#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_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	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_gc_content_full	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	i_t_alt_count_full	i_t_ref_count_full	t_alt_count	t_ref_count
MYO3A	53904	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	26500833	26500833	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-7471-01A-11D-2253-08	TCGA-HT-7471-10B-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	06425414-a57c-40df-905e-290fa2086153	d0b349eb-d50b-43ec-903d-e8494d8705ca	g.chr10:26500833G>A	ENST00000265944.5	+	35	4958	c.4792G>A	c.(4792-4794)Gac>Aac	p.D1598N	MYO3A_ENST00000543632.1_Missense_Mutation_p.R613Q	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	1598					ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						CAACCCCTACGACTTCAGGAG	0.652																																																0													46.0	54.0	52.0					10																	26500833		2203	4300	6503	SO:0001583	missense	53904			AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"""Myosins / Myosin superfamily : Class III"""	7601	protein-coding gene	gene with protein product		606808	"""deafness, autosomal recessive 30"""	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.4792G>A	10.37:g.26500833G>A	ENSP00000265944:p.Asp1598Asn		Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	37	CCDS7148.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.8|20.8	4.047550|4.047550	0.75846|0.75846	.|.	.|.	ENSG00000095777|ENSG00000095777	ENST00000265944|ENST00000543632	D|T	0.83914|0.75704	-1.78|-0.96	4.76|4.76	4.76|4.76	0.60689|0.60689	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.81211|0.81211	0.4775|0.4775	L|L	0.36672|0.36672	1.1|1.1	0.35295|0.35295	D|D	0.782547|0.782547	D|D	0.89917|0.71674	1.0|0.998	D|D	0.83275|0.72982	0.996|0.979	D|D	0.86433|0.86433	0.1762|0.1762	10|9	0.35671|0.87932	T|D	0.21|0	.|.	17.9464|17.9464	0.89040|0.89040	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1598|613	Q8NEV4|F5H0U9	MYO3A_HUMAN|.	N|Q	1598|613	ENSP00000265944:D1598N|ENSP00000445909:R613Q	ENSP00000265944:D1598N|ENSP00000445909:R613Q	D|R	+|+	1|2	0|0	MYO3A|MYO3A	26540839|26540839	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.056000|0.056000	0.15407|0.15407	8.346000|8.346000	0.90060|0.90060	2.478000|2.478000	0.83669|0.83669	0.455000|0.455000	0.32223|0.32223	GAC|CGA		0.652	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		6	15	6	15
CHST15	51363	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	125780796	125780796	+	Missense_Mutation	SNP	G	G	C			TCGA-HT-7471-01A-11D-2253-08	TCGA-HT-7471-10B-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	06425414-a57c-40df-905e-290fa2086153	d0b349eb-d50b-43ec-903d-e8494d8705ca	g.chr10:125780796G>C	ENST00000346248.5	-	6	1965	c.1323C>G	c.(1321-1323)aaC>aaG	p.N441K	CHST15_ENST00000435907.1_Missense_Mutation_p.N441K|CHST15_ENST00000421115.1_Missense_Mutation_p.N441K	NM_015892.4	NP_056976.2	Q7LFX5	CHSTF_HUMAN	carbohydrate (N-acetylgalactosamine 4-sulfate 6-O) sulfotransferase 15	441					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|hexose biosynthetic process (GO:0019319)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity (GO:0050659)			endometrium(4)|kidney(1)|large_intestine(11)|lung(6)|ovary(3)|stomach(1)	26						TGAGGGTGTTGTTGTAGACGC	0.542																																																0													65.0	58.0	60.0					10																	125780796		2203	4300	6503	SO:0001583	missense	51363			AB011170	CCDS7638.1	10q26	2009-07-09			ENSG00000182022	ENSG00000182022	2.8.2.33	"""Sulfotransferases, membrane-bound"""	18137	protein-coding gene	gene with protein product	"""B cell RAG associated protein"", ""N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase"""	608277				9628581, 9754571, 11572857	Standard	NM_014863		Approved	GALNAC4S-6ST, BRAG, KIAA0598	uc001lhm.4	Q7LFX5	OTTHUMG00000019208	ENST00000346248.5:c.1323C>G	10.37:g.125780796G>C	ENSP00000333947:p.Asn441Lys		O60338|O60474|Q86VM4	Missense_Mutation	SNP	ENST00000346248.5	37	CCDS7638.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.026926	0.75390	.	.	ENSG00000182022	ENST00000346248;ENST00000435907;ENST00000546346;ENST00000421115	.	.	.	4.41	3.49	0.39957	Sulfotransferase domain (1);	0.108239	0.64402	D	0.000010	T	0.65811	0.2727	L	0.45422	1.42	0.51233	D	0.99991	D;B	0.89917	1.0;0.408	D;B	0.87578	0.998;0.13	T	0.62923	-0.6751	9	0.31617	T	0.26	-22.8097	12.6393	0.56700	0.0832:0.0:0.9168:0.0	.	441;441	Q7LFX5-2;Q7LFX5	.;CHSTF_HUMAN	K	441	.	ENSP00000333947:N441K	N	-	3	2	CHST15	125770786	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.332000	0.72934	1.996000	0.58369	0.467000	0.42956	AAC		0.542	CHST15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050856.1	NM_015892		10	13	10	13
CHRNA3	1136	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	78894483	78894483	+	Silent	SNP	C	C	T	rs577413653		TCGA-HT-7471-01A-11D-2253-08	TCGA-HT-7471-10B-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	06425414-a57c-40df-905e-290fa2086153	d0b349eb-d50b-43ec-903d-e8494d8705ca	g.chr15:78894483C>T	ENST00000326828.5	-	5	885	c.501G>A	c.