#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
MYEOV	26579	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	69063311	69063311	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-A5R7-01A-11D-A289-08	TCGA-HT-A5R7-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c6a6736-02cf-41d3-9a6b-2d75e0b72bf5	45ec553b-1e7a-4b3c-86a1-c3f1547c1b43	g.chr11:69063311C>T	ENST00000308946.3	+	3	844	c.394C>T	c.(394-396)Cgg>Tgg	p.R132W	MYEOV_ENST00000441339.2_Missense_Mutation_p.R132W|MYEOV_ENST00000535407.1_Missense_Mutation_p.R74W	NM_138768.2	NP_620123.2	Q96EZ4	MYEOV_HUMAN	myeloma overexpressed	132										endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(1)|lung(12)|prostate(2)|skin(1)|urinary_tract(1)	24	all_lung(4;2.21e-19)|Lung NSC(4;6.13e-19)|Melanoma(5;0.00128)		LUSC - Lung squamous cell carcinoma(11;3.33e-11)|STAD - Stomach adenocarcinoma(18;0.00654)|LUAD - Lung adenocarcinoma(13;0.0713)	Kidney(183;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(183;3.23e-08)|Lung(977;0.00361)|LUSC - Lung squamous cell carcinoma(976;0.0153)		GGACGTGTCCCGGGCCAGGAG	0.617																																																0													147.0	142.0	143.0					11																	69063311		2200	4294	6494	SO:0001583	missense	26579			AJ223366	CCDS8190.1, CCDS73340.1	11q13.2	2013-03-27	2013-03-27			ENSG00000172927			7563	protein-coding gene	gene with protein product		605625	"""myeloma overexpressed (in a subset of t(11;14) positive multiple myelomas)"""			10753852	Standard	XM_005273908		Approved	OCIM	uc001oov.3	Q96EZ4		ENST00000308946.3:c.394C>T	11.37:g.69063311C>T	ENSP00000308330:p.Arg132Trp		Q9UGN6|Q9UGN7	Missense_Mutation	SNP	ENST00000308946.3	37	CCDS8190.1	.	.	.	.	.	.	.	.	.	.	C	9.742	1.165196	0.21538	.	.	ENSG00000172927	ENST00000441339;ENST00000308946;ENST00000535407	T;T;T	0.26067	1.77;1.77;1.76	1.4	-0.632	0.11523	.	.	.	.	.	T	0.09818	0.0241	N	0.08118	0	0.09310	N	1	B	0.31241	0.315	B	0.16722	0.016	T	0.19844	-1.0293	9	0.87932	D	0	.	3.8725	0.09042	0.0:0.5246:0.0:0.4754	.	132	Q96EZ4	MYEOV_HUMAN	W	132;132;74	ENSP00000412482:R132W;ENSP00000308330:R132W;ENSP00000438100:R74W	ENSP00000308330:R132W	R	+	1	2	MYEOV	68819887	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.968000	0.01507	-0.218000	0.10018	-0.350000	0.07774	CGG		0.617	MYEOV-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396548.1			19	176	19	176
ANO2	57101	hgsc.bcm.edu;broad.mit.edu	37	12	5672710	5672710	+	Missense_Mutation	SNP	G	G	C			TCGA-HT-A5R7-01A-11D-A289-08	TCGA-HT-A5R7-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c6a6736-02cf-41d3-9a6b-2d75e0b72bf5	45ec553b-1e7a-4b3c-86a1-c3f1547c1b43	g.chr12:5672710G>C	ENST00000356134.5	-	27	2826	c.2755C>G	c.(2755-2757)Ctc>Gtc	p.L919V	ANO2_ENST00000327087.8_Missense_Mutation_p.L918V|ANO2_ENST00000546188.1_Missense_Mutation_p.L919V	NM_001278596.1	NP_001265525.1	Q9NQ90	ANO2_HUMAN	anoctamin 2, calcium activated chloride channel	923					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(1)	58						CAGTCCACGAGGACGCTCAGG	0.552																																																0													85.0	79.0	81.0					12																	5672710		1966	4163	6129	SO:0001583	missense	57101			AJ272204	CCDS44807.1, CCDS44807.2	12p13.3	2014-04-09	2014-04-09	2008-08-28		ENSG00000047617		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	1183	protein-coding gene	gene with protein product	"""transmembrane protein 16B (eight membrane-spanning domains)"""	610109	"""chromosome 12 open reading frame 3"", ""transmembrane protein 16B"", ""anoctamin 2"""	C12orf3, TMEM16B		12739008, 15067359, 24692353	Standard	NM_001278596		Approved		uc001qnm.2	Q9NQ90		ENST00000356134.5:c.2755C>G	12.37:g.5672710G>C	ENSP00000348453:p.Leu919Val		C4N787|Q9H847	Missense_Mutation	SNP	ENST00000356134.5	37		.	.	.	.	.	.	.	.	.	.	G	11.38	1.622208	0.28889	.	.	ENSG00000047617	ENST00000327087;ENST00000356134;ENST00000546188;ENST00000541277;ENST00000543568	T;T;T	0.64618	-0.11;-0.11;-0.11	4.79	4.79	0.61399	.	0.283332	0.31210	N	0.008052	T	0.47619	0.1455	L	0.33293	1	0.47009	D	0.999286	B	0.26975	0.165	B	0.25405	0.06	T	0.45454	-0.9260	10	0.37606	T	0.19	.	8.5691	0.33558	0.085:0.1546:0.7604:0.0	.	918	Q9NQ90-3	.	V	918;919;919;923;6	ENSP00000314048:L918V;ENSP00000348453:L919V;ENSP00000440981:L919V	ENSP00000314048:L918V	L	-	1	0	ANO2	5542971	0.749000	0.28305	0.986000	0.45419	0.943000	0.58893	1.072000	0.30678	2.369000	0.80426	0.555000	0.69702	CTC		0.552	ANO2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000399019.4	NM_020373		9	135	9	135
