#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
PYROXD2	84795	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	100143599	100143599	+	Nonsense_Mutation	SNP	G	G	A	rs148254477	byFrequency	TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chr10:100143599G>A	ENST00000370575.4	-	16	1750	c.1702C>T	c.(1702-1704)Cga>Tga	p.R568*	PYROXD2_ENST00000483923.1_5'UTR	NM_032709.2	NP_116098.2	Q8N2H3	PYRD2_HUMAN	pyridine nucleotide-disulphide oxidoreductase domain 2	568							oxidoreductase activity (GO:0016491)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	12						GCTGCATTTCGCCCAGCAGCT	0.567													G|||	14	0.00279553	0.0	0.0	5008	,	,		15768	0.0		0.0	False		,,,				2504	0.0143															0								G	stop/ARG	0,4406		0,0,2203	169.0	161.0	164.0		1702	3.5	1.0	10	dbSNP_134	164	1,8599	1.2+/-3.3	0,1,4299	yes	stop-gained	PYROXD2	NM_032709.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		568/582	100143599	1,13005	2203	4300	6503	SO:0001587	stop_gained	84795			AK074429	CCDS7474.1	10q24.2	2009-04-22	2009-04-22	2009-04-22	ENSG00000119943	ENSG00000119943			23517	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 33"""	C10orf33			Standard	NM_032709		Approved	FLJ23849	uc001kpc.3	Q8N2H3	OTTHUMG00000018877	ENST00000370575.4:c.1702C>T	10.37:g.100143599G>A	ENSP00000359607:p.Arg568*		D3DR61|Q5TAA9|Q9BRQ1	Nonsense_Mutation	SNP	ENST00000370575.4	37	CCDS7474.1	.	.	.	.	.	.	.	.	.	.	G	36	5.796317	0.96952	0.0	1.16E-4	ENSG00000119943	ENST00000370575	.	.	.	5.39	3.46	0.39613	.	0.106936	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-32.4354	13.9503	0.64113	0.0:0.0:0.7228:0.2772	.	.	.	.	X	568	.	ENSP00000359607:R568X	R	-	1	2	PYROXD2	100133589	1.000000	0.71417	0.993000	0.49108	0.864000	0.49448	3.755000	0.55197	0.584000	0.29591	0.462000	0.41574	CGA		0.567	PYROXD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049782.2	NM_032709		27	228	27	228
CD82	3732	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	44621761	44621761	+	Silent	SNP	C	C	T			TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chr11:44621761C>T	ENST00000227155.4	+	4	365	c.117C>T	c.(115-117)agC>agT	p.S39S	CD82_ENST00000342935.3_Silent_p.S39S	NM_002231.3	NP_002222.1	P27701	CD82_HUMAN	CD82 molecule	39						extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				large_intestine(1)|ovary(1)	2						CCGACAAGAGCAGTTTCATCT	0.602																																																0													147.0	122.0	131.0					11																	44621761		2203	4299	6502	SO:0001819	synonymous_variant	3732			U20770	CCDS7909.1, CCDS31469.1	11p11.2	2013-02-14	2006-03-28	2005-03-03		ENSG00000085117		"""CD molecules"", ""Tetraspanins"""	6210	protein-coding gene	gene with protein product	"""suppression of tumorigenicity 6"", ""R2 leukocyte antigen"""	600623	"""kangai 1 (suppression of tumorigenicity 6, prostate; CD82 antigen (R2 leukocyte antigen, antigen detected by monoclonal and antibody IA4))"", ""CD82 antigen"""	ST6, KAI1			Standard	XM_006718222		Approved	R2, IA4, TSPAN27	uc001myc.3	P27701		ENST00000227155.4:c.117C>T	11.37:g.44621761C>T			D3DQN6|E9PC70|Q7Z2D4|Q7Z5N2	Silent	SNP	ENST00000227155.4	37	CCDS7909.1																																																																																				0.602	CD82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389886.1			37	105	37	105
OR5L2	26338	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	55594988	55594988	+	Missense_Mutation	SNP	G	G	A			TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chr11:55594988G>A	ENST00000378397.1	+	1	294	c.294G>A	c.(292-294)atG>atA	p.M98I		NM_001004739.1	NP_001004739.1	Q8NGL0	OR5L2_HUMAN	olfactory receptor, family 5, subfamily L, member 2	98						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|kidney(1)|large_intestine(1)|lung(42)|ovary(1)|prostate(3)|skin(1)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	59		all_epithelial(135;0.208)				TAGGGTGCATGGTGCAATTCT	0.468										HNSCC(27;0.073)																																						0													192.0	182.0	186.0					11																	55594988		2200	4296	6496	SO:0001583	missense	26338			AB065782	CCDS31511.1	11q11	2012-08-09			ENSG00000205030	ENSG00000205030		"""GPCR / Class A : Olfactory receptors"""	8351	protein-coding gene	gene with protein product						1370859	Standard	NM_001004739		Approved	HTPCRX16, HSHTPCRX16	uc001nhy.1	Q8NGL0	OTTHUMG00000166812	ENST00000378397.1:c.294G>A	11.37:g.55594988G>A	ENSP00000367650:p.Met98Ile		Q6IF66|Q96RB2	Missense_Mutation	SNP	ENST00000378397.1	37	CCDS31511.1	.	.	.	.	.	.	.	.	.	.	.	2.915	-0.224518	0.06061	.	.	ENSG00000205030	ENST00000378397	T	0.00359	7.87	5.21	-10.4	0.00318	GPCR, rhodopsin-like superfamily (1);	1.183400	0.06020	N	0.651176	T	0.00109	0.0003	N	0.11789	0.175	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.37150	-0.9718	10	0.30078	T	0.28	-0.9513	3.3144	0.07027	0.1174:0.2019:0.1874:0.4933	.	98	Q8NGL0	OR5L2_HUMAN	I	98	ENSP00000367650:M98I	ENSP00000367650:M98I	M	+	3	0	OR5L2	55351564	0.000000	0.05858	0.000000	0.03702	0.131000	0.20780	-3.865000	0.00347	-2.079000	0.00871	0.626000	0.83405	ATG		0.468	OR5L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391516.1	NM_001004739		32	246	32	246
ST3GAL4	6484	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	126278326	126278326	+	Missense_Mutation	SNP	G	G	A			TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chr11:126278326G>A	ENST00000526727.1	+	7	936	c.562G>A	c.(562-564)Gtc>Atc	p.V188I	ST3GAL4_ENST00000534457.1_Missense_Mutation_p.V183I|ST3GAL4_ENST00000356132.4_Missense_Mutation_p.V194I|ST3GAL4_ENST00000526756.1_3'UTR|ST3GAL4_ENST00000227495.6_Missense_Mutation_p.V184I|ST3GAL4_ENST00000530591.1_Missense_Mutation_p.V184I|ST3GAL4_ENST00000532243.1_Missense_Mutation_p.V187I|ST3GAL4_ENST00000449406.2_Missense_Mutation_p.V177I|ST3GAL4_ENST00000444328.2_Missense_Mutation_p.V188I|ST3GAL4_ENST00000534083.1_Missense_Mutation_p.V188I|ST3GAL4_ENST00000392669.2_Missense_Mutation_p.V188I			Q11206	SIA4C_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 4	188					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|cognition (GO:0050890)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	beta-galactoside (CMP) alpha-2,3-sialyltransferase activity (GO:0003836)|monosialoganglioside sialyltransferase activity (GO:0047288)			endometrium(1)|large_intestine(2)|lung(5)|stomach(1)	9	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0739)|all_lung(97;0.0798)|all_neural(223;0.138)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0767)		CACACTCCTCGTCCTGGTAGC	0.547																																																0													114.0	90.0	98.0					11																	126278326		2201	4298	6499	SO:0001583	missense	6484			X74570	CCDS8474.1, CCDS58193.1, CCDS58194.1	11q23-q24	2013-03-01	2003-01-14	2005-02-07	ENSG00000110080	ENSG00000110080	2.4.99.4	"""Sialyltransferases"""	10864	protein-coding gene	gene with protein product	"""ST3Gal IV"""	104240	"""sialyltransferase 4C (beta-galactosidase alpha-2,3-sialytransferase)"""	CGS23, SIAT4, NANTA3, SIAT4C		8557707, 8288606	Standard	NM_006278		Approved	STZ, SAT3, FLJ11867	uc001qds.3	Q11206	OTTHUMG00000165830	ENST00000526727.1:c.562G>A	11.37:g.126278326G>A	ENSP00000436047:p.Val188Ile		A8K6B2|O60497|Q8N6A6|Q8NFG7|Q96QQ9	Missense_Mutation	SNP	ENST00000526727.1	37	CCDS58193.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.607252	0.87157	.	.	ENSG00000110080	ENST00000227495;ENST00000444328;ENST00000356132;ENST00000530591;ENST00000534083;ENST00000528858;ENST00000392669;ENST00000526727;ENST00000449406;ENST00000532243;ENST00000534457;ENST00000524860	T;T;T;T;T;T;T;T;T;T;T;T	0.33865	1.39;1.39;1.39;1.39;1.39;1.39;1.39;1.39;1.39;1.39;1.39;1.39	4.55	4.55	0.56014	.	0.117513	0.56097	D	0.000023	T	0.51568	0.1682	L	0.45228	1.405	0.80722	D	1	D;D;D	0.89917	0.977;1.0;1.0	P;D;D	0.79108	0.854;0.979;0.992	T	0.39272	-0.9622	10	0.27082	T	0.32	-15.4274	17.868	0.88801	0.0:0.0:1.0:0.0	.	137;184;188	Q9HAA9;Q6IBE6;Q11206	.;.;SIA4C_HUMAN	I	184;188;194;184;188;188;188;188;177;187;183;24	ENSP00000227495:V184I;ENSP00000394354:V188I;ENSP00000348451:V194I;ENSP00000433989:V184I;ENSP00000433318:V188I;ENSP00000432424:V188I;ENSP00000376437:V188I;ENSP00000436047:V188I;ENSP00000399444:V177I;ENSP00000434349:V187I;ENSP00000434668:V183I;ENSP00000431170:V24I	ENSP00000227495:V184I	V	+	1	0	ST3GAL4	125783536	1.000000	0.71417	0.901000	0.35422	0.910000	0.53928	8.941000	0.92964	2.516000	0.84829	0.561000	0.74099	GTC		0.547	ST3GAL4-003	PUTATIVE	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386470.1	NM_006278		31	75	31	75