(499-501)ccG>ccA	p.P167P	CHRNA3_ENST00000348639.3_Silent_p.P167P	NM_000743.4	NP_000734.2	P32297	ACHA3_HUMAN	cholinergic receptor, nicotinic, alpha 3 (neuronal)	167					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|behavioral response to nicotine (GO:0035095)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of dendrite morphogenesis (GO:0048814)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of membrane potential (GO:0042391)|regulation of smooth muscle contraction (GO:0006940)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission involved in micturition (GO:0060084)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18					Bupropion(DB01156)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Levomethadyl Acetate(DB01227)|Nicotine(DB00184)|Pentolinium(DB01090)|Varenicline(DB01273)	GGTAATCAAACGGGAAGTAGG	0.483													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19157	0.0		0.0	False		,,,				2504	0.0															0													169.0	156.0	160.0					15																	78894483		2196	4293	6489	SO:0001819	synonymous_variant	1136				CCDS10305.1, CCDS53964.1	15q24	2012-02-11	2012-02-07		ENSG00000080644	ENSG00000080644		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1957	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 3 (neuronal)"""	118503	"""cholinergic receptor, nicotinic, alpha polypeptide 3"""			2004777	Standard	NM_000743		Approved		uc002bec.3	P32297	OTTHUMG00000143863	ENST00000326828.5:c.501G>A	15.37:g.78894483C>T			Q15823|Q4KMN8|Q86U77|Q96RH3|Q99553|Q9BQ93|Q9BRR4	Silent	SNP	ENST00000326828.5	37	CCDS10305.1																																																																																				0.483	CHRNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290111.3			34	177	34	177
TMC8	147138	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	76130033	76130033	+	Silent	SNP	G	G	A			TCGA-HT-7471-01A-11D-2253-08	TCGA-HT-7471-10B-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	06425414-a57c-40df-905e-290fa2086153	d0b349eb-d50b-43ec-903d-e8494d8705ca	g.chr17:76130033G>A	ENST00000318430.5	+	7	1142	c.768G>A	c.(766-768)gtG>gtA	p.V256V	TMC8_ENST00000589691.1_Silent_p.V33V|TMC6_ENST00000322914.3_5'Flank	NM_152468.4	NP_689681.2	Q8IU68	TMC8_HUMAN	transmembrane channel-like 8	256					ion transport (GO:0006811)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|regulation of cell growth (GO:0001558)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|zinc ion homeostasis (GO:0055069)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	receptor binding (GO:0005102)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	12			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)|OV - Ovarian serous cystadenocarcinoma(97;0.192)			GCATCCGGGTGCAGGAAGCAG	0.577																																																0													73.0	72.0	73.0					17																	76130033		2203	4300	6503	SO:0001819	synonymous_variant	147138			AY057380	CCDS32749.1	17q25.3	2014-09-17	2005-11-10	2005-11-10	ENSG00000167895	ENSG00000167895			20474	protein-coding gene	gene with protein product		605829	"""epidermodysplasia verruciformis 2"""	EVER2		12426567	Standard	NM_152468		Approved	EVIN2	uc002jup.2	Q8IU68		ENST00000318430.5:c.768G>A	17.37:g.76130033G>A			Q2YDC0|Q8IWU7|Q8N358|Q8NF04	Silent	SNP	ENST00000318430.5	37	CCDS32749.1																																																																																				0.577	TMC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436900.3			36	44	36	44
GATA6	2627	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	18	19751533	19751533	+	Missense_Mutation	SNP	A	A	G			TCGA-HT-7471-01A-11D-2253-08	TCGA-HT-7471-10B-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	06425414-a57c-40df-905e-290fa2086153	d0b349eb-d50b-43ec-903d-e8494d8705ca	g.chr18:19751533A>G	ENST00000269216.3	+	2	705	c.428A>G	c.(427-429)cAg>cGg	p.Q143R	GATA6-AS1_ENST00000583490.1_lincRNA|GATA6_ENST00000581694.1_Missense_Mutation_p.Q143R	NM_005257.4	NP_005248.2	Q92908	GATA6_HUMAN	GATA binding protein 6	143					blood coagulation (GO:0007596)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cardiac vascular smooth muscle cell differentiation (GO:0060947)|cellular response to BMP stimulus (GO:0071773)|cellular response to gonadotropin stimulus (GO:0071371)|cellular response to hypoxia (GO:0071456)|Clara cell differentiation (GO:0060486)|endodermal cell fate determination (GO:0007493)|in utero embryonic development (GO:0001701)|intestinal epithelial cell differentiation (GO:0060575)|liver development (GO:0001889)|lung saccule development (GO:0060430)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta1 production (GO:0032911)|negative regulation of transforming growth factor beta2 production (GO:0032912)|organ formation (GO:0048645)|outflow tract septum morphogenesis (GO:0003148)|pancreatic A cell differentiation (GO:0003310)|phospholipid metabolic process (GO:0006644)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to growth factor (GO:0070848)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)|tube morphogenesis (GO:0035239)|type B pancreatic cell differentiation (GO:0003309)|Type II pneumocyte differentiation (GO:0060510)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(8)|prostate(1)|skin(1)	18	all_cancers(21;0.00271)|all_epithelial(16;7.31e-05)|Ovarian(2;0.116)|Lung NSC(20;0.123)|all_lung(20;0.246)		STAD - Stomach adenocarcinoma(5;0.106)			GCACCCGAGCAGCCGGAGGAG	0.716																																					Colon(8;48 282 46199 46856)|Melanoma(177;170 2725 12489 26999)											0													14.0	19.0	17.0					18																	19751533		2176	4263	6439	SO:0001583	missense	2627			U66075	CCDS11872.1	18q11-q12	2013-01-25	2001-11-28		ENSG00000141448	ENSG00000141448		"""GATA zinc finger domain containing"""	4174	protein-coding gene	gene with protein product		601656	"""GATA-binding protein 6"""			8975704	Standard	XM_005258248		Approved		uc002ktt.2	Q92908	OTTHUMG00000131767	ENST00000269216.3:c.428A>G	18.37:g.19751533A>G	ENSP00000269216:p.Gln143Arg		B0YJ17|P78327	Missense_Mutation	SNP	ENST00000269216.3	37	CCDS11872.1	.	.	.	.	.	.	.	.	.	.	a	14.72	2.620219	0.46736	.	.	ENSG00000141448	ENST00000269216	D	0.97870	-4.58	3.15	1.95	0.26073	.	1.149030	0.06494	N	0.735174	D	0.93284	0.7860	N	0.24115	0.695	0.20926	N	0.999826	P	0.42827	0.791	B	0.38056	0.264	D	0.86812	0.1999	10	0.16420	T	0.52	-23.1144	7.9805	0.30181	0.5901:0.4099:0.0:0.0	.	143	Q92908	GATA6_HUMAN	R	143	ENSP00000269216:Q143R	ENSP00000269216:Q143R	Q	+	2	0	GATA6	18005531	0.998000	0.40836	0.867000	0.34043	0.991000	0.79684	0.922000	0.28734	0.304000	0.22809	0.370000	0.22315	CAG		0.716	GATA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254696.1	NM_005257		6	40	6	40
