#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_Gene_Freq	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_SOL	i_NVarCov_SOL	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_TTotCov_SOL	i_TVarCov_SOL	i_Transcript_Id	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
SP140L	93349	hgsc.bcm.edu	37	2	231256872	231256873	+	Frame_Shift_Ins	INS	-	-	G	rs200753310	byFrequency	TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr2:231256872_231256873insG	ENST00000415673.2	+	12	1121_1122	c.1035_1036insG	c.(1036-1038)ggcfs	p.G346fs	SP140L_ENST00000243810.6_Frame_Shift_Ins_p.G346fs|SP140L_ENST00000396563.4_Frame_Shift_Ins_p.G311fs|SP140L_ENST00000444636.1_Frame_Shift_Ins_p.G346fs	NM_138402.4	NP_612411.4	Q9H930	SP14L_HUMAN	SP140 nuclear body protein-like	346	SAND. {ECO:0000255|PROSITE- ProRule:PRU00185}.					nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|skin(1)	20						AAATCAAAGGAGGCTACGCAAG	0.515																																					p.G345fs		.											.	.	.	0			c.1035_1036insG						.																																			SO:0001589	frameshift_variant	93349	exon12			CAAAGGAGGCTAC	BC004921	CCDS46538.1	2q37.1	2013-01-28			ENSG00000185404	ENSG00000185404		"""Zinc fingers, PHD-type"""	25105	protein-coding gene	gene with protein product						12477932	Standard	NM_138402		Approved		uc010fxm.1	Q9H930	OTTHUMG00000153730	ENST00000415673.2:c.1037dupG	2.37:g.231256874_231256874dupG	ENSP00000397911:p.Gly346fs	Somatic	61	0		WXS	Illumina HiSeq	.	111	42	NM_138402	Q2M375|Q4ZG65|Q9BSP3	Frame_Shift_Ins	INS	ENST00000415673.2	37	CCDS46538.1																																																																																			.		0.515	SP140L-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374538.1	NM_138402	
SRCAP	10847	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	16	30749940	30749940	+	Frame_Shift_Del	DEL	G	G	-			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr16:30749940delG	ENST00000262518.4	+	34	8964	c.8579delG	c.(8578-8580)aggfs	p.R2860fs	SRCAP_ENST00000344771.4_Frame_Shift_Del_p.R2702fs|RP11-2C24.4_ENST00000483578.1_lincRNA|SRCAP_ENST00000395059.2_Frame_Shift_Del_p.R2798fs	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	2860	Pro-rich.				histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			AAACGTCGGAGGGGGAGGCCC	0.617																																					p.R2860fs		.											.	.	.	0			c.8578delA						.						45.0	45.0	45.0					16																	30749940		2197	4300	6497	SO:0001589	frameshift_variant	10847	exon34			GTCGGAGGGGGAG	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"""Swi2/Snf2-related ATPase homolog (S. cerevisiae)"", ""domino homolog 1 (Drosophila)"""	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.8579delG	16.37:g.30749940delG	ENSP00000262518:p.Arg2860fs	Somatic	39	0		WXS	Illumina HiSeq	.	65	17	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Frame_Shift_Del	DEL	ENST00000262518.4	37	CCDS10689.2																																																																																			.		0.617	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662	
BRD2	6046	hgsc.bcm.edu	37	6	32945611	32945612	+	Frame_Shift_Ins	INS	-	-	C			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr6:32945611_32945612insC	ENST00000374825.4	+	9	3108_3109	c.1407_1408insC	c.(1408-1410)cccfs	p.P470fs	BRD2_ENST00000443797.2_Frame_Shift_Ins_p.P350fs|BRD2_ENST00000395289.2_Frame_Shift_Ins_p.P470fs|BRD2_ENST00000395287.1_Frame_Shift_Ins_p.P470fs|BRD2_ENST00000374831.4_Frame_Shift_Ins_p.P470fs|BRD2_ENST00000449085.2_Frame_Shift_Ins_p.P423fs	NM_005104.3	NP_005095.1	P25440	BRD2_HUMAN	bromodomain containing 2	470					chromatin modification (GO:0016568)|nucleosome assembly (GO:0006334)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(3)|stomach(2)	5						CTACTGCCATGCCCCCTGGCTT	0.51																																					p.M469fs		.											.	.	.	0			c.1407_1408insC						.																																			SO:0001589	frameshift_variant	6046	exon9			TGCCATGCCCCCT	X96670	CCDS4762.1, CCDS56420.1, CCDS56421.1	6p21.3	2010-12-23	2002-01-14		ENSG00000204256	ENSG00000204256			1103	protein-coding gene	gene with protein product		601540	"""bromodomain-containing 2"""			1352711, 8781126	Standard	NM_005104		Approved	KIAA9001, RING3, D6S113E, NAT, FSRG1	uc021ywf.1	P25440	OTTHUMG00000031241	ENST00000374825.4:c.1412dupC	6.37:g.32945616_32945616dupC	ENSP00000363958:p.Pro470fs	Somatic	24	0		WXS	Illumina HiSeq	.	18	12	NM_001113182	A2AAU0|B0S7P0|B1AZT1|O00699|O00700|Q15310|Q5STC9|Q63HQ9|Q658Y7|Q6P3U2|Q969U4	Frame_Shift_Ins	INS	ENST00000374825.4	37	CCDS4762.1																																																																																			.		0.510	BRD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076503.2		
MTERF2	80298	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	12	107371419	107371420	+	Frame_Shift_Del	DEL	CT	CT	-			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr12:107371419_107371420delCT	ENST00000552029.1	-	2	3141_3142	c.1073_1074delAG	c.(1072-1074)gagfs	p.E358fs	MTERFD3_ENST00000240050.4_Frame_Shift_Del_p.E358fs|MTERFD3_ENST00000392830.2_Frame_Shift_Del_p.E358fs|C12orf23_ENST00000551237.1_Intron			Q49AM1	MTEF2_HUMAN		358					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)	transcription regulatory region DNA binding (GO:0044212)			breast(1)|kidney(1)|large_intestine(2)|lung(3)	7						TAGCTTCAAACTCTTTTTTTGA	0.356																																					p.358_359del		.											.	.	.	0			c.1074_1075del						.																																			SO:0001589	frameshift_variant	80298	exon3			TTCAAACTCTTTT																												ENST00000552029.1:c.1073_1074delAG	12.37:g.107371421_107371422delCT	ENSP00000447651:p.Glu358fs	Somatic	52	0		WXS	Illumina HiSeq	.	42	15	NM_001033050	Q53HM2|Q9H4L6|Q9H7Y9	Frame_Shift_Del	DEL	ENST00000552029.1	37	CCDS9111.1																																																																																			.		0.356	MTERFD3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406835.1		
CACNA1A	773	hgsc.bcm.edu	37	19	13318673	13318690	+	In_Frame_Del	DEL	CTGCTGCTGCTGCTGCTG	CTGCTGCTGCTGCTGCTG	-	rs16054|rs370146696	byFrequency	TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	CTGCTGCTGCTGCTGCTG	CTGCTGCTGCTGCTGCTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr19:13318673_13318690delCTGCTGCTGCTGCTGCTG	ENST00000360228.5	-	47	6957_6974	c.6958_6975delCAGCAGCAGCAGCAGCAG	c.(6958-6975)cagcagcagcagcagcagdel	p.QQQQQQ2320del	CACNA1A_ENST00000573710.2_3'UTR	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	2319	Poly-Gln.				adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	TGGCCACCGCctgctgctgctgctgctgctgctgctgc	0.771																																					p.2320_2326del		.											.	.	.	0			c.6959_6976del						.																																			SO:0001651	inframe_deletion	773	exon47			CACCGCCTGCTGC	U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.6958_6975delCAGCAGCAGCAGCAGCAG	19.37:g.13318673_13318690delCTGCTGCTGCTGCTGCTG	ENSP00000353362:p.Gln2320_Gln2325del	Somatic	8	0		WXS	Illumina HiSeq	.	10	3	NM_001127222	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	In_Frame_Del	DEL	ENST00000360228.5	37	CCDS45998.1																																																																																			.		0.771	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068	
NFE2L1	4779	hgsc.bcm.edu;broad.mit.edu	37	17	46136201	46136212	+	In_Frame_Del	DEL	CTTCTTCCTCTG	CTTCTTCCTCTG	-	rs539093913		TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	CTTCTTCCTCTG	CTTCTTCCTCTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr17:46136201_46136212delCTTCTTCCTCTG	ENST00000362042.3	+	6	2133_2144	c.1517_1528delCTTCTTCCTCTG	c.(1516-1530)tcttcttcctctgct>tct	p.SSSA511del	NFE2L1_ENST00000582155.1_In_Frame_Del_p.SSSA323del|NFE2L1_ENST00000583378.1_In_Frame_Del_p.SSSA312del|NFE2L1_ENST00000357480.5_In_Frame_Del_p.SSSA481del|NFE2L1_ENST00000536222.1_In_Frame_Del_p.SSSA355del|NFE2L1_ENST00000585291.1_In_Frame_Del_p.SSSA481del|RP5-890E16.4_ENST00000583349.1_RNA|NFE2L1_ENST00000361665.3_In_Frame_Del_p.SSSA500del	NM_003204.2	NP_003195.1	Q14494	NF2L1_HUMAN	nuclear factor, erythroid 2-like 1	511	Poly-Ser.				anatomical structure morphogenesis (GO:0009653)|erythrocyte differentiation (GO:0030218)|heme biosynthetic process (GO:0006783)|inflammatory response (GO:0006954)|transcription from RNA polymerase II promoter (GO:0006366)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)			cervix(1)|endometrium(3)|kidney(9)|large_intestine(7)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						tcctcttcctcttcttcctctgcttcttcctc	0.542																																					p.506_509del		.											.	.	.	0			c.1516_1527del						.			6,4256		0,6,2125						2.5	0.1			67	9,8245		2,5,4120	no	coding	NFE2L1	NM_003204.2		2,11,6245	A1A1,A1R,RR		0.109,0.1408,0.1198				15,12501				SO:0001651	inframe_deletion	4779	exon6			CTTCCTCTTCTTC	AK090459	CCDS11524.1	17q21.3	2013-08-23	2013-08-23			ENSG00000082641		"""basic leucine zipper proteins"""	7781	protein-coding gene	gene with protein product		163260	"""nuclear factor (erythroid-derived 2)-like 1"""	TCF11		8248256, 9501099	Standard	NM_003204		Approved	NRF1, LCR-F1, FLJ00380	uc002imz.4	Q14494		ENST00000362042.3:c.1517_1528delCTTCTTCCTCTG	17.37:g.46136201_46136212delCTTCTTCCTCTG	ENSP00000354855:p.Ser511_Ala514del	Somatic	9	0		WXS	Illumina HiSeq	.	21	6	NM_003204	D3DTU3|D3DTU5|Q12877|Q96FN6	In_Frame_Del	DEL	ENST00000362042.3	37	CCDS11524.1																																																																																			.		0.542	NFE2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443019.1	NM_003204	