POLR3B	55703	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	106850924	106850924	+	Missense_Mutation	SNP	C	C	T	rs371453512		TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chr12:106850924C>T	ENST00000228347.4	+	21	2524	c.2302C>T	c.(2302-2304)Cgt>Tgt	p.R768C	POLR3B_ENST00000539066.1_Missense_Mutation_p.R710C	NM_018082.5	NP_060552.4	Q9NW08	RPC2_HUMAN	polymerase (RNA) III (DNA directed) polypeptide B	768			R -> H (in HLD8). {ECO:0000269|PubMed:22036171}.		defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|ribonucleoside binding (GO:0032549)	p.R768C(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(22)|ovary(1)|prostate(3)|skin(3)|urinary_tract(2)	57						AGGCTTTGGGCGTTGCCTTGT	0.408																																																1	Substitution - Missense(1)	urinary_tract(1)						C	CYS/ARG,CYS/ARG	0,4406		0,0,2203	178.0	164.0	168.0		2128,2302	6.0	1.0	12		168	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	POLR3B	NM_001160708.1,NM_018082.5	180,180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	710/1076,768/1134	106850924	1,13005	2203	4300	6503	SO:0001583	missense	55703			AY092084	CCDS9105.1, CCDS53824.1	12q23.3	2014-08-12			ENSG00000013503	ENSG00000013503		"""RNA polymerase subunits"""	30348	protein-coding gene	gene with protein product		614366				12391170	Standard	NM_018082		Approved	RPC2, FLJ10388	uc001tlp.3	Q9NW08	OTTHUMG00000170077	ENST00000228347.4:c.2302C>T	12.37:g.106850924C>T	ENSP00000228347:p.Arg768Cys		A8K6H0|B3KV73|F5H1E6|Q9NW59	Missense_Mutation	SNP	ENST00000228347.4	37	CCDS9105.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.356160	0.82243	0.0	1.16E-4	ENSG00000013503	ENST00000228347;ENST00000539066	T;T	0.73575	-0.76;-0.76	6.01	6.01	0.97437	DNA-directed RNA polymerase, subunit 2, domain 6 (1);	0.000000	0.85682	D	0.000000	D	0.91922	0.7442	H	0.98701	4.305	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94367	0.7592	10	0.87932	D	0	-17.3304	15.1357	0.72562	0.174:0.826:0.0:0.0	.	768	Q9NW08	RPC2_HUMAN	C	768;710	ENSP00000228347:R768C;ENSP00000445721:R710C	ENSP00000228347:R768C	R	+	1	0	POLR3B	105375054	0.995000	0.38212	0.998000	0.56505	0.998000	0.95712	3.243000	0.51392	2.861000	0.98227	0.650000	0.86243	CGT		0.408	POLR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407166.1	NM_018082		40	96	40	96
FARP1	10160	hgsc.bcm.edu;broad.mit.edu	37	13	99083304	99083304	+	Missense_Mutation	SNP	C	C	T	rs61730891	byFrequency	TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chr13:99083304C>T	ENST00000319562.6	+	18	2178	c.1913C>T	c.(1912-1914)gCg>gTg	p.A638V	FARP1_ENST00000376586.2_Missense_Mutation_p.A638V|FARP1_ENST00000595437.1_Missense_Mutation_p.A638V	NM_005766.2	NP_005757.1	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived)	638	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				dendrite morphogenesis (GO:0048813)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|synapse assembly (GO:0007416)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|synapse (GO:0045202)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|endometrium(6)|kidney(6)|large_intestine(13)|lung(16)|ovary(1)|skin(3)|urinary_tract(1)	49	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			AAGCACCTGGCGGCTCACCTG	0.587													C|||	2	0.000399361	0.0	0.0029	5008	,	,		16276	0.0		0.0	False		,,,				2504	0.0															0								C	VAL/ALA	1,4405		0,1,2202	45.0	50.0	48.0		1913	5.4	1.0	13	dbSNP_129	48	21,8579	16.0+/-53.3	0,21,4279	yes	missense	FARP1	NM_005766.2	64	0,22,6481	TT,TC,CC		0.2442,0.0227,0.1692	benign	638/1046	99083304	22,12984	2203	4300	6503	SO:0001583	missense	10160			AB008430	CCDS9487.1, CCDS32000.1, CCDS66572.1	13q32.2	2013-01-10			ENSG00000152767	ENSG00000152767		"""Rho guanine nucleotide exchange factors"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Pleckstrin homology (PH) domain containing"""	3591	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 75"""	602654				9425278	Standard	NM_005766		Approved	CDEP, PLEKHC2, MGC87400, PPP1R75	uc001vnj.3	Q9Y4F1	OTTHUMG00000017248	ENST00000319562.6:c.1913C>T	13.37:g.99083304C>T	ENSP00000322926:p.Ala638Val		Q5JVI9|Q6IQ29	Missense_Mutation	SNP	ENST00000319562.6	37	CCDS9487.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	18.02	3.530636	0.64860	2.27E-4	0.002442	ENSG00000152767	ENST00000376586;ENST00000319562	T;T	0.66280	-0.2;-0.2	5.42	5.42	0.78866	Dbl homology (DH) domain (5);	0.057306	0.64402	D	0.000002	T	0.43233	0.1238	N	0.03154	-0.405	0.46564	D	0.999107	B;B	0.20459	0.024;0.045	B;B	0.20384	0.008;0.029	T	0.31110	-0.9955	10	0.33940	T	0.23	.	19.577	0.95449	0.0:1.0:0.0:0.0	rs61730891	638;638	Q9Y4F1;C9JME2	FARP1_HUMAN;.	V	638	ENSP00000365771:A638V;ENSP00000322926:A638V	ENSP00000322926:A638V	A	+	2	0	FARP1	97881305	1.000000	0.71417	0.959000	0.39883	0.934000	0.57294	5.536000	0.67180	2.693000	0.91896	0.650000	0.86243	GCG		0.587	FARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045541.3	NM_005766		6	127	6	127
SLC38A6	145389	hgsc.bcm.edu;broad.mit.edu	37	14	61451520	61451520	+	Splice_Site	SNP	A	A	G			TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chr14:61451520A>G	ENST00000267488.4	+	3	425	c.309A>G	c.(307-309)acA>acG	p.T103T	SLC38A6_ENST00000354886.2_Splice_Site_p.T103T|SLC38A6_ENST00000554304.1_3'UTR|RP11-193F5.1_ENST00000553946.1_RNA|SLC38A6_ENST00000456840.2_Splice_Site_p.T80T	NM_153811.2	NP_722518.2	Q8IZM9	S38A6_HUMAN	solute carrier family 38, member 6	103					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(108;0.0981)		GTATTCAGACAGGTGAGTAAA	0.378																																																0													156.0	143.0	147.0					14																	61451520		2203	4300	6503	SO:0001630	splice_region_variant	145389			AF070578	CCDS9751.1, CCDS53900.1	14q23.1	2013-05-22			ENSG00000139974	ENSG00000139974		"""Solute carriers"""	19863	protein-coding gene	gene with protein product							Standard	NM_153811		Approved	NAT-1	uc001xfh.2	Q8IZM9	OTTHUMG00000140335	ENST00000267488.4:c.310+1A>G	14.37:g.61451520A>G			C9JWA6|Q86SY5	Splice_Site	SNP	ENST00000267488.4	37	CCDS9751.1	.	.	.	.	.	.	.	.	.	.	A	11.73	1.727030	0.30593	.	.	ENSG00000139974	ENST00000533744	.	.	.	5.53	1.52	0.23074	.	.	.	.	.	T	0.53594	0.1806	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42932	-0.9422	4	.	.	.	-3.2214	6.1923	0.20530	0.2994:0.3274:0.0:0.3732	.	.	.	.	R	52	.	.	Q	+	2	0	SLC38A6	60521273	0.998000	0.40836	1.000000	0.80357	0.788000	0.44548	0.587000	0.23909	0.353000	0.24079	-0.524000	0.04348	CAG		0.378	SLC38A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276957.1		Silent	14	189	14	189
ATG2B	55102	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	14	96757939	96757939	+	Silent	SNP	A	A	G			TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chr14:96757939A>G	ENST00000359933.4	-	38	6470	c.5577T>C	c.(5575-5577)caT>caC	p.H1859H	ATG2B_ENST00000261834.5_5'UTR	NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	1859					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		TCACTTACCCATGTCGATAGG	0.348																																																0													87.0	92.0	90.0					14																	96757939		2203	4300	6503	SO:0001819	synonymous_variant	55102			AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 103"", ""ATG2 autophagy related 2 homolog B (S. cerevisiae)"""	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.5577T>C	14.37:g.96757939A>G			Q6ZRE7|Q96DQ3|Q9NW80	Silent	SNP	ENST00000359933.4	37	CCDS9944.2																																																																																				0.348	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036		18	157	18	157
SH3GL3	6457	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	84286924	84286924	+	Missense_Mutation	SNP	A	A	G			TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chr15:84286924A>G	ENST00000427482.2	+	9	1235	c.929A>G	c.(928-930)gAc>gGc	p.D310G	SH3GL3_ENST00000535412.1_3'UTR|SH3GL3_ENST00000434347.1_Missense_Mutation_p.D318G|SH3GL3_ENST00000564054.1_3'UTR|SH3GL3_ENST00000324537.5_Missense_Mutation_p.D318G|AC087738.1_ENST00000411248.1_RNA	NM_003027.3	NP_003018.3	Q99963	SH3G3_HUMAN	SH3-domain GRB2-like 3	310	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				central nervous system development (GO:0007417)|endocytosis (GO:0006897)|signal transduction (GO:0007165)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)			central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	30						AAAGAAGGGGACATCATTACA	0.423																																																0													107.0	102.0	104.0					15																	84286924		2203	4300	6503	SO:0001583	missense	6457			AF036271	CCDS10325.2, CCDS73772.1	15q24	2006-11-24			ENSG00000140600	ENSG00000140600			10832	protein-coding gene	gene with protein product		603362				9169142	Standard	NR_026799		Approved	SH3D2C, SH3P13, CNSA3, EEN-B2, HsT19371	uc002bjw.3	Q99963	OTTHUMG00000147361	ENST00000427482.2:c.929A>G	15.37:g.84286924A>G	ENSP00000391372:p.Asp310Gly		O43553|O43554	Missense_Mutation	SNP	ENST00000427482.2	37	CCDS10325.2	.	.	.	.	.	.	.	.	.	.	A	26.9	4.778648	0.90195	.	.	ENSG00000140600	ENST00000427482;ENST00000324537;ENST00000434347	T;T;T	0.63580	-0.05;-0.05;-0.05	5.82	5.82	0.92795	Src homology-3 domain (5);	0.000000	0.85682	D	0.000000	D	0.85401	0.5688	H	0.96430	3.82	0.80722	D	1	D;D	0.71674	0.997;0.998	D;D	0.74023	0.982;0.944	D	0.90012	0.4122	10	0.87932	D	0	-25.5801	15.3729	0.74581	1.0:0.0:0.0:0.0	.	310;318	Q99963;Q99963-3	SH3G3_HUMAN;.	G	310;318;318	ENSP00000391372:D310G;ENSP00000320092:D318G;ENSP00000397871:D318G	ENSP00000320092:D318G	D	+	2	0	SH3GL3	82077928	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.805000	0.91925	2.216000	0.71823	0.533000	0.62120	GAC		0.423	SH3GL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347797.1	NM_003027		10	66	10	66