COLGALT1	79709	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	17690296	17690296	+	Silent	SNP	G	G	A			TCGA-HT-7471-01A-11D-2253-08	TCGA-HT-7471-10B-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	06425414-a57c-40df-905e-290fa2086153	d0b349eb-d50b-43ec-903d-e8494d8705ca	g.chr19:17690296G>A	ENST00000252599.4	+	10	1392	c.1272G>A	c.(1270-1272)gtG>gtA	p.V424V		NM_024656.2	NP_078932.2	Q8NBJ5	GT251_HUMAN	collagen beta(1-O)galactosyltransferase 1	424					extracellular matrix organization (GO:0030198)|lipopolysaccharide biosynthetic process (GO:0009103)	endoplasmic reticulum lumen (GO:0005788)|membrane (GO:0016020)	procollagen galactosyltransferase activity (GO:0050211)										CTCAGGTGGTGGACCGGGGGC	0.562																																																0													79.0	70.0	73.0					19																	17690296		2203	4300	6503	SO:0001819	synonymous_variant	79709			AK075541	CCDS12363.1	19p13.11	2013-02-27	2013-02-27	2013-02-27	ENSG00000130309	ENSG00000130309			26182	protein-coding gene	gene with protein product			"""glycosyltransferase 25 domain containing 1"""	GLT25D1		19075007	Standard	NM_024656		Approved	FLJ22329	uc002nhc.1	Q8NBJ5		ENST00000252599.4:c.1272G>A	19.37:g.17690296G>A			Q8NC64	Silent	SNP	ENST00000252599.4	37	CCDS12363.1																																																																																				0.562	COLGALT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464216.1	NM_024656		29	45	29	45
ZNF761	388561	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	53959188	53959188	+	RNA	SNP	G	G	A			TCGA-HT-7471-01A-11D-2253-08	TCGA-HT-7471-10B-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	06425414-a57c-40df-905e-290fa2086153	d0b349eb-d50b-43ec-903d-e8494d8705ca	g.chr19:53959188G>A	ENST00000454407.1	+	0	1880							Q86XN6	ZN761_HUMAN	zinc finger protein 761						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	30				GBM - Glioblastoma multiforme(134;0.00786)		AAAGCTTTCCGTTTCAAATCA	0.423																																																0													75.0	80.0	78.0					19																	53959188		2203	4300	6503			388561			AB107355		19q13.42	2007-10-05	2006-08-11	2006-08-11	ENSG00000160336	ENSG00000160336		"""Zinc fingers, C2H2-type"""	23179	protein-coding gene	gene with protein product							Standard	NM_001008401		Approved	KIAA2033, FLJ16231, FLJ35333	uc010eqp.3	Q86XN6	OTTHUMG00000156999		19.37:g.53959188G>A			Q6ZNB9	RNA	SNP	ENST00000454407.1	37																																																																																					0.423	ZNF761-203	KNOWN	basic	processed_transcript	processed_transcript		NM_001008401		36	3	36	3
FUBP1	8880	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	78430773	78430773	+	Nonsense_Mutation	SNP	C	C	A			TCGA-HT-7471-01A-11D-2253-08	TCGA-HT-7471-10B-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	06425414-a57c-40df-905e-290fa2086153	d0b349eb-d50b-43ec-903d-e8494d8705ca	g.chr1:78430773C>A	ENST00000370768.2	-	8	697	c.616G>T	c.(616-618)Gaa>Taa	p.E206*	FUBP1_ENST00000436586.2_Nonsense_Mutation_p.E227*|FUBP1_ENST00000370767.1_Nonsense_Mutation_p.E206*	NM_003902.3	NP_003893.2	Q96AE4	FUBP1_HUMAN	far upstream element (FUSE) binding protein 1	206	KH 2. {ECO:0000255|PROSITE- ProRule:PRU00117}.				positive regulation of gene expression (GO:0010628)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)			central_nervous_system(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(1)|upper_aerodigestive_tract(3)	17						TTAATAGTTTCTCCCCCTTTT	0.393			"""F, N"""		oligodendroglioma																																		Rec	yes		1	1p13.1	8880	far upstream element (FUSE) binding protein 1		O	0													182.0	183.0	183.0					1																	78430773		2203	4300	6503	SO:0001587	stop_gained	8880			U05040	CCDS683.1	1p31.1	2008-02-05			ENSG00000162613	ENSG00000162613			4004	protein-coding gene	gene with protein product		603444		FUBP		8125259	Standard	XM_005271309		Approved	FBP	uc001dii.3	Q96AE4	OTTHUMG00000040799	ENST00000370768.2:c.616G>T	1.37:g.78430773C>A	ENSP00000359804:p.Glu206*		Q12828	Nonsense_Mutation	SNP	ENST00000370768.2	37	CCDS683.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.629714	0.87660	.	.	ENSG00000162613	ENST00000370773;ENST00000370767;ENST00000370768;ENST00000394922;ENST00000436586;ENST00000421641	.	.	.	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-14.9192	19.9468	0.97185	0.0:1.0:0.0:0.0	.	.	.	.	X	205;206;206;205;227;226	.	ENSP00000294623:E205X	E	-	1	0	FUBP1	78203361	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.776000	0.85560	2.784000	0.95788	0.650000	0.86243	GAA		0.393	FUBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098030.3	NM_003902		128	39	128	39
