#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_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	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_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_NTotCov	i_NVarCov	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_TTotCov	i_TVarCov	i_Transcript_Id	i_Trna_alt1	i_Trna_alt2	i_Trna_ref	i_Trna_tot	i_Trna_var	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_dbSNPPopFreq	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
DOCK7	85440	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	63119731	63119731	+	Missense_Mutation	SNP	A	A	G			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr1:63119731A>G	ENST00000340370.5	-	3	261	c.244T>C	c.(244-246)Ttt>Ctt	p.F82L	DOCK7_ENST00000404627.2_Missense_Mutation_p.F82L|DOCK7_ENST00000251157.5_Missense_Mutation_p.F82L	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	82					activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						TCTGGAGGAAATTCAATCAAA	0.428																																					p.F82L		.											.	DOCK7-92	0			c.T244C						.						67.0	66.0	66.0					1																	63119731		2203	4300	6503	SO:0001583	missense	85440	exon3			GAGGAAATTCAAT		CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.244T>C	1.37:g.63119731A>G	ENSP00000340742:p.Phe82Leu	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	85	27	NM_001272002	0	0	0	0	0	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Missense_Mutation	SNP	ENST00000340370.5	37	CCDS30734.1	.	.	.	.	.	.	.	.	.	.	A	34	5.346120	0.95807	.	.	ENSG00000116641	ENST00000371140;ENST00000251157;ENST00000340370;ENST00000404627	T;T;T	0.63580	-0.05;-0.05;-0.05	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.73799	0.3633	M	0.84156	2.68	0.80722	D	1	P;D;P	0.56521	0.911;0.976;0.861	P;P;P	0.62382	0.895;0.901;0.73	T	0.78314	-0.2252	10	0.59425	D	0.04	.	15.1374	0.72579	1.0:0.0:0.0:0.0	.	82;82;82	Q96NI0;Q96N67-2;Q96N67-5	.;.;.	L	82	ENSP00000251157:F82L;ENSP00000340742:F82L;ENSP00000384446:F82L	ENSP00000251157:F82L	F	-	1	0	DOCK7	62892319	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.683000	0.91236	2.162000	0.67917	0.533000	0.62120	TTT	.		0.428	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407	
PLEKHO1	51177	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	150131515	150131515	+	Missense_Mutation	SNP	C	C	A			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr1:150131515C>A	ENST00000369124.4	+	6	1305	c.1027C>A	c.(1027-1029)Ccg>Acg	p.P343T	PLEKHO1_ENST00000025469.6_Missense_Mutation_p.P309T|PLEKHO1_ENST00000369126.1_Missense_Mutation_p.P160T	NM_016274.4	NP_057358.2	Q53GL0	PKHO1_HUMAN	pleckstrin homology domain containing, family O member 1	343	Negative regulator of AP-1 activity.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|skin(2)	22	Lung NSC(24;7.78e-28)|Breast(34;0.00211)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			CCCTCGGTCTCCGCCGGATTC	0.607																																					p.P343T		.											.	PLEKHO1-226	0			c.C1027A						.						50.0	54.0	53.0					1																	150131515		2203	4300	6503	SO:0001583	missense	51177	exon6			CGGTCTCCGCCGG	AF073836	CCDS945.1	1q21.2	2013-01-10			ENSG00000023902	ENSG00000023902		"""Pleckstrin homology (PH) domain containing"""	24310	protein-coding gene	gene with protein product		608335				10799509	Standard	NM_016274		Approved	CKIP-1, OC120	uc001ett.3	Q53GL0	OTTHUMG00000012510	ENST00000369124.4:c.1027C>A	1.37:g.150131515C>A	ENSP00000358120:p.Pro343Thr	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	127	19	NM_016274	0	0	101	101	0	Q336K5|Q8IZ51|Q9NRV3|Q9UL48	Missense_Mutation	SNP	ENST00000369124.4	37	CCDS945.1	.	.	.	.	.	.	.	.	.	.	C	15.60	2.880995	0.51801	.	.	ENSG00000023902	ENST00000369126;ENST00000025469;ENST00000369124;ENST00000441340	T;T	0.41758	0.99;0.99	5.24	5.24	0.73138	.	0.515831	0.21943	N	0.066842	T	0.13329	0.0323	N	0.14661	0.345	0.35920	D	0.831769	B	0.34103	0.437	B	0.32090	0.14	T	0.07309	-1.0779	10	0.52906	T	0.07	-17.5791	8.9859	0.35994	0.0:0.899:0.0:0.101	.	343	Q53GL0	PKHO1_HUMAN	T	160;309;343;223	ENSP00000025469:P309T;ENSP00000358120:P343T	ENSP00000025469:P309T	P	+	1	0	PLEKHO1	148398139	0.278000	0.24230	1.000000	0.80357	0.732000	0.41865	1.272000	0.33109	2.726000	0.93360	0.655000	0.94253	CCG	.		0.607	PLEKHO1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034962.1	NM_016274	
ENAH	55740	hgsc.bcm.edu	37	1	225707051	225707051	+	Missense_Mutation	SNP	C	C	A	rs566336314|rs71170086|rs140432837	byFrequency	TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr1:225707051C>A	ENST00000366844.3	-	5	1102	c.651G>T	c.(649-651)gaG>gaT	p.E217D	ENAH_ENST00000284563.6_Missense_Mutation_p.E236D|ENAH_ENST00000366843.2_Missense_Mutation_p.E217D|ENAH_ENST00000391874.2_5'UTR	NM_001008493.1|NM_018212.4	NP_001008493.1|NP_060682.2	Q8N8S7	ENAH_HUMAN	enabled homolog (Drosophila)	217					actin polymerization or depolymerization (GO:0008154)|axon guidance (GO:0007411)|intracellular transport (GO:0046907)|neural tube closure (GO:0001843)|T cell receptor signaling pathway (GO:0050852)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)|synapse (GO:0045202)	WW domain binding (GO:0050699)			NS(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23	Breast(184;0.206)			GBM - Glioblastoma multiforme(131;0.19)		gttcctgccgctccaggcgtt	0.602																																					p.E217D		.											.	ENAH-516	0			c.G651T						.						71.0	66.0	67.0					1																	225707051		2203	4300	6503	SO:0001583	missense	55740	exon5			CTGCCGCTCCAGG	AK001635	CCDS31040.1, CCDS31041.1	1q32.2	2013-08-06			ENSG00000154380	ENSG00000154380			18271	protein-coding gene	gene with protein product	"""mammalian enabled"""	609061				1420303	Standard	XM_005273182		Approved	FLJ10773, NDPP1, MENA	uc001hpc.1	Q8N8S7	OTTHUMG00000037742	ENST00000366844.3:c.651G>T	1.37:g.225707051C>A	ENSP00000355809:p.Glu217Asp	Somatic	143	0		WXS	Illumina HiSeq	Phase_I	142	14	NM_001008493	0	0	5	5	0	D0PQI2|Q502W5|Q5T5M7|Q5VTQ9|Q5VTR0|Q9NVF3|Q9UFB8	Missense_Mutation	SNP	ENST00000366844.3	37	CCDS31041.1	.	.	.	.	.	.	.	.	.	.	C	11.51	1.658764	0.29515	.	.	ENSG00000154380	ENST00000366844;ENST00000366843;ENST00000284563;ENST00000538194	T;T;T	0.55052	0.54;0.54;0.54	.	.	.	.	.	.	.	.	T	0.38585	0.1046	L	0.39898	1.24	0.20074	N	0.999934	.	.	.	.	.	.	T	0.30966	-0.9960	5	0.13853	T	0.58	-3.0228	.	.	.	.	217;217	Q8N8S7-2;Q8N8S7	.;ENAH_HUMAN	D	217;217;236;216	ENSP00000355809:E217D;ENSP00000355808:E217D;ENSP00000284563:E236D	ENSP00000284563:E236D	E	-	3	2	ENAH	223773674	0.529000	0.26322	0.787000	0.31911	0.634000	0.38068	0.000000	0.12993	0.000000	0.14550	0.000000	0.15137	GAG	C|1.000;T|0.000		0.602	ENAH-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000357426.2	NM_018212	
ARHGAP21	57584	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	24873803	24873803	+	Silent	SNP	T	T	C			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr10:24873803T>C	ENST00000396432.2	-	26	5901	c.5415A>G	c.(5413-5415)ggA>ggG	p.G1805G		NM_020824.3	NP_065875.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	1804	Interaction with CTNNA1.				establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(17)|lung(21)|ovary(7)|pancreas(1)|prostate(5)|skin(2)|stomach(2)|urinary_tract(1)	78						CTCTGTGCCCTCCTAGTGTAT	0.488																																					p.G1805G		.											.	ARHGAP21-235	0			c.A5415G						.						50.0	50.0	50.0					10																	24873803		2203	4300	6503	SO:0001819	synonymous_variant	57584	exon26			GTGCCCTCCTAGT	AF480466	CCDS7144.2	10p12.31	2013-01-10			ENSG00000107863	ENSG00000107863		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	23725	protein-coding gene	gene with protein product		609870				12056806	Standard	NM_020824		Approved	KIAA1424, ARHGAP10	uc001isb.2	Q5T5U3	OTTHUMG00000017825	ENST00000396432.2:c.5415A>G	10.37:g.24873803T>C		Somatic	77	0		WXS	Illumina HiSeq	Phase_I	86	32	NM_020824	0	0	14	23	9	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Silent	SNP	ENST00000396432.2	37	CCDS7144.2																																																																																			.		0.488	ARHGAP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047229.4	NM_020824	
PIPSL	266971	ucsc.edu	37	10	95718760	95718760	+	RNA	SNP	G	G	A			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr10:95718760G>A	ENST00000480546.1	-	0	2537					NR_002319.2		A2A3N6	PIPSL_HUMAN	PIP5K1A and PSMD4-like, pseudogene							cytoplasm (GO:0005737)	phosphatidylinositol phosphate kinase activity (GO:0016307)										ATGTGTCCATGGCTGAGCTGG	0.527																																					.													.	.	0			.						.																																					266971	.			GTCCATGGCTGAG	BC068549		10q23.33	2010-10-27	2010-10-27	2007-07-06	ENSG00000180764	ENSG00000180764		"""Proteasome (prosome, macropain) subunits"""	23733	pseudogene	pseudogene			"""proteasome (prosome, macropain) 26S subunit, non-ATPase, 4, pseudogene 2"", ""phosphatidylinositol-4-phosphate 5-kinase, type I-like 1"", ""PIP5K1A and PSMD4-like"""	PSMD4P2, PIP5K1L1		16344562	Standard	NR_002319		Approved	PIP5K1A-PSMD4, PIP5K1P3	uc009xuj.2	A2A3N6	OTTHUMG00000137480		10.37:g.95718760G>A		Somatic	284	0		WXS	Illumina HiSeq		301	1	.	0	0	0	189	189	Q6NUK8	RNA	SNP	ENST00000480546.1	37																																																																																				.		0.527	PIPSL-002	PUTATIVE	basic	processed_transcript	pseudogene	OTTHUMT00000351483.1	NR_002319	
MUC5B	727897	broad.mit.edu	37	11	1281625	1281625	+	Splice_Site	SNP	T	T	G			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr11:1281625T>G	ENST00000529681.1	+	47	17024		c.e47+2		MUC5B_ENST00000447027.1_Splice_Site	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming						cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		GTGAGGAGGGTAAGTGGAAGC	0.667																																					.													.	.	0			c.16966+2T>G						.						25.0	30.0	28.0					11																	1281625		2116	4234	6350	SO:0001630	splice_region_variant	727897	exon47			GGAGGGTAAGTGG	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.16966+2T>G	11.37:g.1281625T>G		Somatic	175	10		WXS	Illumina HiSeq	Phase_I	116	11	NM_002458	0	0	0	0	0	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Splice_Site	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	T	13.72	2.321366	0.41096	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000546052;ENST00000406844	.	.	.	4.68	3.5	0.40072	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.177	0.25751	0.1985:0.0:0.0:0.8015	.	.	.	.	.	-1	.	.	.	+	.	.	MUC5B	1238201	1.000000	0.71417	0.187000	0.23214	0.732000	0.41865	2.167000	0.42415	0.773000	0.33404	0.533000	0.62120	.	.		0.667	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	Intron
KRTAP5-4	387267	hgsc.bcm.edu	37	11	1643082	1643082	+	Missense_Mutation	SNP	T	T	C			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr11:1643082T>C	ENST00000399682.1	-	1	286	c.242A>G	c.(241-243)tAt>tGt	p.Y81C		NM_001012709.1	NP_001012727	Q6L8H1	KRA54_HUMAN	keratin associated protein 5-4	0	9 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				NS(1)|endometrium(9)|kidney(2)|lung(2)|pancreas(1)|prostate(3)|skin(2)	20		all_epithelial(84;0.00819)|Breast(177;0.00832)|Ovarian(85;0.0256)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		ACAAGAGCCATAGCCCCCCTT	0.657																																					p.Y81C		.											.	.	0			c.A242G						.						9.0	16.0	14.0					11																	1643082		684	1578	2262	SO:0001583	missense	387267	exon1			GAGCCATAGCCCC	AB126073		11p15.5	2012-04-19			ENSG00000241598	ENSG00000241598		"""Keratin associated proteins"""	23599	protein-coding gene	gene with protein product						15144888	Standard	NM_001012709		Approved	KRTAP5.4	uc009ycy.1	Q6L8H1	OTTHUMG00000057553	ENST00000399682.1:c.242A>G	11.37:g.1643082T>C	ENSP00000382590:p.Tyr81Cys	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	29	4	NM_001012709	0	0	0	1	1		Missense_Mutation	SNP	ENST00000399682.1	37		.	.	.	.	.	.	.	.	.	.	C	0.053	-1.244643	0.01481	.	.	ENSG00000241598	ENST00000399682;ENST00000328953	T	0.00646	6.0	3.19	3.19	0.36642	.	.	.	.	.	T	0.00144	0.0004	N	0.00004	-3.39	0.20196	N	0.999929	B	0.02656	0.0	B	0.01281	0.0	T	0.41610	-0.9499	9	0.02654	T	1	.	5.8653	0.18771	0.0:0.738:0.0:0.262	rs59610171	81	Q6L8H1	KRA54_HUMAN	C	81	ENSP00000382590:Y81C	ENSP00000331603:Y81C	Y	-	2	0	KRTAP5-4	1599658	0.218000	0.23608	0.997000	0.53966	0.226000	0.24999	0.624000	0.24462	0.452000	0.26830	-0.254000	0.11334	TAT	.		0.657	KRTAP5-4-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000127918.1	NM_001012709	
ARHGAP1	392	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	46702650	46702650	+	Silent	SNP	G	G	A			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr11:46702650G>A	ENST00000311956.4	-	7	643	c.546C>T	c.(544-546)ttC>ttT	p.F182F		NM_004308.3	NP_004299.1	Q07960	RHG01_HUMAN	Rho GTPase activating protein 1	182	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				positive regulation of signal transduction (GO:0009967)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	Rac GTPase activator activity (GO:0030675)|Rho GTPase activator activity (GO:0005100)|SH3/SH2 adaptor activity (GO:0005070)			endometrium(1)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	11		Lung NSC(402;1.76e-12)|all_lung(304;1.3e-11)		GBM - Glioblastoma multiforme(35;5.17e-06)|BRCA - Breast invasive adenocarcinoma(625;0.00112)|Lung(87;0.153)		TCTTCTGCCCGAACTTGAAGC	0.602																																					p.F182F		.											.	ARHGAP1-227	0			c.C546T						.						84.0	90.0	88.0					11																	46702650		2201	4299	6500	SO:0001819	synonymous_variant	392	exon7			CTGCCCGAACTTG	BC018118	CCDS7922.1	11p11.2	2006-04-11			ENSG00000175220	ENSG00000175220		"""Rho GTPase activating proteins"""	673	protein-coding gene	gene with protein product		602732				8288572	Standard	NM_004308		Approved	RhoGAP, p50rhoGAP, CDC42GAP, Cdc42GAP	uc001ndd.4	Q07960	OTTHUMG00000166567	ENST00000311956.4:c.546C>T	11.37:g.46702650G>A		Somatic	106	0		WXS	Illumina HiSeq	Phase_I	58	5	NM_004308	0	0	0	0	0	D3DQQ6	Silent	SNP	ENST00000311956.4	37	CCDS7922.1	.	.	.	.	.	.	.	.	.	.	G	9.301	1.052993	0.19907	.	.	ENSG00000175220	ENST00000528837	.	.	.	5.28	1.37	0.22104	.	.	.	.	.	T	0.57770	0.2076	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51356	-0.8716	4	.	.	.	.	9.3727	0.38264	0.7873:0.0:0.2127:0.0	.	.	.	.	W	136	.	.	R	-	1	2	ARHGAP1	46659226	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	1.205000	0.32308	0.323000	0.23307	-0.459000	0.05422	CGG	.		0.602	ARHGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390472.1	NM_004308	
AHNAK	79026	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	11	62296065	62296065	+	Missense_Mutation	SNP	C	C	T			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr11:62296065C>T	ENST00000378024.4	-	5	6098	c.5824G>A	c.(5824-5826)Gtg>Atg	p.V1942M	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	1942					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				GGCACCGACACATCCACATCC	0.502																																					p.V1942M		.											.	AHNAK-109	0			c.G5824A						.						216.0	226.0	223.0					11																	62296065		2202	4299	6501	SO:0001583	missense	79026	exon5			CCGACACATCCAC	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"""desmoyokin"""	103390	"""AHNAK nucleoprotein (desmoyokin)"""			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.5824G>A	11.37:g.62296065C>T	ENSP00000367263:p.Val1942Met	Somatic	194	0		WXS	Illumina HiSeq	Phase_I	188	14	NM_001620	0	0	6	6	0	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	c	6.228	0.410192	0.11812	.	.	ENSG00000124942	ENST00000244934;ENST00000378024	T	0.01272	5.07	2.29	1.33	0.21861	.	.	.	.	.	T	0.03608	0.0103	M	0.88105	2.93	0.27412	N	0.95455	P	0.41131	0.739	B	0.40602	0.334	T	0.14643	-1.0465	9	0.66056	D	0.02	.	7.0623	0.25133	0.0:0.8577:0.0:0.1423	.	1942	Q09666	AHNK_HUMAN	M	31;1942	ENSP00000367263:V1942M	ENSP00000244934:V31M	V	-	1	0	AHNAK	62052641	0.700000	0.27796	0.013000	0.15412	0.006000	0.05464	-0.172000	0.09868	0.317000	0.23160	0.186000	0.17326	GTG	.		0.502	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060	