ITPR2	3709	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	26755323	26755323	+	Silent	SNP	G	G	A			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr12:26755323G>A	ENST00000381340.3	-	28	4074	c.3658C>T	c.(3658-3660)Ctg>Ttg	p.L1220L		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	1220					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	GGTATCTGCAGAAGATCCAAC	0.353																																					p.L1220L		.											.	.	.	0			c.C3658T						.						100.0	93.0	95.0					12																	26755323		1821	4078	5899	SO:0001819	synonymous_variant	3709	exon28			TCTGCAGAAGATC	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"""Ion channels / Inositol triphosphate receptors"""	6181	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 48"""	600144	"""inositol 1,4,5-triphosphate receptor, type 2"""			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.3658C>T	12.37:g.26755323G>A		Somatic	139	0		WXS	Illumina HiSeq	.	160	49	NM_002223	O94773	Silent	SNP	ENST00000381340.3	37	CCDS41764.1																																																																																			.		0.353	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	
PCDH17	27253	hgsc.bcm.edu	37	13	58207258	58207258	+	Missense_Mutation	SNP	C	C	A			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr13:58207258C>A	ENST00000377918.3	+	1	604	c.578C>A	c.(577-579)cCa>cAa	p.P193Q		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	193	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(30)|liver(2)|lung(54)|ovary(4)|pancreas(2)|prostate(5)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	120		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		ACCAAGTTCCCAGAACTGGTC	0.642																																					p.P193Q	Melanoma(72;952 1291 1619 12849 33676)	.											PCDH17,colon,carcinoma,0,1	PCDH17	0	0			c.C578A						.						32.0	33.0	33.0					13																	58207258		2203	4300	6503	SO:0001583	missense	27253	exon1			AGTTCCCAGAACT	AF029343	CCDS31986.1	13q21.1	2010-01-26			ENSG00000118946	ENSG00000118946		"""Cadherins / Protocadherins : Non-clustered"""	14267	protein-coding gene	gene with protein product		611760				10835267	Standard	NM_001040429		Approved	PCDH68, PCH68	uc001vhq.1	O14917	OTTHUMG00000016992	ENST00000377918.3:c.578C>A	13.37:g.58207258C>A	ENSP00000367151:p.Pro193Gln	Somatic	15	0		WXS	Illumina HiSeq	.	34	2	NM_001040429	A8K1R5|Q5VVW9|Q5VVX0	Missense_Mutation	SNP	ENST00000377918.3	37	CCDS31986.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.937197	0.73557	.	.	ENSG00000118946	ENST00000377918	T	0.55760	0.5	4.8	4.8	0.61643	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.66577	0.2803	L	0.48935	1.535	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.77557	0.983;0.99	T	0.64588	-0.6372	9	.	.	.	.	18.0484	0.89340	0.0:1.0:0.0:0.0	.	193;193	O14917-2;O14917	.;PCD17_HUMAN	Q	193	ENSP00000367151:P193Q	.	P	+	2	0	PCDH17	57105259	1.000000	0.71417	0.982000	0.44146	0.971000	0.66376	7.643000	0.83403	2.511000	0.84671	0.650000	0.86243	CCA	.		0.642	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	NM_001040429	
MROH9	80133	hgsc.bcm.edu	37	1	170941012	170941012	+	Missense_Mutation	SNP	C	C	T	rs377212983		TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr1:170941012C>T	ENST00000367758.3	+	8	703	c.604C>T	c.(604-606)Cgg>Tgg	p.R202W	MROH9_ENST00000367759.4_Missense_Mutation_p.R202W	NM_025063.2	NP_079339.2	Q5TGP6	MROH9_HUMAN	maestro heat-like repeat family member 9	202																	CTACATTGCACGGTGTCAGAA	0.458																																					p.R202W		.											C1orf129_ENST00000367759,NS,carcinoma,0,2	C1orf129_ENST00000367759	0	0			c.C604T						.	C	TRP/ARG,TRP/ARG	1,3921		0,1,1960	279.0	248.0	258.0		604,604	1.0	0.0	1		258	1,8321		0,1,4160	no	missense,missense	C1orf129	NM_001163629.1,NM_025063.2	101,101	0,2,6120	TT,TC,CC		0.012,0.0255,0.0163	possibly-damaging,possibly-damaging	202/862,202/574	170941012	2,12242	1961	4161	6122	SO:0001583	missense	80133	exon8			ATTGCACGGTGTC	AK027203	CCDS41436.1, CCDS53429.1	1q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000117501	ENSG00000117501		"""maestro heat-like repeat containing"""	26287	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 129"""	C1orf129			Standard	NM_025063		Approved	FLJ23550, ARMC11	uc010plz.2	Q5TGP6	OTTHUMG00000041456	ENST00000367758.3:c.604C>T	1.37:g.170941012C>T	ENSP00000356732:p.Arg202Trp	Somatic	20	0		WXS	Illumina HiSeq	.	27	2	NM_025063	A0PJM0|A0PJM2|F5GWX6|Q9H5D7	Missense_Mutation	SNP	ENST00000367758.3	37	CCDS41436.1	.	.	.	.	.	.	.	.	.	.	C	10.37	1.331558	0.24167	2.55E-4	1.2E-4	ENSG00000117501	ENST00000367759;ENST00000367758	T;T	0.67865	-0.29;1.37	4.95	1.04	0.20106	.	0.841682	0.10402	N	0.679044	T	0.15825	0.0381	N	0.08118	0	0.09310	N	1	P;P	0.45078	0.618;0.85	B;B	0.24269	0.032;0.052	T	0.06409	-1.0828	10	0.62326	D	0.03	-4.2567	5.6842	0.17792	0.5043:0.3311:0.0:0.1646	.	202;202	F5GWX6;Q5TGP6	.;CA129_HUMAN	W	202	ENSP00000356733:R202W;ENSP00000356732:R202W	ENSP00000356732:R202W	R	+	1	2	C1orf129	169207636	0.003000	0.15002	0.001000	0.08648	0.008000	0.06430	0.709000	0.25734	-0.019000	0.14055	-0.266000	0.10368	CGG	.		0.458	MROH9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000099327.1	NM_025063	
MTFMT	123263	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	65312553	65312553	+	Missense_Mutation	SNP	T	T	C			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr15:65312553T>C	ENST00000220058.4	-	5	716	c.703A>G	c.(703-705)Atg>Gtg	p.M235V	MTFMT_ENST00000561025.1_5'Flank	NM_139242.3	NP_640335.2	Q96DP5	FMT_HUMAN	mitochondrial methionyl-tRNA formyltransferase	235						mitochondrion (GO:0005739)	methionyl-tRNA formyltransferase activity (GO:0004479)			endometrium(1)|large_intestine(3)|lung(3)|ovary(3)	10					Tetrahydrofolic acid(DB00116)	GCCCCCTCCATTGGCTGCTGC	0.408																																					p.M235V		.											.	.	.	0			c.A703G						.						36.0	39.0	38.0					15																	65312553		1962	4167	6129	SO:0001583	missense	123263	exon5			CCTCCATTGGCTG	AK055688	CCDS45280.1	15q22.31	2006-11-29		2005-08-09		ENSG00000103707			29666	protein-coding gene	gene with protein product		611766				9614118	Standard	NM_139242		Approved	FMT1	uc002aof.4	Q96DP5		ENST00000220058.4:c.703A>G	15.37:g.65312553T>C	ENSP00000220058:p.Met235Val	Somatic	25	0		WXS	Illumina HiSeq	.	21	9	NM_139242	B7Z734	Missense_Mutation	SNP	ENST00000220058.4	37	CCDS45280.1	.	.	.	.	.	.	.	.	.	.	T	7.982	0.751433	0.15778	.	.	ENSG00000103707	ENST00000220058	T	0.76060	-0.99	5.38	-1.84	0.07809	Formyl transferase, N-terminal (2);	0.904156	0.09366	N	0.812066	T	0.50034	0.1592	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34725	-0.9817	10	0.41790	T	0.15	-0.1517	11.4568	0.50187	0.0:0.4566:0.0:0.5434	.	235	Q96DP5	FMT_HUMAN	V	235	ENSP00000220058:M235V	ENSP00000220058:M235V	M	-	1	0	MTFMT	63099606	0.000000	0.05858	0.006000	0.13384	0.668000	0.39293	-0.989000	0.03736	-0.209000	0.10156	0.533000	0.62120	ATG	.		0.408	MTFMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418155.1	NM_139242	
PPARA	5465	hgsc.bcm.edu	37	22	46594338	46594338	+	Nonsense_Mutation	SNP	G	G	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr22:46594338G>T	ENST00000396000.2	+	3	323	c.58G>T	c.(58-60)Gag>Tag	p.E20*	PPARA_ENST00000434345.2_Nonsense_Mutation_p.E20*|PPARA_ENST00000402126.1_Nonsense_Mutation_p.E20*|PPARA_ENST00000407236.1_Nonsense_Mutation_p.E20*|PPARA_ENST00000262735.5_Nonsense_Mutation_p.E20*			Q07869	PPARA_HUMAN	peroxisome proliferator-activated receptor alpha	20					behavioral response to nicotine (GO:0035095)|cellular lipid metabolic process (GO:0044255)|circadian regulation of gene expression (GO:0032922)|enamel mineralization (GO:0070166)|epidermis development (GO:0008544)|fatty acid metabolic process (GO:0006631)|fatty acid transport (GO:0015908)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular receptor signaling pathway (GO:0030522)|lipid metabolic process (GO:0006629)|lipoprotein metabolic process (GO:0042157)|negative regulation of appetite (GO:0032099)|negative regulation of blood pressure (GO:0045776)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of glycolytic process (GO:0045820)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of neuron death (GO:1901215)|negative regulation of protein binding (GO:0032091)|negative regulation of receptor biosynthetic process (GO:0010871)|negative regulation of sequestering of triglyceride (GO:0010891)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular ketone metabolic process by positive regulation of transcription from RNA polymerase II promoter (GO:0072366)|regulation of circadian rhythm (GO:0042752)|regulation of glycolytic by positive regulation of transcription from RNA polymerase II promoter (GO:0072363)|regulation of lipid transport by positive regulation of transcription from RNA polymerase II promoter (GO:0072369)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|wound healing (GO:0042060)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|drug binding (GO:0008144)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|lipid binding (GO:0008289)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|ubiquitin conjugating enzyme binding (GO:0031624)|zinc ion binding (GO:0008270)	p.E20Q(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	15		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00522)	Bezafibrate(DB01393)|Clofibrate(DB00636)|Fenofibrate(DB01039)|Gemfibrozil(DB01241)|Indomethacin(DB00328)	CGGCGATCTAGAGAGCCCGTT	0.562																																					p.E20X		.											