NUTM1	256646	hgsc.bcm.edu;broad.mit.edu	37	15	34646897	34646897	+	Silent	SNP	C	C	A			TCGA-HT-A5R7-01A-11D-A289-08	TCGA-HT-A5R7-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c6a6736-02cf-41d3-9a6b-2d75e0b72bf5	45ec553b-1e7a-4b3c-86a1-c3f1547c1b43	g.chr15:34646897C>A	ENST00000333756.4	+	5	1397	c.1242C>A	c.(1240-1242)atC>atA	p.I414I	NUTM1_ENST00000438749.3_Silent_p.I432I|NUTM1_ENST00000537011.1_Silent_p.I442I	NM_175741.1	NP_786883	Q86Y26	NUTM1_HUMAN	NUT midline carcinoma, family member 1	414						cytoplasm (GO:0005737)|nucleus (GO:0005634)											TGAGCTACATCAATGAGCTGT	0.527																																																0													201.0	179.0	186.0					15																	34646897		2201	4298	6499	SO:0001819	synonymous_variant	256646			AF482429	CCDS32190.1, CCDS61584.1, CCDS61585.1	15q14	2014-01-28	2013-03-14	2013-03-14	ENSG00000184507	ENSG00000184507			29919	protein-coding gene	gene with protein product	"""nuclear protein in testis"""	608963	"""chromosome 15 open reading frame 55"""	C15orf55		12543779	Standard	NM_175741		Approved	NUT, DKFZp434O192, FAM22H	uc001zif.3	Q86Y26	OTTHUMG00000172348	ENST00000333756.4:c.1242C>A	15.37:g.34646897C>A			B4DZ00|B7Z7Y4|E7EVE8|F5H4I6|Q86YS8|Q8N7F2|Q9NTB3	Silent	SNP	ENST00000333756.4	37	CCDS32190.1																																																																																				0.527	NUTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418026.1	NM_175741		11	172	11	172
GRIN2A	2903	hgsc.bcm.edu;broad.mit.edu	37	16	10274071	10274071	+	Silent	SNP	G	G	A			TCGA-HT-A5R7-01A-11D-A289-08	TCGA-HT-A5R7-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c6a6736-02cf-41d3-9a6b-2d75e0b72bf5	45ec553b-1e7a-4b3c-86a1-c3f1547c1b43	g.chr16:10274071G>A	ENST00000396573.2	-	3	507	c.198C>T	c.(196-198)gaC>gaT	p.D66D	GRIN2A_ENST00000404927.2_Silent_p.D66D|GRIN2A_ENST00000562109.1_Silent_p.D66D|GRIN2A_ENST00000330684.3_Silent_p.D66D|GRIN2A_ENST00000396575.2_Silent_p.D66D	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	66					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CCACGTTCACGTCCAGGGGCA	0.642																																																0													74.0	76.0	75.0					16																	10274071		2197	4300	6497	SO:0001819	synonymous_variant	2903				CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.198C>T	16.37:g.10274071G>A			O00669|Q17RZ6	Silent	SNP	ENST00000396573.2	37	CCDS10539.1																																																																																				0.642	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3			12	167	12	167
NOL3	8996	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	16	67208077	67208077	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-A5R7-01A-11D-A289-08	TCGA-HT-A5R7-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c6a6736-02cf-41d3-9a6b-2d75e0b72bf5	45ec553b-1e7a-4b3c-86a1-c3f1547c1b43	g.chr16:67208077G>A	ENST00000568146.1	+	2	58	c.5G>A	c.(4-6)gGc>gAc	p.G2D	NOL3_ENST00000564053.1_Missense_Mutation_p.G64D|NOL3_ENST00000432069.2_Missense_Mutation_p.G2D|NOL3_ENST00000268605.7_Missense_Mutation_p.G2D|KIAA0895L_ENST00000563831.2_5'Flank			O60936	NOL3_HUMAN	nucleolar protein 3 (apoptosis repressor with CARD domain)	2					apoptotic process (GO:0006915)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of gene expression (GO:0010468)|response to hypoxia (GO:0001666)|response to injury involved in regulation of muscle adaptation (GO:0014876)|RNA splicing (GO:0008380)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|sarcoplasm (GO:0016528)	identical protein binding (GO:0042802)|RNA binding (GO:0003723)			ovary(1)	1		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0143)|Epithelial(162;0.0335)|all cancers(182;0.184)		CCGACAATGGGCAACGCGCAG	0.672																																																0													19.0	21.0	20.0					16																	67208077		1832	3911	5743	SO:0001583	missense	8996			AF043244	CCDS42176.1, CCDS58473.1, CCDS61960.1	16q22.1	2008-08-27				ENSG00000140939			7869	protein-coding gene	gene with protein product		605235				9560245	Standard	NM_001276312		Approved	ARC, NOP30, MYP, CARD2	uc010vjd.3	O60936		ENST00000568146.1:c.5G>A	16.37:g.67208077G>A	ENSP00000454598:p.Gly2Asp		B4DFL0|O60937	Missense_Mutation	SNP	ENST00000568146.1	37	CCDS58473.1	.	.	.	.	.	.	.	.	.	.	G	16.01	3.001739	0.54254	.	.	ENSG00000140939	ENST00000432069;ENST00000268605	.	.	.	4.57	3.62	0.41486	.	0.000000	0.50627	D	0.000117	T	0.53997	0.1831	N	0.19112	0.55	0.35245	D	0.778183	D;B	0.89917	1.0;0.266	D;B	0.80764	0.994;0.071	T	0.64711	-0.6343	9	0.87932	D	0	-10.0546	8.6313	0.33922	0.1085:0.0:0.8915:0.0	.	2;64	O60936;B4DFL0	NOL3_HUMAN;.	D	2	.	ENSP00000268605:G2D	G	+	2	0	NOL3	65765578	0.999000	0.42202	0.998000	0.56505	0.095000	0.18619	1.959000	0.40412	0.923000	0.37045	0.455000	0.32223	GGC		0.672	NOL3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422746.1			12	34	12	34
SIGLEC9	27180	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	51628473	51628473	+	Missense_Mutation	SNP	G	G	A	rs151265101		TCGA-HT-A5R7-01A-11D-A289-08	TCGA-HT-A5R7-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c6a6736-02cf-41d3-9a6b-2d75e0b72bf5	45ec553b-1e7a-4b3c-86a1-c3f1547c1b43	g.chr19:51628473G>A	ENST00000250360.3	+	1	309	c.242G>A	c.