																	1	Deletion - In frame(1)	upper_aerodigestive_tract(1)	21							,	2258,1042		849,560,241					,	-0.7	1.0		dbSNP_126	22	6001,1123		2605,791,166	no	coding,intron	TSPEAR,KRTAP10-7	NM_198689.2,NM_144991.2	,	3454,1351,407	A1A1,A1R,RR		15.7636,31.5758,20.7694	,	,		8259,2165				44845098	SO:0001651	inframe_deletion	386675			AJ566385	CCDS74803.1	21q22.3	2014-04-10			ENSG00000205441	ENSG00000272804		"""Keratin associated proteins"""	22970	protein-coding gene	gene with protein product				KRTAP18-7			Standard	NM_198689		Approved	KAP10.7, KAP18.7	uc002zfn.4	P60409	OTTHUMG00000188307	ENST00000380102.2:c.135_149delCTGCTGCGCCCCCAG	21.37:g.46020656_46020670delCTGCTGCGCCCCCAG	ENSP00000369445:p.Cys46_Ser50del	Somatic		Capture	Illumina HiSeq	Phase_I	44845084	Q0VDJ8|Q70LJ2	Frame_Shift_Del	DEL	ENST00000380102.2	37																																																																																					KRTAP10-7-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000128038.1	NM_198689	
NEFH	4744	hgsc.bcm.edu	37	22	29885567	29885568	+	In_Frame_Ins	INS	-	-	AAGTCCCCTGAGAAGGCC	rs147489453|rs559153194|rs75808076|rs59279731		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr22:29885567_29885568insAAGTCCCCTGAGAAGGCC	ENST00000310624.6	+	4	1971_1972	c.1938_1939insAAGTCCCCTGAGAAGGCC	c.(1939-1941)aag>AAGTCCCCTGAGAAGGCCaag	p.647_647K>KSPEKAK		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	653	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.			Missing (in Ref. 1; CAA33366 and 5; AC000035). {ECO:0000305}.	axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						AGGAGGAAGCAAAGTCCCCTGA	0.569																																																	0			22								2816,1448		937,942,253						-5.3	0.0		dbSNP_134	77	5046,3206		1537,1972,617	no	coding	NEFH	NM_021076.3		2474,2914,870	A1A1,A1R,RR		38.8512,33.9587,37.1844				7862,4654				28215568	SO:0001652	inframe_insertion	4744				CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1939_1956dupAAGTCCCCTGAGAAGGCC	22.37:g.29885567_29885568insAAGTCCCCTGAGAAGGCC	Exception_encountered	Somatic		Capture	Illumina HiSeq	Phase_I	28215567	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	In_Frame_Ins	INS	ENST00000310624.6	37	CCDS13858.1																																																																																				NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
FAM47A	158724	hgsc.bcm.edu	37	X	34149658	34149693	+	In_Frame_Del	DEL	ATGGGACACTCCAGTCTCTGGAGGCTCCGGGCGGAG	ATGGGACACTCCAGTCTCTGGAGGCTCCGGGCGGAG	-	rs367563899|rs201090915|rs201363312|rs373732464		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	ATGGGACACTCCAGTCTCTGGAGGCTCCGGGCGGAG	ATGGGACACTCCAGTCTCTGGAGGCTCCGGGCGGAG					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chrX:34149658_34149693delATGGGACACTCCAGTCTCTGGAGGCTCCGGGCGGAG	ENST00000346193.3	-	1	754_789	c.703_738delCTCCGCCCGGAGCCTCCAGAGACTGGAGTGTCCCAT	c.(703-738)ctccgcccggagcctccagagactggagtgtcccatdel	p.LRPEPPETGVSH235del		NM_203408.3	NP_981953.2	Q5JRC9	FA47A_HUMAN	family with sequence similarity 47, member A	235	Pro-rich.							p.L235_H246delLRPEPPETGVSH(1)|p.P240P(1)		NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(5)|large_intestine(17)|lung(44)|ovary(5)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	97						CCGGGCGGATATGGGACACTCCAGTCTCTGGAGGCTCCGGGCGGAGATGGGACACT	0.627														5	0.0013245	0.0	0.0	3775	,	,		15035	0.0		0.004	False		,,,				2504	0.001																2	Substitution - coding silent(1)|Deletion - In frame(1)	ovary(1)|lung(1)	X								33,3667		0,20,13,1562,523						-0.3	0.0			32	98,6373		2,62,32,2290,1731	no	coding	FAM47A	NM_203408.3		2,82,45,3852,2254	A1A1,A1R,A1,RR,R		1.5144,0.8919,1.288				131,10040				34059614	SO:0001651	inframe_deletion	158724			BC026171	CCDS43926.1	Xp21.1	2004-08-09			ENSG00000185448	ENSG00000185448			29962	protein-coding gene	gene with protein product	"""similar to hypothetical protein FLJ35782"""					12477932	Standard	NM_203408		Approved	MGC27003	uc004ddg.3	Q5JRC9	OTTHUMG00000021339	ENST00000346193.3:c.703_738delCTCCGCCCGGAGCCTCCAGAGACTGGAGTGTCCCAT	X.37:g.34149658_34149693delATGGGACACTCCAGTCTCTGGAGGCTCCGGGCGGAG	ENSP00000345029:p.Leu235_His246del	Somatic		Capture	Illumina HiSeq	Phase_I	34059579	A8K8I9|Q8TAA0	In_Frame_Del	DEL	ENST00000346193.3	37	CCDS43926.1																																																																																				FAM47A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056205.1	NM_203408	
NUAK2	81788	hgsc.bcm.edu	37	1	205277835	205277838	+	Frame_Shift_Del	DEL	CACG	CACG	-	rs116063043		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	CACG	CACG					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:205277835_205277838delCACG	ENST00000367157.3	-	3	501_504	c.375_378delCGTG	c.(373-378)atcgtgfs	p.IV127fs		NM_030952.1	NP_112214.1			NUAK family, SNF1-like kinase, 2											breast(3)|kidney(3)|large_intestine(4)|lung(4)|ovary(3)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23	Breast(84;0.186)		BRCA - Breast invasive adenocarcinoma(75;0.117)			CCATGACGATCACGATCTTGCTGC	0.593																																																	0			1																																								203544461	SO:0001589	frameshift_variant	81788			AK074830	CCDS1453.1	1q32.1	2008-02-05			ENSG00000163545	ENSG00000163545			29558	protein-coding gene	gene with protein product	"""SNF1/AMP activated protein kinase"""	608131				11230166	Standard	NM_030952		Approved	SNARK, FLJ90349	uc001hce.3	Q9H093	OTTHUMG00000037196	ENST00000367157.3:c.375_378delCGTG	1.37:g.205277835_205277838delCACG	ENSP00000356125:p.Ile127fs	Somatic		Capture	Illumina HiSeq	Phase_I	203544458		Frame_Shift_Del	DEL	ENST00000367157.3	37	CCDS1453.1																																																																																				NUAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090390.1	NM_030952	