PC	5091	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	66636384	66636384	+	Missense_Mutation	SNP	T	T	C			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr11:66636384T>C	ENST00000393958.2	-	9	1048	c.955A>G	c.(955-957)Aag>Gag	p.K319E	PC_ENST00000524491.1_Missense_Mutation_p.K279E|PC_ENST00000355677.3_Missense_Mutation_p.K319E|PC_ENST00000393960.1_Missense_Mutation_p.K319E|PC_ENST00000393955.2_Missense_Mutation_p.K319E	NM_000920.3	NP_000911.2	P11498	PYC_HUMAN	pyruvate carboxylase	319	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.|Biotin carboxylation.				biotin metabolic process (GO:0006768)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|lipid metabolic process (GO:0006629)|oxaloacetate metabolic process (GO:0006107)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|pyruvate carboxylase activity (GO:0004736)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Melanoma(852;0.0525)		Lung(977;0.153)|LUSC - Lung squamous cell carcinoma(976;0.227)	Biotin(DB00121)|Pyruvic acid(DB00119)	AAGTAGTGCTTGCCGTGCCTG	0.687																																					p.K319E		.											.	PC-228	0			c.A955G						.						92.0	81.0	84.0					11																	66636384		2200	4295	6495	SO:0001583	missense	5091	exon9			AGTGCTTGCCGTG	U04641	CCDS8152.1	11q13.4-q13.5	2012-07-11			ENSG00000173599	ENSG00000173599	6.4.1.1		8636	protein-coding gene	gene with protein product		608786				6548474	Standard	NM_022172		Approved	PCB	uc001ojn.1	P11498	OTTHUMG00000167099	ENST00000393958.2:c.955A>G	11.37:g.66636384T>C	ENSP00000377530:p.Lys319Glu	Somatic	336	1		WXS	Illumina HiSeq	Phase_I	190	65	NM_000920	0	0	1	1	0	B4DN00|Q16705	Missense_Mutation	SNP	ENST00000393958.2	37	CCDS8152.1	.	.	.	.	.	.	.	.	.	.	T	13.76	2.333430	0.41297	.	.	ENSG00000173599	ENST00000393955;ENST00000393958;ENST00000393960;ENST00000524491;ENST00000355677	D;D;D;D;D	0.97256	-4.31;-4.31;-4.31;-4.31;-4.31	4.65	4.65	0.58169	ATP-grasp fold (1);ATP-grasp fold, subdomain 2 (1);Carbamoyl-phosphate synthetase, large subunit, ATP-binding (1);Biotin carboxylation domain (1);	0.063886	0.64402	D	0.000015	D	0.91643	0.7359	N	0.13352	0.335	0.43226	D	0.995117	B	0.09022	0.002	B	0.21360	0.034	D	0.87584	0.2486	10	0.13108	T	0.6	-19.2405	12.029	0.53388	0.0:0.0:0.0:1.0	.	319	P11498	PYC_HUMAN	E	319;319;319;279;319	ENSP00000377527:K319E;ENSP00000377530:K319E;ENSP00000377532:K319E;ENSP00000434192:K279E;ENSP00000347900:K319E	ENSP00000347900:K319E	K	-	1	0	PC	66392960	0.994000	0.37717	1.000000	0.80357	0.938000	0.57974	1.707000	0.37888	1.730000	0.51580	0.459000	0.35465	AAG	.		0.687	PC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393115.1	NM_001040716	
MAML2	84441	hgsc.bcm.edu	37	11	95825248	95825248	+	Silent	SNP	C	C	T			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr11:95825248C>T	ENST00000524717.1	-	2	3231	c.1947G>A	c.(1945-1947)caG>caA	p.Q649Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	649					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)		CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				gttgctgctgctgctgctgtt	0.517			T	"""MECT1, CRTC3"""	salivary gland mucoepidermoid																																p.Q649Q		.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2-850	0			c.G1947A						.						33.0	39.0	37.0					11																	95825248		2115	4166	6281	SO:0001819	synonymous_variant	84441	exon2			CTGCTGCTGCTGC	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"""mastermind (Drosophila)-like 2"""			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.1947G>A	11.37:g.95825248C>T		Somatic	80	0		WXS	Illumina HiSeq	Phase_I	139	25	NM_032427	0	0	0	0	0	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	37	CCDS44714.1																																																																																			.		0.517	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1		
MAML2	84441	ucsc.edu	37	11	95825254	95825254	+	Silent	SNP	C	C	T	rs61749250		TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr11:95825254C>T	ENST00000524717.1	-	2	3225	c.1941G>A	c.(1939-1941)caG>caA	p.Q647Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	647					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)	p.Q647Q(1)	CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				gctgctgctgctgttgttgct	0.512			T	"""MECT1, CRTC3"""	salivary gland mucoepidermoid																																p.Q647Q				Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2-850	1	Substitution - coding silent(1)	endometrium(1)	c.G1941A						.	C		0,4198		0,0,2099	35.0	40.0	38.0		1941	1.7	0.1	11	dbSNP_129	38	5,8237		0,5,4116	no	coding-synonymous	MAML2	NM_032427.1		0,5,6215	TT,TC,CC		0.0607,0.0,0.0402		647/1157	95825254	5,12435	2099	4121	6220	SO:0001819	synonymous_variant	84441	exon2			CTGCTGCTGTTGT	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"""mastermind (Drosophila)-like 2"""			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.1941G>A	11.37:g.95825254C>T		Somatic	113	0		WXS	Illumina HiSeq		146	28	NM_032427	0	0	0	0	0	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	37	CCDS44714.1																																																																																			.		0.512	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1		
SLC6A12	6539	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	306024	306024	+	Missense_Mutation	SNP	A	A	G			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr12:306024A>G	ENST00000428720.1	-	11	1843	c.1100T>C	c.(1099-1101)tTc>tCc	p.F367S	SLC6A12_ENST00000536824.1_Missense_Mutation_p.F367S|SLC6A12_ENST00000424061.2_Missense_Mutation_p.F367S|SLC6A12_ENST00000359674.4_Missense_Mutation_p.F367S|SLC6A12_ENST00000538272.1_5'Flank|SLC6A12_ENST00000397296.2_Missense_Mutation_p.F367S|RP11-283I3.1_ENST00000544067.1_RNA	NM_001122848.2	NP_001116320.1	P48065	S6A12_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 12	367					amino acid transport (GO:0006865)|cellular hyperosmotic response (GO:0071474)|cellular water homeostasis (GO:0009992)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|response to organic substance (GO:0010033)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(8)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0172)|all_epithelial(11;0.0283)|all_lung(10;0.0392)|Lung NSC(10;0.0567)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00227)			AGCCTTGGGGAAGGCGATGAA	0.587																																					p.F367S		.											.	SLC6A12-91	0			c.T1100C						.						107.0	96.0	100.0					12																	306024		2203	4300	6503	SO:0001583	missense	6539	exon11			TTGGGGAAGGCGA	L42300	CCDS8501.1	12p13	2013-07-19	2013-07-19		ENSG00000111181	ENSG00000111181		"""Solute carriers"""	11045	protein-coding gene	gene with protein product	"""betaine/GABA transporter-1"""	603080	"""solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12"""			7589472	Standard	NM_003044		Approved	BGT-1	uc009zdh.2	P48065	OTTHUMG00000090309	ENST00000428720.1:c.1100T>C	12.37:g.306024A>G	ENSP00000388184:p.Phe367Ser	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	85	24	NM_001122848	0	0	5	7	2	A0AV52|B2R992|D3DUN8	Missense_Mutation	SNP	ENST00000428720.1	37	CCDS8501.1	.	.	.	.	.	.	.	.	.	.	A	19.19	3.780522	0.70222	.	.	ENSG00000111181	ENST00000359674;ENST00000397296;ENST00000428720;ENST00000424061;ENST00000536824	T;T;T;T;T	0.79141	-1.24;-1.24;-1.24;-1.24;-1.24	4.26	4.26	0.50523	.	0.067703	0.64402	D	0.000013	D	0.86644	0.5982	M	0.85777	2.775	0.44261	D	0.997113	D	0.58268	0.982	D	0.70935	0.971	D	0.87360	0.2343	10	0.87932	D	0	.	7.5395	0.27729	0.6532:0.0:0.0:0.3468	.	367	P48065	S6A12_HUMAN	S	367	ENSP00000352702:F367S;ENSP00000380464:F367S;ENSP00000388184:F367S;ENSP00000399136:F367S;ENSP00000444268:F367S	ENSP00000352702:F367S	F	-	2	0	SLC6A12	176285	1.000000	0.71417	0.987000	0.45799	0.802000	0.45316	6.483000	0.73617	1.782000	0.52362	0.391000	0.25812	TTC	.		0.587	SLC6A12-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206671.2	NM_003044	
CACNA1C	775	bcgsc.ca	37	12	2794921	2794921	+	Missense_Mutation	SNP	G	G	A	rs200231105	byFrequency	TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr12:2794921G>A	ENST00000347598.4	+	46	5737	c.5737G>A	c.(5737-5739)Gaa>Aaa	p.E1913K	CACNA1C_ENST00000399606.1_Missense_Mutation_p.E1885K|CACNA1C_ENST00000399634.1_Missense_Mutation_p.E1936K|CACNA1C_ENST00000335762.5_Missense_Mutation_p.E1890K|CACNA1C_ENST00000399649.1_Missense_Mutation_p.E1871K|CACNA1C_ENST00000399595.1_Missense_Mutation_p.E1873K|CACNA1C_ENST00000399641.1_Missense_Mutation_p.E1865K|CACNA1C_ENST00000399591.1_Missense_Mutation_p.E1873K|CACNA1C_ENST00000399617.1_Missense_Mutation_p.E1900K|CACNA1C_ENST00000399603.1_Missense_Mutation_p.E1865K|CACNA1C_ENST00000399601.1_Missense_Mutation_p.E1865K|CACNA1C_ENST00000406454.3_Missense_Mutation_p.E1936K|CACNA1C_ENST00000399655.1_Missense_Mutation_p.E1865K|CACNA1C_ENST00000399629.1_Missense_Mutation_p.E1882K|CACNA1C_ENST00000327702.7_Missense_Mutation_p.E1900K|CACNA1C_ENST00000399597.1_Missense_Mutation_p.E1865K|CACNA1C_ENST00000399621.1_Missense_Mutation_p.E1884K|CACNA1C_ENST00000399637.1_Missense_Mutation_p.E1884K|CACNA1C_ENST00000402845.3_Missense_Mutation_p.E1884K|CACNA1C_ENST00000399638.1_Missense_Mutation_p.E1893K|CACNA1C_ENST00000399644.1_Missense_Mutation_p.E1865K|CACNA1C_ENST00000344100.3_Missense_Mutation_p.E1906K|CACNA1C-AS1_ENST00000501371.1_RNA	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	1948					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.E1913K(2)|p.E1906K(2)|p.E1978K(2)|p.E1900K(2)|p.E1400K(2)		NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	CCAGGATGACGAAAATCGGCA	0.592																																					p.E1948K													.	CACNA1C-34	10	Substitution - Missense(10)	kidney(5)|endometrium(5)	c.G5842A						.						47.0	48.0	48.0					12																	2794921		2013	4164	6177	SO:0001583	missense	775	exon47			GATGACGAAAATC	AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.5737G>A	12.37:g.2794921G>A	ENSP00000266376:p.Glu1913Lys	Somatic	139	7		WXS	Illumina HiSeq	Phase_1	175	20	NM_199460	0	0	0	0	0	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Missense_Mutation	SNP	ENST00000347598.4	37	CCDS44788.1	.	.	.	.	.	.	.	.	.	.	G	15.97	2.988512	0.53934	.	.	ENSG00000151067	ENST00000335762;ENST00000399655;ENST00000399644;ENST00000399638;ENST00000399597;ENST00000399621;ENST00000399637;ENST00000399591;ENST00000399641;ENST00000347598;ENST00000399606;ENST00000399601;ENST00000344100;ENST00000399629;ENST00000327702;ENST00000399649;ENST00000402845;ENST00000399603;ENST00000399634;ENST00000399617;ENST00000406454;ENST00000399595;ENST00000322367	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.57595	0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39	4.26	3.35	0.38373	.	1.675690	0.03914	N	0.282339	T	0.64427	0.2597	L	0.39633	1.23	0.24214	N	0.99546	P;D;P;B;D;P;P;D;B;B;D;P;P;B;P;B;P;B;D;P;P;D;D;P;P	0.76494	0.801;0.999;0.941;0.097;0.999;0.921;0.953;0.961;0.11;0.33;0.978;0.941;0.757;0.432;0.902;0.306;0.757;0.062;0.978;0.588;0.769;0.961;0.961;0.882;0.941	B;P;B;B;D;B;B;P;B;B;P;B;B;B;B;B;B;B;P;B;B;P;P;B;B	0.78314	0.21;0.858;0.304;0.03;0.991;0.308;0.378;0.485;0.04;0.071;0.485;0.304;0.122;0.099;0.114;0.033;0.122;0.024;0.485;0.172;0.172;0.485;0.485;0.172;0.304	T	0.56056	-0.8042	10	0.07030	T	0.85	.	14.0749	0.64885	0.0:0.1521:0.8479:0.0	.	556;1906;1862;1948;1900;1884;1865;1882;1893;1865;1885;1865;1896;1913;1865;1900;1936;1873;1871;1873;1854;1884;1884;1865;1865	B7Z7Z5;Q13936-14;Q13936-35;Q13936;Q13936-33;Q13936-13;Q13936-22;Q13936-32;Q13936-31;Q13936-21;Q13936-30;Q13936-23;Q13936-28;Q13936-11;E9PDJ1;E9PDJ0;F5GY28;Q13936-25;Q13936-15;Q13936-29;Q13936-19;Q13936-24;Q13936-27;Q13936-20;Q13936-12	.;.;.;CAC1C_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	K	1890;1865;1865;1893;1865;1884;1884;1873;1865;1913;1885;1865;1906;1882;1900;1871;1884;1865;1936;1900;1936;1873;1766	ENSP00000336982:E1890K;ENSP00000382563:E1865K;ENSP00000382552:E1865K;ENSP00000382547:E1893K;ENSP00000382506:E1865K;ENSP00000382530:E1884K;ENSP00000382546:E1884K;ENSP00000382500:E1873K;ENSP00000382549:E1865K;ENSP00000266376:E1913K;ENSP00000382515:E1885K;ENSP00000382510:E1865K;ENSP00000341092:E1906K;ENSP00000382537:E1882K;ENSP00000329877:E1900K;ENSP00000382557:E1871K;ENSP00000385724:E1884K;ENSP00000382512:E1865K;ENSP00000382542:E1936K;ENSP00000382526:E1900K;ENSP00000385896:E1936K;ENSP00000382504:E1873K	ENSP00000323129:E1766K	E	+	1	0	CACNA1C	2665182	1.000000	0.71417	0.943000	0.38184	0.802000	0.45316	5.486000	0.66856	0.981000	0.38548	0.449000	0.29647	GAA	G|0.500;A|0.500		0.592	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719	
R3HDM2	22864	broad.mit.edu	37	12	57648792	57648792	+	Missense_Mutation	SNP	A	A	C			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr12:57648792A>C	ENST00000347140.3	-	24	3085	c.2695T>G	c.(2695-2697)Tgg>Ggg	p.W899G	R3HDM2_ENST00000403821.2_Missense_Mutation_p.W933G|RP11-123K3.4_ENST00000548184.1_Intron|R3HDM2_ENST00000441731.2_Missense_Mutation_p.W594G|R3HDM2_ENST00000358907.2_Missense_Mutation_p.W899G|R3HDM2_ENST00000413953.2_Intron|R3HDM2_ENST00000402412.1_Missense_Mutation_p.W913G			Q9Y2K5	R3HD2_HUMAN	R3H domain containing 2	899						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	22						TCCTTGAGCCACTGGATCTTG	0.637																																					p.W899G													.	R3HDM2-92	0			c.T2695G						.						63.0	60.0	61.0					12																	57648792		2203	4300	6503	SO:0001583	missense	22864	exon22			TGAGCCACTGGAT	AB023219	CCDS8937.2	12q13.3	2012-11-19			ENSG00000179912	ENSG00000179912			29167	protein-coding gene	gene with protein product							Standard	NM_014925		Approved	KIAA1002	uc009zpm.1	Q9Y2K5	OTTHUMG00000171568	ENST00000347140.3:c.2695T>G	12.37:g.57648792A>C	ENSP00000317903:p.Trp899Gly	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	82	5	NM_014925	0	0	3	3	0	Q2M1T9|Q3ZCT5	Missense_Mutation	SNP	ENST00000347140.3	37	CCDS8937.2	.	.	.	.	.	.	.	.	.	.	A	18.09	3.545615	0.65198	.	.	ENSG00000179912	ENST00000393811;ENST00000347140;ENST00000402412;ENST00000358907;ENST00000441731;ENST00000429355;ENST00000403821	T;T;T;T;T;T;T	0.54279	0.58;1.53;1.55;1.53;0.58;1.18;1.53	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.66655	0.2811	L	0.52573	1.65	0.52099	D	0.999947	P;P;D;P	0.63880	0.487;0.487;0.993;0.578	B;B;D;B	0.72982	0.167;0.167;0.979;0.281	T	0.69409	-0.5153	10	0.87932	D	0	-4.49	14.5277	0.67900	1.0:0.0:0.0:0.0	.	933;913;899;626	B5MCG9;B5MCU0;Q9Y2K5;E9PAL1	.;.;R3HD2_HUMAN;.	G	626;899;913;899;594;664;933	ENSP00000377400:W626G;ENSP00000317903:W899G;ENSP00000385839:W913G;ENSP00000351784:W899G;ENSP00000408536:W594G;ENSP00000394676:W664G;ENSP00000385169:W933G	ENSP00000317903:W899G	W	-	1	0	R3HDM2	55935059	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.710000	0.91388	2.326000	0.78906	0.533000	0.62120	TGG	.		0.637	R3HDM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326570.2	NM_014925	