(241-243)cGg>cAg	p.R81Q	SIGLEC9_ENST00000440804.3_Missense_Mutation_p.R81Q	NM_014441.2	NP_055256.1	Q9Y336	SIGL9_HUMAN	sialic acid binding Ig-like lectin 9	81	Ig-like V-type.				cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(3)|lung(25)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	45		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.000826)|OV - Ovarian serous cystadenocarcinoma(262;0.00295)		AACCCAGCTCGGGCAGTGTGG	0.572																																																0								G	GLN/ARG,GLN/ARG	0,4406		0,0,2203	101.0	91.0	94.0		242,242	-3.2	0.0	19	dbSNP_134	94	1,8599		0,1,4299	no	missense,missense	SIGLEC9	NM_001198558.1,NM_014441.2	43,43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	81/480,81/464	51628473	1,13005	2203	4300	6503	SO:0001583	missense	27180			AF135027	CCDS12825.1, CCDS56100.1	19q13.3-q13.4	2013-01-29			ENSG00000129450	ENSG00000129450		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10878	protein-coding gene	gene with protein product		605640				10903842	Standard	NM_014441		Approved	CD329	uc002pvu.3	Q9Y336		ENST00000250360.3:c.242G>A	19.37:g.51628473G>A	ENSP00000250360:p.Arg81Gln		Q6GTU4|Q9BYI9	Missense_Mutation	SNP	ENST00000250360.3	37	CCDS12825.1	.	.	.	.	.	.	.	.	.	.	.	9.960	1.222425	0.22457	0.0	1.16E-4	ENSG00000129450	ENST00000440804;ENST00000250360	T;T	0.64803	-0.12;-0.12	2.9	-3.16	0.05217	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.288320	0.06255	N	0.692757	T	0.47248	0.1435	L	0.47190	1.495	0.09310	N	1	P	0.38370	0.628	B	0.34180	0.177	T	0.38802	-0.9644	10	0.41790	T	0.15	.	3.9777	0.09481	0.4374:0.1863:0.3763:0.0	.	81	Q9Y336	SIGL9_HUMAN	Q	81	ENSP00000413861:R81Q;ENSP00000250360:R81Q	ENSP00000250360:R81Q	R	+	2	0	SIGLEC9	56320285	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-1.551000	0.02178	-0.531000	0.06340	0.411000	0.27672	CGG		0.572	SIGLEC9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464224.1	NM_014441		27	76	27	76
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-HT-A5R7-01A-11D-A289-08	TCGA-HT-A5R7-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c6a6736-02cf-41d3-9a6b-2d75e0b72bf5	45ec553b-1e7a-4b3c-86a1-c3f1547c1b43	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			12	50	12	50
VIL1	7429	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	219299258	219299258	+	Missense_Mutation	SNP	T	T	C			TCGA-HT-A5R7-01A-11D-A289-08	TCGA-HT-A5R7-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c6a6736-02cf-41d3-9a6b-2d75e0b72bf5	45ec553b-1e7a-4b3c-86a1-c3f1547c1b43	g.chr2:219299258T>C	ENST00000248444.5	+	14	1598	c.1510T>C	c.(1510-1512)Tcc>Ccc	p.S504P	VIL1_ENST00000392114.2_Missense_Mutation_p.S193P	NM_007127.2	NP_009058.2	P09327	VILI_HUMAN	villin 1	504	Core.				actin filament capping (GO:0051693)|actin filament depolymerization (GO:0030042)|actin filament polymerization (GO:0030041)|actin filament severing (GO:0051014)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|cytoplasmic actin-based contraction involved in cell motility (GO:0060327)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell differentiation (GO:0030855)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell migration (GO:0010634)|protein complex assembly (GO:0006461)|regulation of actin nucleation (GO:0051125)|regulation of cell shape (GO:0008360)|regulation of lamellipodium morphogenesis (GO:2000392)|regulation of wound healing (GO:0061041)|response to bacterium (GO:0009617)	actin filament bundle (GO:0032432)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|lamellipodium (GO:0030027)|microvillus (GO:0005902)|ruffle (GO:0001726)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|identical protein binding (GO:0042802)|lysophosphatidic acid binding (GO:0035727)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(20)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Renal(207;0.0474)		Epithelial(149;6.88e-07)|all cancers(144;0.00013)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GGGAGGCACCTCCCGAACTAA	0.607																																																0													65.0	65.0	65.0					2																	219299258		2203	4300	6503	SO:0001583	missense	7429			X12901	CCDS2417.1	2q35	2012-10-02			ENSG00000127831	ENSG00000127831			12690	protein-coding gene	gene with protein product		193040		VIL		2846586	Standard	NM_007127		Approved	D2S1471	uc002via.3	P09327	OTTHUMG00000133112	ENST00000248444.5:c.1510T>C	2.37:g.219299258T>C	ENSP00000248444:p.Ser504Pro		B2R9A7|Q53S11|Q96AC8	Missense_Mutation	SNP	ENST00000248444.5	37	CCDS2417.1	.	.	.	.	.	.	.	.	.	.	T	19.25	3.792143	0.70452	.	.	ENSG00000127831	ENST00000248444;ENST00000392114;ENST00000419986	T;T;T	0.18016	2.58;2.58;2.24	4.32	4.32	0.51571	.	0.000000	0.64402	D	0.000001	T	0.45216	0.1331	M	0.85197	2.74	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	T	0.53415	-0.8442	10	0.72032	D	0.01	-24.2484	13.6306	0.62193	0.0:0.0:0.0:1.0	.	504	P09327	VILI_HUMAN	P	504;193;73	ENSP00000248444:S504P;ENSP00000375962:S193P;ENSP00000394030:S73P	ENSP00000248444:S504P	S	+	1	0	VIL1	219007502	0.994000	0.37717	0.999000	0.59377	0.901000	0.52897	3.210000	0.51129	1.810000	0.52873	0.459000	0.35465	TCC		0.607	VIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256778.3	NM_007127		11	96	11	96