TGOLN2	10618	hgsc.bcm.edu	37	2	85554536	85554577	+	In_Frame_Del	DEL	CTTTTTGGGTCTTTGCCTCCGCACCCGACTTGTTGGAGCTGT	CTTTTTGGGTCTTTGCCTCCGCACCCGACTTGTTGGAGCTGT	-	rs1044964|rs1044965		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	CTTTTTGGGTCTTTGCCTCCGCACCCGACTTGTTGGAGCTGT	CTTTTTGGGTCTTTGCCTCCGCACCCGACTTGTTGGAGCTGT					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr2:85554536_85554577delCTTTTTGGGTCTTTGCCTCCGCACCCGACTTGTTGGAGCTGT	ENST00000409232.3	-	2	339_380	c.278_319delACAGCTCCAACAAGTCGGGTGCGGAGGCAAAGACCCAAAAAG	c.(277-321)gacagctccaacaagtcgggtgcggaggcaaagacccaaaaaggc>ggc	p.DSSNKSGAEAKTQK93del	TGOLN2_ENST00000377386.3_In_Frame_Del_p.DSSNKSGAEAKTQK93del|TGOLN2_ENST00000282120.2_Intron|TGOLN2_ENST00000444342.2_In_Frame_Del_p.DSSNKSGAEAKTQK93del|TGOLN2_ENST00000398263.2_In_Frame_Del_p.DSSNKSGAEAKTQK93del|TGOLN2_ENST00000409015.1_In_Frame_Del_p.DSSNKSGAEAKTQK93del			O43493	TGON2_HUMAN	trans-golgi network protein 2	93	14 X 14 AA tandem repeats.					Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|transport vesicle (GO:0030133)											CTAGTGCTGCCTTTTTGGGTCTTTGCCTCCGCACCCGACTTGTTGGAGCTGTCTTTTTGGGT	0.570																																																	0			2																																								85408088	SO:0001651	inframe_deletion	10618			AF027515	CCDS46351.1, CCDS56126.1, CCDS56127.1	2p11.2	2012-06-25			ENSG00000152291	ENSG00000152291			15450	protein-coding gene	gene with protein product	"""trans-Golgi network protein (46, 48, 51kD isoforms)"""	603062				9422759, 21994457	Standard	NM_001206840		Approved	TGN51, TGN46, TGN48, TGN38, TTGN2	uc021vjw.1	O43493	OTTHUMG00000153017	ENST00000409232.3:c.278_319delACAGCTCCAACAAGTCGGGTGCGGAGGCAAAGACCCAAAAAG	2.37:g.85554536_85554577delCTTTTTGGGTCTTTGCCTCCGCACCCGACTTGTTGGAGCTGT	ENSP00000386443:p.Asp93_Lys106del	Somatic		Capture	Illumina HiSeq	Phase_I	85408047	B2R686|B8ZZ88|D6W5K3|F8WBK2|O15282|O43492|O43499|O43500|O43501|Q53G68|Q53GV2|Q6MZV1|Q6ZTM7|Q8N6T8|Q92760|Q96QL2	In_Frame_Del	DEL	ENST00000409232.3	37	CCDS56126.1																																																																																				TGOLN2-006	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000329045.2	NM_006464	
ZNF717	100131827	hgsc.bcm.edu	37	3	75787042	75787043	+	Frame_Shift_Ins	INS	-	-	AAAT	rs78806516|rs369928577	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr3:75787042_75787043insAAAT	ENST00000478296.1	-	4	1857_1858	c.1581_1582insATTT	c.(1579-1584)ttcctafs	p.L528fs	ZNF717_ENST00000422325.1_Frame_Shift_Ins_p.L578fs|ZNF717_ENST00000491507.1_Intron|ZNF717_ENST00000477374.1_Intron|MIR4273_ENST00000582824.1_RNA|ZNF717_ENST00000400845.3_Frame_Shift_Ins_p.L571fs			Q9BY31	ZN717_HUMAN	zinc finger protein 717	571					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						TGTATAGTTAGGAATGACTTAC	0.366																																																	0			3																																								75869733	SO:0001589	frameshift_variant	100131827			AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124		"""Zinc fingers, C2H2-type"", ""-"""	29448	protein-coding gene	gene with protein product			"""zinc finger protein 838"""	ZNF838			Standard	NM_001128223		Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.1581_1582insATTT	3.37:g.75787042_75787043insAAAT	ENSP00000419377:p.Leu528fs	Somatic		Capture	Illumina HiSeq	Phase_I	75869732		Frame_Shift_Ins	INS	ENST00000478296.1	37																																																																																					ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000352764.2	NM_001128223	
ZNF717	100131827	hgsc.bcm.edu	37	3	75787044	75787045	+	In_Frame_Ins	INS	-	-	CTT	rs373780316		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr3:75787044_75787045insCTT	ENST00000478296.1	-	4	1855_1856	c.1579_1580insAAG	c.(1579-1581)ttc>tAAGtc	p.527_527F>*V	ZNF717_ENST00000422325.1_In_Frame_Ins_p.577_577F>*V|ZNF717_ENST00000491507.1_Intron|ZNF717_ENST00000477374.1_Intron|MIR4273_ENST00000582824.1_RNA|ZNF717_ENST00000400845.3_In_Frame_Ins_p.570_570F>*V			Q9BY31	ZN717_HUMAN	zinc finger protein 717	570					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						TATAGTTAGGAATGACTTACAG	0.361																																																	0			3																																								75869735	SO:0001652	inframe_insertion	100131827			AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124		"""Zinc fingers, C2H2-type"", ""-"""	29448	protein-coding gene	gene with protein product			"""zinc finger protein 838"""	ZNF838			Standard	NM_001128223		Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.1579_1580insAAG	3.37:g.75787044_75787045insCTT	ENSP00000419377:p.Phe527delins*Val	Somatic		Capture	Illumina HiSeq	Phase_I	75869734		In_Frame_Del	INS	ENST00000478296.1	37																																																																																					ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000352764.2	NM_001128223	
MUC4	4585	hgsc.bcm.edu	37	3	195506271	195506318	+	In_Frame_Del	DEL	ACCTGTGGATAATGAGGAAGCATTGGTGACAGGAAGAGGGGTGGTGTC	ACCTGTGGATAATGAGGAAGCATTGGTGACAGGAAGAGGGGTGGTGTC	-	rs199896027|rs201839412|rs192584273|rs62282465|rs199596856|rs62282466|rs77023345|rs551098007|rs563580319|rs201564403|rs201191776|rs200161977|rs377584277|rs202208985|rs200602926|rs201679145	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	ACCTGTGGATAATGAGGAAGCATTGGTGACAGGAAGAGGGGTGGTGTC	ACCTGTGGATAATGAGGAAGCATTGGTGACAGGAAGAGGGGTGGTGTC					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr3:195506271_195506318delACCTGTGGATAATGAGGAAGCATTGGTGACAGGAAGAGGGGTGGTGTC	ENST00000463781.3	-	2	12592_12639	c.12133_12180delGACACCACCCCTCTTCCTGTCACCAATGCTTCCTCATTATCCACAGGT	c.