SEC14L5	9717	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	16	5061202	5061202	+	Missense_Mutation	SNP	C	C	T			TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chr16:5061202C>T	ENST00000251170.7	+	15	2087	c.1907C>T	c.(1906-1908)aCg>aTg	p.T636M	RP11-165E7.1_ENST00000588778.1_RNA	NM_014692.1	NP_055507.1	O43304	S14L5_HUMAN	SEC14-like 5 (S. cerevisiae)	636	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.					integral component of membrane (GO:0016021)|intracellular (GO:0005622)	transporter activity (GO:0005215)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|skin(1)	29						GATGTCCTGACGGCTCTGCAC	0.662																																																0													25.0	29.0	28.0					16																	5061202		1998	4155	6153	SO:0001583	missense	9717			AB007880	CCDS45403.1	16p13.3	2008-02-05				ENSG00000103184			29032	protein-coding gene	gene with protein product						9455477	Standard	NM_014692		Approved	KIAA0420, PRELID4B	uc002cye.2	O43304		ENST00000251170.7:c.1907C>T	16.37:g.5061202C>T	ENSP00000251170:p.Thr636Met			Missense_Mutation	SNP	ENST00000251170.7	37	CCDS45403.1	.	.	.	.	.	.	.	.	.	.	C	10.53	1.376192	0.24857	.	.	ENSG00000103184	ENST00000251170	T	0.42513	0.97	4.45	0.0249	0.14143	GOLD (2);	0.240144	0.32802	N	0.005628	T	0.24509	0.0594	L	0.31294	0.92	0.32802	D	0.500238	B	0.27140	0.169	B	0.17433	0.018	T	0.14227	-1.0480	10	0.45353	T	0.12	-9.5136	7.0081	0.24848	0.1245:0.6608:0.0:0.2147	.	636	O43304	S14L5_HUMAN	M	636	ENSP00000251170:T636M	ENSP00000251170:T636M	T	+	2	0	SEC14L5	5001203	0.870000	0.30015	0.116000	0.21606	0.546000	0.35178	1.730000	0.38125	0.188000	0.20168	0.561000	0.74099	ACG		0.662	SEC14L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434379.1			20	36	20	36
NLRP13	126204	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	56422063	56422063	+	Missense_Mutation	SNP	G	G	C	rs144412914		TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chr19:56422063G>C	ENST00000342929.3	-	6	2147	c.2148C>G	c.(2146-2148)aaC>aaG	p.N716K	NLRP13_ENST00000588751.1_Missense_Mutation_p.N716K	NM_176810.2	NP_789780.2	Q86W25	NAL13_HUMAN	NLR family, pyrin domain containing 13	716							ATP binding (GO:0005524)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(58)|ovary(4)|pancreas(2)|prostate(2)|skin(13)|stomach(2)|urinary_tract(1)	109		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)		GBM - Glioblastoma multiforme(193;0.0642)		AGCAAATGCTGTTCCATGCGT	0.458													G|||	1	0.000199681	0.0	0.0	5008	,	,		20218	0.0		0.001	False		,,,				2504	0.0															0													181.0	157.0	165.0					19																	56422063		2203	4300	6503	SO:0001583	missense	126204			AY154468	CCDS33119.1	19q13.43	2008-02-05	2006-12-08	2006-12-08	ENSG00000173572	ENSG00000173572		"""Nucleotide-binding domain and leucine rich repeat containing"""	22937	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 13"""	609660	"""NACHT, leucine rich repeat and PYD containing 13"""	NALP13		12563287	Standard	NM_176810		Approved	NOD14, PAN13, CLR19.7	uc010ygg.2	Q86W25	OTTHUMG00000167839	ENST00000342929.3:c.2148C>G	19.37:g.56422063G>C	ENSP00000343891:p.Asn716Lys		Q7RTR5	Missense_Mutation	SNP	ENST00000342929.3	37	CCDS33119.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	3.203	-0.163209	0.06502	.	.	ENSG00000173572	ENST00000342929	D	0.84873	-1.91	2.26	-2.95	0.05564	.	.	.	.	.	T	0.58075	0.2097	N	0.01493	-0.835	0.09310	N	1	B	0.22211	0.066	B	0.21917	0.037	T	0.49808	-0.8900	9	0.34782	T	0.22	.	3.4712	0.07567	0.0:0.3326:0.2177:0.4497	.	716	Q86W25	NAL13_HUMAN	K	716	ENSP00000343891:N716K	ENSP00000343891:N716K	N	-	3	2	NLRP13	61113875	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.801000	0.04550	-0.610000	0.05716	-1.234000	0.01563	AAC		0.458	NLRP13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396560.1	NM_176810		41	41	41	41
HSPG2	3339	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	22211318	22211318	+	Silent	SNP	G	G	A	rs529678982		TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chr1:22211318G>A	ENST00000374695.3	-	12	1528	c.1449C>T	c.(1447-1449)aaC>aaT	p.N483N		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	483	Ig-like C2-type 1.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	TGCCCCGGGCGTTCATGGCCT	0.627																																																0													56.0	44.0	49.0					1																	22211318		2202	4300	6502	SO:0001819	synonymous_variant	3339			M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.1449C>T	1.37:g.22211318G>A			Q16287|Q5SZI3|Q9H3V5	Silent	SNP	ENST00000374695.3	37	CCDS30625.1																																																																																				0.627	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		11	19	11	19
TPR	7175	hgsc.bcm.edu;broad.mit.edu	37	1	186315342	186315342	+	Missense_Mutation	SNP	C	C	G			TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chr1:186315342C>G	ENST00000367478.4	-	23	3317	c.3021G>C	c.(3019-3021)aaG>aaC	p.K1007N		NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	1007					carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)			autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		CTTCCATCAACTTCTTTTCCA	0.353			T	NTRK1	papillary thyroid																																		Dom	yes		1	1q25	7175	translocated promoter region		E	0													181.0	161.0	167.0					1																	186315342		1847	4097	5944	SO:0001583	missense	7175			U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"""translocated promoter region (to activated MET oncogene)"""			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.3021G>C	1.37:g.186315342C>G	ENSP00000356448:p.Lys1007Asn		Q15655|Q5SWY0|Q99968	Missense_Mutation	SNP	ENST00000367478.4	37	CCDS41446.1	.	.	.	.	.	.	.	.	.	.	C	17.93	3.508910	0.64410	.	.	ENSG00000047410	ENST00000367478	T	0.26660	1.72	5.66	1.11	0.20524	Prefoldin (1);	0.102278	0.64402	D	0.000004	T	0.26376	0.0644	L	0.29908	0.895	0.36009	D	0.837919	D	0.64830	0.994	P	0.54270	0.747	T	0.19484	-1.0304	10	0.48119	T	0.1	.	9.8887	0.41276	0.0:0.6128:0.0:0.3872	.	1007	P12270	TPR_HUMAN	N	1007	ENSP00000356448:K1007N	ENSP00000356448:K1007N	K	-	3	2	TPR	184581965	0.000000	0.05858	0.997000	0.53966	0.998000	0.95712	-0.344000	0.07780	0.313000	0.23062	0.650000	0.86243	AAG		0.353	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292		12	177	12	177
PREX1	57580	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	20	47305216	47305216	+	Missense_Mutation	SNP	A	A	G			TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chr20:47305216A>G	ENST00000371941.3	-	10	1335	c.1313T>C	c.(1312-1314)gTc>gCc	p.V438A	PREX1_ENST00000396220.1_Missense_Mutation_p.V438A	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	438	DEP 1. {ECO:0000255|PROSITE- ProRule:PRU00066}.				actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			GCACTTGGGGACAGTGCTCAG	0.562																																																0													163.0	119.0	134.0					20																	47305216		2203	4300	6503	SO:0001583	missense	57580			AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.1313T>C	20.37:g.47305216A>G	ENSP00000361009:p.Val438Ala		E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Missense_Mutation	SNP	ENST00000371941.3	37	CCDS13410.1	.	.	.	.	.	.	.	.	.	.	A	18.86	3.712696	0.68730	.	.	ENSG00000124126	ENST00000371941;ENST00000396220	T;T	0.14266	2.52;2.52	5.01	5.01	0.66863	DEP domain (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.124813	0.34725	U	0.003730	T	0.20941	0.0504	M	0.67397	2.05	0.52099	D	0.999941	B	0.30605	0.287	B	0.36092	0.217	T	0.02059	-1.1221	10	0.42905	T	0.14	.	14.7582	0.69583	1.0:0.0:0.0:0.0	.	438	Q8TCU6	PREX1_HUMAN	A	438	ENSP00000361009:V438A;ENSP00000379522:V438A	ENSP00000361009:V438A	V	-	2	0	PREX1	46738623	1.000000	0.71417	0.892000	0.35008	0.996000	0.88848	9.202000	0.95026	1.883000	0.54544	0.460000	0.39030	GTC		0.562	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		9	88	9	88
TTN	7273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	179645981	179645981	+	Silent	SNP	C	C	T			TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chr2:179645981C>T	ENST00000591111.1	-	21	3614	c.3390G>A	c.(3388-3390)gtG>gtA	p.V1130V	TTN_ENST00000589042.1_Silent_p.V1130V|TTN_ENST00000342992.6_Silent_p.V1130V|RP11-88L24.4_ENST00000582038.2_RNA|TTN_ENST00000360870.5_Silent_p.V1130V|TTN_ENST00000342175.6_Silent_p.V1084V|TTN_ENST00000359218.5_Silent_p.V1084V|TTN_ENST00000460472.2_Silent_p.V1084V			Q8WZ42	TITIN_HUMAN	titin	33347	Ig-like 4.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGTTGTAACTCACTTTGTATC	0.353																																																0													198.0	174.0	182.0					2																	179645981		2203	4300	6503	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.3390G>A	2.37:g.179645981C>T			A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.353	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		27	73	27	73
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	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			42	103	42	103