NUP210	23225	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	13363258	13363258	+	Missense_Mutation	SNP	G	G	C			TCGA-HT-A5R7-01A-11D-A289-08	TCGA-HT-A5R7-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c6a6736-02cf-41d3-9a6b-2d75e0b72bf5	45ec553b-1e7a-4b3c-86a1-c3f1547c1b43	g.chr3:13363258G>C	ENST00000254508.5	-	36	5075	c.4993C>G	c.(4993-4995)Ctg>Gtg	p.L1665V		NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa	1665					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|ovary(7)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	66	all_neural(104;0.187)					CTGACCACCAGAGCTGTCTTC	0.582																																																0													166.0	161.0	163.0					3																	13363258		2203	4300	6503	SO:0001583	missense	23225			AB020713	CCDS33704.1	3p25	2008-02-05			ENSG00000132182	ENSG00000132182			30052	protein-coding gene	gene with protein product		607703				2184032, 7504063	Standard	NM_024923		Approved	GP210, POM210, FLJ22389, KIAA0906	uc003bxv.1	Q8TEM1	OTTHUMG00000157268	ENST00000254508.5:c.4993C>G	3.37:g.13363258G>C	ENSP00000254508:p.Leu1665Val		A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Missense_Mutation	SNP	ENST00000254508.5	37	CCDS33704.1	.	.	.	.	.	.	.	.	.	.	G	0.007	-2.011477	0.00422	.	.	ENSG00000132182	ENST00000254508	T	0.05447	3.44	5.45	4.58	0.56647	.	0.000000	0.64402	D	0.000004	T	0.04952	0.0133	L	0.43646	1.37	0.46203	D	0.998927	B	0.28512	0.214	B	0.20767	0.031	T	0.11743	-1.0575	10	0.02654	T	1	-16.5418	9.8185	0.40867	0.0726:0.0:0.7879:0.1395	.	1665	Q8TEM1	PO210_HUMAN	V	1665	ENSP00000254508:L1665V	ENSP00000254508:L1665V	L	-	1	2	NUP210	13338258	1.000000	0.71417	0.851000	0.33527	0.045000	0.14185	3.651000	0.54431	1.299000	0.44798	-0.218000	0.12543	CTG		0.582	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923		77	186	77	186
FBLN2	2199	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	13655525	13655525	+	Silent	SNP	C	C	T	rs368630493		TCGA-HT-A5R7-01A-11D-A289-08	TCGA-HT-A5R7-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c6a6736-02cf-41d3-9a6b-2d75e0b72bf5	45ec553b-1e7a-4b3c-86a1-c3f1547c1b43	g.chr3:13655525C>T	ENST00000295760.7	+	5	1659	c.1590C>T	c.(1588-1590)gcC>gcT	p.A530A	FBLN2_ENST00000404922.3_Silent_p.A530A|FBLN2_ENST00000492059.1_Silent_p.A530A|FBLN2_ENST00000535798.1_Silent_p.A556A	NM_001998.2	NP_001989.2	P98095	FBLN2_HUMAN	fibulin 2	530	Anaphylatoxin-like 3. {ECO:0000255|PROSITE-ProRule:PRU00022}.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(10)|ovary(3)|prostate(3)|urinary_tract(1)	24			UCEC - Uterine corpus endometrioid carcinoma (1;0.00416)			GCGTGCGGGCCGAGGGCCAGT	0.597																																																0													47.0	55.0	52.0					3																	13655525		2058	4190	6248	SO:0001819	synonymous_variant	2199			X82494	CCDS46761.1, CCDS46762.1	3p25-p24	2010-06-15			ENSG00000163520	ENSG00000163520		"""Fibulins"""	3601	protein-coding gene	gene with protein product		135821				7806230	Standard	NM_001165035		Approved		uc011ava.2	P98095	OTTHUMG00000155437	ENST00000295760.7:c.1590C>T	3.37:g.13655525C>T			B7Z9C5|Q8IUI0|Q8IUI1	Silent	SNP	ENST00000295760.7	37	CCDS46762.1																																																																																				0.597	FBLN2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000340083.3	NM_001004019		15	41	15	41
ACKR2	1238	hgsc.bcm.edu;broad.mit.edu	37	3	42906981	42906981	+	Silent	SNP	C	C	T			TCGA-HT-A5R7-01A-11D-A289-08	TCGA-HT-A5R7-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c6a6736-02cf-41d3-9a6b-2d75e0b72bf5	45ec553b-1e7a-4b3c-86a1-c3f1547c1b43	g.chr3:42906981C>T	ENST00000422265.1	+	3	1162	c.987C>T	c.(985-987)gcC>gcT	p.A329A	CYP8B1_ENST00000437102.1_Intron|ACKR2_ENST00000273145.2_Silent_p.A329A|KRBOX1_ENST00000426937.1_Intron|ACKR2_ENST00000442925.1_Silent_p.A329A|RP11-141M3.5_ENST00000471537.1_RNA	NM_001296.4	NP_001287.2	O00590	ACKR2_HUMAN	atypical chemokine receptor 2	329	C-terminal cytoplasmic tail.				chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|multicellular organismal development (GO:0007275)|neutrophil activation (GO:0042119)|receptor-mediated endocytosis (GO:0006898)	actin filament (GO:0005884)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|C-X-C chemokine receptor activity (GO:0016494)|chemokine receptor activity (GO:0004950)|scavenger receptor activity (GO:0005044)										TCCTGGCTGCCGTGCTTGGAT	0.557																																																0													111.0	91.0	98.0					3																	42906981		2203	4300	6503	SO:0001819	synonymous_variant	1238			U94888	CCDS2706.1	3p21.3	2013-07-17	2013-07-16	2013-07-16	ENSG00000144648	ENSG00000144648		"""GPCR / Class A : Chemokine receptors : Atypical"""	1565	protein-coding gene	gene with protein product		602648	"""chemokine binding protein 2"""	CMKBR9, CCBP2		9364936, 9405404, 16148	Standard	NM_001296		Approved	CCR10, D6, CCR9	uc003cme.3	O00590	OTTHUMG00000133040	ENST00000422265.1:c.987C>T	3.37:g.42906981C>T			B2R8Y8|O00537|Q53YA1|Q86UN9|Q96A02	Silent	SNP	ENST00000422265.1	37	CCDS2706.1																																																																																				0.557	ACKR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256645.2	NM_001296		8	104	8	104