ALX1	8092	broad.mit.edu;bcgsc.ca	37	12	85680745	85680745	+	Missense_Mutation	SNP	G	G	A			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr12:85680745G>A	ENST00000316824.3	+	3	801	c.646G>A	c.(646-648)Gac>Aac	p.D216N		NM_006982.2	NP_008913.2	Q15699	ALX1_HUMAN	ALX homeobox 1	216					anterior/posterior pattern specification (GO:0009952)|brain development (GO:0007420)|cartilage condensation (GO:0001502)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|mesenchymal cell development (GO:0014031)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|liver(1)|lung(16)|ovary(1)	26				GBM - Glioblastoma multiforme(134;0.134)		GCCAAGGACTGACAGCTACCC	0.378																																					p.D216N													.	ALX1-24	0			c.G646A						.						130.0	117.0	121.0					12																	85680745		2203	4300	6503	SO:0001583	missense	8092	exon3			AGGACTGACAGCT	U31986	CCDS9028.1	12q21.31	2011-06-20	2007-07-26	2007-07-26		ENSG00000180318		"""Homeoboxes / PRD class"""	1494	protein-coding gene	gene with protein product		601527	"""cartilage paired-class homeoprotein 1"""	CART1		8756334, 7592751	Standard	NM_006982		Approved		uc001tae.4	Q15699	OTTHUMG00000169820	ENST00000316824.3:c.646G>A	12.37:g.85680745G>A	ENSP00000315417:p.Asp216Asn	Somatic	52	1		WXS	Illumina HiSeq	Phase_I	69	6	NM_006982	0	0	0	0	0	Q546C8|Q96FH4	Missense_Mutation	SNP	ENST00000316824.3	37	CCDS9028.1	.	.	.	.	.	.	.	.	.	.	G	19.54	3.847661	0.71603	.	.	ENSG00000180318	ENST00000316824	D	0.92805	-3.11	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	D	0.91717	0.7381	L	0.61218	1.895	0.80722	D	1	B	0.15141	0.012	B	0.19946	0.027	D	0.87471	0.2414	10	0.54805	T	0.06	.	20.0044	0.97430	0.0:0.0:1.0:0.0	.	216	Q15699	ALX1_HUMAN	N	216	ENSP00000315417:D216N	ENSP00000315417:D216N	D	+	1	0	ALX1	84204876	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.864000	0.99589	2.714000	0.92807	0.650000	0.86243	GAC	.		0.378	ALX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406072.1	NM_006982	
GALNT9	50614	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	132834320	132834320	+	Silent	SNP	G	G	A	rs554022886		TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr12:132834320G>A	ENST00000328957.8	-	5	866	c.867C>T	c.(865-867)aaC>aaT	p.N289N	GALNT9_ENST00000535208.1_5'Flank|GALNT9_ENST00000535228.1_5'Flank	NM_001122636.1	NP_001116108.1	Q9HCQ5	GALT9_HUMAN	polypeptide N-acetylgalactosaminyltransferase 9	289					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(1)|endometrium(1)|large_intestine(2)|lung(5)	9	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.49e-08)|Epithelial(86;3.55e-07)|all cancers(50;2.09e-05)		CATGGGCGGCGTTCGCATACT	0.632													g|||	1	0.000199681	0.0008	0.0	5008	,	,		12187	0.0		0.0	False		,,,				2504	0.0				p.N289N	Colon(186;2147 2752 13553 41466)	.											.	GALNT9-90	0			c.C867T						.						27.0	32.0	30.0					12																	132834320		692	1591	2283	SO:0001819	synonymous_variant	50614	exon5			GGCGGCGTTCGCA	AB040672	CCDS41866.1	12q24.33	2014-03-13	2014-03-13		ENSG00000182870	ENSG00000182870	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4131	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 9"""	606251	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 9 (GalNAc-T9)"""			10978536, 12407114	Standard	NM_021808		Approved	GALNAC-T9	uc001ukc.4	Q9HCQ5	OTTHUMG00000168256	ENST00000328957.8:c.867C>T	12.37:g.132834320G>A		Somatic	95	0		WXS	Illumina HiSeq	Phase_I	72	18	NM_001122636	0	0	0	0	0	Q52LR8|Q6NT54|Q8NFR1	Silent	SNP	ENST00000328957.8	37																																																																																				.		0.632	GALNT9-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000402967.1	NM_001122636	
GJA3	2700	broad.mit.edu	37	13	20717168	20717168	+	Missense_Mutation	SNP	G	G	A			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr13:20717168G>A	ENST00000241125.3	-	2	436	c.260C>T	c.(259-261)aCg>aTg	p.T87M		NM_021954.3	NP_068773.2	Q9Y6H8	CXA3_HUMAN	gap junction protein, alpha 3, 46kDa	87			T -> M (in CTRCT14; pearl box cataract). {ECO:0000269|PubMed:17615540}.		cell-cell signaling (GO:0007267)|transport (GO:0006810)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)	gap junction channel activity (GO:0005243)			NS(1)|endometrium(1)|kidney(1)|lung(1)|pancreas(1)|prostate(1)|skin(1)	7		all_cancers(29;1.4e-21)|all_epithelial(30;8.75e-19)|all_lung(29;1.28e-17)|Lung SC(185;0.0257)|Ovarian(182;0.0822)		all cancers(112;0.000554)|Epithelial(112;0.000872)|OV - Ovarian serous cystadenocarcinoma(117;0.0105)|Lung(94;0.0251)|LUSC - Lung squamous cell carcinoma(192;0.0784)		GAGGGTGGGCGTGGACACGAA	0.612																																					p.T87M													.	GJA3-69	0			c.C260T	GRCh37	CM071794	GJA3	M		.						85.0	75.0	78.0					13																	20717168		2203	4300	6503	SO:0001583	missense	2700	exon2			GTGGGCGTGGACA	AF075290	CCDS9289.1	13q12.11	2008-02-05	2007-01-16		ENSG00000121743	ENSG00000121743		"""Ion channels / Gap junction proteins (connexins)"""	4277	protein-coding gene	gene with protein product	"""connexin 46"""	121015	"""gap junction protein, alpha 3, 46kD (connexin 46)"", ""gap junction protein, alpha 3, 46kDa (connexin 46)"""	CZP3		10205266, 7342922	Standard	NM_021954		Approved	CX46	uc001umx.1	Q9Y6H8	OTTHUMG00000016510	ENST00000241125.3:c.260C>T	13.37:g.20717168G>A	ENSP00000241125:p.Thr87Met	Somatic	231	0		WXS	Illumina HiSeq	Phase_I	145	5	NM_021954	0	0	0	0	0	Q0VAB7|Q9H537	Missense_Mutation	SNP	ENST00000241125.3	37	CCDS9289.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.785307	0.90282	.	.	ENSG00000121743	ENST00000241125	D	0.99207	-5.56	5.36	5.36	0.76844	Connexin, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.99423	0.9796	M	0.82716	2.605	0.80722	D	1	D	0.89917	1.0	D	0.70716	0.97	D	0.99000	1.0811	10	0.72032	D	0.01	.	19.094	0.93242	0.0:0.0:1.0:0.0	.	87	Q9Y6H8	CXA3_HUMAN	M	87	ENSP00000241125:T87M	ENSP00000241125:T87M	T	-	2	0	GJA3	19615168	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.735000	0.98825	2.517000	0.84864	0.561000	0.74099	ACG	.		0.612	GJA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044059.3	NM_021954	
GPR12	2835	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	13	27332981	27332981	+	Silent	SNP	C	C	T			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr13:27332981C>T	ENST00000381436.2	-	1	1446	c.984G>A	c.(982-984)gcG>gcA	p.A328A	GPR12_ENST00000405846.3_Silent_p.A328A			P47775	GPR12_HUMAN	G protein-coupled receptor 12	328					cellular calcium ion homeostasis (GO:0006874)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|phosphatidylcholine binding (GO:0031210)			endometrium(7)|kidney(2)|large_intestine(6)|lung(14)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33	Colorectal(5;5.77e-05)	Breast(139;0.198)		Epithelial(112;9.37e-07)|OV - Ovarian serous cystadenocarcinoma(117;1.16e-06)|all cancers(112;8.31e-06)|GBM - Glioblastoma multiforme(144;0.00121)|Lung(94;0.111)|LUSC - Lung squamous cell carcinoma(192;0.184)		TGGGCGAGCGCGCTCTCTGGG	0.537																																					p.A328A		.											.	GPR12-90	0			c.G984A						.						65.0	67.0	66.0					13																	27332981		2203	4300	6503	SO:0001819	synonymous_variant	2835	exon2			CGAGCGCGCTCTC	U18548	CCDS9319.1	13q12	2014-06-12			ENSG00000132975	ENSG00000132975		"""GPCR / Class A : Orphans"""	4466	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 84"""	600752				8262253, 8530049	Standard	NM_005288		Approved	GPCR21, PPP1R84	uc010aal.3	P47775	OTTHUMG00000016620	ENST00000381436.2:c.984G>A	13.37:g.27332981C>T		Somatic	155	0		WXS	Illumina HiSeq	Phase_I	127	56	NM_005288	0	0	0	0	0	Q5T8P3	Silent	SNP	ENST00000381436.2	37	CCDS9319.1																																																																																			.		0.537	GPR12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044257.2		
FRY	10129	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	13	32823745	32823745	+	Missense_Mutation	SNP	G	G	T	rs372186855		TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr13:32823745G>T	ENST00000380250.3	+	49	7587	c.7091G>T	c.(7090-7092)cGg>cTg	p.R2364L		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	2364						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		GCCGTCACCCGGAGCACATCT	0.542																																					p.R2364L		.											.	FRY-142	0			c.G7091T						.						73.0	76.0	75.0					13																	32823745		2015	4173	6188	SO:0001583	missense	10129	exon49			TCACCCGGAGCAC	AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"""chromosome 13 open reading frame 14"""	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.7091G>T	13.37:g.32823745G>T	ENSP00000369600:p.Arg2364Leu	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	77	4	NM_023037	0	0	6	6	0	Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	37	CCDS41875.1	.	.	.	.	.	.	.	.	.	.	G	35	5.453660	0.96223	.	.	ENSG00000073910	ENST00000380250;ENST00000380257;ENST00000380235	T	0.25085	1.82	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	T	0.32823	0.0842	L	0.54323	1.7	0.80722	D	1	P	0.46784	0.884	B	0.42214	0.38	T	0.02821	-1.1106	10	0.54805	T	0.06	.	20.6634	0.99662	0.0:0.0:1.0:0.0	.	2364	Q5TBA9	FRY_HUMAN	L	2364;1174;5	ENSP00000369600:R2364L	ENSP00000369567:R5L	R	+	2	0	FRY	31721745	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.476000	0.97823	2.894000	0.99253	0.655000	0.94253	CGG	.		0.542	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037	
PROSER1	80209	broad.mit.edu	37	13	39600511	39600511	+	Missense_Mutation	SNP	C	C	T			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr13:39600511C>T	ENST00000352251.3	-	6	1216	c.383G>A	c.(382-384)gGc>gAc	p.G128D	PROSER1_ENST00000350125.3_Missense_Mutation_p.G106D|PROSER1_ENST00000484434.3_5'Flank	NM_025138.4	NP_079414.3	Q86XN7	PRSR1_HUMAN	proline and serine rich 1	128																	AGCTTTGCAGCCCCCCTTGAA	0.393																																					p.G128D													.	.	0			c.G383A						.						87.0	92.0	90.0					13																	39600511		2203	4300	6503	SO:0001583	missense	80209	exon6			TTGCAGCCCCCCT	AK022723	CCDS9368.2	13q13.2	2011-08-09	2011-08-09	2011-08-09	ENSG00000120685	ENSG00000120685			20291	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 23"""	C13orf23			Standard	NM_025138		Approved	bA50D16.2, FLJ12661	uc001uwy.4	Q86XN7	OTTHUMG00000016764	ENST00000352251.3:c.383G>A	13.37:g.39600511C>T	ENSP00000332034:p.Gly128Asp	Somatic	17	0		WXS	Illumina HiSeq	Phase_I	13	4	NM_025138	0	0	0	0	0	A6NJ97|Q6P2S2|Q7Z3X5|Q8N3D2|Q8N3P1|Q9H9M1	Missense_Mutation	SNP	ENST00000352251.3	37	CCDS9368.2	.	.	.	.	.	.	.	.	.	.	C	24.7	4.561329	0.86335	.	.	ENSG00000120685	ENST00000352251;ENST00000350125;ENST00000436678	T;T	0.70749	-0.51;-0.4	5.44	5.44	0.79542	.	.	.	.	.	T	0.74898	0.3777	N	0.24115	0.695	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.72763	-0.4195	8	.	.	.	-2.7574	17.1251	0.86712	0.0:1.0:0.0:0.0	.	106;128	A6NJ97;Q86XN7	.;PRSR1_HUMAN	D	128;106;107	ENSP00000332034:G128D;ENSP00000339123:G106D	.	G	-	2	0	PROSER1	38498511	1.000000	0.71417	0.999000	0.59377	0.966000	0.64601	7.019000	0.76412	2.720000	0.93068	0.650000	0.86243	GGC	.		0.393	PROSER1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044607.5	NM_025138	
PRPF39	55015	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	14	45564665	45564665	+	Missense_Mutation	SNP	G	G	A			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr14:45564665G>A	ENST00000355765.6	+	2	393	c.223G>A	c.(223-225)Gca>Aca	p.A75T		NM_017922.3	NP_060392.3	Q86UA1	PRP39_HUMAN	pre-mRNA processing factor 39	75					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(2)|endometrium(2)|kidney(4)|lung(3)|ovary(1)	12						AGAAACAGAAGCAAATTTCCC	0.403																																					p.A75T		.											.	PRPF39-70	0			c.G223A						.						46.0	47.0	46.0					14																	45564665		2031	4212	6243	SO:0001583	missense	55015	exon2			ACAGAAGCAAATT	AK000673	CCDS9682.2	14q21.1	2013-10-03	2013-10-03		ENSG00000185246	ENSG00000185246			20314	protein-coding gene	gene with protein product		614907	"""PRP39 pre-mRNA processing factor 39 homolog (yeast)"", ""PRP39 pre-mRNA processing factor 39 homolog (S. cerevisiae)"""				Standard	NM_017922		Approved	FLJ20666, FLJ11128	uc001wvz.4	Q86UA1	OTTHUMG00000140265	ENST00000355765.6:c.223G>A	14.37:g.45564665G>A	ENSP00000348010:p.Ala75Thr	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	55	23	NM_017922	0	0	0	4	4	Q08AL1|Q08AL2|Q9NUU5	Missense_Mutation	SNP	ENST00000355765.6	37	CCDS9682.2	.	.	.	.	.	.	.	.	.	.	G	12.40	1.927796	0.34002	.	.	ENSG00000185246	ENST00000355765;ENST00000553605	T	0.46819	0.86	5.72	4.83	0.62350	.	.	.	.	.	T	0.32675	0.0837	N	0.20986	0.625	0.26211	N	0.979309	B	0.19817	0.039	B	0.23018	0.043	T	0.20538	-1.0272	9	0.15499	T	0.54	-21.2955	10.525	0.44943	0.1491:0.0:0.8509:0.0	.	75	Q86UA1	PRP39_HUMAN	T	75	ENSP00000348010:A75T	ENSP00000348010:A75T	A	+	1	0	PRPF39	44634415	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.367000	0.52350	1.429000	0.47314	0.591000	0.81541	GCA	.		0.403	PRPF39-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319683.2		
ARG2	384	broad.mit.edu	37	14	68117524	68117524	+	Missense_Mutation	SNP	G	G	T	rs148319106	byFrequency	TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr14:68117524G>T	ENST00000261783.3	+	8	1132	c.952G>T	c.(952-954)Gtg>Ttg	p.V318L	VTI1B_ENST00000554659.1_3'UTR	NM_001172.3	NP_001163.1	P78540	ARGI2_HUMAN	arginase 2	318					arginine metabolic process (GO:0006525)|cellular nitrogen compound metabolic process (GO:0034641)|nitric oxide biosynthetic process (GO:0006809)|small molecule metabolic process (GO:0044281)|striated muscle contraction (GO:0006941)|urea cycle (GO:0000050)|ureteric bud development (GO:0001657)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	arginase activity (GO:0004053)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|ovary(1)|prostate(1)	11				all cancers(60;0.000582)|OV - Ovarian serous cystadenocarcinoma(108;0.00392)|BRCA - Breast invasive adenocarcinoma(234;0.00928)	L-Arginine(DB00125)|L-Ornithine(DB00129)	GGCAGTAGATGTGATTGCTTC	0.473																																					p.V318L													.	ARG2-90	0			c.G952T						.						153.0	116.0	129.0					14																	68117524		2203	4300	6503	SO:0001583	missense	384	exon8			GTAGATGTGATTG	D86724	CCDS9785.1	14q24.1	2013-05-01	2013-05-01			ENSG00000081181			664	protein-coding gene	gene with protein product		107830	"""arginase, type II"""			8954792, 8898077	Standard	NM_001172		Approved		uc001xjs.3	P78540		ENST00000261783.3:c.952G>T	14.37:g.68117524G>T	ENSP00000261783:p.Val318Leu	Somatic	180	0		WXS	Illumina HiSeq	Phase_I	147	4	NM_001172	0	0	9	9	0	B2R690|Q6FHY8	Missense_Mutation	SNP	ENST00000261783.3	37	CCDS9785.1	.	.	.	.	.	.	.	.	.	.	G	8.265	0.812032	0.16537	.	.	ENSG00000081181	ENST00000261783	D	0.82167	-1.58	5.09	5.09	0.68999	Ureohydrolase domain (1);	0.252215	0.39544	N	0.001335	T	0.64080	0.2566	N	0.02751	-0.505	0.80722	D	1	B	0.16802	0.019	B	0.23716	0.048	T	0.63229	-0.6684	10	0.02654	T	1	.	18.6895	0.91578	0.0:0.0:1.0:0.0	.	318	P78540	ARGI2_HUMAN	L	318	ENSP00000261783:V318L	ENSP00000261783:V318L	V	+	1	0	ARG2	67187277	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.586000	0.60984	2.661000	0.90470	0.655000	0.94253	GTG	G|0.999;A|0.001		0.473	ARG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415190.2	NM_001172	