STAG1	10274	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	136117601	136117601	+	Missense_Mutation	SNP	G	G	C	rs371711194		TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chr3:136117601G>C	ENST00000383202.2	-	22	2523	c.2267C>G	c.(2266-2268)tCt>tGt	p.S756C	STAG1_ENST00000536929.1_Missense_Mutation_p.S340C|STAG1_ENST00000434713.2_Missense_Mutation_p.S530C|STAG1_ENST00000236698.5_Missense_Mutation_p.S756C	NM_005862.2	NP_005853.2	Q8WVM7	STAG1_HUMAN	stromal antigen 1	756					chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)	p.S756C(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58						TTTGGAAGGAGAGCCATCAGT	0.313																																																1	Substitution - Missense(1)	breast(1)						G	CYS/SER	0,4406		0,0,2203	66.0	66.0	66.0		2267	5.3	1.0	3		66	1,8599	1.2+/-3.3	0,1,4299	no	missense	STAG1	NM_005862.2	112	0,1,6502	CC,CG,GG		0.0116,0.0,0.0077	benign	756/1259	136117601	1,13005	2203	4300	6503	SO:0001583	missense	10274			Z75330	CCDS3090.1	3q22.2-q22.3	2011-08-12			ENSG00000118007	ENSG00000118007			11354	protein-coding gene	gene with protein product		604358				9305759	Standard	XM_006713471		Approved	SA-1, SCC3A	uc003era.1	Q8WVM7	OTTHUMG00000159798	ENST00000383202.2:c.2267C>G	3.37:g.136117601G>C	ENSP00000372689:p.Ser756Cys		O00539|Q6P275	Missense_Mutation	SNP	ENST00000383202.2	37	CCDS3090.1	.	.	.	.	.	.	.	.	.	.	G	12.29	1.894356	0.33442	0.0	1.16E-4	ENSG00000118007	ENST00000383202;ENST00000236698;ENST00000434713;ENST00000536929	T;T;T;T	0.33216	1.42;1.42;1.42;1.42	5.3	5.3	0.74995	Armadillo-type fold (1);	0.573862	0.19609	N	0.110200	T	0.26268	0.0641	L	0.35723	1.085	0.39352	D	0.965762	B;B	0.06786	0.0;0.001	B;B	0.10450	0.002;0.005	T	0.04930	-1.0917	10	0.42905	T	0.14	.	12.7884	0.57520	0.0:0.0:0.836:0.164	.	756;756	Q6P275;Q8WVM7	.;STAG1_HUMAN	C	756;756;530;340	ENSP00000372689:S756C;ENSP00000236698:S756C;ENSP00000404396:S530C;ENSP00000445787:S340C	ENSP00000236698:S756C	S	-	2	0	STAG1	137600291	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.810000	0.62598	2.473000	0.83533	0.591000	0.81541	TCT		0.313	STAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357366.1	NM_005862		21	62	21	62
RBP1	5947	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	139237308	139237308	+	Silent	SNP	C	C	T			TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chr3:139237308C>T	ENST00000232219.2	-	3	605	c.495G>A	c.(493-495)gaG>gaA	p.E165E	RP11-319G6.1_ENST00000515247.1_RNA	NM_002899.3	NP_002890.2	P09455	RET1_HUMAN	retinol binding protein 1, cellular	103					phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|vitamin A metabolic process (GO:0006776)	cytosol (GO:0005829)	retinal binding (GO:0016918)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|transporter activity (GO:0005215)			endometrium(1)|large_intestine(2)|lung(1)|prostate(1)	5					Acitretin(DB00459)|Vitamin A(DB00162)	AGCCACGCCCCTCCTTCTCAC	0.597																																																0													122.0	97.0	105.0					3																	139237308		2203	4300	6503	SO:0001819	synonymous_variant	5947				CCDS3110.2, CCDS46925.1, CCDS46926.1	3q21-q23	2013-03-01	2001-11-28		ENSG00000114115	ENSG00000114115		"""Fatty acid binding protein family"""	9919	protein-coding gene	gene with protein product		180260	"""retinol-binding protein 1, cellular"""			1654334, 9858824	Standard	NM_002899		Approved	CRABP-I, CRBP1, CRBP, RBPC, CRBPI	uc003eti.2	P09455	OTTHUMG00000155751	ENST00000232219.2:c.495G>A	3.37:g.139237308C>T			A8K2Q0|B7Z7A0|E7EWV0|F2Z2F2|Q6FGX8	Silent	SNP	ENST00000232219.2	37	CCDS3110.2																																																																																				0.597	RBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341495.1	NM_002899		10	110	10	110
C6	729	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	41149347	41149347	+	Silent	SNP	A	A	G			TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chr5:41149347A>G	ENST00000263413.3	-	17	2883	c.2619T>C	c.(2617-2619)tgT>tgC	p.C873C	C6_ENST00000337836.5_Silent_p.C873C	NM_001115131.1	NP_001108603.2	P13671	CO6_HUMAN	complement component 6	873	C5b-binding domain.|Factor I module (FIM) 2.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)				central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(7)|large_intestine(16)|liver(1)|lung(51)|ovary(3)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)	96		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)				ACTTACCTGAACATTTTTCCC	0.398																																																0													255.0	247.0	250.0					5																	41149347		2203	4300	6503	SO:0001819	synonymous_variant	729			J05024	CCDS3936.1	5p13.1	2014-09-17			ENSG00000039537	ENSG00000039537		"""Complement system"""	1339	protein-coding gene	gene with protein product		217050					Standard	NM_001115131		Approved		uc003jmk.3	P13671	OTTHUMG00000094781	ENST00000263413.3:c.2619T>C	5.37:g.41149347A>G				Silent	SNP	ENST00000263413.3	37	CCDS3936.1																																																																																				0.398	C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211592.1			182	252	182	252
MAST4	375449	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	66441064	66441064	+	Missense_Mutation	SNP	A	A	C			TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chr5:66441064A>C	ENST00000403625.2	+	23	3246	c.2951A>C	c.(2950-2952)gAg>gCg	p.E984A	MAST4_ENST00000403666.1_Missense_Mutation_p.E795A|MAST4_ENST00000404260.3_Missense_Mutation_p.E987A|MAST4_ENST00000405643.1_Missense_Mutation_p.E805A|MAST4_ENST00000261569.7_Missense_Mutation_p.E790A	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	987						cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		ATTTCAACAGAGGGAGAGCAA	0.512																																																0													43.0	42.0	43.0					5																	66441064		2012	4198	6210	SO:0001583	missense	375449			AY830839	CCDS47224.1, CCDS47225.1, CCDS54861.1, CCDS75254.1	5q12.3	2007-06-20			ENSG00000069020	ENSG00000069020			19037	protein-coding gene	gene with protein product						9205841	Standard	NM_198828		Approved	KIAA0303	uc021xzk.1	O15021	OTTHUMG00000152471	ENST00000403625.2:c.2951A>C	5.37:g.66441064A>C	ENSP00000385727:p.Glu984Ala		A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Missense_Mutation	SNP	ENST00000403625.2	37	CCDS54861.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.5|24.5	4.543805|4.543805	0.86022|0.86022	.|.	.|.	ENSG00000069020|ENSG00000069020	ENST00000404260;ENST00000403625;ENST00000403666;ENST00000405643;ENST00000380908;ENST00000261569;ENST00000432399|ENST00000443808	T;T;T;T;T|.	0.69306|.	-0.36;-0.36;-0.39;-0.38;-0.36|.	5.26|5.26	5.26|5.26	0.73747|0.73747	.|.	0.252234|.	0.39274|.	N|.	0.001410|.	T|T	0.73651|0.73651	0.3614|0.3614	M|M	0.75615|0.75615	2.305|2.305	0.39531|0.39531	D|D	0.968666|0.968666	D;P;P;D|.	0.58620|.	0.983;0.859;0.849;0.967|.	P;P;P;P|.	0.58266|.	0.834;0.579;0.759;0.836|.	T|T	0.76024|0.76024	-0.3110|-0.3110	10|5	0.54805|.	T|.	0.06|.	-23.8917|-23.8917	13.8888|13.8888	0.63726|0.63726	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	805;987;790;795|.	E7EWQ5;O15021;O15021-2;O15021-3|.	.;MAST4_HUMAN;.;.|.	A|S	987;984;795;805;805;790;790|107	ENSP00000385048:E987A;ENSP00000385727:E984A;ENSP00000384313:E795A;ENSP00000384099:E805A;ENSP00000261569:E790A|.	ENSP00000261569:E790A|.	E|R	+|+	2|3	0|2	MAST4|MAST4	66476820|66476820	1.000000|1.000000	0.71417|0.71417	0.953000|0.953000	0.39169|0.39169	0.862000|0.862000	0.49288|0.49288	8.059000|8.059000	0.89462|0.89462	2.207000|2.207000	0.71202|0.71202	0.482000|0.482000	0.46254|0.46254	GAG|AGA		0.512	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2			15	23	15	23
FEM1C	56929	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	114860125	114860125	+	Missense_Mutation	SNP	G	G	C			TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chr5:114860125G>C	ENST00000274457.3	-	3	2295	c.1734C>G	c.(1732-1734)atC>atG	p.I578M		NM_020177.2	NP_064562.1	Q96JP0	FEM1C_HUMAN	fem-1 homolog c (C. elegans)	578					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				breast(5)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|liver(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	18		all_cancers(142;0.000575)|all_epithelial(76;9.98e-06)|Prostate(80;0.00955)|Ovarian(225;0.0443)|all_lung(232;0.132)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;2.5e-07)|Epithelial(69;2.66e-07)|all cancers(49;1.39e-05)		TTATAGGCTGGATTAAATTTT	0.368																																																0													109.0	110.0	110.0					5																	114860125		2202	4300	6502	SO:0001583	missense	56929				CCDS4118.1	5q22	2013-01-10	2006-11-08		ENSG00000145780	ENSG00000145780		"""Ankyrin repeat domain containing"""	16933	protein-coding gene	gene with protein product		608767				14527725, 11733146	Standard	NM_020177		Approved	KIAA1785, EUROIMAGE686608, EUROIMAGE783647, FEM1A	uc003krb.1	Q96JP0	OTTHUMG00000128895	ENST00000274457.3:c.1734C>G	5.37:g.114860125G>C	ENSP00000274457:p.Ile578Met		B2RE47|Q8N3V8|Q9H704|Q9NPL6|Q9NPL9	Missense_Mutation	SNP	ENST00000274457.3	37	CCDS4118.1	.	.	.	.	.	.	.	.	.	.	G	2.828	-0.243241	0.05906	.	.	ENSG00000145780	ENST00000274457	T	0.69561	-0.41	4.84	3.03	0.35002	Ankyrin repeat-containing domain (2);	0.000000	0.85682	D	0.000000	T	0.54224	0.1845	L	0.49571	1.57	0.48185	D	0.999601	B	0.27117	0.168	B	0.20577	0.03	T	0.44390	-0.9331	10	0.33141	T	0.24	-18.1339	7.118	0.25427	0.1504:0.0:0.7105:0.139	.	578	Q96JP0	FEM1C_HUMAN	M	578	ENSP00000274457:I578M	ENSP00000274457:I578M	I	-	3	3	FEM1C	114888024	1.000000	0.71417	1.000000	0.80357	0.623000	0.37688	3.530000	0.53539	0.435000	0.26365	0.462000	0.41574	ATC		0.368	FEM1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250857.3	NM_020177		69	103	69	103