TOMM70A	9868	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	100096610	100096610	+	Missense_Mutation	SNP	T	T	C			TCGA-HT-A5R7-01A-11D-A289-08	TCGA-HT-A5R7-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c6a6736-02cf-41d3-9a6b-2d75e0b72bf5	45ec553b-1e7a-4b3c-86a1-c3f1547c1b43	g.chr3:100096610T>C	ENST00000284320.5	-	6	1479	c.1031A>G	c.(1030-1032)aAt>aGt	p.N344S		NM_014820.4	NP_055635.3	O94826	TOM70_HUMAN	translocase of outer mitochondrial membrane 70 homolog A (S. cerevisiae)	344					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)|protein transmembrane transport (GO:0071806)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane translocase complex (GO:0005742)|mitochondrion (GO:0005739)	protein transmembrane transporter activity (GO:0008320)			endometrium(11)|large_intestine(5)|lung(10)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	32						TGCATTGGCATTGCCAATAAG	0.348																																																0													183.0	180.0	181.0					3																	100096610		2203	4300	6503	SO:0001583	missense	9868			AB018262	CCDS33807.1	3q12.2	2013-01-10	2006-04-04		ENSG00000154174	ENSG00000154174		"""Tetratricopeptide (TTC) repeat domain containing"""	11985	protein-coding gene	gene with protein product		606081	"""translocase of outer mitochondrial membrane 70 (yeast) homolog A"", ""translocase of outer mitochondrial membrane 70 homolog A (yeast)"""			10582581	Standard	NM_014820		Approved	KIAA0719	uc003dtw.3	O94826	OTTHUMG00000159065	ENST00000284320.5:c.1031A>G	3.37:g.100096610T>C	ENSP00000284320:p.Asn344Ser		D3DN48	Missense_Mutation	SNP	ENST00000284320.5	37	CCDS33807.1	.	.	.	.	.	.	.	.	.	.	T	7.179	0.589130	0.13812	.	.	ENSG00000154174	ENST00000284320;ENST00000544924	T	0.53640	0.61	5.96	2.31	0.28768	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.208622	0.56097	N	0.000023	T	0.28333	0.0700	L	0.28115	0.83	0.45118	D	0.998134	B	0.27882	0.192	B	0.19666	0.026	T	0.05257	-1.0896	10	0.14656	T	0.56	-11.762	9.3111	0.37905	0.0:0.206:0.0:0.794	.	344	O94826	TOM70_HUMAN	S	344;237	ENSP00000284320:N344S	ENSP00000284320:N344S	N	-	2	0	TOMM70A	101579300	1.000000	0.71417	0.982000	0.44146	0.939000	0.58152	3.818000	0.55678	0.168000	0.19655	-0.351000	0.07748	AAT		0.348	TOMM70A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353141.2			26	57	26	57
SEC31A	22872	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	83742201	83742201	+	Silent	SNP	T	T	G			TCGA-HT-A5R7-01A-11D-A289-08	TCGA-HT-A5R7-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c6a6736-02cf-41d3-9a6b-2d75e0b72bf5	45ec553b-1e7a-4b3c-86a1-c3f1547c1b43	g.chr4:83742201T>G	ENST00000395310.2	-	26	3654	c.3472A>C	c.(3472-3474)Agg>Cgg	p.R1158R	SEC31A_ENST00000500777.2_Silent_p.R1005R|SEC31A_ENST00000355196.2_Silent_p.R1158R|SEC31A_ENST00000348405.4_Silent_p.R1119R|SEC31A_ENST00000311785.7_Silent_p.R1044R|SEC31A_ENST00000448323.1_Silent_p.R1158R|SEC31A_ENST00000326950.5_Silent_p.R1119R|SEC31A_ENST00000505472.1_Silent_p.R1189R|SEC31A_ENST00000505984.1_Silent_p.R1104R|SEC31A_ENST00000508502.1_Silent_p.R1143R|SEC31A_ENST00000443462.2_Silent_p.R1138R|SEC31A_ENST00000432794.1_Silent_p.R1171R|SEC31A_ENST00000513858.1_Silent_p.R1005R|SEC31A_ENST00000264405.5_Silent_p.R907R|SEC31A_ENST00000509142.1_Silent_p.R1044R	NM_001077207.2|NM_001077208.2|NM_014933.3	NP_001070675.1|NP_001070676.1|NP_055748.2	O94979	SC31A_HUMAN	SEC31 homolog A (S. cerevisiae)	1158					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)|response to calcium ion (GO:0051592)	COPII vesicle coat (GO:0030127)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle (GO:0030134)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|vesicle coat (GO:0030120)	calcium-dependent protein binding (GO:0048306)		SEC31A/ALK(3)|SEC31A/JAK2(4)	breast(1)	1		Hepatocellular(203;0.114)				GTCTGTTCCCTAAGTTTATCA	0.343																																																0													198.0	208.0	205.0					4																	83742201		2203	4300	6503	SO:0001819	synonymous_variant	22872			AB018358	CCDS3596.1, CCDS3597.1, CCDS43244.1, CCDS47088.1, CCDS54773.1, CCDS75155.1, CCDS75156.1	4q21.3	2013-01-10	2006-10-05	2006-09-07	ENSG00000138674	ENSG00000138674		"""WD repeat domain containing"""	17052	protein-coding gene	gene with protein product		610257	"""SEC31-like 1 (S. cerevisiae)"", ""Sec31 homolog A (S. cerevisiae)"""	SEC31L1		10048485, 10788476	Standard	NM_001077206		Approved	KIAA0905, ABP125, ABP130	uc003hnh.3	O94979	OTTHUMG00000130297	ENST00000395310.2:c.3472A>C	4.37:g.83742201T>G			B4DIW6|B7ZKZ7|B7ZL00|H7C2W3|Q17RR5|Q5H9P6|Q5XG74|Q659G7|Q6ZU90|Q7LCX9|Q86TJ0|Q8IZH4|Q9P048|Q9P0A6|Q9UM05|Q9UM06	Silent	SNP	ENST00000395310.2	37	CCDS3596.1	.	.	.	.	.	.	.	.	.	.	T	9.637	1.138065	0.21123	.	.	ENSG00000138674	ENST00000503937	T	0.70282	-0.47	5.62	4.42	0.53409	.	.	.	.	.	T	0.78541	0.4299	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.79667	-0.1708	6	0.87932	D	0	-13.4754	11.6974	0.51551	0.0:0.0:0.2815:0.7185	.	.	.	.	F	320	ENSP00000422371:L320F	ENSP00000422371:L320F	L	-	3	2	SEC31A	83961225	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.621000	0.36986	0.936000	0.37367	0.533000	0.62120	TTA		0.343	SEC31A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252640.1	NM_016211		53	124	53	124