TGM7	116179	broad.mit.edu	37	15	43571977	43571977	+	Silent	SNP	C	C	A			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr15:43571977C>A	ENST00000452443.2	-	10	1528	c.1524G>T	c.(1522-1524)ctG>ctT	p.L508L		NM_052955.2	NP_443187.1	Q96PF1	TGM7_HUMAN	transglutaminase 7	508					peptide cross-linking (GO:0018149)		metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(2)|prostate(4)|skin(1)	39		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;9.14e-07)	L-Glutamine(DB00130)	TACGCAGCAGCAGCTGCAGGT	0.657																																					p.L508L													.	TGM7-92	0			c.G1524T						.						38.0	44.0	42.0					15																	43571977		2201	4297	6498	SO:0001819	synonymous_variant	116179	exon10			CAGCAGCAGCTGC	AF363393	CCDS32213.1	15q15.2	2004-07-01				ENSG00000159495		"""Transglutaminases"""	30790	protein-coding gene	gene with protein product	"""transglutaminase Z"""	606776				11390390	Standard	NM_052955		Approved	TGMZ	uc001zrf.1	Q96PF1		ENST00000452443.2:c.1524G>T	15.37:g.43571977C>A		Somatic	55	1		WXS	Illumina HiSeq	Phase_I	40	7	NM_052955	0	0	0	0	0		Silent	SNP	ENST00000452443.2	37	CCDS32213.1																																																																																			.		0.657	TGM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432489.1	NM_052955	
SIN3A	25942	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	75673957	75673957	+	Silent	SNP	T	T	A			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr15:75673957T>A	ENST00000394947.3	-	18	3599	c.3285A>T	c.(3283-3285)gcA>gcT	p.A1095A	SIN3A_ENST00000394949.4_Silent_p.A1095A|SIN3A_ENST00000360439.4_Silent_p.A1095A	NM_001145358.1	NP_001138830.1			SIN3 transcription regulator family member A											breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	63						CTCATACCTCTGCTTCCACAG	0.527																																					p.A1095A		.											.	SIN3A-230	0			c.A3285T						.						227.0	191.0	203.0					15																	75673957		2197	4294	6491	SO:0001819	synonymous_variant	25942	exon18			TACCTCTGCTTCC	AK027559	CCDS10279.1	15q22.33	2013-08-21	2013-08-21		ENSG00000169375	ENSG00000169375			19353	protein-coding gene	gene with protein product		607776	"""SIN3 homolog A, transcription regulator (yeast)"", ""SIN3 transcription regulator homolog A (yeast)"""			10773092, 7601471	Standard	NM_001145357		Approved	KIAA0700, DKFZP434K2235	uc002bai.3	Q96ST3	OTTHUMG00000142834	ENST00000394947.3:c.3285A>T	15.37:g.75673957T>A		Somatic	152	0		WXS	Illumina HiSeq	Phase_I	170	77	NM_001145358	0	0	0	0	0		Silent	SNP	ENST00000394947.3	37	CCDS10279.1																																																																																			.		0.527	SIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286469.1	NM_015477	
SIN3A	25942	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	75673982	75673982	+	Missense_Mutation	SNP	T	T	A			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr15:75673982T>A	ENST00000394947.3	-	18	3574	c.3260A>T	c.(3259-3261)gAg>gTg	p.E1087V	SIN3A_ENST00000394949.4_Missense_Mutation_p.E1087V|SIN3A_ENST00000360439.4_Missense_Mutation_p.E1087V	NM_001145358.1	NP_001138830.1			SIN3 transcription regulator family member A											breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	63						ATCCGAATTCTCCTCTTCTGT	0.502																																					p.E1087V		.											.	SIN3A-230	0			c.A3260T						.						219.0	188.0	199.0					15																	75673982		2197	4294	6491	SO:0001583	missense	25942	exon18			GAATTCTCCTCTT	AK027559	CCDS10279.1	15q22.33	2013-08-21	2013-08-21		ENSG00000169375	ENSG00000169375			19353	protein-coding gene	gene with protein product		607776	"""SIN3 homolog A, transcription regulator (yeast)"", ""SIN3 transcription regulator homolog A (yeast)"""			10773092, 7601471	Standard	NM_001145357		Approved	KIAA0700, DKFZP434K2235	uc002bai.3	Q96ST3	OTTHUMG00000142834	ENST00000394947.3:c.3260A>T	15.37:g.75673982T>A	ENSP00000378402:p.Glu1087Val	Somatic	169	0		WXS	Illumina HiSeq	Phase_I	173	75	NM_001145358	0	0	1	1	0		Missense_Mutation	SNP	ENST00000394947.3	37	CCDS10279.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.186474	0.78789	.	.	ENSG00000169375	ENST00000394947;ENST00000394949;ENST00000360439	T;T;T	0.47528	0.84;0.84;0.84	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.47248	0.1435	L	0.61387	1.9	0.80722	D	1	B	0.28998	0.23	B	0.30716	0.119	T	0.41215	-0.9521	10	0.30078	T	0.28	-25.6466	14.6847	0.69042	0.0:0.0:0.0:1.0	.	1087	Q96ST3	SIN3A_HUMAN	V	1087	ENSP00000378402:E1087V;ENSP00000378403:E1087V;ENSP00000353622:E1087V	ENSP00000353622:E1087V	E	-	2	0	SIN3A	73461035	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.939000	0.87685	2.073000	0.62155	0.402000	0.26972	GAG	.		0.502	SIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286469.1	NM_015477	
CARHSP1	23589	bcgsc.ca	37	16	8949067	8949067	+	Missense_Mutation	SNP	G	G	A			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr16:8949067G>A	ENST00000396593.2	-	4	757	c.398C>T	c.(397-399)cCa>cTa	p.P133L	CARHSP1_ENST00000567554.1_Missense_Mutation_p.P133L|CARHSP1_ENST00000311052.5_Missense_Mutation_p.P133L|RP11-77H9.5_ENST00000564919.1_RNA|RP11-77H9.2_ENST00000565934.1_RNA|CARHSP1_ENST00000561530.1_Missense_Mutation_p.P133L	NM_001042476.1|NM_001278260.1|NM_001278261.1|NM_001278262.1|NM_001278263.1|NM_001278264.1|NM_001278265.1|NM_001278266.1|NM_014316.3	NP_001035941.1|NP_001265189.1|NP_001265190.1|NP_001265191.1|NP_001265192.1|NP_001265193.1|NP_001265194.1|NP_001265195.1|NP_055131.2	Q9Y2V2	CHSP1_HUMAN	calcium regulated heat stable protein 1, 24kDa	133					intracellular signal transduction (GO:0035556)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasmic exosome (RNase complex) (GO:0000177)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|P granule (GO:0043186)	DNA binding (GO:0003677)|mRNA 3'-UTR binding (GO:0003730)|phosphatase binding (GO:0019902)			endometrium(2)|lung(1)	3						CTTGGTGCCTGGTGCCAGGTG	0.567																																					p.P133L													.	CARHSP1-90	0			c.C398T						.						188.0	135.0	153.0					16																	8949067		2197	4300	6497	SO:0001583	missense	23589	exon4			GTGCCTGGTGCCA	AF115345	CCDS10537.1	16p13.2	2008-02-05	2002-08-29		ENSG00000153048	ENSG00000153048			17150	protein-coding gene	gene with protein product			"""calcium regulated heat stable protein 1 (24kD)"""			9712905	Standard	NM_014316		Approved	CRHSP-24, CSDC1	uc031quz.1	Q9Y2V2	OTTHUMG00000129695	ENST00000396593.2:c.398C>T	16.37:g.8949067G>A	ENSP00000379838:p.Pro133Leu	Somatic	230	0		WXS	Illumina HiSeq	Phase_1	179	6	NM_001042476	0	0	273	273	0	B2R4C3|D3DUF5|Q2YDX5|Q9BQ53	Missense_Mutation	SNP	ENST00000396593.2	37	CCDS10537.1	.	.	.	.	.	.	.	.	.	.	G	32	5.142560	0.94560	.	.	ENSG00000153048	ENST00000396593;ENST00000311052	.	.	.	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.76154	0.3948	M	0.87269	2.87	0.80722	D	1	D	0.57257	0.979	P	0.49252	0.604	T	0.80594	-0.1313	9	0.87932	D	0	-2.1558	19.6321	0.95713	0.0:0.0:1.0:0.0	.	133	Q9Y2V2	CHSP1_HUMAN	L	133	.	ENSP00000311847:P133L	P	-	2	0	CARHSP1	8856568	1.000000	0.71417	0.701000	0.30321	0.760000	0.43138	9.751000	0.98889	2.884000	0.98904	0.655000	0.94253	CCA	.		0.567	CARHSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251902.1	NM_014316	
FA2H	79152	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	74750468	74750468	+	Missense_Mutation	SNP	G	G	C			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr16:74750468G>C	ENST00000219368.3	-	6	885	c.816C>G	c.(814-816)ttC>ttG	p.F272L	FA2H_ENST00000544337.1_Missense_Mutation_p.F59L	NM_024306.4	NP_077282.3	Q7L5A8	FA2H_HUMAN	fatty acid 2-hydroxylase	272					cell death (GO:0008219)|central nervous system myelin maintenance (GO:0032286)|fatty acid biosynthetic process (GO:0006633)|lipid modification (GO:0030258)|peripheral nervous system myelin maintenance (GO:0032287)|regulation of cell proliferation (GO:0042127)|regulation of hair cycle (GO:0042634)|sebaceous gland cell differentiation (GO:0001949)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	fatty acid alpha-hydroxylase activity (GO:0080132)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			endometrium(2)|large_intestine(4)|lung(3)|skin(1)	10						GCACAGGGGGGAAGACCAGGC	0.677																																					p.F272L		.											.	FA2H-90	0			c.C816G						.						16.0	15.0	15.0					16																	74750468		2194	4297	6491	SO:0001583	missense	79152	exon6			AGGGGGGAAGACC	BC002679	CCDS10911.1	16q23	2013-03-04	2003-10-29	2003-10-31	ENSG00000103089	ENSG00000103089		"""Fatty acid hydroxylase domain containing"""	21197	protein-coding gene	gene with protein product	"""fatty acid hydroxylase"""	611026	"""fatty acid hydroxylase domain containing 1"", ""spastic paraplegia 35 (autosomal recessive)"""	FAXDC1, SPG35		20104589	Standard	NM_024306		Approved	FAAH, FLJ25287	uc002fde.2	Q7L5A8	OTTHUMG00000137603	ENST00000219368.3:c.816C>G	16.37:g.74750468G>C	ENSP00000219368:p.Phe272Leu	Somatic	34	0		WXS	Illumina HiSeq	Phase_I	39	16	NM_024306	0	0	0	0	0	B7Z8T6|O75213|Q96DK1|Q9H1A5	Missense_Mutation	SNP	ENST00000219368.3	37	CCDS10911.1	.	.	.	.	.	.	.	.	.	.	g	23.5	4.426263	0.83667	.	.	ENSG00000103089	ENST00000219368;ENST00000544337	D;D	0.83506	-1.73;-1.73	5.07	3.07	0.35406	Fatty acid hydroxylase (1);	0.000000	0.85682	D	0.000000	D	0.89203	0.6648	M	0.75264	2.295	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.87214	0.2249	10	0.40728	T	0.16	0.1308	11.6853	0.51483	0.1462:0.0:0.8538:0.0	.	272;180	Q7L5A8;B2RDE6	FA2H_HUMAN;.	L	272;59	ENSP00000219368:F272L;ENSP00000442334:F59L	ENSP00000219368:F272L	F	-	3	2	FA2H	73307969	1.000000	0.71417	0.997000	0.53966	0.948000	0.59901	2.233000	0.43027	0.524000	0.28502	0.651000	0.88453	TTC	.		0.677	FA2H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269015.2	NM_024306	
WDR81	124997	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	1630052	1630052	+	Missense_Mutation	SNP	C	C	T			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr17:1630052C>T	ENST00000409644.1	+	1	1799	c.1799C>T	c.(1798-1800)cCc>cTc	p.P600L	WDR81_ENST00000437219.2_Intron|WDR81_ENST00000419248.1_Intron|RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000309182.5_Intron|WDR81_ENST00000446363.1_Intron	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	600	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.				negative regulation of phosphatase activity (GO:0010923)		transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		GCCCTTGCCCCCGAGCCTCCC	0.657																																					p.P600L		.											.	WDR81-91	0			c.C1799T						.						14.0	18.0	17.0					17																	1630052		692	1589	2281	SO:0001583	missense	124997	exon1			TTGCCCCCGAGCC	AK074111	CCDS54061.1, CCDS54062.1, CCDS54063.1	17p13.3	2014-06-13			ENSG00000167716	ENSG00000167716		"""WD repeat domain containing"""	26600	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 166"""	614218					Standard	NM_001163673		Approved	FLJ33817, PPP1R166	uc002ftj.2	Q562E7	OTTHUMG00000153941	ENST00000409644.1:c.1799C>T	17.37:g.1630052C>T	ENSP00000386609:p.Pro600Leu	Somatic	19	0		WXS	Illumina HiSeq	Phase_I	35	20	NM_001163809	0	0	0	0	0	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Missense_Mutation	SNP	ENST00000409644.1	37	CCDS54062.1	.	.	.	.	.	.	.	.	.	.	C	5.306	0.241738	0.10077	.	.	ENSG00000167716	ENST00000409644	T	0.51574	0.7	5.43	5.43	0.79202	.	.	.	.	.	T	0.39545	0.1082	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.12528	-1.0544	6	0.09590	T	0.72	.	12.5648	0.56304	0.0:0.9236:0.0:0.0764	.	.	.	.	L	600	ENSP00000386609:P600L	ENSP00000386609:P600L	P	+	2	0	WDR81	1576802	0.524000	0.26282	0.970000	0.41538	0.006000	0.05464	4.407000	0.59754	2.546000	0.85860	0.462000	0.41574	CCC	.		0.657	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348	
MYBBP1A	10514	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	4445767	4445767	+	Missense_Mutation	SNP	G	G	T	rs200492249	byFrequency	TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr17:4445767G>T	ENST00000254718.4	-	22	3385	c.3079C>A	c.(3079-3081)Cgt>Agt	p.R1027S	MYBBP1A_ENST00000381556.2_Missense_Mutation_p.R1027S			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	1027					cellular response to glucose starvation (GO:0042149)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleocytoplasmic transport (GO:0006913)|osteoblast differentiation (GO:0001649)|positive regulation of cell cycle arrest (GO:0071158)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|NLS-dependent protein nuclear import complex (GO:0042564)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(2)|stomach(1)	24						ACCTGATGACGGGGCCGCACC	0.627																																					p.R1027S		.											.	MYBBP1A-92	0			c.C3079A						.						69.0	80.0	76.0					17																	4445767		2203	4300	6503	SO:0001583	missense	10514	exon22			GATGACGGGGCCG	AF147709	CCDS11046.1, CCDS42238.1	17p13.3	2008-07-18			ENSG00000132382	ENSG00000132382			7546	protein-coding gene	gene with protein product	"""p53-activated protein-2"""	604885				10644447	Standard	NM_014520		Approved	P160, PAP2, FLJ37886	uc002fxz.4	Q9BQG0	OTTHUMG00000090747	ENST00000254718.4:c.3079C>A	17.37:g.4445767G>T	ENSP00000254718:p.Arg1027Ser	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	149	48	NM_014520	0	0	11	18	7	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Missense_Mutation	SNP	ENST00000254718.4	37	CCDS11046.1	.	.	.	.	.	.	.	.	.	.	G	13.30	2.195223	0.38806	.	.	ENSG00000132382	ENST00000381556;ENST00000254718	T;T	0.67698	-0.28;-0.28	5.3	4.12	0.48240	Armadillo-type fold (1);	0.258408	0.43579	D	0.000546	T	0.68568	0.3015	M	0.65975	2.015	0.30663	N	0.754172	P;P	0.48407	0.854;0.91	B;P	0.49683	0.414;0.619	T	0.69591	-0.5104	10	0.38643	T	0.18	-19.6389	9.7224	0.40311	0.1107:0.0:0.8893:0.0	.	1027;1027	Q9BQG0;Q9BQG0-2	MBB1A_HUMAN;.	S	1027	ENSP00000370968:R1027S;ENSP00000254718:R1027S	ENSP00000254718:R1027S	R	-	1	0	MYBBP1A	4392516	1.000000	0.71417	0.995000	0.50966	0.009000	0.06853	2.897000	0.48664	2.473000	0.83533	0.561000	0.74099	CGT	G|0.999;A|0.001		0.627	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520	
NDC80	10403	bcgsc.ca	37	18	2585121	2585121	+	Missense_Mutation	SNP	G	G	T			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr18:2585121G>T	ENST00000261597.4	+	7	771	c.589G>T	c.(589-591)Gcc>Tcc	p.A197S		NM_006101.2	NP_006092.1	O14777	NDC80_HUMAN	NDC80 kinetochore complex component	197	Interaction with RB1.|Interaction with the N-terminus of CDCA1.|Nuclear localization.				attachment of spindle microtubules to kinetochore (GO:0008608)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle organization (GO:0007052)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)				NS(1)|biliary_tract(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(2)|urinary_tract(2)	22						GATACATACTGCCATGAAAGA	0.333																																					p.A197S													.	NDC80-91	0			c.G589T						.						94.0	91.0	92.0					18																	2585121		2203	4300	6503	SO:0001583	missense	10403	exon7			CATACTGCCATGA	AF017790	CCDS11827.1	18p11.31	2013-01-17	2013-01-17	2007-03-02	ENSG00000080986	ENSG00000080986			16909	protein-coding gene	gene with protein product		607272	"""highly expressed in cancer, rich in leucine heptad repeats (yeast)"", ""kinetochore associated 2"", ""NDC80 kinetochore complex component homolog (S. cerevisiae)"""	KNTC2		9315664, 12351790	Standard	NM_006101		Approved	HEC, HEC1, hsNDC80, TID3	uc002kli.3	O14777	OTTHUMG00000131483	ENST00000261597.4:c.589G>T	18.37:g.2585121G>T	ENSP00000261597:p.Ala197Ser	Somatic	43	0		WXS	Illumina HiSeq	Phase_1	55	4	NM_006101	0	0	0	0	0	Q6PJX2	Missense_Mutation	SNP	ENST00000261597.4	37	CCDS11827.1	.	.	.	.	.	.	.	.	.	.	G	3.921	-0.018063	0.07681	.	.	ENSG00000080986	ENST00000261597;ENST00000543946	T	0.64438	-0.1	5.3	4.38	0.52667	.	0.163420	0.56097	D	0.000032	T	0.39462	0.1079	N	0.10874	0.06	0.37731	D	0.925259	B	0.06786	0.001	B	0.14578	0.011	T	0.32903	-0.9889	10	0.09843	T	0.71	-7.1468	13.3687	0.60701	0.0:0.0:0.8439:0.1561	.	197	O14777	NDC80_HUMAN	S	197	ENSP00000261597:A197S	ENSP00000261597:A197S	A	+	1	0	NDC80	2575121	1.000000	0.71417	0.977000	0.42913	0.981000	0.71138	3.611000	0.54132	2.625000	0.88918	0.650000	0.86243	GCC	.		0.333	NDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254327.1	NM_006101	