HLA-DQA2	3118	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	32713716	32713716	+	Missense_Mutation	SNP	G	G	C	rs35633399		TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chr6:32713716G>C	ENST00000374940.3	+	3	582	c.480G>C	c.(478-480)gaG>gaC	p.E160D		NM_020056.4	NP_064440.1	P01906	DQA2_HUMAN	major histocompatibility complex, class II, DQ alpha 2	160	Alpha-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)			endometrium(2)|large_intestine(3)|lung(7)|skin(1)	13					"""""""Insulin(DB00071)"""	GTGTTTCTGAGACCAGCTTCC	0.493																																																0													249.0	228.0	235.0					6																	32713716		1511	2709	4220	SO:0001583	missense	3118				CCDS4753.1	6p21.3	2013-01-11			ENSG00000237541	ENSG00000237541		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4943	protein-coding gene	gene with protein product		613503		HLA-DXA			Standard	NM_020056		Approved		uc003obx.3	P01906	OTTHUMG00000031108	ENST00000374940.3:c.480G>C	6.37:g.32713716G>C	ENSP00000364076:p.Glu160Asp		A2BF37|B0V0E7|O19789|Q5SQ94|Q5SR04	Missense_Mutation	SNP	ENST00000374940.3	37	CCDS4753.1	.	.	.	.	.	.	.	.	.	.	.	9.517	1.107339	0.20714	.	.	ENSG00000237541	ENST00000374940	T	0.03004	4.08	3.06	0.747	0.18371	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.537042	0.19019	U	0.124879	T	0.08088	0.0202	M	0.89287	3.02	0.30450	N	0.775371	D	0.63046	0.992	D	0.68353	0.957	T	0.02244	-1.1189	10	0.72032	D	0.01	.	6.205	0.20598	0.3299:0.0:0.6701:0.0	.	160	P01906	DQA2_HUMAN	D	160	ENSP00000364076:E160D	ENSP00000364076:E160D	E	+	3	2	HLA-DQA2	32821694	1.000000	0.71417	0.993000	0.49108	0.486000	0.33341	0.752000	0.26362	0.005000	0.14708	0.174000	0.16983	GAG		0.493	HLA-DQA2-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076179.2	NM_020056		97	125	97	125
RFX6	222546	hgsc.bcm.edu;broad.mit.edu	37	6	117198501	117198501	+	Silent	SNP	C	C	T			TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chr6:117198501C>T	ENST00000332958.2	+	1	79	c.63C>T	c.(61-63)tcC>tcT	p.S21S		NM_173560.3	NP_775831.2	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6	21					endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|pancreatic A cell differentiation (GO:0003310)|pancreatic D cell differentiation (GO:0003311)|pancreatic epsilon cell differentiation (GO:0090104)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of insulin secretion (GO:0050796)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell differentiation (GO:0003309)	nucleus (GO:0005634)	transcription regulatory region DNA binding (GO:0044212)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(29)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	59						CCCAACTGTCCCCGGGGATCC	0.687																																																0													18.0	20.0	19.0					6																	117198501		2202	4298	6500	SO:0001819	synonymous_variant	222546			BC039248	CCDS5113.1	6q22.31	2008-08-04	2008-08-04	2008-08-04	ENSG00000185002	ENSG00000185002			21478	protein-coding gene	gene with protein product		612659	"""regulatory factor X domain containing 1"""	RFXDC1			Standard	NM_173560		Approved	MGC33442, dJ955L16.1	uc003pxm.3	Q8HWS3	OTTHUMG00000015449	ENST00000332958.2:c.63C>T	6.37:g.117198501C>T			Q5T6B3	Silent	SNP	ENST00000332958.2	37	CCDS5113.1																																																																																				0.687	RFX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041970.2	NM_173560		5	21	5	21
HOXA4	3201	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	27169089	27169089	+	Silent	SNP	G	G	A			TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chr7:27169089G>A	ENST00000360046.5	-	2	783	c.718C>T	c.(718-720)Ctg>Ttg	p.L240L	HOXA4_ENST00000428284.2_Silent_p.L240L|HOXA-AS3_ENST00000518848.1_RNA|HOXA-AS2_ENST00000521687.1_RNA|HOXA3_ENST00000521401.1_Intron|HOXA-AS2_ENST00000521159.1_RNA|RP1-170O19.22_ENST00000467897.2_RNA|HOXA-AS2_ENST00000517550.1_RNA|HOXA3_ENST00000317201.2_5'Flank	NM_002141.4	NP_002132.3	Q00056	HXA4_HUMAN	homeobox A4	240					anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(6)	12						CGCCGGGTCAGGTATCGATTG	0.572																																																0													125.0	116.0	119.0					7																	27169089		2203	4300	6503	SO:0001819	synonymous_variant	3201				CCDS5405.1	7p15.2	2011-06-20	2005-12-22		ENSG00000197576	ENSG00000197576		"""Homeoboxes / ANTP class : HOXL subclass"""	5105	protein-coding gene	gene with protein product		142953	"""homeo box A4"""	HOX1D, HOX1		1973146, 1358459	Standard	NM_002141		Approved		uc003sym.4	Q00056	OTTHUMG00000023213	ENST00000360046.5:c.718C>T	7.37:g.27169089G>A			A4D180|O43366	Silent	SNP	ENST00000360046.5	37	CCDS5405.1	.	.	.	.	.	.	.	.	.	.	G	8.123	0.781313	0.16120	.	.	ENSG00000197576	ENST00000511914	.	.	.	5.29	5.29	0.74685	.	.	.	.	.	T	0.74981	0.3788	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.73830	-0.3859	4	.	.	.	.	18.9816	0.92757	0.0:0.0:1.0:0.0	.	.	.	.	L	59	.	.	P	-	2	0	HOXA4	27135614	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.896000	0.87350	2.485000	0.83878	0.555000	0.69702	CCT		0.572	HOXA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059534.4			40	75	40	75
ACTL7B	10880	hgsc.bcm.edu;broad.mit.edu	37	9	111617665	111617665	+	Silent	SNP	C	C	T			TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chr9:111617665C>T	ENST00000374667.3	-	1	1574	c.546G>A	c.(544-546)tcG>tcA	p.S182S		NM_006686.3	NP_006677.1	Q9Y614	ACL7B_HUMAN	actin-like 7B	182						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	structural constituent of cytoskeleton (GO:0005200)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20						TGGACAGCAACGACTGGGACG	0.647																																																0													46.0	44.0	45.0					9																	111617665		2202	4299	6501	SO:0001819	synonymous_variant	10880			BC033789	CCDS6771.1	9q31	2009-05-15			ENSG00000148156	ENSG00000148156			162	protein-coding gene	gene with protein product		604304				10373328, 12907721	Standard	NM_006686		Approved	Tact1	uc004bdi.3	Q9Y614	OTTHUMG00000020462	ENST00000374667.3:c.546G>A	9.37:g.111617665C>T			B2R9Q2|Q5JSV1	Silent	SNP	ENST00000374667.3	37	CCDS6771.1																																																																																				0.647	ACTL7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053571.1	NM_006686		7	73	7	73
TMEM245	23731	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	111853321	111853321	+	Missense_Mutation	SNP	G	G	C			TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chr9:111853321G>C	ENST00000374586.3	-	5	1062	c.1031C>G	c.(1030-1032)aCg>aGg	p.T344R		NM_032012.3	NP_114401.2	Q9H330	TM245_HUMAN	transmembrane protein 245	344						integral component of membrane (GO:0016021)											TCTAAGAAACGTTCCTATTTC	0.502																																																0													118.0	121.0	120.0					9																	111853321		1951	4144	6095	SO:0001583	missense	23731			AF153415	CCDS43858.1	9q31	2012-03-06	2012-03-06	2012-03-06	ENSG00000106771	ENSG00000106771			1363	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 5"""	C9orf5		10564813	Standard	NM_032012		Approved	CG-2	uc004bdt.4	Q9H330	OTTHUMG00000020469	ENST00000374586.3:c.1031C>G	9.37:g.111853321G>C	ENSP00000363714:p.Thr344Arg		B4DSW7|Q5JTQ5|Q5SS43|Q6ZME3|Q8NDJ5|Q96CG6	Missense_Mutation	SNP	ENST00000374586.3	37	CCDS43858.1	.	.	.	.	.	.	.	.	.	.	G	11.55	1.671436	0.29693	.	.	ENSG00000106771	ENST00000374587;ENST00000374586;ENST00000223608	T	0.22743	1.94	5.9	5.9	0.94986	.	0.338488	0.31358	N	0.007794	T	0.22513	0.0543	L	0.47716	1.5	0.09310	N	1	B;B	0.28082	0.107;0.2	B;B	0.30716	0.119;0.084	T	0.12553	-1.0543	10	0.34782	T	0.22	-7.6891	15.0393	0.71777	0.0:0.0:0.8579:0.1421	.	344;344	Q9H330-2;Q9H330	.;CI005_HUMAN	R	344	ENSP00000363714:T344R	ENSP00000223608:T344R	T	-	2	0	C9orf5	110893142	0.797000	0.28877	0.021000	0.16686	0.534000	0.34807	5.302000	0.65733	2.793000	0.96121	0.563000	0.77884	ACG		0.502	TMEM245-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053587.2	NM_032012		9	75	9	75
MXRA5	25878	hgsc.bcm.edu;broad.mit.edu	37	X	3228182	3228182	+	Missense_Mutation	SNP	C	C	T	rs573265184		TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chrX:3228182C>T	ENST00000217939.6	-	7	8216	c.8062G>A	c.(8062-8064)Gtt>Att	p.V2688I		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	2688	Ig-like C2-type 11.					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)				AGAAGAGAAACGCGTCCCAGG	0.627													c|||	20	0.00529801	0.0	0.0	3775	,	,		12871	0.0		0.0	False		,,,				2504	0.0204															0													37.0	37.0	37.0					X																	3228182		2203	4295	6498	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.8062G>A	X.37:g.3228182C>T	ENSP00000217939:p.Val2688Ile		Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	37	CCDS14124.1	.	.	.	.	.	.	.	.	.	.	C	4.644	0.119809	0.08881	.	.	ENSG00000101825	ENST00000381114;ENST00000217939	T	0.28069	1.63	4.32	-8.65	0.00870	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.201360	0.06423	N	0.722695	T	0.17577	0.0422	N	0.20483	0.58	0.09310	N	1	B	0.23735	0.09	B	0.24394	0.053	T	0.28554	-1.0040	10	0.32370	T	0.25	.	11.8218	0.52242	0.1847:0.6137:0.0:0.2016	.	2688	Q9NR99	MXRA5_HUMAN	I	2688	ENSP00000217939:V2688I	ENSP00000217939:V2688I	V	-	1	0	MXRA5	3238182	1.000000	0.71417	0.000000	0.03702	0.001000	0.01503	1.402000	0.34600	-2.788000	0.00357	-1.886000	0.00541	GTT		0.627	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419		52	86	52	86