PPARA,mouth,carcinoma,0,1	PPARA	0	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.G58T						.						100.0	109.0	106.0					22																	46594338		2203	4300	6503	SO:0001587	stop_gained	5465	exon3			GATCTAGAGAGCC	L02932	CCDS33669.1	22q12-q13.1	2013-01-16	2006-10-17		ENSG00000186951	ENSG00000186951		"""Nuclear hormone receptors"""	9232	protein-coding gene	gene with protein product		170998	"""peroxisome proliferative activated receptor, alpha"""	PPAR		7684926, 10591208	Standard	XM_005261655		Approved	hPPAR, NR1C1	uc003bgx.1	Q07869	OTTHUMG00000150443	ENST00000396000.2:c.58G>T	22.37:g.46594338G>T	ENSP00000379322:p.Glu20*	Somatic	46	0		WXS	Illumina HiSeq	.	40	2	NM_001001928	B0G0X3|Q16241|Q6I9S0|Q92486|Q92689|Q9Y3N1	Nonsense_Mutation	SNP	ENST00000396000.2	37	CCDS33669.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.332774	0.81801	.	.	ENSG00000186951	ENST00000415785;ENST00000396000;ENST00000262735;ENST00000420804;ENST00000407236;ENST00000402126;ENST00000434345	.	.	.	5.7	5.7	0.88788	.	0.407518	0.24841	N	0.035170	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.45353	T	0.12	.	16.9911	0.86354	0.0:0.0:1.0:0.0	.	.	.	.	X	20	.	ENSP00000262735:E20X	E	+	1	0	PPARA	44973002	1.000000	0.71417	0.923000	0.36655	0.020000	0.10135	4.700000	0.61803	2.687000	0.91594	0.655000	0.94253	GAG	.		0.562	PPARA-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318129.3	NM_001001928	
HSF4	3299	hgsc.bcm.edu	37	16	67203243	67203243	+	Missense_Mutation	SNP	C	C	A			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr16:67203243C>A	ENST00000521374.1	+	12	1316	c.1316C>A	c.(1315-1317)cCa>cAa	p.P439Q	NOL3_ENST00000564053.1_5'Flank|HSF4_ENST00000264009.8_Missense_Mutation_p.P439Q|NOL3_ENST00000432069.2_5'Flank|HSF4_ENST00000421453.1_Missense_Mutation_p.P409Q|HSF4_ENST00000584272.1_Missense_Mutation_p.P409Q			Q9ULV5	HSF4_HUMAN	heat shock transcription factor 4	439					camera-type eye development (GO:0043010)|cell development (GO:0048468)|histone H3-K9 demethylation (GO:0033169)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotrimerization (GO:0070207)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	protein phosphatase binding (GO:0019903)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(3)|prostate(1)|skin(1)	12		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0143)|Epithelial(162;0.0335)|all cancers(182;0.184)		TTAAATTCTCCAAGCCCAGGT	0.587																																					p.P439Q		.											.	.	.	0			c.C1316A						.						31.0	34.0	33.0					16																	67203243		1987	4172	6159	SO:0001583	missense	3299	exon14			ATTCTCCAAGCCC	D87673	CCDS42175.1, CCDS45510.1	16q21	2013-01-22			ENSG00000102878	ENSG00000102878			5227	protein-coding gene	gene with protein product		602438	"""cataract, Marner"""	CTM		8972228, 10488131, 12089525	Standard	NM_001538		Approved		uc002erl.2	Q9ULV5	OTTHUMG00000178325	ENST00000521374.1:c.1316C>A	16.37:g.67203243C>A	ENSP00000430947:p.Pro439Gln	Somatic	24	0		WXS	Illumina HiSeq	.	77	4	NM_001040667	Q99472|Q9ULV6	Missense_Mutation	SNP	ENST00000521374.1	37	CCDS42175.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.44|14.44	2.535167|2.535167	0.45176|0.45176	.|.	.|.	ENSG00000102878|ENSG00000102878	ENST00000421453;ENST00000264009;ENST00000517685;ENST00000521374|ENST00000520304	.|.	.|.	.|.	4.6|4.6	3.63|3.63	0.41609|0.41609	.|.	0.610177|.	0.15435|.	N|.	0.262505|.	T|T	0.32496|0.32496	0.0831|0.0831	L|L	0.27053|0.27053	0.805|0.805	0.23876|0.23876	N|N	0.996598|0.996598	B;B|.	0.15473|.	0.013;0.008|.	B;B|.	0.14578|.	0.011;0.003|.	T|T	0.18587|0.18587	-1.0332|-1.0332	9|5	0.72032|.	D|.	0.01|.	1.2143|1.2143	9.3009|9.3009	0.37845|0.37845	0.2467:0.7533:0.0:0.0|0.2467:0.7533:0.0:0.0	.|.	409;439|.	Q9ULV5-2;Q9ULV5|.	.;HSF4_HUMAN|.	Q|K	409;439;363;439|115	.|.	ENSP00000264009:P439Q|.	P|Q	+|+	2|1	0|0	HSF4|HSF4	65760744|65760744	0.013000|0.013000	0.17824|0.17824	0.874000|0.874000	0.34290|0.34290	0.987000|0.987000	0.75469|0.75469	0.948000|0.948000	0.29096|0.29096	1.059000|1.059000	0.40554|0.40554	0.563000|0.563000	0.77884|0.77884	CCA|CAA	.		0.587	HSF4-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375080.1	NM_001538	
GRM8	2918	hgsc.bcm.edu	37	7	126883170	126883170	+	Missense_Mutation	SNP	C	C	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr7:126883170C>T	ENST00000339582.2	-	2	897	c.89G>A	c.(88-90)aGa>aAa	p.R30K	GRM8_ENST00000405249.1_Missense_Mutation_p.R30K|GRM8_ENST00000444921.2_Missense_Mutation_p.R30K|GRM8_ENST00000358373.3_Missense_Mutation_p.R30K			O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8	30					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of cAMP biosynthetic process (GO:0030818)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)	p.R30I(2)		breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(16)|lung(62)|ovary(5)|pancreas(1)|prostate(1)|skin(14)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(4)	125		Prostate(267;0.186)				GCTGTGAGTTCTTTGCATCAT	0.527										HNSCC(24;0.065)																											p.R30K		.											GRM8_ENST00000405249,NS,carcinoma,0,8	GRM8_ENST00000405249	0	2	Substitution - Missense(2)	large_intestine(2)	c.G89A						.						92.0	90.0	91.0					7																	126883170		2203	4300	6503	SO:0001583	missense	2918	exon1			TGAGTTCTTTGCA		CCDS5794.1, CCDS47696.1	7q31.3-q32.1	2012-08-29			ENSG00000179603	ENSG00000179603		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4600	protein-coding gene	gene with protein product		601116				8824806	Standard	NM_000845		Approved	GLUR8, GPRC1H, mGlu8, MGLUR8	uc003vlr.2	O00222	OTTHUMG00000022888	ENST00000339582.2:c.89G>A	7.37:g.126883170C>T	ENSP00000344173:p.Arg30Lys	Somatic	34	0		WXS	Illumina HiSeq	.	50	2	NM_000845	A4D0Y3|B0FZ74|B0M0L0|O15493|O95945|O95946|Q3MIV9|Q52M02|Q6J165	Missense_Mutation	SNP	ENST00000339582.2	37	CCDS5794.1	.	.	.	.	.	.	.	.	.	.	C	5.933	0.356180	0.11239	.	.	ENSG00000179603	ENST00000339582;ENST00000444921;ENST00000358373;ENST00000405249;ENST00000457830	T;T;T;T;T	0.69306	-0.39;-0.39;-0.39;-0.39;-0.39	6.17	6.17	0.99709	.	0.133058	0.53938	D	0.000060	T	0.39358	0.1075	N	0.02802	-0.49	0.25275	N	0.98948	B;B	0.16396	0.017;0.0	B;B	0.13407	0.009;0.0	T	0.07731	-1.0757	10	0.02654	T	1	.	15.3567	0.74431	0.0:0.8613:0.1387:0.0	.	30;30	O00222-2;O00222	.;GRM8_HUMAN	K	30	ENSP00000344173:R30K;ENSP00000409790:R30K;ENSP00000351142:R30K;ENSP00000385731:R30K;ENSP00000415522:R30K	ENSP00000344173:R30K	R	-	2	0	GRM8	126670406	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.262000	0.43285	2.941000	0.99782	0.655000	0.94253	AGA	.		0.527	GRM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059209.4		
SMC5	23137	hgsc.bcm.edu	37	9	72882839	72882839	+	Splice_Site	SNP	G	G	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr9:72882839G>T	ENST00000361138.5	+	3	386	c.328G>T	c.(328-330)Gtt>Ttt	p.V110F		NM_015110.3	NP_055925.2	Q8IY18	SMC5_HUMAN	structural maintenance of chromosomes 5	110					cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|mitotic nuclear division (GO:0007067)|positive regulation of maintenance of mitotic sister chromatid cohesion (GO:0034184)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|telomere maintenance via recombination (GO:0000722)	cell junction (GO:0030054)|chromosome, telomeric region (GO:0000781)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(4)	35						TATGTCTTAGGTTGGGTTTTT	0.313																																					p.V110F		.											.	.	.	0			c.G328T						.						263.0	261.0	261.0					9																	72882839		2203	4300	6503	SO:0001630	splice_region_variant	23137	exon3			TCTTAGGTTGGGT	AB011166	CCDS6632.1	9q21.11	2008-02-05	2006-07-06	2006-07-06	ENSG00000198887	ENSG00000198887		"""Structural maintenance of chromosomes proteins"""	20465	protein-coding gene	gene with protein product		609386	"""SMC5 structural maintenance of chromosomes 5-like 1 (yeast)"""	SMC5L1		9628581	Standard	NM_015110		Approved	KIAA0594	uc004ahr.2	Q8IY18	OTTHUMG00000019992	ENST00000361138.5:c.328-1G>T	9.37:g.72882839G>T		Somatic	57	0		WXS	Illumina HiSeq	.	99	4	NM_015110	A6NM81|O60335|Q05D92|Q5VZ60|Q96SB9	Missense_Mutation	SNP	ENST00000361138.5	37	CCDS6632.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.839900	0.91117	.	.	ENSG00000198887	ENST00000361138	T	0.68331	-0.32	5.8	5.8	0.92144	RecF/RecN/SMC (1);	0.000000	0.85682	D	0.000000	D	0.83110	0.5183	M	0.78637	2.42	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82362	-0.0495	9	.	.	.	-18.9523	20.0493	0.97618	0.0:0.0:1.0:0.0	.	110	Q8IY18	SMC5_HUMAN	F	110	ENSP00000354957:V110F	.	V	+	1	0	SMC5	72072659	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	5.075000	0.64407	2.745000	0.94114	0.491000	0.48974	GTT	.		0.313	SMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052603.1	NM_015110	Missense_Mutation