SHC2	25759	ucsc.edu;bcgsc.ca	37	19	422299	422299	+	Missense_Mutation	SNP	G	G	T	rs375069437		TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr19:422299G>T	ENST00000264554.6	-	11	1466	c.1467C>A	c.(1465-1467)caC>caA	p.H489Q		NM_012435.2	NP_036567.2	P98077	SHC2_HUMAN	SHC (Src homology 2 domain containing) transforming protein 2	489	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				activation of MAPK activity (GO:0000187)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)	cytosol (GO:0005829)				endometrium(2)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	21		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCATCCGGCCGTGGTACCAGG	0.697																																					p.H489Q													.	SHC2-392	0			c.C1467A						.						12.0	15.0	14.0					19																	422299		2093	4207	6300	SO:0001583	missense	25759	exon11			CCGGCCGTGGTAC	AB001451	CCDS45891.1	19p13.3	2013-02-14				ENSG00000129946		"""SH2 domain containing"""	29869	protein-coding gene	gene with protein product	"""neuronal Shc adaptor homolog"""	605217				7527937, 9507002	Standard	NM_012435		Approved	SLI, SCK, SHCB	uc002loq.4	P98077		ENST00000264554.6:c.1467C>A	19.37:g.422299G>T	ENSP00000264554:p.His489Gln	Somatic	72	0		WXS	Illumina HiSeq		32	4	NM_012435	0	0	18	18	0	O60230|Q9NPL5|Q9UCX4	Missense_Mutation	SNP	ENST00000264554.6	37	CCDS45891.1	.	.	.	.	.	.	.	.	.	.	G	15.62	2.888479	0.52014	.	.	ENSG00000129946	ENST00000264554	T	0.68903	-0.36	4.75	-4.42	0.03579	SH2 motif (5);	0.048752	0.85682	D	0.000000	T	0.75982	0.3924	M	0.88031	2.925	0.50632	D	0.999882	D	0.64830	0.994	D	0.67900	0.954	T	0.73711	-0.3897	10	0.31617	T	0.26	-47.0739	7.0621	0.25131	0.5458:0.0:0.3369:0.1173	.	489	P98077	SHC2_HUMAN	Q	489	ENSP00000264554:H489Q	ENSP00000264554:H489Q	H	-	3	2	SHC2	373299	0.022000	0.18835	0.979000	0.43373	0.978000	0.69477	-0.881000	0.04179	-0.519000	0.06444	-0.130000	0.14895	CAC	.		0.697	SHC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451840.3		
MEF2BNB	729991	ucsc.edu	37	19	19293489	19293489	+	Silent	SNP	G	G	A			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr19:19293489G>A	ENST00000462790.3	-	4	690	c.219C>T	c.(217-219)gcC>gcT	p.A73A	MEF2BNB-MEF2B_ENST00000602276.1_5'Flank|MEF2B_ENST00000162023.5_5'UTR|MEF2BNB-MEF2B_ENST00000514819.3_5'UTR|MEF2BNB_ENST00000585679.1_5'UTR|MEF2BNB-MEF2B_ENST00000444486.3_5'UTR|MEF2BNB_ENST00000477565.3_Silent_p.A73A|MEF2B_ENST00000602424.2_5'UTR|MEF2BNB_ENST00000494489.2_5'UTR	NM_001145784.1	NP_001139256.1	Q96FH0	MF2NB_HUMAN	MEF2B neighbor	73					heart development (GO:0007507)												GGTTCTTCACGGCGCTGAAAC	0.627																																					p.A73A													.	.	0			c.C219T						.						54.0	44.0	47.0					19																	19293489		692	1591	2283	SO:0001819	synonymous_variant	729991	exon4			CTTCACGGCGCTG		CCDS46025.1, CCDS54235.1	19p13.11	2011-04-19			ENSG00000254901	ENSG00000254901			37247	protein-coding gene	gene with protein product							Standard	NM_001145783		Approved		uc002nlq.3	Q96FH0	OTTHUMG00000166546	ENST00000462790.3:c.219C>T	19.37:g.19293489G>A		Somatic	58	2		WXS	Illumina HiSeq		39	4	NM_001145784	0	0	0	0	0	B2RXF9|Q9BT01	Silent	SNP	ENST00000462790.3	37	CCDS46025.1																																																																																			.		0.627	MEF2BNB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336091.4		
ZNF880	400713	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	19	52877551	52877551	+	Splice_Site	SNP	G	G	A			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr19:52877551G>A	ENST00000422689.2	+	3	154		c.e3-1		ZNF880_ENST00000597976.1_Splice_Site|ZNF880_ENST00000344085.5_Splice_Site|ZNF880_ENST00000424032.2_Splice_Site|ZNF880_ENST00000600321.1_Splice_Site	NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880						regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						TTTTTAAATAGGAATCTGTCT	0.403																																					.		.											.	.	0			c.140-1G>A						.						52.0	43.0	46.0					19																	52877551		692	1591	2283	SO:0001630	splice_region_variant	400713	exon3			TAAATAGGAATCT	BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"""Zinc fingers, C2H2-type"", ""-"""	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	ENST00000422689.2:c.140-1G>A	19.37:g.52877551G>A		Somatic	58	0		WXS	Illumina HiSeq	Phase_I	78	11	NM_001145434	0	0	0	1	1	B4DNA6	Splice_Site	SNP	ENST00000422689.2	37	CCDS46164.1	.	.	.	.	.	.	.	.	.	.	g	4.728	0.135350	0.09032	.	.	ENSG00000221923	ENST00000424032;ENST00000344085;ENST00000422689	.	.	.	1.13	1.13	0.20643	.	.	.	.	.	.	.	.	.	.	.	0.23483	N	0.997585	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.6302	0.17506	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ZNF880	57569363	0.003000	0.15002	0.027000	0.17364	0.231000	0.25187	0.510000	0.22723	0.920000	0.36970	0.448000	0.29417	.	.		0.403	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434	Intron
C2orf61	285051	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	47382353	47382353	+	Missense_Mutation	SNP	A	A	G			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr2:47382353A>G	ENST00000445927.2	-	1	164	c.38T>C	c.(37-39)aTa>aCa	p.I13T	C2orf61_ENST00000294947.2_Missense_Mutation_p.I13T|RP11-761B3.1_ENST00000422269.1_Intron	NM_001163561.1	NP_001157033.1	Q8N801	CB061_HUMAN	chromosome 2 open reading frame 61	13								p.0?(2)		endometrium(1)|kidney(1)|lung(2)	4		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)			GTCTTCCCTTATTGAGGTGGA	0.632																																					p.I13T		.											.	C2orf61-68	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	c.T38C						.						103.0	86.0	91.0					2																	47382353		2203	4300	6503	SO:0001583	missense	285051	exon1			TCCCTTATTGAGG	AK097491	CCDS1831.1, CCDS54356.1	2p21	2008-02-05			ENSG00000239605	ENSG00000239605			26850	protein-coding gene	gene with protein product							Standard	NM_173649		Approved	FLJ40172	uc010yog.2	Q8N801	OTTHUMG00000128851	ENST00000445927.2:c.38T>C	2.37:g.47382353A>G	ENSP00000408527:p.Ile13Thr	Somatic	118	0		WXS	Illumina HiSeq	Phase_I	100	31	NM_173649	0	0	0	0	0	H7C2Z2	Missense_Mutation	SNP	ENST00000445927.2	37	CCDS54356.1	.	.	.	.	.	.	.	.	.	.	A	7.690	0.690952	0.15039	.	.	ENSG00000239605	ENST00000445927;ENST00000294947	T;T	0.32988	1.43;1.44	3.27	-2.91	0.05631	.	.	.	.	.	T	0.15219	0.0367	N	0.22421	0.69	0.09310	N	1	B	0.16396	0.017	B	0.14023	0.01	T	0.27806	-1.0063	9	0.59425	D	0.04	-0.0687	0.6125	0.00764	0.3325:0.172:0.1132:0.3822	.	13	Q8N801	CB061_HUMAN	T	13	ENSP00000408527:I13T;ENSP00000294947:I13T	ENSP00000294947:I13T	I	-	2	0	C2orf61	47235857	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.157000	0.16402	-0.545000	0.06224	-0.527000	0.04329	ATA	.		0.632	C2orf61-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_173649	
ZNF2	7549	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	95847510	95847510	+	Missense_Mutation	SNP	C	C	G			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr2:95847510C>G	ENST00000340539.5	+	5	1399	c.937C>G	c.(937-939)Cct>Gct	p.P313A	ZNF2_ENST00000425369.1_Missense_Mutation_p.P233A|ZNF2_ENST00000398107.2_Missense_Mutation_p.P271A|ZNF2_ENST00000295210.6_Missense_Mutation_p.P275A|ZNF2_ENST00000453539.2_Missense_Mutation_p.P326A	NM_021088.2	NP_066574	Q9BSG1	ZNF2_HUMAN	zinc finger protein 2	313					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(4)|large_intestine(4)|lung(3)|upper_aerodigestive_tract(1)	12		Ovarian(717;0.00768)		READ - Rectum adenocarcinoma(193;0.0222)		TGGCAGGAAGCCTTATGAGTG	0.468																																					p.P313A		.											.	ZNF2-90	0			c.C937G						.						72.0	78.0	76.0					2																	95847510		2117	4248	6365	SO:0001583	missense	7549	exon5			AGGAAGCCTTATG	X60152	CCDS42712.1, CCDS42713.1, CCDS62957.1	2q11.1	2013-09-24	2005-02-07		ENSG00000163067	ENSG00000275111		"""Zinc fingers, C2H2-type"", ""-"""	12991	protein-coding gene	gene with protein product		194500	"""zinc finger protein 2 (A1-5)"""			8183940, 1945843	Standard	NM_021088		Approved	A1-5, ZNF661, Zfp661	uc002suf.3	Q9BSG1	OTTHUMG00000155150	ENST00000340539.5:c.937C>G	2.37:g.95847510C>G	ENSP00000345392:p.Pro313Ala	Somatic	168	0		WXS	Illumina HiSeq	Phase_I	153	53	NM_021088	0	0	0	0	0	A8MWV7|B4DIR4|Q4ZFY6|Q96G44|Q9UMC5	Missense_Mutation	SNP	ENST00000340539.5	37	CCDS42712.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.197452	0.79015	.	.	ENSG00000163067	ENST00000398107;ENST00000340539;ENST00000425369;ENST00000295210;ENST00000453539	T;T;T;T;T	0.16457	2.34;2.34;2.34;2.34;2.34	5.31	5.31	0.75309	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.49305	D	0.000154	T	0.43233	0.1238	M	0.77406	2.37	0.53688	D	0.999974	D;D;D	0.76494	0.986;0.999;0.962	P;D;P	0.66847	0.766;0.947;0.514	T	0.35051	-0.9804	10	0.87932	D	0	-19.4509	16.5178	0.84305	0.0:1.0:0.0:0.0	.	275;271;312	B4DIR4;A8MWV7;Q9BSG1	.;.;ZNF2_HUMAN	A	271;313;233;275;326	ENSP00000381178:P271A;ENSP00000345392:P313A;ENSP00000406017:P233A;ENSP00000295210:P275A;ENSP00000411051:P326A	ENSP00000295210:P275A	P	+	1	0	ZNF2	95211237	1.000000	0.71417	0.998000	0.56505	0.591000	0.36615	7.297000	0.78799	2.765000	0.95021	0.655000	0.94253	CCT	.		0.468	ZNF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338595.2	NM_021088	
PGAP1	80055	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	2	197750195	197750195	+	Missense_Mutation	SNP	G	G	T			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr2:197750195G>T	ENST00000354764.4	-	12	1339	c.1225C>A	c.(1225-1227)Caa>Aaa	p.Q409K	PGAP1_ENST00000409188.1_3'UTR|PGAP1_ENST00000409475.1_Missense_Mutation_p.Q409K	NM_024989.3	NP_079265.2	Q75T13	PGAP1_HUMAN	post-GPI attachment to proteins 1	409					anterior/posterior axis specification (GO:0009948)|attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|embryonic pattern specification (GO:0009880)|forebrain regionalization (GO:0021871)|head development (GO:0060322)|intracellular protein transport (GO:0006886)|myo-inositol transport (GO:0015798)|post-translational protein modification (GO:0043687)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	nuclease activity (GO:0004518)|phosphoric ester hydrolase activity (GO:0042578)			breast(4)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(11)|ovary(6)|stomach(1)|urinary_tract(1)	40						TCAACCCCTTGCAGGCTTTGA	0.284																																					p.Q409K		.											.	PGAP1-93	0			c.C1225A						.						52.0	59.0	57.0					2																	197750195		2191	4286	6477	SO:0001583	missense	80055	exon12			CCCCTTGCAGGCT		CCDS2318.1	2q33.1	2014-03-03			ENSG00000197121	ENSG00000197121			25712	protein-coding gene	gene with protein product	"""GPI inositol-deacylase"""	611655				14734546, 17711852, 24482476	Standard	XM_005246866		Approved	FLJ12377, Bst1, SPG67	uc002utw.3	Q75T13	OTTHUMG00000132743	ENST00000354764.4:c.1225C>A	2.37:g.197750195G>T	ENSP00000346809:p.Gln409Lys	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	71	5	NM_024989	0	0	0	0	0	Q4G0R8|Q4ZG47|Q53SM0|Q6AW92|Q6UWV4|Q9HA24	Missense_Mutation	SNP	ENST00000354764.4	37	CCDS2318.1	.	.	.	.	.	.	.	.	.	.	G	14.07	2.425404	0.43020	.	.	ENSG00000197121	ENST00000422382;ENST00000354764;ENST00000409475	.	.	.	5.26	5.26	0.73747	.	0.261976	0.38778	N	0.001561	T	0.56630	0.1998	N	0.24115	0.695	0.80722	D	1	B;P	0.49447	0.228;0.924	B;P	0.62298	0.083;0.9	T	0.46373	-0.9196	9	0.06891	T	0.86	-10.914	14.225	0.65853	0.0:0.0:1.0:0.0	.	409;409	Q75T13-3;Q75T13	.;PGAP1_HUMAN	K	189;409;409	.	ENSP00000346809:Q409K	Q	-	1	0	PGAP1	197458440	0.997000	0.39634	0.967000	0.41034	0.825000	0.46686	3.380000	0.52448	2.732000	0.93576	0.591000	0.81541	CAA	.		0.284	PGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256103.5	NM_024989	
EEF1B2	1933	broad.mit.edu	37	2	207025358	207025358	+	Missense_Mutation	SNP	A	A	G			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr2:207025358A>G	ENST00000392222.2	+	2	502	c.127A>G	c.(127-129)Agc>Ggc	p.S43G	EEF1B2_ENST00000392221.1_Missense_Mutation_p.S43G|NDUFS1_ENST00000440274.1_5'Flank|NDUFS1_ENST00000423725.1_5'Flank|NDUFS1_ENST00000449699.1_5'Flank|SNORA41_ENST00000384675.1_RNA|SNORD51_ENST00000384320.2_RNA|EEF1B2_ENST00000236957.5_Missense_Mutation_p.S43G|NDUFS1_ENST00000455934.2_5'Flank|NDUFS1_ENST00000457011.1_5'Flank|NDUFS1_ENST00000233190.6_5'Flank|NDUFS1_ENST00000432169.1_5'Flank	NM_001959.3	NP_001950.1	P24534	EF1B_HUMAN	eukaryotic translation elongation factor 1 beta 2	43	GST C-terminal.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|translation (GO:0006412)|translational elongation (GO:0006414)	cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)	translation elongation factor activity (GO:0003746)	p.S43G(4)		breast(1)|endometrium(5)|kidney(3)|large_intestine(1)|lung(6)	16						AGCCGTGTCCAGCCCACCGCC	0.468																																					p.S43G													.	EEF1B2-227	4	Substitution - Missense(4)	endometrium(2)|lung(1)|kidney(1)	c.A127G						.						109.0	99.0	102.0					2																	207025358		2203	4300	6503	SO:0001583	missense	1933	exon3			GTGTCCAGCCCAC	X60489	CCDS2367.1	2q33.3	2011-04-28			ENSG00000114942	ENSG00000114942			3208	protein-coding gene	gene with protein product		600655				8250921	Standard	NM_001959		Approved		uc002vbf.1	P24534	OTTHUMG00000132891	ENST00000392222.2:c.127A>G	2.37:g.207025358A>G	ENSP00000376056:p.Ser43Gly	Somatic	209	1		WXS	Illumina HiSeq	Phase_I	195	5	NM_021121	0	0	103	103	0	A8K795|Q6IBH9	Missense_Mutation	SNP	ENST00000392222.2	37	CCDS2367.1	.	.	.	.	.	.	.	.	.	.	A	0.014	-1.585588	0.00872	.	.	ENSG00000114942	ENST00000236957;ENST00000392221;ENST00000392222;ENST00000445505	T;T;T;T	0.44482	0.92;0.92;0.92;0.92	5.47	0.911	0.19343	Glutathione S-transferase, C-terminal-like (2);	0.442134	0.26800	N	0.022437	T	0.19846	0.0477	N	0.16098	0.37	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.18745	-1.0327	10	0.17832	T	0.49	-2.1703	6.3337	0.21285	0.2348:0.0:0.6384:0.1268	.	43	P24534	EF1B_HUMAN	G	43	ENSP00000236957:S43G;ENSP00000376055:S43G;ENSP00000376056:S43G;ENSP00000407730:S43G	ENSP00000236957:S43G	S	+	1	0	EEF1B2	206733603	0.049000	0.20398	0.145000	0.22337	0.051000	0.14879	0.879000	0.28146	-0.027000	0.13873	-0.252000	0.11476	AGC	.		0.468	EEF1B2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336436.1	NM_001037663	