TLR7	51284	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	12906720	12906720	+	Silent	SNP	C	C	T	rs201628325		TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chrX:12906720C>T	ENST00000380659.3	+	3	3232	c.3093C>T	c.(3091-3093)aaC>aaT	p.N1031N		NM_016562.3	NP_057646.1	Q9NYK1	TLR7_HUMAN	toll-like receptor 7	1031	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of chemokine production (GO:0032722)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|toll-like receptor 7 signaling pathway (GO:0034154)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	cytoplasm (GO:0005737)|early phagosome (GO:0032009)|endolysosome membrane (GO:0036020)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|single-stranded RNA binding (GO:0003727)|siRNA binding (GO:0035197)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(4)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	44					Hydroxychloroquine(DB01611)|Imiquimod(DB00724)	GTCTAAAGAACGCCCTGGCCA	0.517																																																0								C		0,3835		0,0,1632,571	105.0	103.0	104.0		3093	0.8	1.0	X		104	1,6727		0,1,2427,1872	no	coding-synonymous	TLR7	NM_016562.3		0,1,4059,2443	TT,TC,CC,C		0.0149,0.0,0.0095		1031/1050	12906720	1,10562	2203	4300	6503	SO:0001819	synonymous_variant	51284			AF240467	CCDS14151.1	Xp22.3	2008-02-05			ENSG00000196664	ENSG00000196664			15631	protein-coding gene	gene with protein product		300365				11022119	Standard	NM_016562		Approved		uc004cvc.3	Q9NYK1	OTTHUMG00000021137	ENST00000380659.3:c.3093C>T	X.37:g.12906720C>T			D1CS69|Q9NR98	Silent	SNP	ENST00000380659.3	37	CCDS14151.1																																																																																				0.517	TLR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055769.1	NM_016562		77	167	77	167
GLUD2	2747	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	120181766	120181766	+	Silent	SNP	C	C	T			TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chrX:120181766C>T	ENST00000328078.1	+	1	305	c.228C>T	c.(226-228)cgC>cgT	p.R76R		NM_012084.3	NP_036216.2	P49448	DHE4_HUMAN	glutamate dehydrogenase 2	76					glutamate biosynthetic process (GO:0006537)|glutamate catabolic process (GO:0006538)|glutamate metabolic process (GO:0006536)|oxidation-reduction process (GO:0055114)	mitochondrion (GO:0005739)	ADP binding (GO:0043531)|glutamate dehydrogenase (NAD+) activity (GO:0004352)|glutamate dehydrogenase [NAD(P)+] activity (GO:0004353)|GTP binding (GO:0005525)|leucine binding (GO:0070728)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|urinary_tract(1)	38						TCTTCGATCGCGGCGCCAGCA	0.647																																																0													84.0	72.0	76.0					X																	120181766		2203	4300	6503	SO:0001819	synonymous_variant	2747			U08997	CCDS14603.1	Xq24-q25	2008-02-05	2003-02-24	2003-02-28	ENSG00000182890	ENSG00000182890			4336	protein-coding gene	gene with protein product		300144	"""glutamate dehydrogenase pseudogene 1"""	GLUDP1		8207021, 9109504	Standard	NM_012084		Approved		uc004eto.3	P49448	OTTHUMG00000022320	ENST00000328078.1:c.228C>T	X.37:g.120181766C>T			B2R8G0|Q9UDQ4	Silent	SNP	ENST00000328078.1	37	CCDS14603.1																																																																																				0.647	GLUD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058133.1	NM_012084		16	134	16	134
SLITRK4	139065	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	142717275	142717275	+	Silent	SNP	G	G	A			TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chrX:142717275G>A	ENST00000381779.4	-	2	1875	c.1650C>T	c.(1648-1650)agC>agT	p.S550S	SLITRK4_ENST00000338017.4_Silent_p.S550S|SLITRK4_ENST00000356928.1_Silent_p.S550S	NM_001184749.2|NM_001184750.1|NM_173078.4	NP_001171678.1|NP_001171679.1|NP_775101.1	Q8IW52	SLIK4_HUMAN	SLIT and NTRK-like family, member 4	550	LRRCT 2.					integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(27)|ovary(2)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	60	Acute lymphoblastic leukemia(192;6.56e-05)					CAATCCCGTCGCTCAACTTCT	0.438																																																0													143.0	136.0	139.0					X																	142717275		2203	4300	6503	SO:0001819	synonymous_variant	139065			BC040986	CCDS14679.1	Xq27.3	2004-06-23			ENSG00000179542	ENSG00000179542			23502	protein-coding gene	gene with protein product		300562				14557068	Standard	NM_001184749		Approved	DKFZp547M2010	uc004fby.3	Q8IW52	OTTHUMG00000022580	ENST00000381779.4:c.1650C>T	X.37:g.142717275G>A			Q5JXG3|Q8TCM8|Q96DL3	Silent	SNP	ENST00000381779.4	37	CCDS14679.1																																																																																				0.438	SLITRK4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058617.1	NM_173078		82	152	82	152
ZNF41	7592	broad.mit.edu;ucsc.edu	37	X	47307606	47307606	+	Missense_Mutation	SNP	T	T	G			TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chrX:47307606T>G	ENST00000377065.4	-	5	2202	c.1563A>C	c.(1561-1563)aaA>aaC	p.K521N	ZNF41_ENST00000313116.7_Missense_Mutation_p.K521N|ZNF41_ENST00000465311.1_5'Flank|ZNF41_ENST00000397050.2_Missense_Mutation_p.K531N	NM_153380.2	NP_700359.1	P51814	ZNF41_HUMAN	zinc finger protein 41	563					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|upper_aerodigestive_tract(2)	24		all_lung(315;0.000129)				ACATATAGGGTTTTTCCCCAG	0.418																																																0													106.0	102.0	104.0					X																	47307606		2203	4300	6503	SO:0001583	missense	7592			X60155	CCDS14279.1	Xp11.23	2013-01-08			ENSG00000147124	ENSG00000147124		"""Zinc fingers, C2H2-type"", ""-"""	13107	protein-coding gene	gene with protein product		314995				2037297	Standard	NM_007130		Approved	MGC8941, MRX89	uc004dhy.4	P51814	OTTHUMG00000021448	ENST00000377065.4:c.1563A>C	X.37:g.47307606T>G	ENSP00000366265:p.Lys521Asn		A8K1V6|B4DH01|Q96LE8|Q9UMC4|Q9UMV5|Q9UMV6|Q9UMV7|Q9UMV8|Q9UMV9|Q9UMW0|Q9UMW1	Missense_Mutation	SNP	ENST00000377065.4	37	CCDS14279.1	.	.	.	.	.	.	.	.	.	.	T	16.50	3.141623	0.57044	.	.	ENSG00000147124	ENST00000313116;ENST00000377065;ENST00000397050	T;T;T	0.26067	1.76;1.76;1.76	3.98	-1.0	0.10196	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.37012	N	0.002292	T	0.43233	0.1238	M	0.73962	2.25	0.24834	N	0.992502	D;D;D;D;D	0.89917	1.0;1.0;0.979;1.0;1.0	D;D;P;D;D	0.80764	0.985;0.985;0.559;0.985;0.994	T	0.26608	-1.0098	10	0.87932	D	0	.	7.8916	0.29682	0.0:0.4208:0.0:0.5792	.	521;523;531;555;563	P51814-6;P51814-2;P51814-3;P51814-5;P51814	.;.;.;.;ZNF41_HUMAN	N	521;521;531	ENSP00000315173:K521N;ENSP00000366265:K521N;ENSP00000380243:K531N	ENSP00000315173:K521N	K	-	3	2	ZNF41	47192550	0.099000	0.21834	0.327000	0.25402	0.969000	0.65631	-0.341000	0.07811	-0.298000	0.08921	0.486000	0.48141	AAA		0.418	ZNF41-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056429.1	NM_153380		22	189	22	189
BGN	633	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	152770259	152770259	+	Missense_Mutation	SNP	C	C	T			TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chrX:152770259C>T	ENST00000331595.4	+	2	356	c.170C>T	c.(169-171)cCc>cTc	p.P57L	BGN_ENST00000480756.1_3'UTR	NM_001711.4	NP_001702.1	P21810	PGS1_HUMAN	biglycan	57					blood vessel remodeling (GO:0001974)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|small molecule metabolic process (GO:0044281)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|transport vesicle (GO:0030133)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|glycosaminoglycan binding (GO:0005539)			breast(2)|endometrium(3)|large_intestine(1)|lung(9)|ovary(1)	16	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TCTGTCACACCCACCTACAGC	0.622																																																0													94.0	81.0	85.0					X																	152770259		2203	4300	6503	SO:0001583	missense	633			AK092954	CCDS14721.1	Xq28	2008-02-05			ENSG00000182492	ENSG00000182492		"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	1044	protein-coding gene	gene with protein product	"""biglycan proteoglycan"""	301870				1612609	Standard	NM_001711		Approved	DSPG1, SLRR1A	uc004fhr.2	P21810	OTTHUMG00000024205	ENST00000331595.4:c.170C>T	X.37:g.152770259C>T	ENSP00000327336:p.Pro57Leu		D3DWU3|P13247	Missense_Mutation	SNP	ENST00000331595.4	37	CCDS14721.1	.	.	.	.	.	.	.	.	.	.	C	12.34	1.909430	0.33721	.	.	ENSG00000182492	ENST00000331595;ENST00000431891	T;T	0.69040	0.49;-0.37	4.73	4.73	0.59995	.	0.286793	0.32736	N	0.005718	T	0.63628	0.2527	L	0.61218	1.895	0.80722	D	1	B	0.06786	0.001	B	0.08055	0.003	T	0.60449	-0.7261	10	0.25106	T	0.35	-28.9095	15.9127	0.79485	0.0:1.0:0.0:0.0	.	57	P21810	PGS1_HUMAN	L	57	ENSP00000327336:P57L;ENSP00000402525:P57L	ENSP00000327336:P57L	P	+	2	0	BGN	152423453	0.006000	0.16342	0.983000	0.44433	0.153000	0.21895	1.346000	0.33964	2.090000	0.63153	0.529000	0.55759	CCC		0.622	BGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060981.1	NM_001711		79	102	79	102