HFM1	164045	hgsc.bcm.edu;bcgsc.ca	37	1	91726906	91726906	+	Missense_Mutation	SNP	G	G	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr1:91726906G>T	ENST00000370425.3	-	39	4347	c.4249C>A	c.(4249-4251)Cct>Act	p.P1417T	HFM1_ENST00000462405.1_5'UTR|HFM1_ENST00000294696.5_3'UTR|HFM1_ENST00000370424.3_Missense_Mutation_p.P1096T|Y_RNA_ENST00000384090.1_RNA	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	1417					resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		TCATCATCAGGATGATACATA	0.224																																					p.P1417T		.											.	.	.	0			c.C4249A						.						24.0	20.0	21.0					1																	91726906		1760	4005	5765	SO:0001583	missense	164045	exon39			CATCAGGATGATA	AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"""SEC63 domain containing 1"""	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.4249C>A	1.37:g.91726906G>T	ENSP00000359454:p.Pro1417Thr	Somatic	72	0		WXS	Illumina HiSeq	.	74	4	NM_001017975	B1B0B6|Q8N9Q0	Missense_Mutation	SNP	ENST00000370425.3	37	CCDS30769.2	.	.	.	.	.	.	.	.	.	.	G	7.819	0.717393	0.15372	.	.	ENSG00000162669	ENST00000370425;ENST00000370424	T;T	0.64260	0.34;-0.09	5.36	-0.0398	0.13874	.	.	.	.	.	T	0.18551	0.0445	L	0.27053	0.805	0.80722	D	1	B	0.24186	0.099	B	0.22601	0.04	T	0.15809	-1.0424	9	0.07325	T	0.83	.	5.6121	0.17410	0.3884:0.139:0.4726:0.0	.	1417	A2PYH4	HFM1_HUMAN	T	1417;1096	ENSP00000359454:P1417T;ENSP00000359453:P1096T	ENSP00000359453:P1096T	P	-	1	0	HFM1	91499494	0.998000	0.40836	0.982000	0.44146	0.274000	0.26718	0.257000	0.18369	0.108000	0.17862	-0.182000	0.12963	CCT	.		0.224	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975	
DNAH2	146754	hgsc.bcm.edu	37	17	7630469	7630469	+	Silent	SNP	G	G	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr17:7630469G>T	ENST00000572933.1	+	4	1718	c.258G>T	c.(256-258)ctG>ctT	p.L86L	DNAH2_ENST00000570791.1_Silent_p.L86L|DNAH2_ENST00000082259.3_Silent_p.L86L|DNAH2_ENST00000389173.2_Silent_p.L86L			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	86	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				GAGCTGCGCTGACAGGACTGG	0.532																																					p.L86L		.											.	.	.	0			c.G258T						.						146.0	115.0	125.0					17																	7630469		2203	4300	6503	SO:0001819	synonymous_variant	146754	exon3			TGCGCTGACAGGA	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"""Axonemal dyneins"""	2948	protein-coding gene	gene with protein product		603333	"""dynein, axonemal, heavy polypeptide 2"", ""dynein heavy chain domain 3"""	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.258G>T	17.37:g.7630469G>T		Somatic	37	0		WXS	Illumina HiSeq	.	32	3	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Silent	SNP	ENST00000572933.1	37	CCDS32551.1																																																																																			.		0.532	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877	
RPS28	6234	hgsc.bcm.edu	37	19	8386428	8386428	+	Missense_Mutation	SNP	G	G	A			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr19:8386428G>A	ENST00000600659.2	+	1	45	c.14G>A	c.(13-15)cGt>cAt	p.R5H	NDUFA7_ENST00000598884.1_5'Flank|NDUFA7_ENST00000301457.2_5'Flank	NM_001031.4	NP_001022.1	P62857	RS28_HUMAN	ribosomal protein S28	5					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosomal small subunit biogenesis (GO:0042274)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|small ribosomal subunit (GO:0015935)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)										GACACCAGCCGTGTGCAGCCT	0.657																																					p.R5H		.											.	.	.	0			c.G14A						.						5.0	6.0	6.0					19																	8386428		1905	4030	5935	SO:0001583	missense	6234	exon1			CCAGCCGTGTGCA	D14530	CCDS45953.1	19p13.2	2011-04-06				ENSG00000233927		"""S ribosomal proteins"""	10418	protein-coding gene	gene with protein product	"""40S ribosomal protein S28"""	603685				8415000, 9582194	Standard	NM_001031		Approved	S28	uc002mjn.3	P62857		ENST00000600659.2:c.14G>A	19.37:g.8386428G>A	ENSP00000472469:p.Arg5His	Somatic	58	0		WXS	Illumina HiSeq	.	83	4	NM_001031	P25112	Missense_Mutation	SNP	ENST00000600659.2	37	CCDS45953.1	.	.	.	.	.	.	.	.	.	.	G	13.14	2.147238	0.37923	.	.	ENSG00000233927	ENST00000417088	.	.	.	5.08	4.0	0.46444	Nucleic acid-binding, OB-fold-like (1);	.	.	.	.	T	0.36496	0.0969	.	.	.	0.80722	D	1	B	0.15473	0.013	B	0.10450	0.005	T	0.14615	-1.0466	7	0.07325	T	0.83	.	13.8376	0.63419	0.0:0.0:0.8473:0.1527	.	5	P62857	RS28_HUMAN	H	5	.	ENSP00000397872:R5H	R	+	2	0	RPS28	8292428	1.000000	0.71417	0.675000	0.29917	0.148000	0.21650	5.803000	0.69129	2.626000	0.88956	0.561000	0.74099	CGT	.		0.657	RPS28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461377.3	NM_001031	
LMTK2	22853	hgsc.bcm.edu	37	7	97820972	97820972	+	Missense_Mutation	SNP	G	G	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr7:97820972G>T	ENST00000297293.5	+	11	1488	c.1195G>T	c.(1195-1197)Gcg>Tcg	p.A399S		NM_014916.3	NP_055731.2	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2	399	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				early endosome to late endosome transport (GO:0045022)|endocytic recycling (GO:0032456)|negative regulation of catalytic activity (GO:0043086)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|receptor recycling (GO:0001881)|transferrin transport (GO:0033572)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|myosin VI binding (GO:0070853)|protein phosphatase inhibitor activity (GO:0004864)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|pancreas(2)|skin(2)|stomach(3)	59	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)					AAAGAGACCCGCGGCTGAAGA	0.507																																					p.A399S		.											LMTK2_ENST00000297293,colon,carcinoma,0,2	LMTK2_ENST00000297293	0	0			c.G1195T						.						57.0	55.0	56.0					7																	97820972		2203	4300	6503	SO:0001583	missense	22853	exon11			AGACCCGCGGCTG	AB029002	CCDS5654.1	7q22.1	2014-06-12			ENSG00000164715	ENSG00000164715			17880	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 100"""	610989				15005709	Standard	NM_014916		Approved	KIAA1079, KPI2, KPI-2, cprk, LMR2, BREK, AATYK2, PPP1R100	uc003upd.2	Q8IWU2	OTTHUMG00000154256	ENST00000297293.5:c.1195G>T	7.37:g.97820972G>T	ENSP00000297293:p.Ala399Ser	Somatic	29	0		WXS	Illumina HiSeq	.	46	3	NM_014916	A4D272|Q75MG7|Q9UPS3	Missense_Mutation	SNP	ENST00000297293.5	37	CCDS5654.1	.	.	.	.	.	.	.	.	.	.	G	11.77	1.737906	0.30774	.	.	ENSG00000164715	ENST00000297293	T	0.58506	0.33	5.52	4.41	0.53225	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.097851	0.64402	D	0.000002	T	0.20740	0.0499	N	0.00456	-1.48	0.29917	N	0.823058	B	0.19706	0.038	B	0.25140	0.058	T	0.06643	-1.0815	10	0.38643	T	0.18	.	4.6036	0.12366	0.275:0.0:0.725:0.0	.	399	Q8IWU2	LMTK2_HUMAN	S	399	ENSP00000297293:A399S	ENSP00000297293:A399S	A	+	1	0	LMTK2	97658908	1.000000	0.71417	0.025000	0.17156	0.156000	0.22039	6.086000	0.71352	2.767000	0.95098	0.655000	0.94253	GCG	.		0.507	LMTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334560.1	NM_014916	
EXD3	54932	hgsc.bcm.edu;broad.mit.edu	37	9	140201611	140201611	+	Missense_Mutation	SNP	C	C	T	rs540192818		TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr9:140201611C>T	ENST00000340951.4	-	22	2617	c.2422G>A	c.(2422-2424)Ggc>Agc	p.G808S	EXD3_ENST00000342129.4_Missense_Mutation_p.G446S	NM_017820.3	NP_060290.3	Q9NX53	MUT7B_HUMAN	exonuclease 3'-5' domain containing 3	0										NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)	12						AGCCGGGTGCCGTCGGCCAGC	0.692													C|||	1	0.000199681	0.0008	0.0	5008	,	,		12512	0.0		0.0	False		,,,				2504	0.0				p.G808S		.											.	.	.	0			c.G2422A						.						10.0	13.0	12.0					9																	140201611		1992	4163	6155	SO:0001583	missense	54932	exon22			GGGTGCCGTCGGC		CCDS48066.1, CCDS75942.1	9q34.3	2009-03-04			ENSG00000187609	ENSG00000187609			26023	protein-coding gene	gene with protein product							Standard	XM_005266093		Approved	LOC54932, FLJ20433, mut-7	uc004cmp.2	Q8N9H8	OTTHUMG00000156149	ENST00000340951.4:c.2422G>A	9.37:g.140201611C>T	ENSP00000340474:p.Gly808Ser	Somatic	9	0		WXS	Illumina HiSeq	.	15	7	NM_017820	Q6P1M1|Q8IXT8	Missense_Mutation	SNP	ENST00000340951.4	37	CCDS48066.1	.	.	.	.	.	.	.	.	.	.	C	18.33	3.599387	0.66332	.	.	ENSG00000187609	ENST00000342129;ENST00000340951	T;T	0.72835	-0.69;0.45	4.42	2.52	0.30459	.	.	.	.	.	T	0.64527	0.2606	L	0.29908	0.895	0.19300	N	0.999971	D;D	0.61697	0.989;0.99	P;P	0.51582	0.674;0.561	T	0.53968	-0.8363	9	0.59425	D	0.04	.	6.7559	0.23514	0.0:0.7217:0.1792:0.0991	.	446;808	Q8N9H8-3;Q8N9H8	.;MUT7_HUMAN	S	446;808	ENSP00000343705:G446S;ENSP00000340474:G808S	ENSP00000340474:G808S	G	-	1	0	EXD3	139321432	.	.	0.091000	0.20842	0.007000	0.05969	.	.	0.300000	0.22699	0.561000	0.74099	GGC	.		0.692	EXD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343182.1	NM_017820	