STK11IP	114790	broad.mit.edu;bcgsc.ca	37	2	220465972	220465972	+	Missense_Mutation	SNP	C	C	T	rs564151932		TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr2:220465972C>T	ENST00000456909.1	+	3	167	c.77C>T	c.(76-78)tCt>tTt	p.S26F	STK11IP_ENST00000459692.1_3'UTR|STK11IP_ENST00000295641.10_Missense_Mutation_p.S37F			Q8N1F8	S11IP_HUMAN	serine/threonine kinase 11 interacting protein	37					protein localization (GO:0008104)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)	protein kinase binding (GO:0019901)			breast(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|urinary_tract(1)	23		Renal(207;0.0183)		Epithelial(149;2.69e-07)|all cancers(144;5.91e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GTGGTCCTGTCTGGCTGTAGC	0.517																																					p.S37F													.	STK11IP-91	0			c.C110T						.						55.0	58.0	57.0					2																	220465972		2166	4274	6440	SO:0001583	missense	114790	exon3			TCCTGTCTGGCTG	AF450267	CCDS46521.1	2q35	2008-06-03			ENSG00000144589	ENSG00000144589			19184	protein-coding gene	gene with protein product	"""LKB1 interacting protein"""	607172				11741830	Standard	NM_052902		Approved	LIP1, KIAA1898, LKB1IP, STK11IP1	uc002vml.3	Q8N1F8	OTTHUMG00000059239	ENST00000456909.1:c.77C>T	2.37:g.220465972C>T	ENSP00000389383:p.Ser26Phe	Somatic	124	1		WXS	Illumina HiSeq	Phase_I	108	7	NM_052902	0	0	0	0	0	Q8NAW9|Q8WXE4|Q96CN3|Q96PY9	Missense_Mutation	SNP	ENST00000456909.1	37		.	.	.	.	.	.	.	.	.	.	C	18.45	3.626530	0.66901	.	.	ENSG00000144589	ENST00000456909;ENST00000426736;ENST00000295641	T;T	0.05996	3.36;3.36	4.93	4.93	0.64822	.	0.137054	0.45606	D	0.000355	T	0.19248	0.0462	M	0.62723	1.935	0.44000	D	0.996702	D;D;D;D;D	0.76494	0.999;0.996;0.999;0.999;0.999	D;P;D;D;D	0.71656	0.961;0.804;0.961;0.974;0.965	T	0.00057	-1.2174	10	0.49607	T	0.09	-16.0901	11.0821	0.48066	0.3078:0.6922:0.0:0.0	.	37;37;26;37;37	B4DUE4;B4DII2;E7ERV2;Q8N1F8-2;Q8N1F8	.;.;.;.;S11IP_HUMAN	F	26;37;37	ENSP00000389383:S26F;ENSP00000295641:S37F	ENSP00000295641:S37F	S	+	2	0	STK11IP	220174216	1.000000	0.71417	1.000000	0.80357	0.816000	0.46133	4.825000	0.62708	2.568000	0.86640	0.650000	0.86243	TCT	.		0.517	STK11IP-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000131432.1	NM_052902	
FRG1B	284802	bcgsc.ca	37	20	29623219	29623219	+	Missense_Mutation	SNP	A	A	G			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr20:29623219A>G	ENST00000278882.3	+	3	411	c.31A>G	c.(31-33)Atg>Gtg	p.M11V	FRG1B_ENST00000439954.2_Missense_Mutation_p.N12S|FRG1B_ENST00000358464.4_Missense_Mutation_p.M11V			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	11										endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						GCACTCGACAATGGTCTTTTT	0.413																																					.													.	FRG1B-22	0			.						.																																			SO:0001583	missense	284802	.			TCGACAATGGTCT			20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531			15792	other	unknown			"""chromosome 20 open reading frame 80"""	C20orf80			Standard	NR_003579		Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.31A>G	20.37:g.29623219A>G	ENSP00000278882:p.Met11Val	Somatic	812	13		WXS	Illumina HiSeq	Phase_1	917	54	.	0	0	25	25	0	C4AME5	RNA	SNP	ENST00000278882.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	a|a	0.925|0.925	-0.714671|-0.714671	0.03206|0.03206	.|.	.|.	ENSG00000149531|ENSG00000149531	ENST00000278882;ENST00000358464|ENST00000439954	.|T	.|0.53206	.|0.63	1.93|1.93	1.93|1.93	0.25924|0.25924	.|.	0.114289|.	0.56097|.	U|.	0.000024|.	T|T	0.42040|0.42040	0.1185|0.1185	.|.	.|.	.|.	0.18873|0.18873	N|N	0.999983|0.999983	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.36648|0.36648	-0.9739|-0.9739	6|6	0.66056|0.54805	D|T	0.02|0.06	.|.	4.9441|4.9441	0.13980|0.13980	0.6812:0.3188:0.0:0.0|0.6812:0.3188:0.0:0.0	.|.	.|.	.|.	.|.	V|S	11|12	.|ENSP00000408863:N12S	ENSP00000278882:M11V|ENSP00000408863:N12S	M|N	+|+	1|2	0|0	FRG1B|FRG1B	28236880|28236880	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.107000|0.107000	0.19398|0.19398	3.154000|3.154000	0.50693|0.50693	1.147000|1.147000	0.42369|0.42369	0.347000|0.347000	0.21830|0.21830	ATG|AAT	.		0.413	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078494.2	NR_003579	
PCK1	5105	broad.mit.edu	37	20	56140434	56140434	+	Silent	SNP	C	C	T			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr20:56140434C>T	ENST00000319441.4	+	10	1607	c.1443C>T	c.(1441-1443)gcC>gcT	p.A481A	PCK1_ENST00000543666.1_Silent_p.A164A|PCK1_ENST00000535860.1_3'UTR	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	481					carbohydrate metabolic process (GO:0005975)|drug metabolic process (GO:0017144)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process from pyruvate (GO:0046327)|internal protein amino acid acetylation (GO:0006475)|oxaloacetate metabolic process (GO:0006107)|response to activity (GO:0014823)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxylic acid binding (GO:0031406)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)			endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(19)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	34	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			ACCCCTTTGCCATGCGGCCCT	0.507																																					p.A481A													.	PCK1-227	0			c.C1443T						.						94.0	93.0	93.0					20																	56140434		2203	4300	6503	SO:0001819	synonymous_variant	5105	exon10			CTTTGCCATGCGG		CCDS13460.1	20q13.31	2007-11-06			ENSG00000124253	ENSG00000124253	4.1.1.32		8724	protein-coding gene	gene with protein product		614168				1492743	Standard	NM_002591		Approved	PEPCK-C	uc002xyn.4	P35558	OTTHUMG00000032825	ENST00000319441.4:c.1443C>T	20.37:g.56140434C>T		Somatic	75	0		WXS	Illumina HiSeq	Phase_I	100	5	NM_002591	0	0	24	24	0	A8K437|B4DT64|Q8TCA3|Q9UJD2	Silent	SNP	ENST00000319441.4	37	CCDS13460.1																																																																																			.		0.507	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2		
PFKFB4	5210	broad.mit.edu	37	3	48576038	48576038	+	Silent	SNP	G	G	T			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr3:48576038G>T	ENST00000232375.3	-	7	637	c.525C>A	c.(523-525)ggC>ggA	p.G175G	PFKFB4_ENST00000383734.2_Silent_p.G175G|PFKFB4_ENST00000490115.1_5'UTR|PFKFB4_ENST00000416568.1_Silent_p.G175G|PFKFB4_ENST00000545984.1_3'UTR|PFKFB4_ENST00000536104.1_Silent_p.G164G|PFKFB4_ENST00000541519.1_Silent_p.G141G	NM_004567.2	NP_004558.1	Q16877	F264_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4	175	6-phosphofructo-2-kinase.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|fructose metabolic process (GO:0006000)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	6-phosphofructo-2-kinase activity (GO:0003873)|ATP binding (GO:0005524)|fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)			breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|urinary_tract(1)	14				BRCA - Breast invasive adenocarcinoma(193;0.0003)|KIRC - Kidney renal clear cell carcinoma(197;0.00596)|Kidney(197;0.00684)		AGTCAGGGCTGCCCAGTTTCA	0.592																																					p.G175G													.	PFKFB4-153	0			c.C525A						.						61.0	53.0	55.0					3																	48576038		2203	4300	6503	SO:0001819	synonymous_variant	5210	exon7			AGGGCTGCCCAGT	BC010269	CCDS2771.1	3p22-p21	2004-03-02			ENSG00000114268	ENSG00000114268			8875	protein-coding gene	gene with protein product		605320				8830046, 10095107	Standard	NM_004567		Approved		uc003ctv.3	Q16877	OTTHUMG00000133528	ENST00000232375.3:c.525C>A	3.37:g.48576038G>T		Somatic	136	1		WXS	Illumina HiSeq	Phase_I	105	6	NM_004567	0	0	1	1	0	Q5S3G5|Q5XLC2|Q64EX5	Silent	SNP	ENST00000232375.3	37	CCDS2771.1																																																																																			.		0.592	PFKFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257503.2	NM_004567	
RRP9	9136	broad.mit.edu	37	3	51968675	51968675	+	Silent	SNP	G	G	A			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr3:51968675G>A	ENST00000232888.6	-	12	1225	c.1152C>T	c.(1150-1152)gcC>gcT	p.A384A		NM_004704.3	NP_004695.1	O43818	U3IP2_HUMAN	ribosomal RNA processing 9, small subunit (SSU) processome component, homolog (yeast)	384					rRNA processing (GO:0006364)	nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(1)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|ovary(1)|skin(1)	21				BRCA - Breast invasive adenocarcinoma(193;8.04e-05)|Kidney(197;0.000553)|KIRC - Kidney renal clear cell carcinoma(197;0.000724)		TGTTGAGGAGGGCTGCCACCG	0.662																																					p.A384A													.	RRP9-154	0			c.C1152T						.						50.0	53.0	52.0					3																	51968675		2203	4300	6503	SO:0001819	synonymous_variant	9136	exon12			GAGGAGGGCTGCC	AJ001340	CCDS2837.1	3p21.31	2013-01-10	2008-02-26	2006-10-24	ENSG00000114767	ENSG00000114767		"""WD repeat domain containing"""	16829	protein-coding gene	gene with protein product			"""RNA, U3 small nucleolar interacting protein 2"""	RNU3IP2		9418896, 12032086	Standard	NM_004704		Approved	U3-55K	uc003dbw.2	O43818	OTTHUMG00000156930	ENST00000232888.6:c.1152C>T	3.37:g.51968675G>A		Somatic	172	0		WXS	Illumina HiSeq	Phase_I	110	3	NM_004704	0	0	30	30	0	B2R996|Q8IZ30	Silent	SNP	ENST00000232888.6	37	CCDS2837.1																																																																																			.		0.662	RRP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346637.1	NM_004704	
MFSD1	64747	broad.mit.edu	37	3	158539426	158539426	+	Missense_Mutation	SNP	G	G	T			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr3:158539426G>T	ENST00000264266.8	+	10	966	c.904G>T	c.(904-906)Gca>Tca	p.A302S	MFSD1_ENST00000415822.2_Missense_Mutation_p.A351S|MFSD1_ENST00000392813.4_Missense_Mutation_p.A312S			Q9H3U5	MFSD1_HUMAN	major facilitator superfamily domain containing 1	302					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(15)|skin(1)	26			Lung(72;0.00372)|LUSC - Lung squamous cell carcinoma(72;0.00523)			TTCCCAGGCAGCAAGTGCAAT	0.289																																					p.A351S	Pancreas(62;1186 1654 36636 37908)												.	MFSD1-90	0			c.G1051T						.						56.0	62.0	60.0					3																	158539426		2189	4298	6487	SO:0001583	missense	64747	exon10			CAGGCAGCAAGTG	BC017661	CCDS3185.1, CCDS3185.2, CCDS54666.1	3q25.32	2005-11-17			ENSG00000118855	ENSG00000118855			25874	protein-coding gene	gene with protein product							Standard	NM_022736		Approved	FLJ14153, UG0581B09	uc003fcl.2	Q9H3U5	OTTHUMG00000158835	ENST00000264266.8:c.904G>T	3.37:g.158539426G>T	ENSP00000264266:p.Ala302Ser	Somatic	68	1		WXS	Illumina HiSeq	Phase_I	102	4	NM_022736	0	0	1	1	0	B4DGJ8|B4DMR8|B4DU49|B4DWU1|C9JS94|J3KQL7|Q05C07|Q5XKJ1|Q8IVS1|Q8IXG4|Q9H7X1	Missense_Mutation	SNP	ENST00000264266.8	37		.	.	.	.	.	.	.	.	.	.	G	26.8	4.776906	0.90195	.	.	ENSG00000118855	ENST00000415822;ENST00000392813;ENST00000264266;ENST00000361159	T;D;T	0.82433	0.06;-1.61;0.06	5.46	5.46	0.80206	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.217978	0.47093	D	0.000256	D	0.88514	0.6457	M	0.74258	2.255	0.80722	D	1	P;P	0.50272	0.933;0.809	P;P	0.53102	0.718;0.512	D	0.88012	0.2763	10	0.42905	T	0.14	.	18.9102	0.92481	0.0:0.0:1.0:0.0	.	312;302	C9JS94;Q9H3U5	.;MFSD1_HUMAN	S	351;312;302;226	ENSP00000403117:A351S;ENSP00000376560:A312S;ENSP00000264266:A302S	ENSP00000264266:A302S	A	+	1	0	MFSD1	160022120	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.593000	0.67550	2.549000	0.85964	0.655000	0.94253	GCA	.		0.289	MFSD1-018	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470730.1	NM_022736	
TPRG1	285386	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	188925189	188925189	+	Missense_Mutation	SNP	A	A	G			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr3:188925189A>G	ENST00000345063.3	+	2	183	c.16A>G	c.(16-18)Agt>Ggt	p.S6G	TPRG1_ENST00000433971.1_Missense_Mutation_p.S6G	NM_198485.3	NP_940887.1	Q6ZUI0	TPRG1_HUMAN	tumor protein p63 regulated 1	6						cytoplasm (GO:0005737)				endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|skin(2)|urinary_tract(1)	16	all_cancers(143;6.12e-12)|all_hematologic(3;0.0359)|Ovarian(172;0.0925)	all_lung(153;8.23e-09)|Lung NSC(153;3.55e-06)|all_neural(597;0.0019)|Myeloproliferative disorder(1037;0.0255)	Lung(62;6.93e-06)	GBM - Glioblastoma multiforme(93;4.77e-14)		AACAATTGGGAGTTTTGAAGG	0.458																																					p.S6G		.											.	TPRG1-90	0			c.A16G						.						97.0	95.0	96.0					3																	188925189		2203	4300	6503	SO:0001583	missense	285386	exon2			ATTGGGAGTTTTG	AK125682	CCDS3292.1	3q28	2008-02-04	2008-01-16	2008-01-16	ENSG00000188001	ENSG00000188001			24759	protein-coding gene	gene with protein product			"""family with sequence similarity 79, member B"""	FAM79B			Standard	NM_198485		Approved	FLJ41238, FLJ43694	uc003frw.2	Q6ZUI0	OTTHUMG00000156321	ENST00000345063.3:c.16A>G	3.37:g.188925189A>G	ENSP00000341031:p.Ser6Gly	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	149	23	NM_198485	0	0	0	0	0		Missense_Mutation	SNP	ENST00000345063.3	37	CCDS3292.1	.	.	.	.	.	.	.	.	.	.	A	14.92	2.678779	0.47886	.	.	ENSG00000188001	ENST00000433971;ENST00000412373;ENST00000345063;ENST00000456832	.	.	.	5.83	5.83	0.93111	.	0.488214	0.25631	N	0.029360	T	0.39410	0.1077	L	0.34521	1.04	0.31374	N	0.679799	B	0.26363	0.147	B	0.29077	0.098	T	0.48681	-0.9014	9	0.45353	T	0.12	-5.1687	12.5927	0.56451	1.0:0.0:0.0:0.0	.	6	Q6ZUI0	TPRG1_HUMAN	G	6	.	ENSP00000341031:S6G	S	+	1	0	TPRG1	190407883	1.000000	0.71417	0.982000	0.44146	0.737000	0.42083	2.764000	0.47613	2.235000	0.73313	0.533000	0.62120	AGT	.		0.458	TPRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343931.1	NM_198485	
MUC4	4585	broad.mit.edu;bcgsc.ca	37	3	195490958	195490958	+	Missense_Mutation	SNP	G	G	A			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr3:195490958G>A	ENST00000346145.4	-	10	1333	c.1294C>T	c.(1294-1296)Cgg>Tgg	p.R432W	MUC4_ENST00000349607.4_Missense_Mutation_p.R381W|MUC4_ENST00000475231.1_Missense_Mutation_p.R4616W|MUC4_ENST00000463781.3_Missense_Mutation_p.R4668W	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	1425					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACGTGGGGCCGCCTCTGCTGG	0.662																																					p.R4668W													.	MUC4-90	0			c.C14002T						.						18.0	16.0	16.0					3																	195490958		2200	4299	6499	SO:0001583	missense	4585	exon11			GGGGCCGCCTCTG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000346145.4:c.1294C>T	3.37:g.195490958G>A	ENSP00000304207:p.Arg432Trp	Somatic	330	0		WXS	Illumina HiSeq	Phase_I	210	10	NM_018406	0	0	0	0	0	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000346145.4	37	CCDS3310.1	.	.	.	.	.	.	.	.	.	.	.	9.013	0.982982	0.18889	.	.	ENSG00000145113	ENST00000349607;ENST00000346145;ENST00000463781;ENST00000475231	T;T;T;T	0.78126	-1.15;-0.44;-0.46;-0.33	5.25	-4.79	0.03200	AMOP (2);	0.750787	0.11391	N	0.568766	T	0.73814	0.3635	M	0.76002	2.32	0.25565	N	0.986958	P;P;P;P;B;B;D	0.53619	0.469;0.922;0.779;0.91;0.027;0.027;0.961	B;P;B;B;B;B;P	0.49451	0.107;0.611;0.199;0.303;0.019;0.019;0.466	T	0.65553	-0.6140	10	0.87932	D	0	-4.1234	1.1024	0.01687	0.3996:0.1018:0.1745:0.324	.	4540;1425;381;432;4668;4616;1373	E7ESK3;Q99102;Q99102-12;Q99102-13;E9PDY6;E7ENC5;Q99102-10	.;MUC4_HUMAN;.;.;.;.;.	W	381;432;4668;4616	ENSP00000338109:R381W;ENSP00000304207:R432W;ENSP00000417498:R4668W;ENSP00000420243:R4616W	ENSP00000304207:R432W	R	-	1	2	MUC4	196976629	0.021000	0.18746	0.104000	0.21259	0.021000	0.10359	-0.327000	0.07955	-0.553000	0.06158	-0.187000	0.12897	CGG	.		0.662	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341862.1	NM_018406	
UBA6	55236	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	4	68534339	68534339	+	Silent	SNP	T	T	C			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr4:68534339T>C	ENST00000322244.5	-	9	782	c.723A>G	c.(721-723)acA>acG	p.T241T	UBA6_ENST00000420827.2_Silent_p.T241T	NM_018227.5	NP_060697.4	A0AVT1	UBA6_HUMAN	ubiquitin-like modifier activating enzyme 6	241					protein ubiquitination (GO:0016567)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|FAT10 activating enzyme activity (GO:0019780)|ligase activity (GO:0016874)			central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(6)|liver(1)|lung(23)|skin(2)|upper_aerodigestive_tract(2)	44						GGAATTGTCCTGTCTCCAGTT	0.303																																					p.T241T		.											.	UBA6-90	0			c.A723G						.						123.0	120.0	121.0					4																	68534339		2203	4300	6503	SO:0001819	synonymous_variant	55236	exon9			TTGTCCTGTCTCC	AK094164	CCDS3516.1	4q13.2	2008-02-05	2007-11-30	2007-11-30	ENSG00000033178	ENSG00000033178		"""Ubiquitin-like modifier activating enzymes"""	25581	protein-coding gene	gene with protein product	"""UBA6, ubiquitin-activating enzyme E1"""	611361	"""ubiquitin-activating enzyme E1-like 2"""	UBE1L2		17580310	Standard	NM_018227		Approved	FLJ10808	uc003hdg.4	A0AVT1	OTTHUMG00000129299	ENST00000322244.5:c.723A>G	4.37:g.68534339T>C		Somatic	76	0		WXS	Illumina HiSeq	Phase_I	94	5	NM_018227	0	0	0	0	0	A6N8M7|B2RAV3|Q4W5K0|Q6UV21|Q86T78|Q86TC7|Q8N5T3|Q8N9E4|Q9H3T7|Q9NVC9	Silent	SNP	ENST00000322244.5	37	CCDS3516.1																																																																																			.		0.303	UBA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251429.2	NM_018227	