MUC17	140453	hgsc.bcm.edu;broad.mit.edu	37	7	100684757	100684757	+	Missense_Mutation	SNP	A	A	T			TCGA-HT-A5R7-01A-11D-A289-08	TCGA-HT-A5R7-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c6a6736-02cf-41d3-9a6b-2d75e0b72bf5	45ec553b-1e7a-4b3c-86a1-c3f1547c1b43	g.chr7:100684757A>T	ENST00000306151.4	+	3	10124	c.10060A>T	c.(10060-10062)Agt>Tgt	p.S3354C		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	3354	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					GCCAGTGGTCAGTTCTGAGGC	0.483																																																0													295.0	307.0	303.0					7																	100684757		2203	4300	6503	SO:0001583	missense	140453			AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"""Mucins"""	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.10060A>T	7.37:g.100684757A>T	ENSP00000302716:p.Ser3354Cys		O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	a	4.635	0.118040	0.08881	.	.	ENSG00000169876	ENST00000306151	T	0.02709	4.19	0.823	0.823	0.18812	.	.	.	.	.	T	0.04634	0.0126	N	0.14661	0.345	0.09310	N	1	D	0.76494	0.999	D	0.76071	0.987	T	0.44421	-0.9329	9	0.56958	D	0.05	.	3.5513	0.07847	0.5848:0.4152:0.0:0.0	.	3354	Q685J3	MUC17_HUMAN	C	3354	ENSP00000302716:S3354C	ENSP00000302716:S3354C	S	+	1	0	MUC17	100471477	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.024000	0.12435	0.166000	0.19597	0.165000	0.16767	AGT		0.483	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		32	479	32	479
AOC1	26	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	150553856	150553856	+	Missense_Mutation	SNP	G	G	A	rs577618065		TCGA-HT-A5R7-01A-11D-A289-08	TCGA-HT-A5R7-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c6a6736-02cf-41d3-9a6b-2d75e0b72bf5	45ec553b-1e7a-4b3c-86a1-c3f1547c1b43	g.chr7:150553856G>A	ENST00000493429.1	+	4	882	c.298G>A	c.(298-300)Gtc>Atc	p.V100I	AOC1_ENST00000360937.4_Missense_Mutation_p.V100I|AOC1_ENST00000467291.1_Missense_Mutation_p.V100I|AOC1_ENST00000416793.2_Missense_Mutation_p.V100I			P19801	AOC1_HUMAN	amine oxidase, copper containing 1	100					amine metabolic process (GO:0009308)|cellular response to azide (GO:0097185)|cellular response to copper ion (GO:0071280)|cellular response to copper ion starvation (GO:0035874)|cellular response to heparin (GO:0071504)|cellular response to histamine (GO:0071420)|oxidation-reduction process (GO:0055114)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	calcium ion binding (GO:0005509)|cation channel activity (GO:0005261)|copper ion binding (GO:0005507)|diamine oxidase activity (GO:0052597)|drug binding (GO:0008144)|heparin binding (GO:0008201)|histamine oxidase activity (GO:0052598)|methylputrescine oxidase activity (GO:0052599)|primary amine oxidase activity (GO:0008131)|propane-1,3-diamine oxidase activity (GO:0052600)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|quinone binding (GO:0048038)|receptor activity (GO:0004872)|sodium channel activity (GO:0005272)|zinc ion binding (GO:0008270)									Amiloride(DB00594)	AGCCCGTGCCGTCATCTTCTT	0.582													G|||	1	0.000199681	0.0	0.0	5008	,	,		19281	0.0		0.0	False		,,,				2504	0.001															0													109.0	107.0	108.0					7																	150553856		1983	4159	6142	SO:0001583	missense	26			AK092514	CCDS43679.1, CCDS64797.1	7q36.1	2013-06-19	2013-06-19	2013-06-19	ENSG00000002726	ENSG00000002726	1.4.3.22		80	protein-coding gene	gene with protein product	"""diamine oxidase"""	104610	"""amiloride binding protein 1 (amine oxidase (copper-containing))"""	ABP1		8182053	Standard	NM_001091		Approved	DAO	uc003wia.2	P19801	OTTHUMG00000158306	ENST00000493429.1:c.298G>A	7.37:g.150553856G>A	ENSP00000418614:p.Val100Ile		C9J690|Q16683|Q16684|Q56II4|Q6GU42	Missense_Mutation	SNP	ENST00000493429.1	37	CCDS43679.1	.	.	.	.	.	.	.	.	.	.	G	2.901	-0.227597	0.06022	.	.	ENSG00000002726	ENST00000493429;ENST00000467291;ENST00000460213;ENST00000360937;ENST00000416793;ENST00000483043	T;T;T;T;T;T	0.37235	1.21;1.21;1.21;1.21;1.21;1.21	5.32	-4.83	0.03161	Copper amine oxidase, N2/N3-terminal (1);Copper amine oxidase, N-terminal (1);Copper amine oxidase, N2-terminal (1);	0.564860	0.18326	N	0.144636	T	0.16769	0.0403	N	0.16166	0.38	0.21527	N	0.999657	B;B	0.15141	0.012;0.008	B;B	0.18263	0.021;0.009	T	0.30001	-0.9993	10	0.11182	T	0.66	-11.239	13.5265	0.61597	0.6106:0.0:0.3894:0.0	.	100;100	C9J690;P19801	.;ABP1_HUMAN	I	100	ENSP00000418614:V100I;ENSP00000418328:V100I;ENSP00000418557:V100I;ENSP00000354193:V100I;ENSP00000411613:V100I;ENSP00000417392:V100I	ENSP00000354193:V100I	V	+	1	0	ABP1	150184789	0.002000	0.14202	0.002000	0.10522	0.345000	0.29048	-0.049000	0.11924	-0.875000	0.04022	-0.137000	0.14449	GTC		0.582	AOC1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350628.1	NM_001091		54	82	54	82