(12133-12180)gacaccacccctcttcctgtcaccaatgcttcctcattatccacaggtdel	p.DTTPLPVTNASSLSTG4045del	MUC4_ENST00000475231.1_In_Frame_Del_p.DTTPLPVTNASSLSTG4045del|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.P4050T(3)|p.T4046A(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGGTGGCGTGACCTGTGGATAATGAGGAAGCATTGGTGACAGGAAGAGGGGTGGTGTCACCTGTGGAT	0.589																																																	5	Substitution - Missense(5)	kidney(3)|haematopoietic_and_lymphoid_tissue(2)	3							,,	213,2197		69,75,1061					,,		0.0			23	808,3672		295,218,1727	no	intron,coding,intron	MUC4	NM_138297.4,NM_018406.6,NM_004532.5	,,	364,293,2788	A1A1,A1R,RR		18.0357,8.8382,14.8186	,,	,,		1021,5869				196991097	SO:0001651	inframe_deletion	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12133_12180delGACACCACCCCTCTTCCTGTCACCAATGCTTCCTCATTATCCACAGGT	3.37:g.195506271_195506318delACCTGTGGATAATGAGGAAGCATTGGTGACAGGAAGAGGGGTGGTGTC	ENSP00000417498:p.Asp4045_Gly4060del	Somatic		Capture	Illumina HiSeq	Phase_I	196991050	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	In_Frame_Del	DEL	ENST00000463781.3	37	CCDS54700.1																																																																																				MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MUC4	4585	hgsc.bcm.edu	37	3	195506713	195506760	+	In_Frame_Del	DEL	GCTGAGGAAGTGTCGGTGACAGGAAGAGGGGTGGCGTGACGTGTGGAT	GCTGAGGAAGTGTCGGTGACAGGAAGAGGGGTGGCGTGACGTGTGGAT	-	rs62282473|rs550221890|rs62282471|rs200597845|rs201121891|rs9882363|rs192522651|rs62282470|rs554841787|rs201914190|rs200055147|rs181895767|rs374267078|rs199635197|rs201530419|rs200381819|rs201961213	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	GCTGAGGAAGTGTCGGTGACAGGAAGAGGGGTGGCGTGACGTGTGGAT	GCTGAGGAAGTGTCGGTGACAGGAAGAGGGGTGGCGTGACGTGTGGAT					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr3:195506713_195506760delGCTGAGGAAGTGTCGGTGACAGGAAGAGGGGTGGCGTGACGTGTGGAT	ENST00000463781.3	-	2	12150_12197	c.11691_11738delATCCACACGTCACGCCACCCCTCTTCCTGTCACCGACACTTCCTCAGC	c.(11689-11739)gcatccacacgtcacgccacccctcttcctgtcaccgacacttcctcagct>gct	p.3897_3913ASTRHATPLPVTDTSSA>A	MUC4_ENST00000475231.1_In_Frame_Del_p.3897_3913ASTRHATPLPVTDTSSA>A|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.A3902V(2)|p.P3904S(2)|p.A3902T(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ATCTGTGGAAGCTGAGGAAGTGTCGGTGACAGGAAGAGGGGTGGCGTGACGTGTGGATGCTGAGGAAG	0.593																																																	5	Substitution - Missense(5)	kidney(2)|skin(2)|endometrium(1)	3							,,	327,1561		144,39,761					,,		0.0			8	1397,2107		610,177,965	no	intron,coding,intron	MUC4	NM_138297.4,NM_018406.6,NM_004532.5	,,	754,216,1726	A1A1,A1R,RR		39.8687,17.3199,31.9733	,,	,,		1724,3668				196991539	SO:0001651	inframe_deletion	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11691_11738delATCCACACGTCACGCCACCCCTCTTCCTGTCACCGACACTTCCTCAGC	3.37:g.195506713_195506760delGCTGAGGAAGTGTCGGTGACAGGAAGAGGGGTGGCGTGACGTGTGGAT	ENSP00000417498:p.Ala3897_Ser3912del	Somatic		Capture	Illumina HiSeq	Phase_I	196991492	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	In_Frame_Del	DEL	ENST00000463781.3	37	CCDS54700.1																																																																																				MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MUC4	4585	hgsc.bcm.edu	37	3	195515367	195515414	+	In_Frame_Del	DEL	GGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT	GGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT	-	rs369312980|rs547775645|rs201510137|rs200193644|rs531942134|rs13060431|rs200400545|rs71180964|rs199583597|rs55868431|rs55803325|rs550428312|rs199702053|rs13065584	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	GGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT	GGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr3:195515367_195515414delGGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT	ENST00000463781.3	-	2	3496_3543	c.3037_3084delAGCCCTTCCTCAGTATCCACAGGTCACACCACCCCTCTTCCTGTCACC	c.(3037-3084)agcccttcctcagtatccacaggtcacaccacccctcttcctgtcaccdel	p.SPSSVSTGHTTPLPVT1013del	MUC4_ENST00000475231.1_In_Frame_Del_p.SPSSVSTGHTTPLPVT1013del|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	448	Repeat.|Ser-rich.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.S1013_T1028delSPSSVSTGHTTPLPVT(4)|p.S1013G(2)|p.T1022A(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGGAAGTGTCGGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCTGGTGACAGGA	0.573																																																	8	Substitution - Missense(4)|Deletion - In frame(4)	stomach(6)|prostate(2)	3																																								196999809	SO:0001651	inframe_deletion	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.3037_3084delAGCCCTTCCTCAGTATCCACAGGTCACACCACCCCTCTTCCTGTCACC	3.37:g.195515367_195515414delGGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT	ENSP00000417498:p.Ser1013_Thr1028del	Somatic		Capture	Illumina HiSeq	Phase_I	196999762	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	In_Frame_Del	DEL	ENST00000463781.3	37	CCDS54700.1																																																																																				MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
FAT1	2195	hgsc.bcm.edu	37	4	187540871	187540871	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr4:187540871delA	ENST00000441802.2	-	10	7078	c.6869delT	c.(6868-6870)gtgfs	p.V2290fs		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2290	Cadherin 21. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						AGACAGGGTCACCGCATAAGA	0.453										HNSCC(5;0.00058)																											Colon(197;1040 2055 4143 4984 49344)												0			4											94.0	97.0	96.0					4																	187540871		1991	4160	6151	187777865	SO:0001589	frameshift_variant	2195			X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.6869delT	4.37:g.187540871delA	ENSP00000406229:p.Val2290fs	Somatic		Capture	Illumina HiSeq	Phase_I	187777865		Frame_Shift_Del	DEL	ENST00000441802.2	37	CCDS47177.1																																																																																				FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