MRGPRX3	117195	broad.mit.edu;ucsc.edu	37	11	18158870	18158870	+	Missense_Mutation	SNP	G	G	A	rs184402606	byFrequency	TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chr11:18158870G>A	ENST00000396275.2	+	3	482	c.121G>A	c.(121-123)Gcg>Acg	p.A41T		NM_054031.3	NP_473372.3	Q96LB0	MRGX3_HUMAN	MAS-related GPR, member X3	41						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27						TTCCCTTGTCGCGCTGACAGG	0.592													g|||	4	0.000798722	0.0023	0.0	5008	,	,		21199	0.001		0.0	False		,,,				2504	0.0															0													141.0	136.0	138.0					11																	18158870		2200	4293	6493	SO:0001583	missense	117195				CCDS7830.1	11p15.1	2013-10-10			ENSG00000179826	ENSG00000179826		"""GPCR / Class A : Orphans"""	17980	protein-coding gene	gene with protein product		607229				11551509	Standard	NM_054031		Approved	MRGX3	uc001mnu.3	Q96LB0	OTTHUMG00000166435	ENST00000396275.2:c.121G>A	11.37:g.18158870G>A	ENSP00000379571:p.Ala41Thr		B0M0L1|Q8TDE0|Q8TDE1	Missense_Mutation	SNP	ENST00000396275.2	37	CCDS7830.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	12.71	2.018974	0.35606	.	.	ENSG00000179826	ENST00000396275;ENST00000531264	T;T	0.09350	2.99;2.99	1.46	0.495	0.16890	.	0.000000	0.64402	D	0.000005	T	0.03095	0.0091	N	0.08118	0	0.21020	N	0.999809	B	0.12013	0.005	B	0.04013	0.001	T	0.33650	-0.9860	10	0.87932	D	0	.	5.8267	0.18558	0.2002:0.0:0.7998:0.0	.	41	Q96LB0	MRGX3_HUMAN	T	41	ENSP00000379571:A41T;ENSP00000436242:A41T	ENSP00000379571:A41T	A	+	1	0	MRGPRX3	18115446	0.967000	0.33354	0.063000	0.19743	0.001000	0.01503	1.858000	0.39408	0.167000	0.19631	-0.450000	0.05554	GCG		0.592	MRGPRX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389767.1	NM_054031		64	171	64	171
FUBP1	8880	broad.mit.edu;hgsc.bcm.edu	37	1	78432402	78432405	+	Frame_Shift_Del	DEL	AACA	AACA	-			TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chr1:78432402_78432405delAACA	ENST00000370768.2	-	7	527_530	c.446_449delTGTT	c.(445-450)atgttafs	p.ML149fs	FUBP1_ENST00000436586.2_Frame_Shift_Del_p.ML170fs|FUBP1_ENST00000370767.1_Frame_Shift_Del_p.ML149fs	NM_003902.3	NP_003893.2	Q96AE4	FUBP1_HUMAN	far upstream element (FUSE) binding protein 1	149	KH 1. {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						TGTTCCAGTTAACATACAGGACCT	0.338			"""F, N"""		oligodendroglioma																																		Rec	yes		1	1p13.1	8880	far upstream element (FUSE) binding protein 1		O	0																																										SO:0001589	frameshift_variant	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.446_449delTGTT	1.37:g.78432402_78432405delAACA	ENSP00000359804:p.Met149fs		Q12828	Frame_Shift_Del	DEL	ENST00000370768.2	37	CCDS683.1																																																																																				0.338	FUBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098030.3	NM_003902		30	42	30	42
C1orf56	54964	broad.mit.edu;hgsc.bcm.edu	37	1	151021328	151021331	+	Splice_Site	DEL	AGTA	AGTA	-			TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chr1:151021328_151021331delAGTA	ENST00000368926.5	+	1	1113	c.1005delAGTA	c.(1003-1005)cca>cc	p.P335fs	C1orf56_ENST00000465135.1_3'UTR	NM_017860.3	NP_060330.2	Q9BUN1	MENT_HUMAN	chromosome 1 open reading frame 56	335						cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|lung(3)|ovary(1)|prostate(1)	7	Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			AGATGCAACCAGTAAGTGTTTGGT	0.505											OREG0013793	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									GBM(146;891 3320 6873)											0																																										SO:0001630	splice_region_variant	0			BC002469	CCDS980.1	1q21.2	2013-09-20			ENSG00000143443	ENSG00000143443			26045	protein-coding gene	gene with protein product	"""methylated in normal thymocytes"""					12975309, 22133874	Standard	NM_017860		Approved	FLJ20519, MENT	uc001ewn.3	Q9BUN1	OTTHUMG00000035159	ENST00000368926.5:c.1005+1AGTA>-	1.37:g.151021328_151021331delAGTA		1737	B2RDU8|Q9NWZ4	Splice_Site	DEL	ENST00000368926.5	37	CCDS980.1																																																																																				0.505	C1orf56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085101.1	NM_017860	Frame_Shift_Del	40	120	40	120
EPC2	26122	broad.mit.edu;hgsc.bcm.edu	37	2	149511681	149511682	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chr2:149511681_149511682delAG	ENST00000258484.6	+	4	679_680	c.645_646delAG	c.(643-648)acagagfs	p.E216fs		NM_015630.3	NP_056445.3	Q52LR7	EPC2_HUMAN	enhancer of polycomb homolog 2 (Drosophila)	216					chromatin modification (GO:0016568)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Piccolo NuA4 histone acetyltransferase complex (GO:0032777)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.0516)		GGAGAAGAACAGAGAAAATGCA	0.361																																																0																																										SO:0001589	frameshift_variant	26122			AF286904	CCDS46422.1	2q23	2008-02-05			ENSG00000135999	ENSG00000135999			24543	protein-coding gene	gene with protein product		611000					Standard	NM_015630		Approved	DKFZP566F2124	uc010zbt.2	Q52LR7	OTTHUMG00000153739	ENST00000258484.6:c.645_646delAG	2.37:g.149511683_149511684delAG	ENSP00000258484:p.Glu216fs		B3KWT7|D3DP89|Q7L9J1|Q96RR7|Q9NUT8|Q9NVR1|Q9UFM9	Frame_Shift_Del	DEL	ENST00000258484.6	37	CCDS46422.1																																																																																				0.361	EPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332278.1	NM_015630		13	13	13	13
MYH15	22989	broad.mit.edu;hgsc.bcm.edu	37	3	108103610	108103612	+	In_Frame_Del	DEL	TTC	TTC	-			TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chr3:108103610_108103612delTTC	ENST00000273353.3	-	40	5669_5671	c.5613_5615delGAA	c.(5611-5616)aagaat>aat	p.K1871del		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	1871						cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						CCTGCTCAGATTCTTCTTGTCTT	0.473																																																0																																										SO:0001651	inframe_deletion	22989			AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"""Myosins / Myosin superfamily : Class II"""	31073	protein-coding gene	gene with protein product		609929	"""myosin, heavy polypeptide 15"""			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.5613_5615delGAA	3.37:g.108103613_108103615delTTC	ENSP00000273353:p.Lys1871del			In_Frame_Del	DEL	ENST00000273353.3	37	CCDS43127.1																																																																																				0.473	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988		55	130	55	130
PCDH18	54510	broad.mit.edu;hgsc.bcm.edu	37	4	138442647	138442649	+	In_Frame_Del	DEL	TCT	TCT	-			TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chr4:138442647_138442649delTCT	ENST00000344876.4	-	4	3328_3330	c.2942_2944delAGA	c.(2941-2946)aagagt>agt	p.K981del	PCDH18_ENST00000507846.1_In_Frame_Del_p.K760del|PCDH18_ENST00000510305.1_In_Frame_Del_p.K192del|PCDH18_ENST00000511115.1_In_Frame_Del_p.K161del|PCDH18_ENST00000412923.2_In_Frame_Del_p.K980del	NM_019035.3	NP_061908.1	Q9HCL0	PCD18_HUMAN	protocadherin 18	981	Interaction with DAB1. {ECO:0000250}.				brain development (GO:0007420)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(27)|lung(21)|ovary(2)|pancreas(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86	all_hematologic(180;0.24)					GTGGAAAAACTCTTCTTCTTTTC	0.512																																																0																																										SO:0001651	inframe_deletion	54510			AL137471	CCDS34064.1, CCDS75193.1	4q28.3	2010-01-26			ENSG00000189184	ENSG00000189184		"""Cadherins / Protocadherins : Non-clustered"""	14268	protein-coding gene	gene with protein product		608287				10835267, 11549318	Standard	XM_005263070		Approved	KIAA1562, PCDH68L	uc003ihe.4	Q9HCL0	OTTHUMG00000161348	ENST00000344876.4:c.2942_2944delAGA	4.37:g.138442653_138442655delTCT	ENSP00000355082:p.Lys981del		A8K7K3|B7ZKT1|Q52LS2	In_Frame_Del	DEL	ENST00000344876.4	37	CCDS34064.1																																																																																				0.512	PCDH18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364614.1	NM_019035		20	106	20	106
PABPC1	26986	broad.mit.edu;hgsc.bcm.edu	37	8	101733783	101733784	+	Frame_Shift_Ins	INS	-	-	T			TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chr8:101733783_101733784insT	ENST00000318607.5	-	1	1156_1157	c.28_29insA	c.(28-30)atgfs	p.M10fs	PABPC1_ENST00000519004.1_Intron|PABPC1_ENST00000522387.1_Frame_Shift_Ins_p.M10fs	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	10					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|mRNA stabilization (GO:0048255)|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|translation activator activity (GO:0008494)			breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	40	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			GAGCGAGGCCATGGGGTAGCTG	0.698																																																0																																										SO:0001589	frameshift_variant	26986			Y00345	CCDS6289.1	8q22.2-q23	2013-02-12	2004-04-20		ENSG00000070756	ENSG00000070756		"""RNA binding motif (RRM) containing"""	8554	protein-coding gene	gene with protein product		604679	"""poly(A)-binding protein, cytoplasmic 2"""	PAB1, PABPC2		2885805	Standard	XM_005250861		Approved	PABP1, PABPL1	uc003yjs.1	P11940	OTTHUMG00000164779	ENST00000318607.5:c.29dupA	8.37:g.101733784_101733784dupT	ENSP00000313007:p.Met10fs		Q15097|Q93004	Frame_Shift_Ins	INS	ENST00000318607.5	37	CCDS6289.1																																																																																				0.698	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568		10	30	10	30