NOLC1	9221	hgsc.bcm.edu;bcgsc.ca	37	10	103916788	103916788	+	Missense_Mutation	SNP	G	G	A			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr10:103916788G>A	ENST00000605788.1	+	2	368	c.133G>A	c.(133-135)Gcc>Acc	p.A45T	NOLC1_ENST00000405356.1_Missense_Mutation_p.A45T|NOLC1_ENST00000488254.2_Missense_Mutation_p.A45T|NOLC1_ENST00000603742.1_5'UTR	NM_001284389.1|NM_004741.3	NP_001271318.1|NP_004732.2	Q14978	NOLC1_HUMAN	nucleolar and coiled-body phosphoprotein 1	45					cell cycle (GO:0007049)|mitotic nuclear division (GO:0007067)|nucleolus organization (GO:0007000)|rRNA processing (GO:0006364)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	31		Colorectal(252;0.122)		Epithelial(162;5.19e-08)|all cancers(201;9.43e-07)		ACAGCAGGATGCCAATGCCTC	0.413																																					p.A45T		.											.	.	.	0			c.G133A						.						242.0	237.0	239.0					10																	103916788		2203	4300	6503	SO:0001583	missense	9221	exon2			CAGGATGCCAATG	Z34289	CCDS7530.1, CCDS65925.1, CCDS65926.1	10q24.32	2008-08-01			ENSG00000166197	ENSG00000166197			15608	protein-coding gene	gene with protein product		602394				7657714, 10567578	Standard	XM_005270273		Approved	P130, KIAA0035, NOPP140, NOPP130	uc001kuo.2	Q14978	OTTHUMG00000018944	ENST00000605788.1:c.133G>A	10.37:g.103916788G>A	ENSP00000474710:p.Ala45Thr	Somatic	50	0		WXS	Illumina HiSeq	.	75	4	NM_004741	Q15030|Q5VV70|Q9BUV3	Missense_Mutation	SNP	ENST00000605788.1	37	CCDS7530.1	.	.	.	.	.	.	.	.	.	.	G	16.13	3.036421	0.54896	.	.	ENSG00000166197	ENST00000405356;ENST00000370007	T	0.43688	0.94	5.92	2.96	0.34315	.	0.165024	0.43416	D	0.000578	T	0.36799	0.0980	M	0.63428	1.95	0.33234	D	0.556268	P;P;B	0.34724	0.465;0.465;0.335	B;B;B	0.34242	0.178;0.178;0.086	T	0.50491	-0.8822	10	0.48119	T	0.1	-7.9818	7.511	0.27573	0.0:0.2461:0.4983:0.2556	.	45;45;45	Q14978-3;Q14978-2;Q14978	.;.;NOLC1_HUMAN	T	45	ENSP00000385410:A45T	ENSP00000359024:A45T	A	+	1	0	NOLC1	103906778	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.435000	0.44811	0.819000	0.34492	0.655000	0.94253	GCC	.		0.413	NOLC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050012.2	NM_004741	
LRP1B	53353	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	141660609	141660609	+	Missense_Mutation	SNP	C	C	G			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr2:141660609C>G	ENST00000389484.3	-	23	4617	c.3646G>C	c.(3646-3648)Gat>Cat	p.D1216H		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1216	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CTACAATAATCCACAATTTCA	0.433										TSP Lung(27;0.18)																											p.D1216H	Colon(99;50 2074 2507 20106)	.											.	.	.	0			c.G3646C						.						184.0	163.0	170.0					2																	141660609		2203	4300	6503	SO:0001583	missense	53353	exon23			AATAATCCACAAT	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.3646G>C	2.37:g.141660609C>G	ENSP00000374135:p.Asp1216His	Somatic	20	0		WXS	Illumina HiSeq	.	47	15	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	C	19.30	3.801151	0.70567	.	.	ENSG00000168702	ENST00000389484;ENST00000544579;ENST00000434794	D;D	0.88277	-2.36;-2.36	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	D	0.95108	0.8415	M	0.86805	2.84	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.87578	0.947;0.998	D	0.93106	0.6512	10	0.25106	T	0.35	.	19.8389	0.96675	0.0:1.0:0.0:0.0	.	399;1216	Q96NT6;Q9NZR2	.;LRP1B_HUMAN	H	1216;1154;361	ENSP00000374135:D1216H;ENSP00000413239:D361H	ENSP00000374135:D1216H	D	-	1	0	LRP1B	141377079	1.000000	0.71417	0.984000	0.44739	0.508000	0.34012	4.881000	0.63114	2.755000	0.94549	0.650000	0.86243	GAT	.		0.433	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
CCDC173	129881	hgsc.bcm.edu	37	2	170510628	170510628	+	Missense_Mutation	SNP	G	G	T	rs530807316	byFrequency	TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr2:170510628G>T	ENST00000447353.1	-	6	1021	c.916C>A	c.(916-918)Cgt>Agt	p.R306S		NM_001085447.1	NP_001078916.1	Q0VFZ6	CC173_HUMAN	coiled-coil domain containing 173	306																	TGTATAAGACGCTTTTTTGCT	0.323																																					p.R306S		.											.	.	.	0			c.C916A						.						133.0	115.0	121.0					2																	170510628		1812	4088	5900	SO:0001583	missense	129881	exon6			TAAGACGCTTTTT	BC015980, BC117445	CCDS46445.1	2q31.1	2012-08-07	2012-08-07	2012-08-07	ENSG00000154479	ENSG00000154479			25064	protein-coding gene	gene with protein product	"""hypothetical LOC129881"""		"""chromosome 2 open reading frame 77"""	C2orf77		12477932	Standard	NM_001085447		Approved	LOC129881	uc002ufe.2	Q0VFZ6	OTTHUMG00000154116	ENST00000447353.1:c.916C>A	2.37:g.170510628G>T	ENSP00000391504:p.Arg306Ser	Somatic	81	0		WXS	Illumina HiSeq	.	92	4	NM_001085447	Q6PJF6	Missense_Mutation	SNP	ENST00000447353.1	37	CCDS46445.1	.	.	.	.	.	.	.	.	.	.	G	10.48	1.361782	0.24684	.	.	ENSG00000154479	ENST00000447353	T	0.10288	2.89	5.04	0.98	0.19750	.	3.818340	0.00166	N	0.000001	T	0.14356	0.0347	M	0.65975	2.015	0.24973	N	0.99166	B	0.15141	0.012	B	0.23419	0.046	T	0.31503	-0.9941	10	0.33141	T	0.24	.	3.0791	0.06256	0.1773:0.1371:0.545:0.1406	.	306	Q0VFZ6	CB077_HUMAN	S	306	ENSP00000391504:R306S	ENSP00000391504:R306S	R	-	1	0	C2orf77	170218874	0.751000	0.28327	1.000000	0.80357	0.979000	0.70002	0.138000	0.16016	0.632000	0.30432	-0.961000	0.02630	CGT	.		0.323	CCDC173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333954.2	NM_001085447	
PRAMEF12	390999	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	12835030	12835030	+	Missense_Mutation	SNP	C	C	A			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr1:12835030C>A	ENST00000357726.4	+	1	47	c.20C>A	c.(19-21)cCt>cAt	p.P7H		NM_001080830.1	NP_001074299.1	O95522	PRA12_HUMAN	PRAME family member 12	7					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					NS(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(9)|ovary(3)|skin(1)|urinary_tract(1)	23	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00818)|Colorectal(212;5.04e-06)|Kidney(185;4.99e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000198)|COAD - Colon adenocarcinoma(227;0.000245)|BRCA - Breast invasive adenocarcinoma(304;0.000295)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		CAGGCCCCACCTAGACTCCTG	0.542																																					p.P7H		.											.	.	.	0			c.C20A						.						45.0	53.0	51.0					1																	12835030		2193	4299	6492	SO:0001583	missense	390999	exon1			CCCCACCTAGACT		CCDS41254.1	1p36.21	2013-01-17			ENSG00000116726	ENSG00000116726		"""-"""	22125	protein-coding gene	gene with protein product							Standard	NM_001080830		Approved	OTTHUMG00000001927	uc001aui.3	O95522	OTTHUMG00000001927	ENST00000357726.4:c.20C>A	1.37:g.12835030C>A	ENSP00000350358:p.Pro7His	Somatic	46	0		WXS	Illumina HiSeq	.	38	23	NM_001080830		Missense_Mutation	SNP	ENST00000357726.4	37	CCDS41254.1	.	.	.	.	.	.	.	.	.	.	.	12.49	1.955049	0.34471	.	.	ENSG00000116726	ENST00000357726	T	0.11169	2.8	2.68	0.576	0.17380	.	0.739872	0.11778	N	0.530441	T	0.28896	0.0717	M	0.79805	2.47	0.09310	N	1	D	0.89917	1.0	D	0.74348	0.983	T	0.06499	-1.0823	10	0.72032	D	0.01	.	5.8762	0.18830	0.2065:0.3877:0.4058:0.0	.	7	O95522	PRA12_HUMAN	H	7	ENSP00000350358:P7H	ENSP00000350358:P7H	P	+	2	0	PRAMEF12	12757617	0.000000	0.05858	0.020000	0.16555	0.181000	0.23173	-0.095000	0.11077	0.141000	0.18875	0.195000	0.17529	CCT	.		0.542	PRAMEF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005457.1	XM_372760	
GTF3C4	9329	hgsc.bcm.edu	37	9	135564267	135564267	+	Splice_Site	SNP	G	G	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr9:135564267G>T	ENST00000372146.4	+	5	2968		c.e5-1			NM_012204.2	NP_036336.2	Q9UKN8	TF3C4_HUMAN	general transcription factor IIIC, polypeptide 4, 90kDa						5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|positive regulation of catalytic activity (GO:0043085)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase III promoter (GO:0006384)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)|enzyme activator activity (GO:0008047)|histone acetyltransferase activity (GO:0004402)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|skin(1)	20				OV - Ovarian serous cystadenocarcinoma(145;8.15e-07)|Epithelial(140;2.6e-05)		TCCTTTTGCAGATCCCGACTG	0.478																																					.	Pancreas(142;417 1875 11086 31973 47667)	.											GTF3C4,right_upper_lobe,carcinoma,0,1	GTF3C4	0	0			c.2405-1G>T						.						173.0	151.0	158.0					9																	135564267		2203	4300	6503	SO:0001630	splice_region_variant	9329	exon5			TTTGCAGATCCCG	AF142328	CCDS6953.1	9q34.3	2011-07-01	2002-08-29		ENSG00000125484	ENSG00000125484		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""General transcription factors"""	4667	protein-coding gene	gene with protein product		604892	"""general transcription factor IIIC, polypeptide 4 (90kD)"""			10523658	Standard	NM_012204		Approved	TFIIIC90, KAT12	uc010mzv.3	Q9UKN8	OTTHUMG00000020842	ENST00000372146.4:c.2405-1G>T	9.37:g.135564267G>T		Somatic	33	0		WXS	Illumina HiSeq	.	39	2	NM_012204	Q5VZJ7	Splice_Site	SNP	ENST00000372146.4	37	CCDS6953.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.318522	0.81469	.	.	ENSG00000125484	ENST00000372146	.	.	.	5.71	5.71	0.89125	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.5914	0.84766	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GTF3C4	134554088	1.000000	0.71417	1.000000	0.80357	0.896000	0.52359	8.116000	0.89574	2.701000	0.92244	0.462000	0.41574	.	.		0.478	GTF3C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054792.1		Intron