TAS2R3	50831	hgsc.bcm.edu	37	7	141464569	141464571	+	In_Frame_Del	DEL	TCT	TCT	-			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	TCT	TCT					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr7:141464569_141464571delTCT	ENST00000247879.2	+	1	673_675	c.611_613delTCT	c.(610-615)atcttc>atc	p.F205del	SSBP1_ENST00000465582.1_Intron	NM_016943.2	NP_058639.1	Q9NYW6	TA2R3_HUMAN	taste receptor, type 2, member 3	205					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|sensory perception of taste (GO:0050909)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)	14	Melanoma(164;0.0171)					TCTTTGCTCATCTTCTCCCTGGG	0.512																																																	0			7																																								141111040	SO:0001651	inframe_deletion	50831			AF227130	CCDS5867.1	7q31.3-q32	2012-08-22			ENSG00000127362	ENSG00000127362		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14910	protein-coding gene	gene with protein product		604868					Standard	NM_016943		Approved	T2R3	uc003vwp.1	Q9NYW6	OTTHUMG00000157637	ENST00000247879.2:c.611_613delTCT	7.37:g.141464572_141464574delTCT	ENSP00000247879:p.Phe205del	Somatic		Capture	Illumina HiSeq	Phase_I	141111038	A4D1U2|Q645W2|Q75MV6	In_Frame_Del	DEL	ENST00000247879.2	37	CCDS5867.1																																																																																				TAS2R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349288.1		
RP1L1	94137	hgsc.bcm.edu	37	8	10467671	10467673	+	In_Frame_Del	DEL	CTC	CTC	-	rs200084961|rs374739066		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	CTC	CTC					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr8:10467671_10467673delCTC	ENST00000382483.3	-	4	4158_4160	c.3935_3937delGAG	c.(3934-3939)ggagaa>gaa	p.G1312del		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1328	8 X 16 AA approximate tandem repeats of T-E-E-G-L-Q-E-E-G-V-Q-L-E-E-T-K.				cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		tgcagcccttctccttctgttcc	0.488																																																	0			8																																								10505083	SO:0001651	inframe_deletion	94137			AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.3935_3937delGAG	8.37:g.10467671_10467673delCTC	ENSP00000371923:p.Gly1312del	Somatic		Capture	Illumina HiSeq	Phase_I	10505081	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	In_Frame_Del	DEL	ENST00000382483.3	37	CCDS43708.1																																																																																				RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
RP1L1	94137	hgsc.bcm.edu	37	8	10467681	10467686	+	In_Frame_Del	DEL	TCCTTC	TCCTTC	-	rs386722181		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	TCCTTC	TCCTTC					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr8:10467681_10467686delTCCTTC	ENST00000382483.3	-	4	4145_4150	c.3922_3927delGAAGGA	c.(3922-3927)gaaggadel	p.EG1308del		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1326	8 X 16 AA approximate tandem repeats of T-E-E-G-L-Q-E-E-G-V-Q-L-E-E-T-K.				cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		ctccttctgttccttcttTAGTTTCC	0.485																																																	0			8								43,79,3686		3,0,37,3,73,1788						-0.4	0.0			135	362,29,7561		4,0,354,0,29,3589	no	codingComplex	RP1L1	NM_178857.5		7,0,391,3,102,5377	A1A1,A1A2,A1R,A2A2,A2R,RR		4.917,3.2038,4.3622				405,108,11247				10505096	SO:0001651	inframe_deletion	94137			AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.3922_3927delGAAGGA	8.37:g.10467681_10467686delTCCTTC	ENSP00000371923:p.Glu1308_Gly1309del	Somatic		Capture	Illumina HiSeq	Phase_I	10505091	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	In_Frame_Del	DEL	ENST00000382483.3	37	CCDS43708.1																																																																																				RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
RUNX1T1	862	hgsc.bcm.edu	37	8	93026961	93026963	+	In_Frame_Del	DEL	GAA	GAA	-			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	GAA	GAA					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr8:93026961_93026963delGAA	ENST00000523629.1	-	4	766_768	c.312_314delTTC	c.(310-315)tcttcc>tcc	p.104_105SS>S	RUNX1T1_ENST00000422361.2_In_Frame_Del_p.67_68SS>S|RUNX1T1_ENST00000396218.1_In_Frame_Del_p.77_78SS>S|RUNX1T1_ENST00000518844.1_In_Frame_Del_p.77_78SS>S|RUNX1T1_ENST00000521553.1_In_Frame_Del_p.67_68SS>S|RUNX1T1_ENST00000360348.2_In_Frame_Del_p.67_68SS>S|RUNX1T1_ENST00000265814.3_In_Frame_Del_p.104_105SS>S|RUNX1T1_ENST00000436581.2_In_Frame_Del_p.115_116SS>S|RUNX1T1_ENST00000522163.1_5'Flank|RUNX1T1_ENST00000520724.1_In_Frame_Del_p.67_68SS>S	NM_001198626.1|NM_001198630.1|NM_001198633.1|NM_175634.2	NP_001185555.1|NP_001185559.1|NP_001185562.1|NP_783552.1	Q06455	MTG8_HUMAN	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	104	Poly-Ser.				fat cell differentiation (GO:0045444)|generation of precursor metabolites and energy (GO:0006091)|regulation of DNA binding (GO:0051101)|transcription, DNA-templated (GO:0006351)	nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(54)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	86			BRCA - Breast invasive adenocarcinoma(11;0.0141)			AGAGGAGGAGGAAGAAGAGGAAG	0.542																																																	0			8																																								93096139	SO:0001651	inframe_deletion	862			D43638	CCDS6256.1, CCDS6257.1, CCDS47891.1, CCDS56544.1, CCDS75766.1, CCDS75767.1	8q22	2007-01-29	2005-01-20	2005-01-22	ENSG00000079102	ENSG00000079102		"""Zinc fingers, MYND-type"""	1535	protein-coding gene	gene with protein product		133435	"""core-binding factor, runt domain, alpha subunit 2; translocated to, 1; cyclin D-related"""	AML1T1, CBFA2T1		1391946, 9790752	Standard	NM_004349		Approved	CDR, ETO, MTG8, ZMYND2	uc011lgi.2	Q06455	OTTHUMG00000164066	ENST00000523629.1:c.312_314delTTC	8.37:g.93026964_93026966delGAA	ENSP00000428543:p.Ser108del	Somatic		Capture	Illumina HiSeq	Phase_I	93096137	B7Z4P4|E7EPN4|O14784|Q06456|Q14873|Q16239|Q16346|Q16347|Q6IBL1|Q6NXH1|Q7Z4J5|Q92479|Q9BRZ0	In_Frame_Del	DEL	ENST00000523629.1	37	CCDS6256.1																																																																																				RUNX1T1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377045.3	NM_004349, NM_175635	