KIAA1324	57535	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	109707134	109707134	+	Silent	SNP	C	C	T	rs144842352		TCGA-HT-7471-01A-11D-2253-08	TCGA-HT-7471-10B-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	06425414-a57c-40df-905e-290fa2086153	d0b349eb-d50b-43ec-903d-e8494d8705ca	g.chr1:109707134C>T	ENST00000369939.3	+	3	471	c.288C>T	c.(286-288)aaC>aaT	p.N96N	KIAA1324_ENST00000529753.1_Silent_p.N96N	NM_020775.4	NP_065826	Q6UXG2	K1324_HUMAN	KIAA1324	96					cellular response to starvation (GO:0009267)|macroautophagy (GO:0016236)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|positive regulation of autophagic vacuole assembly (GO:2000786)|positive regulation of vacuole organization (GO:0044090)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34		all_epithelial(167;0.000102)|all_lung(203;0.000323)|Lung NSC(277;0.00063)		Colorectal(144;0.0188)|Lung(183;0.0527)|COAD - Colon adenocarcinoma(174;0.14)|Epithelial(280;0.21)|all cancers(265;0.249)		TCTCCTGCAACGCCGGGGAGT	0.592																																																0								C		1,4405	2.1+/-5.4	0,1,2202	109.0	108.0	108.0		288	-7.5	0.9	1	dbSNP_134	108	0,8600		0,0,4300	no	coding-synonymous	KIAA1324	NM_020775.3		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		96/1014	109707134	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	57535			AK057647	CCDS794.1, CCDS58015.1	1p13.3	2008-09-18			ENSG00000116299	ENSG00000116299			29618	protein-coding gene	gene with protein product	"""estrogen induced gene 121"""	611298				10718198, 16322283	Standard	NM_020775		Approved	maba1, EIG121	uc021orb.1	Q6UXG2	OTTHUMG00000011725	ENST00000369939.3:c.288C>T	1.37:g.109707134C>T			Q08AE6|Q5T5C9|Q5T5D0|Q5T5D1|Q9P2M2	Silent	SNP	ENST00000369939.3	37	CCDS794.1																																																																																				0.592	KIAA1324-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032389.2	NM_020775		103	21	103	21
ADCY10	55811	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	167870912	167870912	+	Nonsense_Mutation	SNP	G	G	A			TCGA-HT-7471-01A-11D-2253-08	TCGA-HT-7471-10B-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	06425414-a57c-40df-905e-290fa2086153	d0b349eb-d50b-43ec-903d-e8494d8705ca	g.chr1:167870912G>A	ENST00000367851.4	-	5	608	c.424C>T	c.(424-426)Cga>Tga	p.R142*	ADCY10_ENST00000545172.1_Intron|ADCY10_ENST00000367848.1_Nonsense_Mutation_p.R50*	NM_018417.4	NP_060887.2	Q96PN6	ADCYA_HUMAN	adenylate cyclase 10 (soluble)	142	Guanylate cyclase 1. {ECO:0000255|PROSITE-ProRule:PRU00099}.				cAMP biosynthetic process (GO:0006171)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|spermatogenesis (GO:0007283)	apical part of cell (GO:0045177)|axon (GO:0030424)|basal part of cell (GO:0045178)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)			autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(26)|ovary(2)|prostate(4)|skin(6)|stomach(1)|urinary_tract(1)	63						ATCTTGACTCGGATGTCTAGG	0.463																																																0													170.0	164.0	166.0					1																	167870912		2203	4300	6503	SO:0001587	stop_gained	55811			AF271058	CCDS1265.1, CCDS53426.1, CCDS72977.1	1q24	2013-02-04			ENSG00000143199	ENSG00000143199	4.6.1.1	"""Adenylate cyclases"""	21285	protein-coding gene	gene with protein product	"""soluble adenylyl cyclase"", ""Hypercalciuria, absorptive, 2"""	605205					Standard	XM_006711449		Approved	SAC, Sacy, SACI, HCA2, RP1-313L4.2	uc001ger.3	Q96PN6	OTTHUMG00000034573	ENST00000367851.4:c.424C>T	1.37:g.167870912G>A	ENSP00000356825:p.Arg142*		B4DZF0|F5GWS5|O95558|Q5R329|Q5R330|Q8WXV4|Q9NNX0	Nonsense_Mutation	SNP	ENST00000367851.4	37	CCDS1265.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.613178	0.87359	.	.	ENSG00000143199	ENST00000367851;ENST00000367848	.	.	.	5.76	3.84	0.44239	.	0.270367	0.26983	N	0.021504	.	.	.	.	.	.	0.80722	A	1.000000	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.6457	9.3555	0.38164	0.0:0.1576:0.6786:0.1638	.	.	.	.	X	142;50	.	ENSP00000356822:R50X	R	-	1	2	ADCY10	166137536	0.994000	0.37717	0.106000	0.21319	0.087000	0.18053	2.743000	0.47442	0.734000	0.32515	-0.323000	0.08544	CGA		0.463	ADCY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083663.1	NM_018417		87	102	87	102
CACNA1E	777	hgsc.bcm.edu;broad.mit.edu	37	1	181765891	181765891	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-7471-01A-11D-2253-08	TCGA-HT-7471-10B-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	06425414-a57c-40df-905e-290fa2086153	d0b349eb-d50b-43ec-903d-e8494d8705ca	g.chr1:181765891G>A	ENST00000367573.2	+	47	6296	c.6296G>A	c.(6295-6297)cGc>cAc	p.R2099H	CACNA1E_ENST00000367567.4_Missense_Mutation_p.R1663H|CACNA1E_ENST00000367570.1_Missense_Mutation_p.R2056H|CACNA1E_ENST00000358338.5_Missense_Mutation_p.R1988H|CACNA1E_ENST00000526775.1_Missense_Mutation_p.R2037H|CACNA1E_ENST00000357570.5_Missense_Mutation_p.R2050H|CACNA1E_ENST00000360108.3_Missense_Mutation_p.R2080H	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	2099					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						GATGTCTCCCGCTGCAATTCA	0.602																																																0													36.0	39.0	38.0					1																	181765891		1969	4166	6135	SO:0001583	missense	777			AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.6296G>A	1.37:g.181765891G>A	ENSP00000356545:p.Arg2099His		B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	37	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	G	36	5.659027	0.96734	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.99158	-5.33;-5.31;-4.67;-5.3;-5.5;-4.67;-4.67	5.91	5.91	0.95273	.	0.000000	0.50627	D	0.000113	D	0.98842	0.9609	L	0.36672	1.1	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.984;0.996	D	0.99924	1.1272	10	0.62326	D	0.03	.	19.8936	0.96942	0.0:0.0:1.0:0.0	.	2037;2056	Q15878-2;Q15878-3	.;.	H	2056;2037;2050;1988;1663;2080;2099	ENSP00000356542:R2056H;ENSP00000434814:R2037H;ENSP00000350183:R2050H;ENSP00000351101:R1988H;ENSP00000356539:R1663H;ENSP00000353222:R2080H;ENSP00000356545:R2099H	ENSP00000350183:R2050H	R	+	2	0	CACNA1E	180032514	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.050000	0.93843	2.793000	0.96121	0.655000	0.94253	CGC		0.602	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		3	18	3	18