AGBL2	79841	hgsc.bcm.edu	37	11	47727437	47727437	+	Missense_Mutation	SNP	G	G	T	rs200616669		TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr11:47727437G>T	ENST00000525123.1	-	5	550	c.265C>A	c.(265-267)Cag>Aag	p.Q89K	AGBL2_ENST00000529712.1_Intron|AGBL2_ENST00000298861.4_Missense_Mutation_p.Q89K|AGBL2_ENST00000357610.3_Missense_Mutation_p.Q89K|AGBL2_ENST00000528244.1_Missense_Mutation_p.Q89K	NM_024783.3	NP_079059.2	Q5U5Z8	CBPC2_HUMAN	ATP/GTP binding protein-like 2	89						cytosol (GO:0005829)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|endometrium(5)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(1)	34						GCTTCTATCTGTCTGTGCACA	0.463																																					p.Q89K		.											.	.	.	0			c.C265A						.						224.0	206.0	212.0					11																	47727437		2201	4298	6499	SO:0001583	missense	79841	exon5			CTATCTGTCTGTG		CCDS7944.1	11p11.2	2014-06-23			ENSG00000165923	ENSG00000165923			26296	protein-coding gene	gene with protein product	"""cytoplasmic carboxypeptidase 2"""					12738998, 21303978	Standard	NM_024783		Approved	FLJ23598, CCP2	uc001ngg.3	Q5U5Z8	OTTHUMG00000165368	ENST00000525123.1:c.265C>A	11.37:g.47727437G>T	ENSP00000435582:p.Gln89Lys	Somatic	68	0		WXS	Illumina HiSeq	.	97	4	NM_024783	A8MPX2|Q53FV5|Q8IV57|Q9H5C0	Missense_Mutation	SNP	ENST00000525123.1	37	CCDS7944.1	.	.	.	.	.	.	.	.	.	.	G	10.22	1.289684	0.23478	.	.	ENSG00000165923	ENST00000525123;ENST00000357610;ENST00000298861;ENST00000528244;ENST00000530577;ENST00000529154	T;T;T;T;T;T	0.42900	2.98;2.97;2.98;2.98;0.96;2.04	3.26	2.34	0.29019	.	1.966240	0.02879	N	0.132609	T	0.31167	0.0788	N	0.25647	0.755	0.09310	N	1	B;B	0.19817	0.039;0.013	B;B	0.18871	0.023;0.006	T	0.15983	-1.0418	10	0.22706	T	0.39	-0.5543	6.452	0.21908	0.1341:0.0:0.8659:0.0	.	89;89	F6U0I4;Q5U5Z8	.;CBPC2_HUMAN	K	89;89;89;89;69;89	ENSP00000435582:Q89K;ENSP00000350228:Q89K;ENSP00000298861:Q89K;ENSP00000436630:Q89K;ENSP00000432264:Q69K;ENSP00000436518:Q89K	ENSP00000298861:Q89K	Q	-	1	0	AGBL2	47684013	0.040000	0.19996	0.009000	0.14445	0.167000	0.22549	2.842000	0.48230	0.946000	0.37632	0.543000	0.68304	CAG	0.001		0.463	AGBL2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383726.2	NM_024783	
DDX10	1662	hgsc.bcm.edu;bcgsc.ca	37	11	108590611	108590611	+	Splice_Site	SNP	C	C	A			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr11:108590611C>A	ENST00000322536.3	+	12	1627	c.1498C>A	c.(1498-1500)Ctg>Atg	p.L500M	DDX10_ENST00000526794.1_Splice_Site_p.L500M	NM_004398.2	NP_004389.2	Q13206	DDX10_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10	500					metabolic process (GO:0008152)		ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			breast(2)|endometrium(5)|kidney(2)|large_intestine(4)|lung(11)|pancreas(1)|prostate(2)	27		all_cancers(61;1.29e-11)|all_epithelial(67;2.96e-07)|Melanoma(852;1.54e-05)|Acute lymphoblastic leukemia(157;4.24e-05)|all_hematologic(158;0.000141)|Breast(348;0.026)|all_neural(223;0.0729)		BRCA - Breast invasive adenocarcinoma(274;2.48e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.000609)|OV - Ovarian serous cystadenocarcinoma(223;0.133)		TGAATATGCCCTGTAAGTATT	0.348			T	NUP98	AML*																																p.L500M		.		Dom	yes		11	11q22-q23	1662	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10		L	.	.	.	0			c.C1498A						.						89.0	87.0	88.0					11																	108590611		2200	4298	6498	SO:0001630	splice_region_variant	1662	exon12			TATGCCCTGTAAG	U28042	CCDS8342.1	11q22-q23	2005-10-11	2003-06-13		ENSG00000178105	ENSG00000178105		"""DEAD-boxes"""	2735	protein-coding gene	gene with protein product		601235	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 10 (RNA helicase)"""			8660968	Standard	NM_004398		Approved	HRH-J8	uc001pkm.3	Q13206	OTTHUMG00000166540	ENST00000322536.3:c.1499+1C>A	11.37:g.108590611C>A		Somatic	74	0		WXS	Illumina HiSeq	.	97	4	NM_004398	B2RCQ3|Q5BJD8	Missense_Mutation	SNP	ENST00000322536.3	37	CCDS8342.1	.	.	.	.	.	.	.	.	.	.	C	9.691	1.151985	0.21371	.	.	ENSG00000178105	ENST00000322536;ENST00000456020;ENST00000526794	T;T	0.39787	1.06;1.06	5.5	3.63	0.41609	.	0.273852	0.35970	N	0.002865	T	0.38161	0.1030	L	0.39397	1.21	0.29801	N	0.832449	P;P	0.34909	0.475;0.475	B;B	0.40329	0.222;0.326	T	0.33214	-0.9877	10	0.36615	T	0.2	-8.914	12.1085	0.53825	0.0:0.8609:0.0:0.1391	.	500;500	Q13206;E9PIF2	DDX10_HUMAN;.	M	500;406;500	ENSP00000314348:L500M;ENSP00000432032:L500M	ENSP00000314348:L500M	L	+	1	2	DDX10	108095821	0.945000	0.32115	1.000000	0.80357	0.258000	0.26162	1.638000	0.37165	0.801000	0.34066	0.650000	0.86243	CTG	.		0.348	DDX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390343.1	NM_004398	Missense_Mutation
BAGE2	85319	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	21	11049582	11049582	+	RNA	SNP	C	C	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr21:11049582C>T	ENST00000470054.1	-	0	526							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2							extracellular region (GO:0005576)								Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TAAGAGGTCTCCCGGGCTGTC	0.398																																					p.E107K		.											.	.	.	0			c.G319A						.						71.0	56.0	61.0					21																	11049582		692	1590	2282			85318	exon4			AGGTCTCCCGGGC	AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172			15723	protein-coding gene	gene with protein product	"""cancer/testis antigen family 2, member 2"""					12461691	Standard	NM_182482		Approved	CT2.2		Q86Y30	OTTHUMG00000074128		21.37:g.11049582C>T		Somatic	114	0		WXS	Illumina HiSeq	.	147	8	NM_182481	A8K925|Q08ER0	Missense_Mutation	SNP	ENST00000470054.1	37																																																																																				.		0.398	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	NM_182482	
ZBBX	79740	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	167023497	167023497	+	Silent	SNP	G	G	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr3:167023497G>T	ENST00000392766.2	-	17	1999	c.1659C>A	c.(1657-1659)tcC>tcA	p.S553S	ZBBX_ENST00000392764.1_Silent_p.S524S|ZBBX_ENST00000392767.2_Silent_p.S553S|ZBBX_ENST00000455345.2_Silent_p.S553S|ZBBX_ENST00000307529.5_Silent_p.S553S	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	553						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(9)|liver(1)|lung(38)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	70						TCAATTCCAAGGATTCTTTGA	0.328																																					p.S553S		.											.	.	.	0			c.C1659A						.						72.0	64.0	67.0					3																	167023497		1810	4065	5875	SO:0001819	synonymous_variant	79740	exon17			TTCCAAGGATTCT	AK026702	CCDS3199.2, CCDS56295.1, CCDS56296.1	3q26.1	2010-03-23			ENSG00000169064	ENSG00000169064			26245	protein-coding gene	gene with protein product						12477932	Standard	NM_024687		Approved	FLJ23049	uc011bpc.2	A8MT70	OTTHUMG00000133560	ENST00000392766.2:c.1659C>A	3.37:g.167023497G>T		Somatic	51	0		WXS	Illumina HiSeq	.	109	48	NM_024687	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Silent	SNP	ENST00000392766.2	37	CCDS3199.2																																																																																			.		0.328	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687	
ZKSCAN3	80317	hgsc.bcm.edu	37	6	28333606	28333606	+	Silent	SNP	G	G	A			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr6:28333606G>A	ENST00000377255.3	+	7	1458	c.1161G>A	c.(1159-1161)aaG>aaA	p.K387K	ZKSCAN3_ENST00000341464.5_Silent_p.K239K|ZKSCAN3_ENST00000252211.2_Silent_p.K387K	NM_001242894.1	NP_001229823.1	Q9BRR0	ZKSC3_HUMAN	zinc finger with KRAB and SCAN domains 3	387					autophagy (GO:0006914)|lysosome organization (GO:0007040)|negative regulation of autophagy (GO:0010507)|negative regulation of cellular senescence (GO:2000773)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(4)|large_intestine(3)|lung(8)|pancreas(1)|skin(2)|stomach(2)|urinary_tract(1)	21						ACCTTATCAAGCATCAGAGAA	0.502																																					p.K387K		.											.	.	.	0			c.G1161A						.						93.0	92.0	93.0					6																	28333606		2203	4300	6503	SO:0001819	synonymous_variant	80317	exon6			TATCAAGCATCAG	U71601	CCDS4650.1, CCDS56408.1	6p22.1	2013-01-09	2007-02-20	2007-02-20		ENSG00000189298		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13853	protein-coding gene	gene with protein product		612791	"""zinc finger protein 306"", ""zinc finger protein 309"""	ZNF306, ZNF309		10520746, 22531714	Standard	NM_024493		Approved	Zfp47, ZF47, ZSCAN35	uc003nle.4	Q9BRR0	OTTHUMG00000014521	ENST00000377255.3:c.1161G>A	6.37:g.28333606G>A		Somatic	29	0		WXS	Illumina HiSeq	.	35	4	NM_024493	B2R8W2|B3KVC0|H7BXX1|Q5VXH3|Q92972|Q9H4T3	Silent	SNP	ENST00000377255.3	37	CCDS4650.1																																																																																			.		0.502	ZKSCAN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040189.3	NM_024493	