CEL	1056	hgsc.bcm.edu	37	9	135947002	135947034	+	In_Frame_Del	DEL	CCCACGGGTGACTCCGAGACCGCCCCCGTGCCG	CCCACGGGTGACTCCGAGACCGCCCCCGTGCCG	-	rs368091098|rs374263839|rs530591081|rs201411101|rs75294797	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	CCCACGGGTGACTCCGAGACCGCCCCCGTGCCG	CCCACGGGTGACTCCGAGACCGCCCCCGTGCCG					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr9:135947002_135947034delCCCACGGGTGACTCCGAGACCGCCCCCGTGCCG	ENST00000372080.4	+	11	2138_2170	c.2122_2154delCCCACGGGTGACTCCGAGACCGCCCCCGTGCCG	c.(2122-2154)cccacgggtgactccgagaccgcccccgtgccgdel	p.PTGDSETAPVP708del	CEL_ENST00000351304.7_In_Frame_Del_p.PTGDSETAPVP639del	NM_001807.3	NP_001798.2	P19835	CEL_HUMAN	carboxyl ester lipase	705	17 X 11 AA tandem repeats, glycodomain, O-linked (mucin type).				cholesterol catabolic process (GO:0006707)|fatty acid catabolic process (GO:0009062)|intestinal cholesterol absorption (GO:0030299)|intestinal lipid catabolic process (GO:0044258)|lipid digestion (GO:0044241)|lipid metabolic process (GO:0006629)|pancreatic juice secretion (GO:0030157)|protein esterification (GO:0018350)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	acylglycerol lipase activity (GO:0047372)|catalytic activity (GO:0003824)|heparin binding (GO:0008201)|hydrolase activity (GO:0016787)|sterol esterase activity (GO:0004771)|triglyceride lipase activity (GO:0004806)	p.P718T(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(9)|pancreas(2)|skin(1)	20				OV - Ovarian serous cystadenocarcinoma(145;1.03e-40)|Epithelial(140;3.58e-37)|GBM - Glioblastoma multiforme(294;0.00164)|READ - Rectum adenocarcinoma(205;0.196)		CCCCGTGACCCCCACGGGTGACTCCGAGACCGCCCCCGTGCCGCCCACGGGTG	0.777																																																	1	Substitution - Missense(1)	lung(1)	9																																								134936855	SO:0001651	inframe_deletion	1056			M54994	CCDS43896.1	9q34.3	2013-03-13	2013-03-13		ENSG00000170835	ENSG00000170835	3.1.1.3, 3.1.1.13		1848	protein-coding gene	gene with protein product	"""bile salt-stimulated lipase"""	114840				1676983	Standard	NM_001807		Approved	BSSL, MODY8	uc010naa.2	P19835	OTTHUMG00000020855	ENST00000372080.4:c.2122_2154delCCCACGGGTGACTCCGAGACCGCCCCCGTGCCG	9.37:g.135947002_135947034delCCCACGGGTGACTCCGAGACCGCCCCCGTGCCG	ENSP00000361151:p.Pro708_Pro718del	Somatic		Capture	Illumina HiSeq	Phase_I	134936823	Q16398|Q5T7U7|Q9UCH1|Q9UP41	In_Frame_Del	DEL	ENST00000372080.4	37	CCDS43896.1																																																																																				CEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054823.1		
OR6C76	390326	hgsc.bcm.edu	37	12	55820959	55820959	+	Frame_Shift_Del	DEL	A	A	-	rs397719965|rs57387180		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr12:55820959delA	ENST00000328314.3	+	1	922	c.922delA	c.(922-924)aaafs	p.K311fs		NM_001005183.1	NP_001005183.1	A6NM76	O6C76_HUMAN	olfactory receptor, family 6, subfamily C, member 76	311						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|large_intestine(3)|lung(4)|prostate(1)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						GATTTCCCACAAAAAAAAAAA	0.338																																																	0			12											19.0	20.0	19.0					12																	55820959		2110	4120	6230	54107226	SO:0001589	frameshift_variant	390326				CCDS31823.1	12q13.2	2013-09-23			ENSG00000185821	ENSG00000185821		"""GPCR / Class A : Olfactory receptors"""	31305	protein-coding gene	gene with protein product							Standard	NM_001005183		Approved		uc010spm.2	A6NM76	OTTHUMG00000169956	ENST00000328314.3:c.922delA	12.37:g.55820959delA	ENSP00000328402:p.Lys311fs	Somatic		Capture	Illumina HiSeq	Phase_I	54107226		Frame_Shift_Del	DEL	ENST00000328314.3	37	CCDS31823.1																																																																																				OR6C76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406675.1	NM_001005183	
LRRIQ1	84125	hgsc.bcm.edu	37	12	85638646	85638646	+	Frame_Shift_Del	DEL	A	A	-	rs5799725|rs398102301	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr12:85638646delA	ENST00000393217.2	+	27	5157	c.5096delA	c.(5095-5097)gaafs	p.E1699fs	LRRIQ1_ENST00000528777.3_3'UTR	NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	1699										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|liver(1)|lung(28)|ovary(5)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	83				GBM - Glioblastoma multiforme(134;0.212)		GTGAACAGAGAAAAAAAAAAT	0.388													|||unknown(HR)	991	0.197883	0.0893	0.2522	5008	,	,		15671	0.1776		0.2753	False		,,,				2504	0.2474																0			12											79.0	61.0	67.0					12																	85638646		1828	4079	5907	84162777	SO:0001589	frameshift_variant	84125			AK022365	CCDS41816.1	12q21	2008-02-05			ENSG00000133640	ENSG00000133640			25708	protein-coding gene	gene with protein product						11347906	Standard	NM_001079910		Approved	FLJ12303, KIAA1801	uc001tac.3	Q96JM4	OTTHUMG00000166185	ENST00000393217.2:c.5096delA	12.37:g.85638646delA	ENSP00000376910:p.Glu1699fs	Somatic		Capture	Illumina HiSeq	Phase_I	84162777	Q567P4|Q9BS17|Q9HA36	Frame_Shift_Del	DEL	ENST00000393217.2	37	CCDS41816.1																																																																																				LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165	