SON	6651	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	21	34924118	34924118	+	Missense_Mutation	SNP	A	A	G	rs142324795		TCGA-HT-7471-01A-11D-2253-08	TCGA-HT-7471-10B-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	06425414-a57c-40df-905e-290fa2086153	d0b349eb-d50b-43ec-903d-e8494d8705ca	g.chr21:34924118A>G	ENST00000356577.4	+	3	3056	c.2581A>G	c.(2581-2583)Atg>Gtg	p.M861V	SON_ENST00000381679.4_Missense_Mutation_p.M861V|SON_ENST00000300278.4_Missense_Mutation_p.M861V|SON_ENST00000290239.6_Missense_Mutation_p.M861V|SON_ENST00000381692.2_Intron	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	861	17 X 10 AA tandem repeats of L-A-[ST]- [NSG]-[TS]-MDSQM.				cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of cell cycle (GO:0051726)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleic acid binding (GO:0003676)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(25)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	72						AACTAGCTCAATGGATTCCCA	0.493													A|||	1	0.000199681	0.0	0.0014	5008	,	,		26099	0.0		0.0	False		,,,				2504	0.0															0								A	VAL/MET,VAL/MET	1,4405	2.1+/-5.4	0,1,2202	173.0	169.0	170.0		2581,2581	5.7	1.0	21	dbSNP_134	170	0,8600		0,0,4300	yes	missense,missense	SON	NM_032195.1,NM_138927.1	21,21	0,1,6502	GG,GA,AA		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging	861/2304,861/2427	34924118	1,13005	2203	4300	6503	SO:0001583	missense	6651			AF380181	CCDS13629.1, CCDS13631.1, CCDS74784.1	21q22.1-q22.2	2013-01-28			ENSG00000159140	ENSG00000159140		"""G patch domain containing"""	11183	protein-coding gene	gene with protein product	"""NRE-binding protein"", ""negative regulatory element-binding protein"", ""Bax antagonist selected in Saccharomyces 1"""	182465		C21orf50		8318737, 21551269	Standard	NM_032195		Approved	DBP-5, NREBP, KIAA1019, BASS1, FLJ21099, FLJ33914	uc002yse.1	P18583	OTTHUMG00000065806	ENST00000356577.4:c.2581A>G	21.37:g.34924118A>G	ENSP00000348984:p.Met861Val		D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Missense_Mutation	SNP	ENST00000356577.4	37	CCDS13629.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	A	13.29	2.193512	0.38707	2.27E-4	0.0	ENSG00000159140	ENST00000356577;ENST00000290239;ENST00000300278;ENST00000381679	T;T;T;T	0.80653	-1.4;-1.4;-1.4;-1.4	5.69	5.69	0.88448	.	0.000000	0.64402	D	0.000003	D	0.86418	0.5928	M	0.63843	1.955	0.29292	N	0.869312	P;P;B	0.50369	0.891;0.934;0.02	P;D;B	0.65684	0.867;0.937;0.041	T	0.80930	-0.1162	10	0.21014	T	0.42	.	13.9442	0.64075	1.0:0.0:0.0:0.0	.	861;861;861	P18583;P18583-3;P18583-6	SON_HUMAN;.;.	V	861	ENSP00000348984:M861V;ENSP00000290239:M861V;ENSP00000300278:M861V;ENSP00000371095:M861V	ENSP00000290239:M861V	M	+	1	0	SON	33845988	0.861000	0.29849	1.000000	0.80357	0.955000	0.61496	1.578000	0.36525	2.168000	0.68352	0.524000	0.50904	ATG		0.493	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927		102	140	102	140
LRRC3	81543	hgsc.bcm.edu;broad.mit.edu	37	21	45876870	45876870	+	Silent	SNP	C	C	T	rs138458454		TCGA-HT-7471-01A-11D-2253-08	TCGA-HT-7471-10B-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	06425414-a57c-40df-905e-290fa2086153	d0b349eb-d50b-43ec-903d-e8494d8705ca	g.chr21:45876870C>T	ENST00000291592.4	+	2	660	c.343C>T	c.(343-345)Ctg>Ttg	p.L115L	LRRC3DN_ENST00000596691.1_5'Flank|LRRC3-AS1_ENST00000426578.1_RNA	NM_030891.3	NP_112153.1	Q9BY71	LRRC3_HUMAN	leucine rich repeat containing 3	115						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|lung(1)|urinary_tract(1)	5		Breast(209;0.00908)		COAD - Colon adenocarcinoma(84;0.148)|Lung(125;0.195)		GGCCGGGGGCCTGCGGCTGCT	0.672																																																0								C		0,4370		0,0,2185	26.0	30.0	28.0		343	3.9	1.0	21	dbSNP_134	28	1,8525		0,1,4262	no	coding-synonymous	LRRC3	NM_030891.3		0,1,6447	TT,TC,CC		0.0117,0.0,0.0078		115/258	45876870	1,12895	2185	4263	6448	SO:0001819	synonymous_variant	81543			AB058646	CCDS13711.1	21q22.3	2011-12-07	2002-06-20		ENSG00000160233	ENSG00000160233			14965	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 102"""	C21orf102		12036297	Standard	NM_030891		Approved		uc002zfa.3	Q9BY71	OTTHUMG00000040847	ENST00000291592.4:c.343C>T	21.37:g.45876870C>T			Q0VDJ2	Silent	SNP	ENST00000291592.4	37	CCDS13711.1																																																																																				0.672	LRRC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098095.3			4	59	4	59
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-HT-7471-01A-11D-2253-08	TCGA-HT-7471-10B-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	06425414-a57c-40df-905e-290fa2086153	d0b349eb-d50b-43ec-903d-e8494d8705ca	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000345146.2_Missense_Mutation_p.R132H|IDH1_ENST00000446179.1_Missense_Mutation_p.R132H	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393			Mis		gliobastoma																																Pancreas(158;264 1958 3300 35450 36047)		Dom	yes		2	2q33.3	3417	"""isocitrate dehydrogenase 1 (NADP+), soluble"""		O	2835	Substitution - Missense(2834)|Complex - compound substitution(1)	central_nervous_system(2579)|haematopoietic_and_lymphoid_tissue(205)|bone(43)|prostate(4)|biliary_tract(2)|urinary_tract(1)|skin(1)											79.0	73.0	75.0					2																	209113112		2203	4300	6503	SO:0001583	missense	3417				CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.395G>A	2.37:g.209113112C>T	ENSP00000390265:p.Arg132His		Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.657324	0.88154	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	5.57	4.69	0.59074	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.93145	0.7817	H	0.99379	4.54	0.80722	D	1	B	0.25486	0.127	B	0.25405	0.06	D	0.92324	0.5868	10	0.87932	D	0	-20.0399	14.3783	0.66895	0.0:0.9288:0.0:0.0712	.	132	O75874	IDHC_HUMAN	H	132	ENSP00000260985:R132H;ENSP00000410513:R132H;ENSP00000390265:R132H;ENSP00000391075:R132H	ENSP00000260985:R132H	R	-	2	0	IDH1	208821357	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	6.088000	0.71371	1.356000	0.45884	0.555000	0.69702	CGT		0.393	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			55	70	55	70