ASIC5	51802	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	4	156784757	156784757	+	Missense_Mutation	SNP	G	G	A			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr4:156784757G>A	ENST00000537611.2	-	2	236	c.190C>T	c.(190-192)Ctc>Ttc	p.L64F	TDO2_ENST00000506181.1_Intron	NM_017419.2	NP_059115.1	Q9NY37	ASIC5_HUMAN	acid-sensing (proton-gated) ion channel family member 5	64					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrogen ion channel activity (GO:0015252)|ligand-gated sodium channel activity (GO:0015280)										ACCAACCAGAGCACCCTGCGA	0.483																																					p.L64F		.											.	.	0			c.C190T						.						131.0	116.0	121.0					4																	156784757		2203	4300	6503	SO:0001583	missense	51802	exon2			ACCAGAGCACCCT	AJ252011	CCDS3793.1	4q32.1	2012-10-03	2012-03-02	2012-03-02	ENSG00000256394	ENSG00000256394			17537	protein-coding gene	gene with protein product			"""amiloride-sensitive cation channel 5, intestinal"""	ACCN5		10767424	Standard	NM_017419		Approved	INAC, HINAC	uc003ipe.1	Q9NY37	OTTHUMG00000161941	ENST00000537611.2:c.190C>T	4.37:g.156784757G>A	ENSP00000442477:p.Leu64Phe	Somatic	144	0		WXS	Illumina HiSeq	Phase_I	149	56	NM_017419	0	0	0	0	0		Missense_Mutation	SNP	ENST00000537611.2	37	CCDS3793.1	.	.	.	.	.	.	.	.	.	.	G	6.118	0.390031	0.11581	.	.	ENSG00000256394	ENST00000537611	T	0.65732	-0.17	4.24	1.65	0.23941	.	0.825563	0.10479	N	0.669867	T	0.38878	0.1057	N	0.11651	0.15	0.58432	D	0.999998	B	0.10296	0.003	B	0.17979	0.02	T	0.26744	-1.0094	10	0.02654	T	1	-0.483	12.6071	0.56529	0.0:0.0:0.5103:0.4896	.	64	Q9NY37	ACCN5_HUMAN	F	64	ENSP00000442477:L64F	ENSP00000264432:L64F	L	-	1	0	ACCN5	157004207	0.075000	0.21258	0.386000	0.26170	0.148000	0.21650	0.106000	0.15354	0.224000	0.20940	-0.271000	0.10264	CTC	.		0.483	ASIC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366464.1		
C6orf15	29113	broad.mit.edu	37	6	31079878	31079878	+	Silent	SNP	G	G	T			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr6:31079878G>T	ENST00000259870.3	-	2	261	c.258C>A	c.(256-258)ggC>ggA	p.G86G	PSORS1C1_ENST00000259881.9_5'Flank	NM_014070.2	NP_054789.2	Q6UXA7	CF015_HUMAN	chromosome 6 open reading frame 15	86					extracellular matrix organization (GO:0030198)	interstitial matrix (GO:0005614)	heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			endometrium(3)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|stomach(1)	17						CAGGTGGGAAGCCATCTGATG	0.607																																					p.G86G													.	C6orf15-90	0			c.C258A						.						52.0	56.0	55.0					6																	31079878		2203	4300	6503	SO:0001819	synonymous_variant	29113	exon2			TGGGAAGCCATCT	AB031481	CCDS4693.1	6p21	2011-12-12			ENSG00000204542	ENSG00000204542			13927	protein-coding gene	gene with protein product		611401					Standard	NM_014070		Approved	STG	uc003nsk.1	Q6UXA7	OTTHUMG00000031111	ENST00000259870.3:c.258C>A	6.37:g.31079878G>T		Somatic	156	1		WXS	Illumina HiSeq	Phase_I	117	7	NM_014070	0	0	0	0	0	B0S7V8|Q0EFA6|Q2L6G7|Q5SQ81|Q86Z05|Q9UIG3	Silent	SNP	ENST00000259870.3	37	CCDS4693.1																																																																																			.		0.607	C6orf15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076184.2	NM_014070	
SYNGAP1	8831	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	33400480	33400480	+	Missense_Mutation	SNP	C	C	T			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr6:33400480C>T	ENST00000418600.2	+	5	507	c.406C>T	c.(406-408)Cgg>Tgg	p.R136W	SYNGAP1_ENST00000293748.5_Missense_Mutation_p.R136W|SYNGAP1_ENST00000496374.1_3'UTR|SYNGAP1_ENST00000428982.2_Missense_Mutation_p.R77W	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	136					dendrite development (GO:0016358)|negative regulation of axonogenesis (GO:0050771)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|pattern specification process (GO:0007389)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|receptor clustering (GO:0043113)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of MAPK cascade (GO:0043408)|regulation of synapse structure and activity (GO:0050803)|regulation of synaptic plasticity (GO:0048167)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Rab GTPase activator activity (GO:0005097)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(15)|ovary(7)|pancreas(1)|stomach(1)|urinary_tract(1)	43						CCTGAGCCGACGGCTAAAAAG	0.577																																					p.R136W		.											.	SYNGAP1-48	0			c.C406T						.						56.0	49.0	51.0					6																	33400480		2203	4300	6503	SO:0001583	missense	8831	exon5			AGCCGACGGCTAA	AB067525	CCDS34434.2	6p21.3	2010-06-25	2010-06-25		ENSG00000197283	ENSG00000197283			11497	protein-coding gene	gene with protein product		603384	"""synaptic Ras GTPase activating protein 1 homolog (rat)"""			9581761, 18323856	Standard	NM_006772		Approved	SYNGAP, RASA5, KIAA1938	uc011dri.2	Q96PV0	OTTHUMG00000031096	ENST00000418600.2:c.406C>T	6.37:g.33400480C>T	ENSP00000403636:p.Arg136Trp	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	54	16	NM_006772	0	0	2	2	0	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Missense_Mutation	SNP	ENST00000418600.2	37	CCDS34434.2	.	.	.	.	.	.	.	.	.	.	C	15.30	2.792591	0.50102	.	.	ENSG00000197283	ENST00000293748;ENST00000418600;ENST00000449372;ENST00000428982	T;T;T	0.28666	1.6;1.71;1.77	4.06	-1.15	0.09709	Pleckstrin homology domain (1);	0.000000	0.85682	D	0.000000	T	0.34048	0.0884	M	0.69358	2.11	0.58432	D	0.999996	D;D;D	0.71674	0.965;0.98;0.998	B;P;P	0.62382	0.416;0.621;0.901	T	0.43065	-0.9414	10	0.87932	D	0	.	11.9927	0.53184	0.6778:0.3221:0.0:0.0	.	136;136;136	Q96PV0;Q96PV0-4;B7ZCA0	SYGP1_HUMAN;.;.	W	136;136;136;77	ENSP00000293748:R136W;ENSP00000403636:R136W;ENSP00000412475:R77W	ENSP00000293748:R136W	R	+	1	2	SYNGAP1	33508458	0.994000	0.37717	0.996000	0.52242	0.938000	0.57974	1.265000	0.33027	0.002000	0.14630	0.467000	0.42956	CGG	.		0.577	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407	
RRP36	88745	broad.mit.edu	37	6	42994982	42994982	+	Nonsense_Mutation	SNP	C	C	T			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr6:42994982C>T	ENST00000244496.5	+	5	527	c.517C>T	c.(517-519)Cag>Tag	p.Q173*		NM_033112.2	NP_149103.1	Q96EU6	RRP36_HUMAN	ribosomal RNA processing 36 homolog (S. cerevisiae)	173					ribosomal small subunit biogenesis (GO:0042274)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|central_nervous_system(1)|large_intestine(5)|lung(1)|ovary(1)|prostate(1)	11						GCAACTGCTTCAGCGAATGGT	0.438																																					p.Q173X													.	RRP36-90	0			c.C517T						.						132.0	122.0	125.0					6																	42994982		2203	4300	6503	SO:0001587	stop_gained	88745	exon5			CTGCTTCAGCGAA	BC011933	CCDS34453.1	6p21.1	2010-07-06	2010-07-06	2010-07-06	ENSG00000124541	ENSG00000124541			21374	protein-coding gene	gene with protein product		613475	"""chromosome 6 open reading frame 153"""	C6orf153		20038530	Standard	NM_033112		Approved	dJ20C7.4	uc003otp.1	Q96EU6	OTTHUMG00000014715	ENST00000244496.5:c.517C>T	6.37:g.42994982C>T	ENSP00000244496:p.Gln173*	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	73	4	NM_033112	0	0	0	0	0	Q9BRF6|Q9P0C8	Nonsense_Mutation	SNP	ENST00000244496.5	37	CCDS34453.1	.	.	.	.	.	.	.	.	.	.	C	12.77	2.038361	0.35989	.	.	ENSG00000124541	ENST00000244496	.	.	.	5.81	4.89	0.63831	.	0.276138	0.29040	N	0.013327	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10111	T	0.7	.	11.6759	0.51430	0.2645:0.7355:0.0:0.0	.	.	.	.	X	173	.	ENSP00000244496:Q173X	Q	+	1	0	RRP36	43102960	0.922000	0.31269	1.000000	0.80357	0.087000	0.18053	1.686000	0.37669	2.741000	0.93983	0.650000	0.86243	CAG	.		0.438	RRP36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040572.1	NM_033112	
HMGN3	9324	broad.mit.edu	37	6	79918284	79918284	+	Silent	SNP	G	G	T			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr6:79918284G>T	ENST00000344726.5	-	3	204	c.76C>A	c.(76-78)Cgg>Agg	p.R26R	HMGN3_ENST00000275036.7_Silent_p.R26R	NM_001201362.1|NM_001201363.1|NM_004242.3	NP_001188291.1|NP_001188292.1|NP_004233.1	Q15651	HMGN3_HUMAN	high mobility group nucleosomal binding domain 3	26					chromatin modification (GO:0016568)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|thyroid hormone receptor binding (GO:0046966)			central_nervous_system(1)|kidney(2)|lung(1)	4		all_cancers(76;0.000116)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.0393)		BRCA - Breast invasive adenocarcinoma(397;0.125)		CTGGCAGACCGTCTTGTGGGC	0.353																																					p.R26R													.	HMGN3-226	0			c.C76A						.						159.0	160.0	160.0					6																	79918284		2203	4300	6503	SO:0001819	synonymous_variant	9324	exon3			CAGACCGTCTTGT	L40357	CCDS4988.1, CCDS4989.1, CCDS75485.1	6q14.3	2011-07-01	2002-07-25	2002-07-26	ENSG00000118418	ENSG00000118418		"""High-mobility group / Canonical"""	12312	protein-coding gene	gene with protein product		604502	"""thyroid hormone receptor interactor 7"""	TRIP7		7776974, 11356838	Standard	NM_004242		Approved		uc021zbz.1	Q15651	OTTHUMG00000015073	ENST00000344726.5:c.76C>A	6.37:g.79918284G>T		Somatic	206	1		WXS	Illumina HiSeq	Phase_I	211	5	NM_001201362	0	0	2	2	0	B2RD37|Q5HYD3|Q7RTT0|Q969M5|Q9BZT7	Silent	SNP	ENST00000344726.5	37	CCDS4988.1																																																																																			.		0.353	HMGN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041300.1	NM_004242	
LPA	4018	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	161026202	161026202	+	Missense_Mutation	SNP	A	A	G			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr6:161026202A>G	ENST00000316300.5	-	18	2865	c.2821T>C	c.(2821-2823)Tac>Cac	p.Y941H	LPA_ENST00000447678.1_Missense_Mutation_p.Y941H			P08519	APOA_HUMAN	lipoprotein, Lp(a)	3449	Kringle 9. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood circulation (GO:0008015)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|negative regulation of endopeptidase activity (GO:0010951)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|plasma lipoprotein particle (GO:0034358)	apolipoprotein binding (GO:0034185)|endopeptidase inhibitor activity (GO:0004866)|fibronectin binding (GO:0001968)|heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|lung(54)|ovary(4)|pancreas(1)|prostate(2)|skin(10)|stomach(1)|urinary_tract(1)	107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	TTTCCGTGGTAGCACTCCTGC	0.458																																					p.Y941H		.											.	LPA-74	0			c.T2821C						.						269.0	278.0	275.0					6																	161026202		2200	4298	6498	SO:0001583	missense	4018	exon19			CGTGGTAGCACTC	X06290	CCDS43523.1	6q25-q26	2012-10-02			ENSG00000198670	ENSG00000198670			6667	protein-coding gene	gene with protein product		152200		LP		3670400	Standard	NM_005577		Approved		uc003qtl.3	P08519	OTTHUMG00000015956	ENST00000316300.5:c.2821T>C	6.37:g.161026202A>G	ENSP00000321334:p.Tyr941His	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	55	32	NM_005577	0	0	0	0	0	Q5VTD7|Q9UD88	Missense_Mutation	SNP	ENST00000316300.5	37	CCDS43523.1	.	.	.	.	.	.	.	.	.	.	a	10.16	1.275243	0.23307	.	.	ENSG00000198670	ENST00000316300;ENST00000447678	T;T	0.65364	-0.15;-0.15	2.16	2.16	0.27623	Kringle (4);Kringle-like fold (1);	.	.	.	.	T	0.72087	0.3417	H	0.95816	3.725	0.21782	N	0.999546	D	0.60160	0.987	D	0.70227	0.968	T	0.61004	-0.7150	9	0.26408	T	0.33	.	6.2159	0.20656	1.0:0.0:0.0:0.0	.	3449	P08519	APOA_HUMAN	H	941	ENSP00000321334:Y941H;ENSP00000395608:Y941H	ENSP00000321334:Y941H	Y	-	1	0	LPA	160946192	0.988000	0.35896	0.913000	0.36048	0.097000	0.18754	2.967000	0.49216	0.999000	0.39023	0.155000	0.16302	TAC	.		0.458	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577	
TAX1BP1	8887	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	27856559	27856559	+	Nonsense_Mutation	SNP	A	A	T			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr7:27856559A>T	ENST00000396319.2	+	15	2075	c.1987A>T	c.(1987-1989)Aga>Tga	p.R663*	TAX1BP1_ENST00000409980.1_Nonsense_Mutation_p.R687*|TAX1BP1_ENST00000433216.2_Nonsense_Mutation_p.R464*|TAX1BP1_ENST00000265393.6_Nonsense_Mutation_p.R621*|TAX1BP1_ENST00000543117.1_Nonsense_Mutation_p.R621*	NM_006024.6	NP_006015.4	Q86VP1	TAXB1_HUMAN	Tax1 (human T-cell leukemia virus type I) binding protein 1	663					apoptotic process (GO:0006915)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)	cytosol (GO:0005829)	kinase binding (GO:0019900)			breast(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(8)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31			GBM - Glioblastoma multiforme(3;0.0823)			GCCACCTGTCAGAGTCCCCTC	0.453																																					p.R663X		.											.	TAX1BP1-153	0			c.A1987T						.						63.0	65.0	65.0					7																	27856559		2203	4300	6503	SO:0001587	stop_gained	8887	exon15			CCTGTCAGAGTCC	U33821	CCDS5415.1, CCDS43561.1, CCDS56471.1	7p15	2010-08-05			ENSG00000106052	ENSG00000106052			11575	protein-coding gene	gene with protein product		605326				10435631	Standard	NM_006024		Approved	TXBP151, CALCOCO3	uc003szl.3	Q86VP1	OTTHUMG00000023377	ENST00000396319.2:c.1987A>T	7.37:g.27856559A>T	ENSP00000379612:p.Arg663*	Somatic	31	0		WXS	Illumina HiSeq	Phase_I	74	44	NM_006024	0	0	14	17	3	B4DKU7|E7ENV2|O60398|O95770|Q13311|Q9BQG5|Q9UI88	Nonsense_Mutation	SNP	ENST00000396319.2	37	CCDS5415.1	.	.	.	.	.	.	.	.	.	.	A	28.1	4.886755	0.91814	.	.	ENSG00000106052	ENST00000543117;ENST00000265393;ENST00000409980;ENST00000433216;ENST00000396319;ENST00000457186	.	.	.	5.67	4.5	0.54988	.	0.000000	0.56097	D	0.000023	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05620	T	0.96	-17.6197	12.6545	0.56780	0.857:0.143:0.0:0.0	.	.	.	.	X	621;621;687;464;663;200	.	ENSP00000265393:R621X	R	+	1	2	TAX1BP1	27823084	1.000000	0.71417	0.999000	0.59377	0.808000	0.45660	2.947000	0.49058	0.975000	0.38392	0.533000	0.62120	AGA	.		0.453	TAX1BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214142.1	NM_006024	