ORAI1	84876	hgsc.bcm.edu	37	12	122064774	122064779	+	In_Frame_Del	DEL	CCGCCA	CCGCCA	-	rs141919534|rs531278468		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	CCGCCA	CCGCCA					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr12:122064774_122064779delCCGCCA	ENST00000330079.7	+	1	320_325	c.127_132delCCGCCA	c.(127-132)ccgccadel	p.PP47del		NM_032790.3	NP_116179	Q96D31	CRCM1_HUMAN	ORAI calcium release-activated calcium modulator 1	0	Pro-rich.				blood coagulation (GO:0007596)|immune system process (GO:0002376)|positive regulation of calcium ion transport (GO:0051928)|regulation of calcium ion transport (GO:0051924)|store-operated calcium entry (GO:0002115)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|protein complex (GO:0043234)	identical protein binding (GO:0042802)|store-operated calcium channel activity (GO:0015279)	p.P43_P44delPP(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)	11	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000415)|Epithelial(86;0.00148)		cccgggggccccgccaccgccaccgc	0.748														5007	0.9998	1.0	1.0	5008	,	,		5795	1.0		1.0	False		,,,				2504	0.999																1	Deletion - In frame(1)	breast(1)	12																																								120549162	SO:0001651	inframe_deletion	84876			AK027372		12q24.31	2014-09-17	2007-08-14	2007-08-14	ENSG00000182500	ENSG00000276045		"""ORAI calcium release-activated calcium modulators"""	25896	protein-coding gene	gene with protein product	"""calcium release-activated calcium modulator 1"""	610277	"""transmembrane protein 142A"""	TMEM142A		16582901	Standard	NM_032790		Approved	FLJ14466, CRACM1	uc021rff.1	Q96D31		ENST00000330079.7:c.127_132delCCGCCA	12.37:g.122064780_122064785delCCGCCA	ENSP00000328216:p.Pro47_Pro48del	Somatic		Capture	Illumina HiSeq	Phase_I	120549157	Q3MHV3|Q6DHX2|Q96BP7|Q96K71	In_Frame_Del	DEL	ENST00000330079.7	37	CCDS41851.1																																																																																				ORAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402151.1	NM_032790	
WDR66	144406	hgsc.bcm.edu	37	12	122359397	122359398	+	In_Frame_Ins	INS	-	-	GAGGAGGAGGAGAAA	rs142042908|rs386767074|rs58098972|rs142971083|rs377641095|rs71082910		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr12:122359397_122359398insGAGGAGGAGGAGAAA	ENST00000288912.4	+	2	1040_1041	c.186_187insGAGGAGGAGGAGAAA	c.(187-189)gag>GAGGAGGAGGAGAAAgag	p.63_63E>EEEEKE	WDR66_ENST00000397454.2_In_Frame_Ins_p.63_63E>EEEEKE	NM_144668.5	NP_653269.3	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	63	Glu-rich.						calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(13)|ovary(2)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	all_neural(191;0.0496)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248)		aggaggaaggggaggaggaggg	0.465																																					Esophageal Squamous(85;849 1794 49757 52143)												0			12																																								120843781	SO:0001652	inframe_insertion	144406			AL833930	CCDS41853.1, CCDS53840.1	12q24.31	2014-07-31			ENSG00000158023	ENSG00000158023		"""WD repeat domain containing"""	28506	protein-coding gene	gene with protein product						17967944	Standard	NM_001178003		Approved	MGC33630, CaM-IP4	uc009zxk.3	Q8TBY9	OTTHUMG00000168948	Exception_encountered	12.37:g.122359397_122359398insGAGGAGGAGGAGAAA	Exception_encountered	Somatic		Capture	Illumina HiSeq	Phase_I	120843780	C9J1W2|Q8IYA3|Q8N898|Q8NDE7	In_Frame_Ins	INS	ENST00000288912.4	37	CCDS41853.1																																																																																				WDR66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401700.1	NM_144668	
GPHN	10243	hgsc.bcm.edu	37	14	67525469	67525470	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr14:67525469_67525470insC	ENST00000315266.5	+	10	2132_2133	c.1011_1012insC	c.(1012-1014)ccgfs	p.P338fs	GPHN_ENST00000478722.1_Frame_Shift_Ins_p.P371fs|GPHN_ENST00000459628.1_Frame_Shift_Ins_p.P353fs|GPHN_ENST00000543237.1_Frame_Shift_Ins_p.P384fs|GPHN_ENST00000305960.9_Frame_Shift_Ins_p.P307fs|GPHN_ENST00000544752.2_3'UTR	NM_001024218.1	NP_001019389.1	Q9NQX3	GEPH_HUMAN	gephyrin	338	MPT adenylyltransferase.				establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycine receptor clustering (GO:0072579)|Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|molybdopterin cofactor biosynthetic process (GO:0032324)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|inhibitory synapse (GO:0060077)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|molybdopterin adenylyltransferase activity (GO:0061598)|molybdopterin molybdotransferase activity (GO:0061599)|transferase activity (GO:0016740)			large_intestine(8)|liver(1)|ovary(2)|stomach(1)	12		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)		TGGAGATGACTCCGGTGCTTGG	0.406			T	MLL	AL																																			Dom	yes		14	14q24	10243	gephyrin (GPH)		L	0			14																																								66595223	SO:0001589	frameshift_variant	10243			AB037806	CCDS9777.1, CCDS32103.1	14q23.3	2008-04-22			ENSG00000171723	ENSG00000171723			15465	protein-coding gene	gene with protein product		603930				1319186, 10325225, 18403029	Standard	XM_005267250		Approved	KIAA1385	uc001xix.3	Q9NQX3	OTTHUMG00000029785	ENST00000315266.5:c.1013dupC	14.37:g.67525471_67525471dupC	ENSP00000312771:p.Pro338fs	Somatic		Capture	Illumina HiSeq	Phase_I	66595222	Q9H4E9|Q9P2G2	Frame_Shift_Ins	INS	ENST00000315266.5	37	CCDS32103.1																																																																																				GPHN-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000074299.2	NM_020806	