STAB1	23166	hgsc.bcm.edu;broad.mit.edu	37	3	52552602	52552602	+	Silent	SNP	C	C	T			TCGA-HT-7471-01A-11D-2253-08	TCGA-HT-7471-10B-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	06425414-a57c-40df-905e-290fa2086153	d0b349eb-d50b-43ec-903d-e8494d8705ca	g.chr3:52552602C>T	ENST00000321725.6	+	47	4936	c.4860C>T	c.(4858-4860)caC>caT	p.H1620H		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	1620	FAS1 5. {ECO:0000255|PROSITE- ProRule:PRU00082, ECO:0000305}.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|oxidation-reduction process (GO:0055114)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|protein disulfide oxidoreductase activity (GO:0015035)|scavenger receptor activity (GO:0005044)			breast(4)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(13)|liver(1)|lung(27)|ovary(1)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	76				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		TCGTGCCGCACGCAGATCTAA	0.627																																																0													43.0	34.0	37.0					3																	52552602		2199	4295	6494	SO:0001819	synonymous_variant	23166			AJ275213	CCDS33768.1	3p21.31	2008-07-18			ENSG00000010327	ENSG00000010327			18628	protein-coding gene	gene with protein product	"""MS-1 antigen"", ""fasciclin egf-like, laminin-type egf-like, and link domain-containing scavenger receptor-1"", ""common lymphatic endothelial and vascular endothelial receptor-1"""	608560				11829752, 12077138	Standard	XM_005264973		Approved	KIAA0246, STAB-1, FEEL-1, CLEVER-1, FELE-1, FEX1	uc003dej.3	Q9NY15	OTTHUMG00000158574	ENST00000321725.6:c.4860C>T	3.37:g.52552602C>T			A7E297|Q8IUH0|Q8IUH1|Q93072	Silent	SNP	ENST00000321725.6	37	CCDS33768.1																																																																																				0.627	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136		5	8	5	8
SLC6A3	6531	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	1409836	1409836	+	Splice_Site	SNP	G	G	A	rs2270912	byFrequency	TCGA-HT-7471-01A-11D-2253-08	TCGA-HT-7471-10B-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	06425414-a57c-40df-905e-290fa2086153	d0b349eb-d50b-43ec-903d-e8494d8705ca	g.chr5:1409836G>A	ENST00000270349.9	-	10	1525	c.1398C>T	c.(1396-1398)aaC>aaT	p.N466N	SLC6A3_ENST00000453492.2_Splice_Site_p.N466N	NM_001044.4	NP_001035.1	Q01959	SC6A3_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 3	466					adenohypophysis development (GO:0021984)|aging (GO:0007568)|cation transmembrane transport (GO:0098655)|cell death (GO:0008219)|dopamine biosynthetic process (GO:0042416)|dopamine catabolic process (GO:0042420)|dopamine transport (GO:0015872)|lactation (GO:0007595)|locomotory behavior (GO:0007626)|monoamine transport (GO:0015844)|neurotransmitter biosynthetic process (GO:0042136)|positive regulation of multicellular organism growth (GO:0040018)|prepulse inhibition (GO:0060134)|regulation of dopamine metabolic process (GO:0042053)|response to cAMP (GO:0051591)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to iron ion (GO:0010039)|response to nicotine (GO:0035094)|sensory perception of smell (GO:0007608)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	axon (GO:0030424)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine transmembrane transporter activity (GO:0005329)|dopamine:sodium symporter activity (GO:0005330)|drug binding (GO:0008144)|monoamine transmembrane transporter activity (GO:0008504)			breast(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(19)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	38			OV - Ovarian serous cystadenocarcinoma(19;0.00928)|all cancers(22;0.0262)		Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Benzatropine(DB00245)|Benzphetamine(DB00865)|Bupropion(DB01156)|Chloroprocaine(DB01161)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Cocaine(DB00907)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Diethylpropion(DB00937)|Diphenylpyraline(DB01146)|Dopamine(DB00988)|Duloxetine(DB00476)|Ephedra(DB01363)|Escitalopram(DB01175)|Fencamfamine(DB01463)|Imipramine(DB00458)|Ioflupane I 123(DB08824)|Lisdexamfetamine(DB01255)|Loxapine(DB00408)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Mirtazapine(DB00370)|Modafinil(DB00745)|Nefazodone(DB01149)|Pethidine(DB00454)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Procaine(DB00721)|Pseudoephedrine(DB00852)|Sertraline(DB01104)|Sibutramine(DB01105)|Trimipramine(DB00726)|Venlafaxine(DB00285)	TGGTACGTACGTTGGTGACGC	0.617													G|||	23	0.00459265	0.0061	0.0043	5008	,	,		22372	0.0089		0.0	False		,,,				2504	0.0031															0								G		20,4386	27.2+/-55.0	0,20,2183	192.0	142.0	159.0		1398	-3.6	0.5	5	dbSNP_100	159	1,8597	1.2+/-3.3	0,1,4298	yes	coding-synonymous-near-splice	SLC6A3	NM_001044.4		0,21,6481	AA,AG,GG		0.0116,0.4539,0.1615		466/621	1409836	21,12983	2203	4299	6502	SO:0001630	splice_region_variant	6531				CCDS3863.1	5p15.3	2013-07-19	2013-07-19		ENSG00000142319	ENSG00000142319		"""Solute carriers"""	11049	protein-coding gene	gene with protein product	"""dopamine transporter"""	126455	"""solute carrier family 6 (neurotransmitter transporter, dopamine), member 3"", ""dopamine transporter 1"""	DAT1		1406597	Standard	NM_001044		Approved	DAT	uc003jck.3	Q01959	OTTHUMG00000131016	ENST00000270349.9:c.1398+1C>T	5.37:g.1409836G>A			A2RUN4|Q14996	Splice_Site	SNP	ENST00000270349.9	37	CCDS3863.1																																																																																				0.617	SLC6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253650.3	NM_001044	Silent	45	51	45	51