NOTCH2	4853	hgsc.bcm.edu	37	1	120539668	120539668	+	Missense_Mutation	SNP	T	T	A	rs200464440		TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr1:120539668T>A	ENST00000256646.2	-	4	922	c.703A>T	c.(703-705)Acc>Tcc	p.T235S	NOTCH2_ENST00000602566.1_Missense_Mutation_p.T196S	NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	235	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.				apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)			breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		TGCCGACAGGTGCCTCCATTG	0.572			"""N, F, Mis"""		"""marginal zone lymphoma, DLBCL"""				Alagille Syndrome																												p.T235S		.		Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	NOTCH2_ENST00000369342,NS,carcinoma,0,2	NOTCH2_ENST00000369342	0	0			c.A703T						.						50.0	40.0	43.0					1																	120539668		2203	4299	6502	SO:0001583	missense	4853	exon4	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	GACAGGTGCCTCC	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"""Ankyrin repeat domain containing"""	7882	protein-coding gene	gene with protein product		600275	"""Notch (Drosophila) homolog 2"", ""Notch homolog 2 (Drosophila)"""			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.703A>T	1.37:g.120539668T>A	ENSP00000256646:p.Thr235Ser	Somatic	11	0		WXS	Illumina HiSeq	.	35	2	NM_001200001	Q5T3X7|Q99734|Q9H240	Missense_Mutation	SNP	ENST00000256646.2	37	CCDS908.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.508758	0.85282	.	.	ENSG00000134250	ENST00000256646;ENST00000539617;ENST00000401649;ENST00000369342	T	0.33438	1.41	5.83	5.83	0.93111	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.38897	U	0.001527	T	0.42471	0.1204	L	0.58510	1.815	0.80722	D	1	P;D;D	0.71674	0.924;0.998;0.965	P;D;P	0.77004	0.585;0.989;0.834	T	0.25082	-1.0142	10	0.41790	T	0.15	.	15.3661	0.74523	0.0:0.0:0.0:1.0	.	196;235;235	D2WEZ3;Q6IQ50;Q04721	.;.;NOTC2_HUMAN	S	235;196;208;196	ENSP00000256646:T235S	ENSP00000256646:T235S	T	-	1	0	NOTCH2	120341191	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	6.185000	0.72013	2.216000	0.71823	0.477000	0.44152	ACC	.		0.572	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408	
SPICE1	152185	hgsc.bcm.edu	37	3	113187725	113187725	+	Missense_Mutation	SNP	G	G	A			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr3:113187725G>A	ENST00000295872.4	-	9	1032	c.773C>T	c.(772-774)gCt>gTt	p.A258V		NM_144718.3	NP_653319.1	Q8N0Z3	SPICE_HUMAN	spindle and centriole associated protein 1	258					metaphase plate congression (GO:0051310)|regulation of centriole replication (GO:0046599)|spindle assembly involved in mitosis (GO:0090307)	centriole (GO:0005814)|centrosome (GO:0005813)|spindle (GO:0005819)				NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(3)|large_intestine(9)|lung(10)|ovary(2)|skin(2)|urinary_tract(1)	33						TCTCTTGACAGCATTGGTAGC	0.413																																					p.A258V		.											SPICE1_ENST00000295872,rectum,carcinoma,0,2	SPICE1_ENST00000295872	0	0			c.C773T						.						88.0	79.0	82.0					3																	113187725		2203	4300	6503	SO:0001583	missense	152185	exon9			TTGACAGCATTGG	AY099107	CCDS2973.1	3q13.2	2010-09-01	2010-09-01	2010-09-01	ENSG00000163611	ENSG00000163611			25083	protein-coding gene	gene with protein product	"""spindle and centriole protein"""	613447	"""coiled-coil domain containing 52"""	CCDC52		20736305	Standard	NM_144718		Approved	SPICE	uc003eag.4	Q8N0Z3	OTTHUMG00000159261	ENST00000295872.4:c.773C>T	3.37:g.113187725G>A	ENSP00000295872:p.Ala258Val	Somatic	42	0		WXS	Illumina HiSeq	.	45	2	NM_144718	D3DN72|Q8WUX6	Missense_Mutation	SNP	ENST00000295872.4	37	CCDS2973.1	.	.	.	.	.	.	.	.	.	.	G	10.73	1.433986	0.25813	.	.	ENSG00000163611	ENST00000295872	T	0.32515	1.45	5.05	3.24	0.37175	.	0.289600	0.37906	N	0.001898	T	0.17323	0.0416	L	0.33245	0.995	0.41048	D	0.985286	P;P	0.41393	0.748;0.506	B;B	0.36134	0.218;0.218	T	0.04268	-1.0964	10	0.23891	T	0.37	-8.2206	5.4437	0.16523	0.3329:0.0:0.6671:0.0	.	154;258	B3KX77;Q8N0Z3	.;SPICE_HUMAN	V	258	ENSP00000295872:A258V	ENSP00000295872:A258V	A	-	2	0	SPICE1	114670415	0.995000	0.38212	0.996000	0.52242	0.045000	0.14185	2.968000	0.49224	1.263000	0.44181	-0.218000	0.12543	GCT	.		0.413	SPICE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354177.2	NM_144718	
PRMT3	10196	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	11	20473693	20473693	+	Missense_Mutation	SNP	T	T	G			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr11:20473693T>G	ENST00000331079.6	+	11	1228	c.1011T>G	c.(1009-1011)ttT>ttG	p.F337L	PRMT3_ENST00000437750.2_Missense_Mutation_p.F275L	NM_001145167.1|NM_005788.3	NP_001138639.1|NP_005779	O60678	ANM3_HUMAN	protein arginine methyltransferase 3	337	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				histone arginine methylation (GO:0034969)|negative regulation of protein ubiquitination (GO:0031397)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|ribosome (GO:0005840)	histone-arginine N-methyltransferase activity (GO:0008469)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|modified amino acid binding (GO:0072341)|protein-arginine N-methyltransferase activity (GO:0016274)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)			endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|prostate(1)	17						TTCTTCTGTTTGAGTCTATGT	0.338																																					p.F337L		.											.	.	.	0			c.T1011G						.						156.0	150.0	152.0					11																	20473693		2203	4300	6503	SO:0001583	missense	10196	exon11			TCTGTTTGAGTCT	AF059531	CCDS7853.1, CCDS44554.1	11p15.1	2008-02-05	2006-02-16	2006-02-16	ENSG00000185238	ENSG00000185238		"""Protein arginine methyltransferases"""	30163	protein-coding gene	gene with protein product		603190	"""HMT1 hnRNP methyltransferase-like 3 (S. cerevisiae)"""	HRMT1L3		9642256	Standard	NM_005788		Approved		uc001mqb.3	O60678	OTTHUMG00000166022	ENST00000331079.6:c.1011T>G	11.37:g.20473693T>G	ENSP00000331879:p.Phe337Leu	Somatic	85	0		WXS	Illumina HiSeq	.	110	7	NM_005788	B4DUC7	Missense_Mutation	SNP	ENST00000331079.6	37	CCDS7853.1	.	.	.	.	.	.	.	.	.	.	T	15.10	2.732060	0.48939	.	.	ENSG00000185238	ENST00000331079;ENST00000541255;ENST00000437750	T;T	0.21932	1.98;1.98	5.69	2.15	0.27550	.	0.044001	0.85682	N	0.000000	T	0.12178	0.0296	N	0.13168	0.305	0.53688	D	0.999979	B;B	0.31949	0.348;0.011	B;B	0.32624	0.149;0.031	T	0.11842	-1.0571	10	0.72032	D	0.01	-12.6888	9.1974	0.37237	0.0:0.208:0.0:0.792	.	275;337	O60678-2;O60678	.;ANM3_HUMAN	L	337;337;275	ENSP00000331879:F337L;ENSP00000397766:F275L	ENSP00000331879:F337L	F	+	3	2	PRMT3	20430269	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	0.987000	0.29603	0.120000	0.18254	-0.262000	0.10625	TTT	.		0.338	PRMT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387489.1	NM_005788	
BCO2	83875	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	112070469	112070469	+	Missense_Mutation	SNP	G	G	A			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr11:112070469G>A	ENST00000357685.5	+	6	919	c.784G>A	c.(784-786)Ggg>Agg	p.G262R	BCO2_ENST00000438022.1_Missense_Mutation_p.G228R|BCO2_ENST00000526088.1_Missense_Mutation_p.G228R|AP002884.3_ENST00000532612.1_Missense_Mutation_p.G160R|BCO2_ENST00000393032.2_Missense_Mutation_p.G228R|BCO2_ENST00000532593.1_Missense_Mutation_p.G157R|BCO2_ENST00000531169.1_Missense_Mutation_p.G228R|BCO2_ENST00000361053.4_Missense_Mutation_p.G189R			Q9BYV7	BCDO2_HUMAN	beta-carotene oxygenase 2	262					carotene catabolic process (GO:0016121)|carotene metabolic process (GO:0016119)|carotenoid metabolic process (GO:0016116)|oxidation-reduction process (GO:0055114)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of reactive oxygen species metabolic process (GO:2000377)|retinal metabolic process (GO:0042574)|retinoic acid metabolic process (GO:0042573)	intracellular (GO:0005622)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			NS(1)|breast(1)|kidney(3)|large_intestine(1)|lung(9)|skin(1)	16						GGTGGACCTTGGGGAGACAAT	0.403																																					p.G262R	GBM(177;1916 2099 21049 29541 39946)	.											.	.	.	0			c.G784A						.						162.0	163.0	162.0					11																	112070469		2201	4297	6498	SO:0001583	missense	83875	exon6			GACCTTGGGGAGA	AJ290393	CCDS8358.2, CCDS41716.1, CCDS58181.1, CCDS58182.1, CCDS58183.1	11q23.1	2014-05-12	2008-04-15	2008-04-15	ENSG00000197580	ENSG00000197580	1.13.11.71		18503	protein-coding gene	gene with protein product	"""beta-carotene 9',10' oxygenase"", ""carotenoid-9',10'-cleaving dioxygenase"""	611740	"""beta-carotene dioxygenase 2"""	BCDO2		11278918, 15983114, 15949678	Standard	NM_031938		Approved	FLJ34464, B-DIOX-II	uc001pnf.3	Q9BYV7	OTTHUMG00000167155	ENST00000357685.5:c.784G>A	11.37:g.112070469G>A	ENSP00000350314:p.Gly262Arg	Somatic	37	0		WXS	Illumina HiSeq	.	64	21	NM_031938	B0YIX5|B4DNC3|E9PBI8|E9PJJ1|Q8IUS0|Q96JC8|Q96JY5	Missense_Mutation	SNP	ENST00000357685.5	37	CCDS8358.2	.	.	.	.	.	.	.	.	.	.	G	4.780	0.144983	0.09134	.	.	ENSG00000197580	ENST00000357685;ENST00000393032;ENST00000361053;ENST00000438022;ENST00000526088;ENST00000532593;ENST00000531169	D;D;D;D;D;D;D	0.95788	-3.81;-3.8;-3.5;-3.8;-3.79;-3.65;-3.8	5.72	3.81	0.43845	.	0.729507	0.14194	N	0.335146	D	0.92890	0.7738	L	0.31065	0.9	0.09310	N	1	B;P;B;B	0.50369	0.188;0.934;0.119;0.311	B;P;B;B	0.50537	0.222;0.643;0.222;0.158	D	0.85463	0.1168	10	0.25751	T	0.34	-4.6846	10.0107	0.41984	0.1241:0.1145:0.7613:0.0	.	239;189;262;89	C9JEZ9;E9PBI8;Q9BYV7;Q8NAZ7	.;.;BCDO2_HUMAN;.	R	262;228;189;228;228;157;228	ENSP00000350314:G262R;ENSP00000376752:G228R;ENSP00000354338:G189R;ENSP00000414843:G228R;ENSP00000436615:G228R;ENSP00000431802:G157R;ENSP00000437053:G228R	ENSP00000350314:G262R	G	+	1	0	BCO2	111575679	0.007000	0.16637	0.043000	0.18650	0.060000	0.15804	1.399000	0.34566	1.411000	0.46957	0.655000	0.94253	GGG	.		0.403	BCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256570.3	NM_001037290	