XG	7499	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	2729413	2729413	+	Missense_Mutation	SNP	C	C	G			TCGA-HT-A5R7-01A-11D-A289-08	TCGA-HT-A5R7-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c6a6736-02cf-41d3-9a6b-2d75e0b72bf5	45ec553b-1e7a-4b3c-86a1-c3f1547c1b43	g.chrX:2729413C>G	ENST00000381174.5	+	9	671	c.446C>G	c.(445-447)tCc>tGc	p.S149C	XG_ENST00000419513.2_Missense_Mutation_p.S164C|snoU13_ENST00000516039.1_RNA|XG_ENST00000426774.1_Missense_Mutation_p.S150C			P55808	XG_HUMAN	Xg blood group	149						integral component of plasma membrane (GO:0005887)				endometrium(1)|large_intestine(3)|lung(3)|ovary(1)	8		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				CCCATCGTATCCGTGGTGGTG	0.448																																																0													65.0	59.0	61.0					X																	2729413		2203	4298	6501	SO:0001583	missense	7499			AF380356	CCDS14120.1, CCDS48073.1	Xp22.32	2014-07-19	2006-01-12		ENSG00000124343	ENSG00000124343		"""Blood group antigens"", ""Pseudoautosomal regions / PAR1"""	12806	protein-coding gene	gene with protein product		300879	"""Xg blood group (pseudoautosomal boundary-divided on the X chromosome)"""	PBDX		8054981	Standard	NM_175569		Approved		uc004cqp.3	P55808	OTTHUMG00000021075	ENST00000381174.5:c.446C>G	X.37:g.2729413C>G	ENSP00000370566:p.Ser149Cys		E9PCH1|Q496N8|Q496N9|Q496P0|Q71BZ5	Missense_Mutation	SNP	ENST00000381174.5	37	CCDS14120.1	.	.	.	.	.	.	.	.	.	.	C	10.28	1.305681	0.23736	.	.	ENSG00000124343	ENST00000381174;ENST00000419513;ENST00000426774;ENST00000509484;ENST00000533923	T;T;T;T	0.37058	1.22;1.22;1.22;1.22	3.6	2.71	0.32032	.	0.342724	0.26765	U	0.022613	T	0.34629	0.0904	M	0.67397	2.05	0.09310	N	1	B;B	0.22146	0.065;0.053	B;B	0.20384	0.029;0.017	T	0.35375	-0.9791	10	0.87932	D	0	.	8.6942	0.34284	0.0:0.77:0.23:0.0	.	149;164	P55808;P55808-3	XG_HUMAN;.	C	149;164;150;127;11	ENSP00000370566:S149C;ENSP00000411004:S164C;ENSP00000398503:S150C;ENSP00000430005:S127C	ENSP00000370566:S149C	S	+	2	0	XG	2739413	0.009000	0.17119	0.002000	0.10522	0.196000	0.23810	0.853000	0.27777	0.517000	0.28361	0.384000	0.25694	TCC		0.448	XG-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055633.2	NM_175569		6	21	6	21
FAM47B	170062	hgsc.bcm.edu;broad.mit.edu	37	X	34961355	34961355	+	Missense_Mutation	SNP	A	A	G			TCGA-HT-A5R7-01A-11D-A289-08	TCGA-HT-A5R7-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c6a6736-02cf-41d3-9a6b-2d75e0b72bf5	45ec553b-1e7a-4b3c-86a1-c3f1547c1b43	g.chrX:34961355A>G	ENST00000329357.5	+	1	443	c.407A>G	c.(406-408)aAt>aGt	p.N136S		NM_152631.2	NP_689844.2	Q8NA70	FA47B_HUMAN	family with sequence similarity 47, member B	136										breast(3)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	71						ATGTACCCCAATCTGGGAAAA	0.567																																																0													92.0	81.0	85.0					X																	34961355		2202	4300	6502	SO:0001583	missense	170062			BC035026	CCDS14236.1	Xp21.1	2004-08-09			ENSG00000189132	ENSG00000189132			26659	protein-coding gene	gene with protein product						14702039	Standard	NM_152631		Approved	FLJ35782	uc004ddi.2	Q8NA70	OTTHUMG00000021345	ENST00000329357.5:c.407A>G	X.37:g.34961355A>G	ENSP00000328307:p.Asn136Ser		Q5JQN5|Q6PIG3	Missense_Mutation	SNP	ENST00000329357.5	37	CCDS14236.1	.	.	.	.	.	.	.	.	.	.	A	1.094	-0.663069	0.03428	.	.	ENSG00000189132	ENST00000329357	T	0.18502	2.21	0.843	-0.587	0.11690	.	.	.	.	.	T	0.10680	0.0261	L	0.38838	1.175	0.09310	N	1	B	0.13594	0.008	B	0.14578	0.011	T	0.38585	-0.9654	9	0.21014	T	0.42	.	4.282	0.10838	0.7589:0.0:0.2411:0.0	.	136	Q8NA70	FA47B_HUMAN	S	136	ENSP00000328307:N136S	ENSP00000328307:N136S	N	+	2	0	FAM47B	34871276	0.313000	0.24554	0.002000	0.10522	0.016000	0.09150	-2.264000	0.01173	-0.239000	0.09710	-1.064000	0.02280	AAT		0.567	FAM47B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056211.1	NM_152631		8	81	8	81
FOXN1	8456	broad.mit.edu;ucsc.edu	37	17	26861989	26861989	+	Missense_Mutation	SNP	C	C	A			TCGA-HT-A5R7-01A-11D-A289-08	TCGA-HT-A5R7-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c6a6736-02cf-41d3-9a6b-2d75e0b72bf5	45ec553b-1e7a-4b3c-86a1-c3f1547c1b43	g.chr17:26861989C>A	ENST00000226247.2	+	7	1429	c.1400C>A	c.(1399-1401)cCc>cAc	p.P467H	FOXN1_ENST00000579795.1_Missense_Mutation_p.P467H	NM_003593.2	NP_003584.2	O15353	FOXN1_HUMAN	forkhead box N1	467					defense response (GO:0006952)|epidermis development (GO:0008544)|epithelial cell proliferation (GO:0050673)|hair follicle development (GO:0001942)|keratinocyte differentiation (GO:0030216)|lymphocyte homeostasis (GO:0002260)|nail development (GO:0035878)|organ morphogenesis (GO:0009887)|regulation of T cell differentiation in thymus (GO:0033081)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|thymus development (GO:0048538)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(3)|lung(8)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Lung NSC(42;0.00431)					CCTCCTGGACCCCCGCAGCCA	0.677																																																0													35.0	35.0	35.0					17																	26861989		2203	4300	6503	SO:0001583	missense	8456			Y11739	CCDS11232.1	17q11-q12	2014-09-17	2003-06-12	2003-06-13	ENSG00000109101	ENSG00000109101		"""Forkhead boxes"""	12765	protein-coding gene	gene with protein product		600838	"""winged-helix nude"", ""Rowett nude"""	WHN, RONU		9321431	Standard	NM_003593		Approved	FKHL20	uc002hbj.3	O15353	OTTHUMG00000132603	ENST00000226247.2:c.1400C>A	17.37:g.26861989C>A	ENSP00000226247:p.Pro467His		B2R9Q7|O15352	Missense_Mutation	SNP	ENST00000226247.2	37	CCDS11232.1	.	.	.	.	.	.	.	.	.	.	C	7.395	0.631516	0.14322	.	.	ENSG00000109101	ENST00000226247	D	0.93247	-3.19	4.35	2.12	0.27331	.	0.794130	0.11240	N	0.584700	T	0.81645	0.4866	N	0.08118	0	0.27391	N	0.955129	B	0.06786	0.001	B	0.06405	0.002	T	0.69491	-0.5131	10	0.25751	T	0.34	.	2.6089	0.04885	0.2721:0.51:0.0:0.2179	.	467	O15353	FOXN1_HUMAN	H	467	ENSP00000226247:P467H	ENSP00000226247:P467H	P	+	2	0	FOXN1	23886116	0.999000	0.42202	0.967000	0.41034	0.726000	0.41606	0.909000	0.28558	0.982000	0.38575	0.561000	0.74099	CCC		0.677	FOXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255832.1			8	70	8	70