ZNF713	349075	bcgsc.ca	37	7	55991337	55991337	+	Missense_Mutation	SNP	G	G	T			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr7:55991337G>T	ENST00000429591.2	+	3	251	c.213G>T	c.(211-213)ttG>ttT	p.L71F	ZNF713_ENST00000482436.1_3'UTR|MRPS17_ENST00000426595.1_Missense_Mutation_p.L71F	NM_182633.1	NP_872439.1	Q8N859	ZN713_HUMAN	zinc finger protein 713	71	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	25	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			TCGCGCAGTTGGAGCTAGAGG	0.453																																					p.L71F													.	ZNF713-92	0			c.G213T						.						93.0	77.0	83.0					7																	55991337		2203	4300	6503	SO:0001583	missense	349075	exon3			GCAGTTGGAGCTA	AK097282	CCDS34639.1	7p11.2	2013-01-08			ENSG00000178665	ENSG00000178665		"""Zinc fingers, C2H2-type"", ""-"""	22043	protein-coding gene	gene with protein product							Standard	NM_182633		Approved	FLJ39963	uc003trc.1	Q8N859	OTTHUMG00000156175	ENST00000429591.2:c.213G>T	7.37:g.55991337G>T	ENSP00000416662:p.Leu71Phe	Somatic	98	0		WXS	Illumina HiSeq	Phase_1	99	5	NM_182633	0	0	2	2	0		Missense_Mutation	SNP	ENST00000429591.2	37	CCDS34639.1	.	.	.	.	.	.	.	.	.	.	G	11.44	1.640080	0.29157	.	.	ENSG00000249773;ENSG00000178665	ENST00000426595;ENST00000429591	T;T	0.01015	5.44;5.44	3.48	1.65	0.23941	Krueppel-associated box (3);	0.000000	0.31531	N	0.007495	T	0.03348	0.0097	M	0.73217	2.22	0.24694	N	0.993298	D	0.71674	0.998	D	0.80764	0.994	T	0.25047	-1.0143	10	0.87932	D	0	.	5.346	0.16010	0.2585:0.0:0.7415:0.0	.	71	Q8N859	ZN713_HUMAN	F	71	ENSP00000390331:L71F;ENSP00000416662:L71F	ENSP00000390331:L71F	L	+	3	2	RP11-15K19.2;ZNF713	55958831	1.000000	0.71417	0.958000	0.39756	0.229000	0.25112	1.556000	0.36288	0.460000	0.27045	0.655000	0.94253	TTG	.		0.453	ZNF713-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343297.1	NM_182633	
GIMAP8	155038	broad.mit.edu	37	7	150174500	150174500	+	Missense_Mutation	SNP	G	G	T			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr7:150174500G>T	ENST00000307271.3	+	5	2204	c.1630G>T	c.(1630-1632)Gct>Tct	p.A544S		NM_175571.2	NP_783161.1	Q8ND71	GIMA8_HUMAN	GTPase, IMAP family member 8	544	AIG1-type G 3.					cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	GTP binding (GO:0005525)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(11)|lung(26)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.17)		GGACAAAACAGCTGTGGCGAA	0.502																																					p.A544S													.	GIMAP8-95	0			c.G1630T						.						80.0	77.0	78.0					7																	150174500		2203	4300	6503	SO:0001583	missense	155038	exon5			AAAACAGCTGTGG	AL834361	CCDS34777.1	7q36.1	2014-04-04			ENSG00000171115	ENSG00000171115		"""GTPases, IMAP"""	21792	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 9"""					15474311	Standard	XM_005249951		Approved	DKFZp667I133, hIAN6, IAN9	uc003whj.3	Q8ND71	OTTHUMG00000158327	ENST00000307271.3:c.1630G>T	7.37:g.150174500G>T	ENSP00000305107:p.Ala544Ser	Somatic	75	1		WXS	Illumina HiSeq	Phase_I	100	6	NM_175571	0	0	5	5	0		Missense_Mutation	SNP	ENST00000307271.3	37	CCDS34777.1	.	.	.	.	.	.	.	.	.	.	G	14.77	2.633250	0.47049	.	.	ENSG00000171115	ENST00000307271	T	0.34859	1.34	4.44	1.39	0.22231	AIG1 (1);	3.096750	0.01386	N	0.013095	T	0.33673	0.0871	L	0.41236	1.265	0.09310	N	1	P	0.35793	0.521	B	0.38378	0.272	T	0.23833	-1.0177	10	0.45353	T	0.12	.	5.6382	0.17548	0.3651:0.0:0.6349:0.0	.	544	Q8ND71	GIMA8_HUMAN	S	544	ENSP00000305107:A544S	ENSP00000305107:A544S	A	+	1	0	GIMAP8	149805433	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.442000	0.21628	0.518000	0.28383	-0.150000	0.13652	GCT	.		0.502	GIMAP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350701.1	NM_175571	
CHD7	55636	broad.mit.edu	37	8	61775123	61775123	+	Missense_Mutation	SNP	C	C	T			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr8:61775123C>T	ENST00000423902.2	+	37	8467	c.7988C>T	c.(7987-7989)gCg>gTg	p.A2663V	CHD7_ENST00000524602.1_Missense_Mutation_p.A614V	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	2663					adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			GGAGCTATGGCGCCTCCAATG	0.448																																					p.A2663V													.	CHD7-141	0			c.C7988T						.						48.0	52.0	51.0					8																	61775123		1869	4092	5961	SO:0001583	missense	55636	exon37			CTATGGCGCCTCC	AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"""CHARGE association"""	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.7988C>T	8.37:g.61775123C>T	ENSP00000392028:p.Ala2663Val	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	69	3	NM_017780	0	0	3	3	0	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Missense_Mutation	SNP	ENST00000423902.2	37	CCDS47865.1	.	.	.	.	.	.	.	.	.	.	C	36	5.614620	0.96649	.	.	ENSG00000171316	ENST00000307121;ENST00000423902;ENST00000524602	T;T	0.71817	-0.6;-0.6	5.59	5.59	0.84812	BRK domain (2);	0.000000	0.64402	D	0.000007	D	0.84723	0.5535	M	0.76328	2.33	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	D	0.85891	0.1428	10	0.87932	D	0	-14.5932	19.592	0.95518	0.0:1.0:0.0:0.0	.	2663	Q9P2D1	CHD7_HUMAN	V	2663;2663;614	ENSP00000392028:A2663V;ENSP00000437061:A614V	ENSP00000307304:A2663V	A	+	2	0	CHD7	61937677	1.000000	0.71417	0.966000	0.40874	0.981000	0.71138	7.800000	0.85949	2.628000	0.89032	0.655000	0.94253	GCG	.		0.448	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762	
LAMC3	10319	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	133948708	133948708	+	Splice_Site	SNP	G	G	A			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr9:133948708G>A	ENST00000361069.4	+	20	3627	c.3494G>A	c.(3493-3495)aGc>aAc	p.S1165N	LAMC3_ENST00000480883.1_Intron	NM_006059.3	NP_006050.3	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3	1165	Domain II and I.				astrocyte development (GO:0014002)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|extracellular matrix organization (GO:0030198)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	structural molecule activity (GO:0005198)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(31)|ovary(3)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	69	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		CTCGCCAGGAGGTGAGTCCCA	0.607																																					p.S1165N		.											.	LAMC3-93	0			c.G3494A						.						46.0	46.0	46.0					9																	133948708		2203	4300	6503	SO:0001630	splice_region_variant	10319	exon20			CCAGGAGGTGAGT	AF041835	CCDS6938.1	9q31-q34	2013-03-01			ENSG00000050555	ENSG00000050555		"""Laminins"""	6494	protein-coding gene	gene with protein product		604349				10225960	Standard	NM_006059		Approved	DKFZp434E202	uc004caa.1	Q9Y6N6	OTTHUMG00000020819	ENST00000361069.4:c.3494+1G>A	9.37:g.133948708G>A		Somatic	55	0		WXS	Illumina HiSeq	Phase_I	17	7	NM_006059	0	0	0	0	0	B1APX9|B1APY0|Q59H72	Missense_Mutation	SNP	ENST00000361069.4	37	CCDS6938.1	.	.	.	.	.	.	.	.	.	.	G	10.79	1.450700	0.26074	.	.	ENSG00000050555	ENST00000361069;ENST00000355048	T	0.29655	1.56	4.23	4.23	0.50019	.	0.177619	0.64402	D	0.000012	T	0.34221	0.0890	M	0.68317	2.08	0.39455	D	0.967477	P	0.36789	0.57	B	0.40038	0.317	T	0.15093	-1.0449	10	0.17832	T	0.49	.	14.3309	0.66556	0.0:0.0:1.0:0.0	.	1165	Q9Y6N6	LAMC3_HUMAN	N	1165	ENSP00000354360:S1165N	ENSP00000347156:S1165N	S	+	2	0	LAMC3	132938529	1.000000	0.71417	1.000000	0.80357	0.811000	0.45836	6.044000	0.71012	2.365000	0.80145	0.555000	0.69702	AGC	.		0.607	LAMC3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054717.3	NM_006059	Missense_Mutation
TSPYL2	64061	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	X	53114044	53114044	+	Silent	SNP	C	C	A			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chrX:53114044C>A	ENST00000375442.4	+	3	1125	c.993C>A	c.(991-993)cgC>cgA	p.R331R		NM_022117.3	NP_071400.1	Q9H2G4	TSYL2_HUMAN	TSPY-like 2	331					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell cycle (GO:0007049)|cellular protein metabolic process (GO:0044267)|chromatin modification (GO:0016568)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|negative regulation of DNA replication (GO:0008156)|nucleosome assembly (GO:0006334)|regulation of protein kinase activity (GO:0045859)|regulation of signal transduction (GO:0009966)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	rDNA binding (GO:0000182)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(1)	19						AGCGCAACCGCTCAGGTAAGT	0.498																																					p.R331R		.											.	TSPYL2-130	0			c.C993A						.						105.0	85.0	92.0					X																	53114044		2203	4300	6503	SO:0001819	synonymous_variant	64061	exon3			CAACCGCTCAGGT	AF273046	CCDS14350.1	Xp11	2014-06-09			ENSG00000184205	ENSG00000184205			24358	protein-coding gene	gene with protein product		300564				11318608, 11395479	Standard	NM_022117		Approved	SE20-4, HRIHFB2216, CTCL, DENTT, CDA1, CINAP, TSPX	uc004drw.3	Q9H2G4	OTTHUMG00000021597	ENST00000375442.4:c.993C>A	X.37:g.53114044C>A		Somatic	75	0		WXS	Illumina HiSeq	Phase_I	60	56	NM_022117	0	0	0	0	0	O94799|Q96DG7|Q9BZW6	Silent	SNP	ENST00000375442.4	37	CCDS14350.1																																																																																			.		0.498	TSPYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056718.1	NM_022117	
STAG2	10735	bcgsc.ca	37	X	123185066	123185066	+	Silent	SNP	C	C	T			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chrX:123185066C>T	ENST00000371160.1	+	12	1403	c.1113C>T	c.(1111-1113)ttC>ttT	p.F371F	STAG2_ENST00000371145.3_Silent_p.F371F|STAG2_ENST00000354548.5_Silent_p.F302F|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000218089.9_Silent_p.F371F|STAG2_ENST00000371157.3_Silent_p.F371F|STAG2_ENST00000371144.3_Silent_p.F371F	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	371	SCD. {ECO:0000255|PROSITE- ProRule:PRU00750}.				meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						CCAGTCGGTTCAAGGTTAGTA	0.303																																					p.F371F													.	STAG2-134	0			c.C1113T						.						31.0	32.0	32.0					X																	123185066		2203	4282	6485	SO:0001819	synonymous_variant	10735	exon12			TCGGTTCAAGGTT	Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.1113C>T	X.37:g.123185066C>T		Somatic	53	0		WXS	Illumina HiSeq	Phase_1	50	4	NM_001042749	0	0	0	0	0	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Silent	SNP	ENST00000371160.1	37	CCDS14607.1																																																																																			.		0.303	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603	
LAMTOR5	10542	hgsc.bcm.edu;bcgsc.ca	37	1	110950347	110950347	+	5'Flank	DEL	C	C	-	rs201420127		TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr1:110950347delC	ENST00000602318.1	-	0	0				LAMTOR5-AS1_ENST00000609709.1_RNA|LAMTOR5-AS1_ENST00000608067.1_RNA|LAMTOR5-AS1_ENST00000608499.1_RNA|LAMTOR5-AS1_ENST00000590826.1_RNA|LAMTOR5-AS1_ENST00000608602.1_RNA|LAMTOR5-AS1_ENST00000457535.1_RNA|LAMTOR5-AS1_ENST00000609244.1_RNA|LAMTOR5_ENST00000602858.1_5'Flank|LAMTOR5_ENST00000256644.4_Frame_Shift_Del_p.A48fs|LAMTOR5-AS1_ENST00000610148.1_RNA|LAMTOR5-AS1_ENST00000598454.1_RNA|LAMTOR5_ENST00000474861.2_5'Flank|LAMTOR5-AS1_ENST00000608253.1_RNA|LAMTOR5-AS1_ENST00000608486.1_RNA|LAMTOR5_ENST00000483260.1_5'Flank|LAMTOR5-AS1_ENST00000587691.1_RNA|LAMTOR5-AS1_ENST00000609512.1_RNA|LAMTOR5-AS1_ENST00000590413.1_RNA			O43504	LTOR5_HUMAN	late endosomal/lysosomal adaptor, MAPK and MTOR activator 5						cellular response to amino acid stimulus (GO:0071230)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of GTPase activity (GO:0043547)|positive regulation of TOR signaling (GO:0032008)|protein localization to lysosome (GO:0061462)|regulation of cell size (GO:0008361)|response to virus (GO:0009615)|viral genome replication (GO:0019079)	cytosol (GO:0005829)|lysosome (GO:0005764)|Ragulator complex (GO:0071986)											CGTAACGGCGCCTCCAAAGGG	0.617																																					p.A48fs		.											.	.	0			c.142delG						.						87.0	74.0	78.0					1																	110950347		2203	4300	6503	SO:0001631	upstream_gene_variant	10542	exon1			.	AF029890	CCDS824.1	1p12	2012-09-24	2012-09-24	2012-09-24	ENSG00000134248	ENSG00000134248			17955	protein-coding gene	gene with protein product	"""HBx-interacting protein"", ""hepatitis B virus x-interacting protein (9.6kD)"""	608521	"""hepatitis B virus x interacting protein"""	HBXIP		9499022, 22980980	Standard	NM_006402		Approved	XIP, MGC71071	uc001dzr.3	O43504	OTTHUMG00000011568		1.37:g.110950347delC	Exception_encountered	Somatic	297	0		WXS	Illumina HiSeq	Phase_I	216	42	NM_006402	0	0	0	0	0	Q6IBD8	Frame_Shift_Del	DEL	ENST00000602318.1	37																																																																																				.		0.617	LAMTOR5-007	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467909.1	NM_006402	
PIGB	9488	broad.mit.edu	37	15	55631503	55631503	+	Frame_Shift_Del	DEL	T	T	-			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr15:55631503delT	ENST00000164305.5	+	7	1124	c.833delT	c.(832-834)attfs	p.I278fs	CCPG1_ENST00000563294.1_5'Flank|PIGB_ENST00000539642.1_Frame_Shift_Del_p.I83fs	NM_004855.4	NP_004846.4	Q92521	PIGB_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class B	278					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	mannosyltransferase activity (GO:0000030)			endometrium(3)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)	11				all cancers(107;0.0255)		ATTGATCGTATTTTTTTTGGC	0.284																																					p.I278fs													.	PIGB-226	0			c.833delT						.			11,43,3402		0,0,11,0,43,1674	132.0	109.0	116.0			4.4	1.0	15		117	28,109,7593		0,0,28,3,103,3731	no	codingComplex	PIGB	NM_004855.4		0,0,39,3,146,5405	A1A1,A1A2,A1R,A2A2,A2R,RR		1.7723,1.5625,1.7075			55631503	39,152,10995	1790	4032	5822	SO:0001589	frameshift_variant	9488	exon7			ATCGTATTTTTTT	D42138	CCDS61641.1	15q21.3	2013-02-26	2006-06-28		ENSG00000069943	ENSG00000069943		"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"", ""Phosphatidylinositol glycan anchor biosynthesis"""	8959	protein-coding gene	gene with protein product	"""GPI mannosyltransferase 3"", ""dol-P-Man dependent GPI mannosyltransferase"""	604122	"""phosphatidylinositol glycan, class B"""			8861954	Standard	NM_004855		Approved		uc002act.3	Q92521	OTTHUMG00000172654	ENST00000164305.5:c.833delT	15.37:g.55631503delT	ENSP00000164305:p.Ile278fs	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	96	7	NM_004855	0	0	0	0	0	Q53FF9|Q8WVN7	Frame_Shift_Del	DEL	ENST00000164305.5	37																																																																																				.		0.284	PIGB-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000419687.1	NM_004855	
HOXD8	3234	hgsc.bcm.edu;bcgsc.ca	37	2	176996164	176996165	+	Frame_Shift_Ins	INS	-	-	CCCTAGCCCT			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr2:176996164_176996165insCCCTAGCCCT	ENST00000313173.4	+	2	1324_1325	c.697_698insCCCTAGCCCT	c.(697-699)gccfs	p.-236fs	HOXD8_ENST00000450510.2_Frame_Shift_Ins_p.-235fs|HOXD8_ENST00000429017.1_Frame_Shift_Ins_p.-52fs|HOXD8_ENST00000548663.1_Frame_Shift_Ins_p.-132fs|HOXD8_ENST00000544999.1_Frame_Shift_Ins_p.-235fs|HOXD-AS2_ENST00000440016.2_RNA	NM_001199746.1|NM_019558.3	NP_001186675.1|NP_062458.1	P13378	HXD8_HUMAN	homeobox D8						anterior/posterior axis specification, embryo (GO:0008595)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(2)|lung(5)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.195)	Colorectal(32;0.0224)|READ - Rectum adenocarcinoma(9;0.0556)		GGTTTCCCACGCCCTAGCCCTC	0.446																																					p.A233fs		.											.	HOXD8-90	0			c.697_698insCCCTAGCCCT						.																																			SO:0001589	frameshift_variant	3234	exon2			.		CCDS2268.1, CCDS56148.1, CCDS56149.1	2q31.1	2011-06-20	2005-12-22		ENSG00000175879	ENSG00000175879		"""Homeoboxes / ANTP class : HOXL subclass"""	5139	protein-coding gene	gene with protein product		142985	"""homeo box D8"""	HOX4, HOX4E		1973146, 1358459	Standard	NM_001199747		Approved		uc002uko.3	P13378	OTTHUMG00000132513	ENST00000313173.4:c.698_707dupCCCTAGCCCT	2.37:g.176996165_176996174dupCCCTAGCCCT	ENSP00000315949:p.Leu236fs	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	53	14	NM_019558	0	0	0	0	0	F8WBG7|Q5BL00|Q8IXZ1	Frame_Shift_Ins	INS	ENST00000313173.4	37	CCDS2268.1																																																																																			.		0.446	HOXD8-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255694.1		