TTYH3	80727	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	2698612	2698612	+	Missense_Mutation	SNP	A	A	G			TCGA-HT-7471-01A-11D-2253-08	TCGA-HT-7471-10B-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	06425414-a57c-40df-905e-290fa2086153	d0b349eb-d50b-43ec-903d-e8494d8705ca	g.chr7:2698612A>G	ENST00000258796.7	+	13	1668	c.1463A>G	c.(1462-1464)aAc>aGc	p.N488S	TTYH3_ENST00000403167.1_Missense_Mutation_p.N317S|TTYH3_ENST00000407643.1_Missense_Mutation_p.N456S	NM_025250.2	NP_079526.1	Q9C0H2	TTYH3_HUMAN	tweety family member 3	488					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)|intracellular calcium activated chloride channel activity (GO:0005229)			kidney(1)|large_intestine(3)|lung(9)|prostate(2)|upper_aerodigestive_tract(2)	17		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;2.04e-14)		CGCTGTGAGAACACCCCACTC	0.642																																																0													136.0	130.0	132.0					7																	2698612		2203	4300	6503	SO:0001583	missense	80727				CCDS34588.1	7p22	2013-09-02	2013-09-02		ENSG00000136295	ENSG00000136295			22222	protein-coding gene	gene with protein product		608919	"""tweety homolog 3 (Drosophila)"""				Standard	NM_025250		Approved	KIAA1691	uc003smp.3	Q9C0H2	OTTHUMG00000152050	ENST00000258796.7:c.1463A>G	7.37:g.2698612A>G	ENSP00000258796:p.Asn488Ser		A4D201|B7WP98|Q6L749|Q6ZVG3|Q8TEG6	Missense_Mutation	SNP	ENST00000258796.7	37	CCDS34588.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.390116	0.82902	.	.	ENSG00000136295	ENST00000258796;ENST00000407643;ENST00000403167;ENST00000429448	T;T;T;T	0.37235	1.21;1.21;1.21;1.71	4.11	4.11	0.48088	.	0.000000	0.85682	U	0.000000	T	0.52041	0.1710	L	0.54323	1.7	0.54753	D	0.999988	D;D	0.89917	0.998;1.0	D;D	0.80764	0.994;0.994	T	0.46978	-0.9152	10	0.30078	T	0.28	.	13.409	0.60931	1.0:0.0:0.0:0.0	.	317;488	Q9C0H2-3;Q9C0H2	.;TTYH3_HUMAN	S	488;456;317;148	ENSP00000258796:N488S;ENSP00000385316:N456S;ENSP00000385015:N317S;ENSP00000413757:N148S	ENSP00000258796:N488S	N	+	2	0	TTYH3	2665138	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.744000	0.68664	1.631000	0.50456	0.379000	0.24179	AAC		0.642	TTYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325082.2	XM_166523		124	165	124	165
TMEM248	55069	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	66416082	66416082	+	Missense_Mutation	SNP	A	A	G			TCGA-HT-7471-01A-11D-2253-08	TCGA-HT-7471-10B-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	06425414-a57c-40df-905e-290fa2086153	d0b349eb-d50b-43ec-903d-e8494d8705ca	g.chr7:66416082A>G	ENST00000341567.4	+	5	995	c.740A>G	c.(739-741)tAt>tGt	p.Y247C		NM_017994.4	NP_060464.1	Q9NWD8	TM248_HUMAN	transmembrane protein 248	247						integral component of membrane (GO:0016021)											GGAAAAGTCTATCATGCTTTA	0.428																																																0													112.0	105.0	107.0					7																	66416082		2203	4300	6503	SO:0001583	missense	55069				CCDS5536.1	7q11.21	2012-05-30	2012-05-30	2012-05-30	ENSG00000106609	ENSG00000106609			25476	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 42"""	C7orf42		12477932	Standard	XM_005250482		Approved	FLJ10099, FLJ13090	uc003tvk.3	Q9NWD8	OTTHUMG00000129553	ENST00000341567.4:c.740A>G	7.37:g.66416082A>G	ENSP00000340668:p.Tyr247Cys		Q53H07|Q96FR2	Missense_Mutation	SNP	ENST00000341567.4	37	CCDS5536.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.455030	0.84209	.	.	ENSG00000106609	ENST00000341567	.	.	.	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.66915	0.2838	L	0.34521	1.04	0.80722	D	1	D	0.71674	0.998	D	0.72338	0.977	T	0.69892	-0.5022	9	0.72032	D	0.01	-11.6184	15.5232	0.75881	1.0:0.0:0.0:0.0	.	247	Q9NWD8	CG042_HUMAN	C	247	.	ENSP00000340668:Y247C	Y	+	2	0	C7orf42	66053517	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.833000	0.92089	2.317000	0.78254	0.460000	0.39030	TAT		0.428	TMEM248-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251745.2	NM_017994		38	65	38	65
MXRA5	25878	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	3238337	3238337	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-7471-01A-11D-2253-08	TCGA-HT-7471-10B-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	06425414-a57c-40df-905e-290fa2086153	d0b349eb-d50b-43ec-903d-e8494d8705ca	g.chrX:3238337C>T	ENST00000217939.6	-	5	5543	c.5389G>A	c.(5389-5391)Gga>Aga	p.G1797R		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	1797						extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				GAGGGTGATCCCGTGGTCTGC	0.493																																																0													88.0	83.0	85.0					X																	3238337		2203	4300	6503	SO:0001583	missense	25878			AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7539	protein-coding gene	gene with protein product	"""adlican"""					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.5389G>A	X.37:g.3238337C>T	ENSP00000217939:p.Gly1797Arg		Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	37	CCDS14124.1	.	.	.	.	.	.	.	.	.	.	c	8.335	0.827310	0.16749	.	.	ENSG00000101825	ENST00000381114;ENST00000217939	T	0.62232	0.04	3.53	-1.14	0.09741	.	1.982520	0.03569	U	0.228242	T	0.36880	0.0983	N	0.08118	0	0.09310	N	1	B	0.19583	0.037	B	0.15484	0.013	T	0.20940	-1.0260	10	0.48119	T	0.1	.	0.2047	0.00149	0.2188:0.2104:0.2271:0.3437	.	1797	Q9NR99	MXRA5_HUMAN	R	1797	ENSP00000217939:G1797R	ENSP00000217939:G1797R	G	-	1	0	MXRA5	3248337	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.607000	0.05648	-0.005000	0.14395	-0.381000	0.06696	GGA		0.493	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419		20	27	20	27