MED23	9439	broad.mit.edu;ucsc.edu	37	6	131913582	131913582	+	Silent	SNP	T	T	C			TCGA-HT-A5R7-01A-11D-A289-08	TCGA-HT-A5R7-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c6a6736-02cf-41d3-9a6b-2d75e0b72bf5	45ec553b-1e7a-4b3c-86a1-c3f1547c1b43	g.chr6:131913582T>C	ENST00000368068.3	-	25	3596	c.3417A>G	c.(3415-3417)agA>agG	p.R1139R	MED23_ENST00000354577.4_Silent_p.R1145R|MED23_ENST00000403834.3_Silent_p.R1145R|MED23_ENST00000479213.1_5'UTR|MED23_ENST00000368058.1_Silent_p.R1145R|MED23_ENST00000545957.1_Silent_p.R780R|MED23_ENST00000368060.3_Silent_p.R1139R	NM_004830.3	NP_004821.2	Q9ULK4	MED23_HUMAN	mediator complex subunit 23	1139					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(12)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	44	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0115)|OV - Ovarian serous cystadenocarcinoma(155;0.0608)		TAATGTTCTCTCTTGGCACTA	0.353																																																0													152.0	139.0	143.0					6																	131913582		2203	4300	6503	SO:0001819	synonymous_variant	9439			AF104255	CCDS5146.1, CCDS5147.1, CCDS59039.1	6q22.33-q24.1	2008-02-05	2007-08-08	2007-07-30	ENSG00000112282	ENSG00000112282			2372	protein-coding gene	gene with protein product		605042	"""cofactor required for Sp1 transcriptional activation, subunit 3, 130kDa"""	CRSP3		9989412	Standard	NM_004830		Approved	CRSP130, DRIP130, Sur2	uc003qcs.2	Q9ULK4	OTTHUMG00000015565	ENST00000368068.3:c.3417A>G	6.37:g.131913582T>C			B9TX55|O95403|Q5JWT3|Q5JWT4|Q6P9H6|Q9H0J2|Q9NTT9|Q9NTU0|Q9Y5P7|Q9Y667	Silent	SNP	ENST00000368068.3	37	CCDS5147.1																																																																																				0.353	MED23-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042215.1			20	80	20	80
TMPRSS15	5651	broad.mit.edu;ucsc.edu	37	21	19647644	19647644	+	Missense_Mutation	SNP	G	G	T			TCGA-HT-A5R7-01A-11D-A289-08	TCGA-HT-A5R7-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c6a6736-02cf-41d3-9a6b-2d75e0b72bf5	45ec553b-1e7a-4b3c-86a1-c3f1547c1b43	g.chr21:19647644G>T	ENST00000284885.3	-	24	2807	c.2774C>A	c.(2773-2775)gCa>gAa	p.A925E		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	925	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						CAATATGTTTGCAGTAGTACC	0.398																																																0													109.0	98.0	102.0					21																	19647644		2203	4300	6503	SO:0001583	missense	5651				CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"""Serine peptidases / Transmembrane"""	9490	protein-coding gene	gene with protein product	"""proenterokinase"", ""enteropeptidase"""	606635	"""protease, serine, 7 (enterokinase)"""	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.2774C>A	21.37:g.19647644G>T	ENSP00000284885:p.Ala925Glu		Q2NKL7	Missense_Mutation	SNP	ENST00000284885.3	37	CCDS13571.1	.	.	.	.	.	.	.	.	.	.	G	15.69	2.907449	0.52333	.	.	ENSG00000154646	ENST00000284885	D	0.88354	-2.37	5.75	3.93	0.45458	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.215520	0.39985	N	0.001202	D	0.85626	0.5740	L	0.46885	1.475	0.09310	N	1	P	0.48294	0.908	P	0.44359	0.447	T	0.76940	-0.2773	9	.	.	.	.	11.2104	0.48795	0.15:0.0:0.85:0.0	.	925	P98073	ENTK_HUMAN	E	925	ENSP00000284885:A925E	.	A	-	2	0	TMPRSS15	18569515	0.982000	0.34865	0.033000	0.17914	0.896000	0.52359	4.078000	0.57606	0.872000	0.35775	0.650000	0.86243	GCA		0.398	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772		7	61	7	61
ATRX	546	broad.mit.edu;hgsc.bcm.edu	37	X	76920179	76920180	+	Frame_Shift_Ins	INS	-	-	C			TCGA-HT-A5R7-01A-11D-A289-08	TCGA-HT-A5R7-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c6a6736-02cf-41d3-9a6b-2d75e0b72bf5	45ec553b-1e7a-4b3c-86a1-c3f1547c1b43	g.chrX:76920179_76920180insC	ENST00000373344.5	-	11	4111_4112	c.3897_3898insG	c.(3895-3900)gggaaafs	p.K1300fs	ATRX_ENST00000395603.3_Frame_Shift_Ins_p.K1262fs|ATRX_ENST00000480283.1_5'UTR	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	1300	Interaction with DAXX.				ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						GTTCTTTTTTTCCCTTCTTCTG	0.371			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome																																Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	1	Unknown(1)	bone(1)																																								SO:0001589	frameshift_variant	546			U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"""RAD54 homolog (S. cerevisiae)"""	300032	"""alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)"", ""Juberg-Marsidi syndrome"""	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.3898dupG	X.37:g.76920182_76920182dupC	ENSP00000362441:p.Lys1300fs		D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Frame_Shift_Ins	INS	ENST00000373344.5	37	CCDS14434.1																																																																																				0.371	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		31	71	31	71