SULT1A4	445329	hgsc.bcm.edu	37	16	29466211	29466211	+	5'Flank	DEL	A	A	-			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr16:29466211delA	ENST00000395400.3	+	0	0				SLX1B-SULT1A4_ENST00000564950.1_RNA|RP11-345J4.5_ENST00000565417.1_5'Flank|SLX1B_ENST00000351581.4_Frame_Shift_Del_p.K51fs|SNX29P2_ENST00000398878.3_lincRNA|SLX1B_ENST00000330181.5_Frame_Shift_Del_p.K51fs|BOLA2_ENST00000330978.3_5'UTR|SULT1A4_ENST00000344620.6_5'Flank			P0DMN0	ST1A4_HUMAN	sulfotransferase family, cytosolic, 1A, phenol-preferring, member 4						catecholamine metabolic process (GO:0006584)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)	aryl sulfotransferase activity (GO:0004062)										TGGGGGCCGCAAAAAAGGCGG	0.697																																																	0			16																																								29373712	SO:0001631	upstream_gene_variant	0			L34160	CCDS32427.1	16p11.2	2013-05-10			ENSG00000213648	ENSG00000213648	2.8.2.1	"""Sulfotransferases, cytosolic"""	30004	protein-coding gene	gene with protein product		615819				15358107, 15752422	Standard	NM_001017390		Approved		uc002dxk.3	P0DMN0	OTTHUMG00000170468		16.37:g.29466211delA	Exception_encountered	Somatic		Capture	Illumina HiSeq	Phase_I	29373712	B4DNV0|O95603|P50224|Q1ET66|Q6ZWJ5	Frame_Shift_Del	DEL	ENST00000395400.3	37	CCDS32427.1																																																																																				SULT1A4-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_001017389	
RLTPR	146206	hgsc.bcm.edu	37	16	67681232	67681234	+	In_Frame_Del	DEL	ATG	ATG	-	rs201801777		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	ATG	ATG					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr16:67681232_67681234delATG	ENST00000334583.6	+	10	1046_1048	c.718_720delATG	c.(718-720)atgdel	p.M241del	RLTPR_ENST00000545661.1_In_Frame_Del_p.M241del	NM_001013838.1	NP_001013860.1	Q6F5E8	LR16C_HUMAN	RGD motif, leucine rich repeats, tropomodulin domain and proline-rich containing	241					cell migration (GO:0016477)|establishment of protein localization (GO:0045184)|homeostasis of number of cells (GO:0048872)|maintenance of cell polarity (GO:0030011)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interferon-gamma secretion (GO:1902715)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|F-actin capping protein complex (GO:0008290)|immunological synapse (GO:0001772)|membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(4)|kidney(1)|lung(9)|urinary_tract(2)	18		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232)		GATTCTGCACATGATGAGTCAGT	0.645																																																	0			16																																								66238735	SO:0001651	inframe_deletion	146206			AB113647	CCDS45513.1	16q22.1	2010-09-10				ENSG00000159753			27089	protein-coding gene	gene with protein product	"""RGD, leucine-rich repeat, tropomodulin and proline-rich containing protein"", ""leucine rich repeat containing 16C"""	610859				15588584, 19846667	Standard	XM_005255807		Approved	LRRC16C, CARMIL2	uc002etn.3	Q6F5E8		ENST00000334583.6:c.718_720delATG	16.37:g.67681235_67681237delATG	ENSP00000334958:p.Met241del	Somatic		Capture	Illumina HiSeq	Phase_I	66238733	B8X2Z3	In_Frame_Del	DEL	ENST00000334583.6	37	CCDS45513.1																																																																																				RLTPR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467858.1	NM_001013838	
KRTAP4-1	85285	hgsc.bcm.edu	37	17	39340796	39340852	+	In_Frame_Del	DEL	CGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG	CGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG	-	rs483929|rs543483191|rs79048996|rs1985673|rs2320229|rs483893|rs572749|rs543006020|rs71155126|rs554407371|rs2320230	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	CGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG	CGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr17:39340796_39340852delCGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG	ENST00000398472.1	-	1	742_798	c.255_311delCCCACTCTGCTGTCAGACCACCTGCCACCCCAGCTGTGGTATGTCCAGCTGCTGCCG	c.(253-312)cgcccactctgctgtcagaccacctgccaccccagctgtggtatgtccagctgctgccgt>cgt	p.85_104RPLCCQTTCHPSCGMSSCCR>R				Q9BYQ7	KRA41_HUMAN	keratin associated protein 4-1	85	18 X 5 AA repeats of C-C-[GRQC]-[SPT]- [VSTL].		Missing (in allele KAP4.10). {ECO:0000269|PubMed:15955084}.			keratin filament (GO:0045095)		p.H90_C108delHPSCGMSSCCRPLCCQTTC(2)|p.H94_C112delHPSCGMSSCCRPLCCQTTC(2)		kidney(1)|large_intestine(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	5		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			ACAGAGTGGACGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGGCGGCAGCAGC	0.646																																																	4	Deletion - In frame(4)	upper_aerodigestive_tract(2)|prostate(2)	17																																								36594378	SO:0001651	inframe_deletion	85285			AC006070		17q21.2	2013-06-25			ENSG00000198443	ENSG00000198443		"""Keratin associated proteins"""	18907	protein-coding gene	gene with protein product			"""keratin associated protein 4-10"""	KRTAP4-10		11279113	Standard	NM_033060		Approved	KAP4.1, KAP4.10	uc002hwe.4	Q9BYQ7	OTTHUMG00000132081	ENST00000398472.1:c.255_311delCCCACTCTGCTGTCAGACCACCTGCCACCCCAGCTGTGGTATGTCCAGCTGCTGCCG	17.37:g.39340796_39340852delCGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG	ENSP00000381489:p.Arg85_Cys103del	Somatic		Capture	Illumina HiSeq	Phase_I	36594322	A8MWS7|Q3SYF2	Frame_Shift_Del	DEL	ENST00000398472.1	37																																																																																					KRTAP4-1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255108.1	NM_033060	
RALY	22913	hgsc.bcm.edu	37	20	32664864	32664865	+	In_Frame_Ins	INS	-	-	CAG	rs10649600|rs57852506	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr20:32664864_32664865insCAG	ENST00000246194.3	+	8	1191_1192	c.689_690insCAG	c.(688-693)gccggc>gcCAGcggc	p.230_231AG>ASG	RALY_ENST00000375114.3_In_Frame_Ins_p.214_215AG>ASG	NM_016732.2	NP_057951.1	Q9UKM9	RALY_HUMAN	RALY heterogeneous nuclear ribonucleoprotein	230	Epitope (recognized by BKRF1 antibodies).|Poly-Gly.			A -> AS (in Ref. 2; AAC28898). {ECO:0000305}.	mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			kidney(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12						GGAggtggcgccggcggcggcg	0.658																																																	0			20																																								32128526	SO:0001652	inframe_insertion	22913			AF148457	CCDS13229.1, CCDS13230.1	20q11.21-q11.23	2013-08-06	2013-08-06		ENSG00000125970	ENSG00000125970		"""RNA binding motif (RRM) containing"""	15921	protein-coding gene	gene with protein product		614663	"""RNA-binding protein (autoantigenic, hnRNP-associated with lethal yellow)"", ""RNA binding protein, autoantigenic (hnRNP-associated with lethal yellow homolog (mouse))"""			10500250, 23614458	Standard	NM_016732		Approved	P542, HNRPCL2	uc002xab.3	Q9UKM9	OTTHUMG00000032283	Exception_encountered	20.37:g.32664864_32664865insCAG	ENSP00000246194:p.Ala230_Gly231insSer	Somatic		Capture	Illumina HiSeq	Phase_I	32128525	Q14621|Q2M365|Q5QPL8|Q9BQX6|Q9UJE3	In_Frame_Ins	INS	ENST00000246194.3	37	CCDS13230.1																																																																																				RALY-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078753.1		