CCNT1	904	broad.mit.edu;ucsc.edu	37	12	49087565	49087565	+	Nonsense_Mutation	SNP	C	C	A			TCGA-HT-7471-01A-11D-2253-08	TCGA-HT-7471-10B-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	06425414-a57c-40df-905e-290fa2086153	d0b349eb-d50b-43ec-903d-e8494d8705ca	g.chr12:49087565C>A	ENST00000261900.3	-	9	1654	c.1432G>T	c.(1432-1434)Gag>Tag	p.E478*		NM_001240.3	NP_001231.2	O60563	CCNT1_HUMAN	cyclin T1	478					cell cycle (GO:0007049)|cell division (GO:0051301)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|positive transcription elongation factor complex b (GO:0008024)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|snRNA binding (GO:0017069)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(3)|skin(2)	27						TTTATCTCCTCTGGTTTTGAA	0.453																																																0													95.0	94.0	94.0					12																	49087565		2203	4300	6503	SO:0001587	stop_gained	904			AF048730	CCDS8766.1, CCDS61109.1	12q13.11	2010-11-15			ENSG00000129315	ENSG00000129315			1599	protein-coding gene	gene with protein product		143055	"""human immunodeficiency virus type 1 (HIV-1) expression (elevated) 1"""	HIVE1		9491887, 9499409	Standard	NM_001240		Approved	CCNT, CYCT1	uc001rsd.4	O60563	OTTHUMG00000170393	ENST00000261900.3:c.1432G>T	12.37:g.49087565C>A	ENSP00000261900:p.Glu478*		A9XU13|E7EX76|O60581	Nonsense_Mutation	SNP	ENST00000261900.3	37	CCDS8766.1	.	.	.	.	.	.	.	.	.	.	C	36	5.803314	0.96960	.	.	ENSG00000129315	ENST00000261900	.	.	.	4.8	4.8	0.61643	.	0.458255	0.24590	N	0.037239	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	-7.8064	16.968	0.86291	0.0:1.0:0.0:0.0	.	.	.	.	X	478	.	ENSP00000261900:E478X	E	-	1	0	CCNT1	47373832	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.983000	0.70540	2.368000	0.80403	0.561000	0.74099	GAG		0.453	CCNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408853.1	NM_001240		36	66	36	66
RBM4	5936	broad.mit.edu;hgsc.bcm.edu	37	11	66411034	66411035	+	Frame_Shift_Ins	INS	-	-	CGATAGAT			TCGA-HT-7471-01A-11D-2253-08	TCGA-HT-7471-10B-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	06425414-a57c-40df-905e-290fa2086153	d0b349eb-d50b-43ec-903d-e8494d8705ca	g.chr11:66411034_66411035insCGATAGAT	ENST00000409406.1	+	2	1303_1304	c.526_527insCGATAGAT	c.(526-528)ccgfs	p.-178fs	RBM4_ENST00000514361.3_Frame_Shift_Ins_p.-153fs|RBM4_ENST00000408993.2_Frame_Shift_Ins_p.-178fs|RBM4_ENST00000398692.4_Intron|RBM4_ENST00000506523.2_Intron|RBM14-RBM4_ENST00000412278.2_Frame_Shift_Ins_p.-153fs|RBM14-RBM4_ENST00000500635.2_Intron|RBM4_ENST00000530235.1_Intron|RBM4_ENST00000396053.4_Intron|RBM4_ENST00000310092.7_Frame_Shift_Ins_p.-178fs|RBM4_ENST00000578778.1_Intron|RBM4_ENST00000503028.2_Frame_Shift_Ins_p.-178fs			Q9BWF3	RBM4_HUMAN	RNA binding motif protein 4						cap-independent translational initiation (GO:0002190)|cell differentiation (GO:0030154)|circadian regulation of translation (GO:0097167)|entrainment of circadian clock by photoperiod (GO:0043153)|IRES-dependent translational initiation (GO:0002192)|mRNA processing (GO:0006397)|negative regulation of translation (GO:0017148)|negative regulation of translation in response to stress (GO:0032055)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|negative regulation of translational initiation (GO:0045947)|positive regulation of muscle cell differentiation (GO:0051149)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of nucleocytoplasmic transport (GO:0046822)|response to arsenic-containing substance (GO:0046685)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|stress-activated MAPK cascade (GO:0051403)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	miRNA binding (GO:0035198)|mRNA 3'-UTR binding (GO:0003730)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|pre-mRNA intronic binding (GO:0097157)|pre-mRNA intronic pyrimidine-rich binding (GO:0097158)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(4)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13				Lung(977;0.0112)|LUSC - Lung squamous cell carcinoma(976;0.0266)		CAAAGAGTGTCCGATAGATCGT	0.579																																																0																																										SO:0001589	frameshift_variant	5936			U89505	CCDS41676.1, CCDS55776.1, CCDS55777.1	11q13	2013-02-12			ENSG00000173933	ENSG00000173933		"""Zinc fingers, CCHC domain containing"", ""RNA binding motif (RRM) containing"""	9901	protein-coding gene	gene with protein product		602571				9169144, 16260624	Standard	NM_002896		Approved	LARK, RBM4A, ZCRB3A, ZCCHC21		Q9BWF3	OTTHUMG00000154171	ENST00000409406.1:c.527_534dupCGATAGAT	11.37:g.66411035_66411042dupCGATAGAT	ENSP00000386894:p.Asp178fs		B3KUN0|B4E1U0|E7EQS3|O02916|Q4VC48|Q6P1P2|Q8WU85	Frame_Shift_Ins	INS	ENST00000409406.1	37	CCDS41676.1																																																																																				0.579	RBM4-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334212.1	NM_002896		14	80	14	80
CIC	23152	broad.mit.edu;hgsc.bcm.edu	37	19	42794411	42794411	+	Frame_Shift_Del	DEL	T	T	-			TCGA-HT-7471-01A-11D-2253-08	TCGA-HT-7471-10B-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	06425414-a57c-40df-905e-290fa2086153	d0b349eb-d50b-43ec-903d-e8494d8705ca	g.chr19:42794411delT	ENST00000575354.2	+	10	1531	c.1491delT	c.(1489-1491)cctfs	p.P497fs	CIC_ENST00000572681.2_Frame_Shift_Del_p.P1406fs|CIC_ENST00000160740.3_Frame_Shift_Del_p.P497fs	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	497					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				TGTTTTCACCTGTGATCCGTT	0.617			"""Mis, F, S"""		oligodendroglioma																																		Rec	yes		19	19q13.2	23152	capicua homolog		O	0													101.0	96.0	98.0					19																	42794411		2203	4300	6503	SO:0001589	frameshift_variant	23152			AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"""capicua (Drosophila) homolog"", ""capicua homolog (Drosophila)"""			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.1491delT	19.37:g.42794411delT	ENSP00000458663:p.Pro497fs		Q7LGI1|Q9UEG5|Q9Y6T1	Frame_Shift_Del	DEL	ENST00000575354.2	37	CCDS12601.1																																																																																				0.617	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2			82	26	82	26