ESR2	2100	broad.mit.edu;hgsc.bcm.edu	37	14	64699865	64699866	+	Frame_Shift_Del	DEL	TG	TG	-			TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chr14:64699865_64699866delTG	ENST00000341099.4	-	9	1999_2000	c.1582_1583delCA	c.(1582-1584)cagfs	p.Q528fs	ESR2_ENST00000357782.2_Intron|ESR2_ENST00000555483.1_5'UTR|ESR2_ENST00000554572.1_Intron|ESR2_ENST00000555278.1_Intron|ESR2_ENST00000557772.1_3'UTR|ESR2_ENST00000267525.6_Frame_Shift_Del_p.Q437fs|ESR2_ENST00000353772.3_Intron|ESR2_ENST00000542956.1_Intron|ESR2_ENST00000358599.5_Intron|ESR2_ENST00000553796.1_Intron	NM_001437.2	NP_001428.1	Q92731	ESR2_HUMAN	estrogen receptor 2 (ER beta)	528	Steroid-binding.				brain development (GO:0007420)|cell-cell signaling (GO:0007267)|epithelial cell maturation involved in prostate gland development (GO:0060743)|extracellular negative regulation of signal transduction (GO:1900116)|gene expression (GO:0010467)|hormone-mediated apoptotic signaling pathway (GO:0008628)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|ovarian follicle development (GO:0001541)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|prostate gland epithelium morphogenesis (GO:0060740)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|uterus development (GO:0060065)|vagina development (GO:0060068)	extracellular region (GO:0005576)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|estrogen receptor activity (GO:0030284)|estrogen response element binding (GO:0034056)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|receptor antagonist activity (GO:0048019)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	23				all cancers(60;0.00916)|OV - Ovarian serous cystadenocarcinoma(108;0.0111)|BRCA - Breast invasive adenocarcinoma(234;0.0437)	Diethylstilbestrol(DB00255)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estropipate(DB04574)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Trilostane(DB01108)	TCACTGAGACTGTGGGTTCTGG	0.604																																																0									,,,	3,4261		0,3,2129					,,,	2.6	0.0			111	0,8254		0,0,4127	no	frameshift,intron,intron,intron	ESR2	NM_001437.2,NM_001214902.1,NM_001040276.1,NM_001040275.1	,,,	0,3,6256	A1A1,A1R,RR		0.0,0.0704,0.024	,,,	,,,		3,12515				SO:0001589	frameshift_variant	2100			X99101	CCDS9762.1, CCDS32096.1, CCDS55920.1, CCDS61469.1, CCDS61470.1	14q21-q22	2013-01-16			ENSG00000140009	ENSG00000140009		"""Nuclear hormone receptors"""	3468	protein-coding gene	gene with protein product		601663				8769313	Standard	NM_001214902		Approved	NR3A2, Erb	uc001xha.1	Q92731	OTTHUMG00000141306	ENST00000341099.4:c.1582_1583delCA	14.37:g.64699867_64699868delTG	ENSP00000343925:p.Gln528fs		A8K8K5|G3V5M5|O60608|O60685|O60702|O60703|O75583|O75584|Q0MWT5|Q0MWT6|Q86Z31|Q9UEV6|Q9UHD3|Q9UQK9	Frame_Shift_Del	DEL	ENST00000341099.4	37	CCDS9762.1																																																																																				0.604	ESR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280621.1			17	87	17	87
ABCA8	10351	broad.mit.edu;hgsc.bcm.edu	37	17	66887644	66887645	+	Frame_Shift_Ins	INS	-	-	G			TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chr17:66887644_66887645insG	ENST00000269080.2	-	22	3146_3147	c.3009_3010insC	c.(3007-3012)agcatcfs	p.I1004fs	ABCA8_ENST00000430352.2_Frame_Shift_Ins_p.I1044fs|ABCA8_ENST00000586539.1_Frame_Shift_Ins_p.I1044fs	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	1004					transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(3)|central_nervous_system(2)|endometrium(9)|kidney(5)|large_intestine(19)|liver(1)|lung(30)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|urinary_tract(4)	83	Breast(10;4.56e-13)					TAATCATCGATGCTGCTCATGG	0.347																																																0																																										SO:0001589	frameshift_variant	10351			AB020629	CCDS11680.1, CCDS74138.1, CCDS74139.1	17q24	2012-03-14			ENSG00000141338	ENSG00000141338		"""ATP binding cassette transporters / subfamily A"""	38	protein-coding gene	gene with protein product		612505					Standard	XM_005256938		Approved	KIAA0822	uc002jhp.3	O94911		ENST00000269080.2:c.3010dupC	17.37:g.66887645_66887645dupG	ENSP00000269080:p.Ile1004fs		A1L3U3|C9JQE6|Q86WW0	Frame_Shift_Ins	INS	ENST00000269080.2	37	CCDS11680.1																																																																																				0.347	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168		26	58	26	58
ZNF334	55713	broad.mit.edu;hgsc.bcm.edu	37	20	45130734	45130736	+	In_Frame_Del	DEL	AAG	AAG	-			TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chr20:45130734_45130736delAAG	ENST00000347606.4	-	5	1424_1426	c.1242_1244delCTT	c.(1240-1245)ttcttt>ttt	p.414_415FF>F	ZNF334_ENST00000457685.2_In_Frame_Del_p.376_377FF>F|ZNF334_ENST00000593880.1_In_Frame_Del_p.437_438FF>F	NM_018102.4	NP_060572.3	Q9HCZ1	ZN334_HUMAN	zinc finger protein 334	414					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	32		Myeloproliferative disorder(115;0.0122)				AGATTGACAAAAGAAGGTTTTCT	0.424																																																0									,	5,4259		2,1,2129					,	-2.3	0.0			119	4,8250		2,0,4125	no	coding,coding	ZNF334	NM_199441.1,NM_018102.3	,	4,1,6254	A1A1,A1R,RR		0.0485,0.1173,0.0719	,	,		9,12509				SO:0001651	inframe_deletion	55713			AK001331	CCDS33480.1, CCDS74736.1	20q13.12	2013-09-20			ENSG00000198185	ENSG00000198185		"""Zinc fingers, C2H2-type"", ""-"""	15806	protein-coding gene	gene with protein product							Standard	NM_018102		Approved	bA179N14.1	uc002xsc.4	Q9HCZ1	OTTHUMG00000032654	ENST00000347606.4:c.1242_1244delCTT	20.37:g.45130737_45130739delAAG	ENSP00000255129:p.Phe415del		Q5T6U2|Q9NVW4	In_Frame_Del	DEL	ENST00000347606.4	37	CCDS33480.1																																																																																				0.424	ZNF334-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079575.1			41	156	41	156
OGT	8473	broad.mit.edu;hgsc.bcm.edu	37	X	70756047	70756050	+	Frame_Shift_Del	DEL	TTCC	TTCC	-			TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chrX:70756047_70756050delTTCC	ENST00000373719.3	+	2	274_277	c.57_60delTTCC	c.(55-60)ctttccfs	p.LS19fs	OGT_ENST00000373701.3_Intron|OGT_ENST00000498566.1_3'UTR	NM_181672.2|NM_181673.2	NP_858058.1|NP_858059.1	O15294	OGT1_HUMAN	O-linked N-acetylglucosamine (GlcNAc) transferase	19					apoptotic process (GO:0006915)|cellular response to retinoic acid (GO:0071300)|chromatin organization (GO:0006325)|circadian regulation of gene expression (GO:0032922)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of protein ubiquitination (GO:0031397)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of catalytic activity (GO:0043085)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of histone H3-K27 methylation (GO:0061087)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of proteolysis (GO:0045862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glycolytic process (GO:0006110)|regulation of insulin receptor signaling pathway (GO:0046626)|regulation of Rac protein signal transduction (GO:0035020)|response to insulin (GO:0032868)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone acetyltransferase complex (GO:0000123)|microtubule organizing center (GO:0005815)|mitochondrion (GO:0005739)|MLL5-L complex (GO:0070688)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	acetylglucosaminyltransferase activity (GO:0008375)|enzyme activator activity (GO:0008047)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein N-acetylglucosaminyltransferase activity (GO:0016262)|protein O-GlcNAc transferase activity (GO:0097363)			breast(6)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|liver(3)|lung(9)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Renal(35;0.156)					AACGTATGCTTTCCTTCCAAGGGT	0.426																																																0																																										SO:0001589	frameshift_variant	8473			U77413	CCDS14414.1, CCDS35502.1	Xq13	2013-07-24	2012-05-04		ENSG00000147162	ENSG00000147162	2.4.1.255	"""Tetratricopeptide (TTC) repeat domain containing"""	8127	protein-coding gene	gene with protein product	"""UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase"""	300255	"""O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)"""			9083068	Standard	NM_181672		Approved	O-GLCNAC, HRNT1, MGC22921, FLJ23071	uc004eaa.2	O15294	OTTHUMG00000033316	ENST00000373719.3:c.57_60delTTCC	X.37:g.70756051_70756054delTTCC	ENSP00000362824:p.Leu19fs		Q7Z3K0|Q8WWM8|Q96CC1|Q9UG57	Frame_Shift_Del	DEL	ENST00000373719.3	37	CCDS14414.1																																																																																				0.426	OGT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000081829.3	NM_003605, NM_181672		44	86	44	86
CIC	23152	broad.mit.edu	37	19	42795593	42795594	+	Frame_Shift_Del	DEL	TG	TG	-			TCGA-DB-5274-01A-01D-1468-08	TCGA-DB-5274-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad0bc157-fb99-4b6c-80b7-384aac4304c0	f4361c01-824e-4b40-9f03-767a2796e586	g.chr19:42795593_42795594delTG	ENST00000575354.2	+	10	2713_2714	c.2673_2674delTG	c.(2671-2676)tctgtafs	p.V892fs	CIC_ENST00000572681.2_Frame_Shift_Del_p.V1801fs|CIC_ENST00000160740.3_Frame_Shift_Del_p.V892fs	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	892	Pro-rich.				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)				TCCTGCAGTCTGTACCCTCCGC	0.624			"""Mis, F, S"""		oligodendroglioma																																		Rec	yes		19	19q13.2	23152	capicua homolog		O	0																																										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.2673_2674delTG	19.37:g.42795593_42795594delTG	ENSP00000458663:p.Val892fs		Q7LGI1|Q9UEG5|Q9Y6T1	Frame_Shift_Del	DEL	ENST00000575354.2	37	CCDS12601.1																																																																																				0.624	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2			7	64	7	64