KRTAP10-7	386675	hgsc.bcm.edu	37	21	46020656	46020670	+	In_Frame_Del	DEL	CTGCTGCGCCCCCAG	CTGCTGCGCCCCCAG	-	rs36208679|rs60739860|rs373191083		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	CTGCTGCGCCCCCAG	CTGCTGCGCCCCCAG					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr21:46020656_46020670delCTGCTGCGCCCCCAG	ENST00000380102.2	+	1	160_174	c.135_149delCTGCTGCGCCCCCAG	c.(133-150)ccctgctgcgcccccagc>ccc	p.CCAPS46del	TSPEAR_ENST00000323084.4_Intron	NM_198689.2	NP_941962.1	P60409	KR107_HUMAN	keratin associated protein 10-7	46	30 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)		p.S50_P54delSCCAP(1)		breast(1)|large_intestine(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	8						GCGAGCCCCCCTGCTGCGCCCCCAGCTGCTGCGCC	0.698																																																	1	Deletion - In frame(1)	upper_aerodigestive_tract(1)	21							,	2258,1042		849,560,241					,	-0.7	1.0		dbSNP_126	22	6001,1123		2605,791,166	no	coding,intron	TSPEAR,KRTAP10-7	NM_198689.2,NM_144991.2	,	3454,1351,407	A1A1,A1R,RR		15.7636,31.5758,20.7694	,	,		8259,2165				44845098	SO:0001651	inframe_deletion	386675			AJ566385	CCDS74803.1	21q22.3	2014-04-10			ENSG00000205441	ENSG00000272804		"""Keratin associated proteins"""	22970	protein-coding gene	gene with protein product				KRTAP18-7			Standard	NM_198689		Approved	KAP10.7, KAP18.7	uc002zfn.4	P60409	OTTHUMG00000188307	ENST00000380102.2:c.135_149delCTGCTGCGCCCCCAG	21.37:g.46020656_46020670delCTGCTGCGCCCCCAG	ENSP00000369445:p.Cys46_Ser50del	Somatic		Capture	Illumina HiSeq	Phase_I	44845084	Q0VDJ8|Q70LJ2	Frame_Shift_Del	DEL	ENST00000380102.2	37																																																																																					KRTAP10-7-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000128038.1	NM_198689	
NEFH	4744	hgsc.bcm.edu	37	22	29885567	29885568	+	In_Frame_Ins	INS	-	-	AAGTCCCCTGAGAAGGCC	rs147489453|rs559153194|rs75808076|rs59279731		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr22:29885567_29885568insAAGTCCCCTGAGAAGGCC	ENST00000310624.6	+	4	1971_1972	c.1938_1939insAAGTCCCCTGAGAAGGCC	c.(1939-1941)aag>AAGTCCCCTGAGAAGGCCaag	p.647_647K>KSPEKAK		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	653	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.			Missing (in Ref. 1; CAA33366 and 5; AC000035). {ECO:0000305}.	axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						AGGAGGAAGCAAAGTCCCCTGA	0.569																																																	0			22								2816,1448		937,942,253						-5.3	0.0		dbSNP_134	77	5046,3206		1537,1972,617	no	coding	NEFH	NM_021076.3		2474,2914,870	A1A1,A1R,RR		38.8512,33.9587,37.1844				7862,4654				28215568	SO:0001652	inframe_insertion	4744				CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1939_1956dupAAGTCCCCTGAGAAGGCC	22.37:g.29885567_29885568insAAGTCCCCTGAGAAGGCC	Exception_encountered	Somatic		Capture	Illumina HiSeq	Phase_I	28215567	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	In_Frame_Ins	INS	ENST00000310624.6	37	CCDS13858.1																																																																																				NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
FAM47A	158724	hgsc.bcm.edu	37	X	34149658	34149693	+	In_Frame_Del	DEL	ATGGGACACTCCAGTCTCTGGAGGCTCCGGGCGGAG	ATGGGACACTCCAGTCTCTGGAGGCTCCGGGCGGAG	-	rs367563899|rs201090915|rs201363312|rs373732464		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	ATGGGACACTCCAGTCTCTGGAGGCTCCGGGCGGAG	ATGGGACACTCCAGTCTCTGGAGGCTCCGGGCGGAG					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chrX:34149658_34149693delATGGGACACTCCAGTCTCTGGAGGCTCCGGGCGGAG	ENST00000346193.3	-	1	754_789	c.703_738delCTCCGCCCGGAGCCTCCAGAGACTGGAGTGTCCCAT	c.(703-738)ctccgcccggagcctccagagactggagtgtcccatdel	p.LRPEPPETGVSH235del		NM_203408.3	NP_981953.2	Q5JRC9	FA47A_HUMAN	family with sequence similarity 47, member A	235	Pro-rich.							p.L235_H246delLRPEPPETGVSH(1)|p.P240P(1)		NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(5)|large_intestine(17)|lung(44)|ovary(5)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	97						CCGGGCGGATATGGGACACTCCAGTCTCTGGAGGCTCCGGGCGGAGATGGGACACT	0.627														5	0.0013245	0.0	0.0	3775	,	,		15035	0.0		0.004	False		,,,				2504	0.001																2	Substitution - coding silent(1)|Deletion - In frame(1)	ovary(1)|lung(1)	X								33,3667		0,20,13,1562,523						-0.3	0.0			32	98,6373		2,62,32,2290,1731	no	coding	FAM47A	NM_203408.3		2,82,45,3852,2254	A1A1,A1R,A1,RR,R		1.5144,0.8919,1.288				131,10040				34059614	SO:0001651	inframe_deletion	158724			BC026171	CCDS43926.1	Xp21.1	2004-08-09			ENSG00000185448	ENSG00000185448			29962	protein-coding gene	gene with protein product	"""similar to hypothetical protein FLJ35782"""					12477932	Standard	NM_203408		Approved	MGC27003	uc004ddg.3	Q5JRC9	OTTHUMG00000021339	ENST00000346193.3:c.703_738delCTCCGCCCGGAGCCTCCAGAGACTGGAGTGTCCCAT	X.37:g.34149658_34149693delATGGGACACTCCAGTCTCTGGAGGCTCCGGGCGGAG	ENSP00000345029:p.Leu235_His246del	Somatic		Capture	Illumina HiSeq	Phase_I	34059579	A8K8I9|Q8TAA0	In_Frame_Del	DEL	ENST00000346193.3	37	CCDS43926.1																																																																																				FAM47A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056205.1	NM_203408	