GBE1	2632	hgsc.bcm.edu	37	3	81539564	81539564	+	Silent	SNP	C	C	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr3:81539564C>T	ENST00000429644.2	-	16	2746	c.2103G>A	c.(2101-2103)ccG>ccA	p.P701P	GBE1_ENST00000489715.1_Silent_p.P660P	NM_000158.3	NP_000149	Q04446	GLGB_HUMAN	glucan (1,4-alpha-), branching enzyme 1	701					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	1,4-alpha-glucan branching enzyme activity (GO:0003844)|cation binding (GO:0043169)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			breast(1)|endometrium(5)|large_intestine(2)|lung(4)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Lung NSC(201;0.0117)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0654)|Epithelial(33;0.00305)|LUSC - Lung squamous cell carcinoma(29;0.00646)|BRCA - Breast invasive adenocarcinoma(55;0.00813)|Lung(72;0.0129)|KIRC - Kidney renal clear cell carcinoma(39;0.212)|Kidney(39;0.247)		CTCTTCAATTCGGCAGATCCA	0.418									Glycogen Storage Disease, type IV																												p.P701P		.											GBE1_ENST00000429644,NS,carcinoma,0,2	GBE1_ENST00000429644	0	0			c.G2103A						.						138.0	128.0	131.0					3																	81539564		1933	4130	6063	SO:0001819	synonymous_variant	2632	exon16	Familial Cancer Database	Andersen Disease, Brancher deficiency	TCAATTCGGCAGA		CCDS54612.1	3p12.2	2013-09-20	2008-08-01		ENSG00000114480	ENSG00000114480	2.4.1.18		4180	protein-coding gene	gene with protein product	"""glycogen branching enzyme"", ""Andersen disease"", ""glycogen storage disease type IV"""	607839				8463281	Standard	NM_000158		Approved		uc021xav.1	Q04446	OTTHUMG00000158978	ENST00000429644.2:c.2103G>A	3.37:g.81539564C>T		Somatic	30	0		WXS	Illumina HiSeq	.	26	2	NM_000158	B3KWV3|Q96EN0	Silent	SNP	ENST00000429644.2	37	CCDS54612.1																																																																																			.		0.418	GBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352760.2		
XIRP2	129446	hgsc.bcm.edu	37	2	168104508	168104508	+	Missense_Mutation	SNP	G	G	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr2:168104508G>T	ENST00000409195.1	+	9	6695	c.6606G>T	c.(6604-6606)aaG>aaT	p.K2202N	XIRP2_ENST00000295237.9_Missense_Mutation_p.K2202N|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.K1980N|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409043.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2027					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						TAAAGAAAAAGAATATAAACC	0.353																																					p.K2202N		.											XIRP2,colon,carcinoma,0,1	XIRP2	0	0			c.G6606T						.						36.0	34.0	35.0					2																	168104508		1818	4075	5893	SO:0001583	missense	129446	exon9			GAAAAAGAATATA	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.6606G>T	2.37:g.168104508G>T	ENSP00000386840:p.Lys2202Asn	Somatic	28	0		WXS	Illumina HiSeq	.	49	2	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	37	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	G	0.005	-2.200634	0.00296	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.22336	1.96;1.96;1.96	5.92	-4.28	0.03732	.	0.755817	0.12987	N	0.422788	T	0.07773	0.0195	N	0.14661	0.345	0.19575	N	0.999967	B;B;B	0.11235	0.001;0.002;0.004	B;B;B	0.08055	0.001;0.003;0.003	T	0.36578	-0.9742	10	0.13853	T	0.58	-3.01	4.1761	0.10353	0.077:0.206:0.3995:0.3175	.	2027;2027;1980	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	N	2202;2202;1980	ENSP00000386840:K2202N;ENSP00000295237:K2202N;ENSP00000387255:K1980N	ENSP00000295237:K2202N	K	+	3	2	XIRP2	167812754	0.001000	0.12720	0.007000	0.13788	0.005000	0.04900	-0.259000	0.08721	-0.621000	0.05633	-0.188000	0.12872	AAG	.		0.353	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
ANK1	286	hgsc.bcm.edu	37	8	41571689	41571689	+	Silent	SNP	C	C	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr8:41571689C>T	ENST00000347528.4	-	16	1868	c.1785G>A	c.(1783-1785)ccG>ccA	p.P595P	ANK1_ENST00000289734.7_Silent_p.P595P|ANK1_ENST00000352337.4_Silent_p.P595P|ANK1_ENST00000396945.1_Silent_p.P595P|ANK1_ENST00000265709.8_Silent_p.P628P|ANK1_ENST00000396942.1_Silent_p.P595P|ANK1_ENST00000379758.2_Silent_p.P595P	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	595	89 kDa domain.				axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|ER to Golgi vesicle-mediated transport (GO:0006888)|erythrocyte development (GO:0048821)|exocytosis (GO:0006887)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|monovalent inorganic cation transport (GO:0015672)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of organelle organization (GO:0010638)|protein targeting to plasma membrane (GO:0072661)|signal transduction (GO:0007165)	axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|M band (GO:0031430)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|cytoskeletal adaptor activity (GO:0008093)|enzyme binding (GO:0019899)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(4)|endometrium(9)|kidney(1)|large_intestine(26)|lung(62)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	122	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			CAGGGCTGTGCGGGGAGCCGC	0.667																																					p.P628P		.											.	.	.	0			c.G1884A						.						15.0	18.0	17.0					8																	41571689		2200	4295	6495	SO:0001819	synonymous_variant	286	exon16			GCTGTGCGGGGAG	M28880	CCDS6119.1, CCDS6121.1, CCDS6122.1, CCDS47849.1, CCDS55227.1	8p11.21	2013-01-10			ENSG00000029534	ENSG00000029534		"""Ankyrin repeat domain containing"""	492	protein-coding gene	gene with protein product		612641		ANK		1689849	Standard	NM_001142445		Approved	SPH1	uc003xom.3	P16157	OTTHUMG00000150281	ENST00000347528.4:c.1785G>A	8.37:g.41571689C>T		Somatic	77	0		WXS	Illumina HiSeq	.	116	5	NM_001142446	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Silent	SNP	ENST00000347528.4	37	CCDS6119.1																																																																																			.		0.667	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475	
FAT3	120114	hgsc.bcm.edu	37	11	92599977	92599977	+	Missense_Mutation	SNP	G	G	T	rs376837097		TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr11:92599977G>T	ENST00000298047.6	+	21	11746	c.11729G>T	c.(11728-11730)cGt>cTt	p.R3910L	FAT3_ENST00000533797.1_Missense_Mutation_p.R245L|FAT3_ENST00000409404.2_Missense_Mutation_p.R3910L|FAT3_ENST00000525166.1_Missense_Mutation_p.R3760L			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	3910	Laminin G-like. {ECO:0000255|PROSITE- ProRule:PRU00122}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R3910L(2)|p.R485L(1)		NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				ATCTCGGGCCGTGCTGTCAAC	0.627										TCGA Ovarian(4;0.039)																											p.R3910L		.											FAT3_ENST00000409404,NS,carcinoma,0,3	FAT3_ENST00000409404	0	3	Substitution - Missense(3)	lung(3)	c.G11729T						.	G	LEU/ARG	0,4088		0,0,2044	34.0	39.0	37.0		11729	5.8	1.0	11		37	1,8383		0,1,4191	no	missense	FAT3	NM_001008781.2	102	0,1,6235	TT,TG,GG		0.0119,0.0,0.0080	possibly-damaging	3910/4558	92599977	1,12471	2044	4192	6236	SO:0001583	missense	120114	exon21			CGGGCCGTGCTGT	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"""Cadherins / Cadherin-related"""	23112	protein-coding gene	gene with protein product	"""cadherin-related family member 10"""	612483	"""FAT tumor suppressor homolog 3 (Drosophila)"""			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.11729G>T	11.37:g.92599977G>T	ENSP00000298047:p.Arg3910Leu	Somatic	27	0		WXS	Illumina HiSeq	.	54	3	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	37		.	.	.	.	.	.	.	.	.	.	G	16.94	3.261193	0.59431	0.0	1.19E-4	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166;ENST00000533797	T;T;T;T	0.78246	-1.16;-1.16;-1.16;-1.16	5.77	5.77	0.91146	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	.	.	.	.	T	0.81992	0.4940	L	0.43152	1.355	0.80722	D	1	D;B	0.67145	0.996;0.073	P;B	0.61722	0.893;0.115	T	0.75306	-0.3364	9	0.11485	T	0.65	.	19.9934	0.97376	0.0:0.0:1.0:0.0	.	3910;3910	Q8TDW7-3;Q8TDW7	.;FAT3_HUMAN	L	3910;3910;3760;245	ENSP00000298047:R3910L;ENSP00000387040:R3910L;ENSP00000432586:R3760L;ENSP00000436399:R245L	ENSP00000298047:R3910L	R	+	2	0	FAT3	92239625	1.000000	0.71417	0.964000	0.40570	0.724000	0.41520	6.323000	0.72891	2.732000	0.93576	0.561000	0.74099	CGT	.		0.627	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
MIR3689A	100500846	hgsc.bcm.edu	37	9	137741921	137741921	+	RNA	SNP	G	G	C			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr9:137741921G>C	ENST00000578854.1	-	0	0				AL603650.2_ENST00000581079.1_RNA|AL603650.3_ENST00000582742.1_RNA|MIR3689F_ENST00000579617.1_RNA|MIR3689D2_ENST00000580187.1_RNA|MIR3689D1_ENST00000579706.1_RNA|MIR3689E_ENST00000582479.1_RNA|AL603650.1_ENST00000583957.1_RNA|AL603650.4_ENST00000583817.1_RNA|MIR3689C_ENST00000581239.1_RNA|MIR3689B_ENST00000581772.1_RNA	NR_037460.1				microRNA 3689a																		CAGGGAGCACGGGATCACACC	0.607																																					.		.											.	.	.	0			.						.																																					100500846	.			GAGCACGGGATCA			9	2011-09-12				ENSG00000265872		"""ncRNAs / Micro RNAs"""	38904	non-coding RNA	RNA, micro							Standard	NR_037460		Approved	hsa-mir-3689a	uc022bpb.1				9.37:g.137741921G>C		Somatic	42	0		WXS	Illumina HiSeq	.	54	6	.		RNA	SNP	ENST00000578854.1	37																																																																																				.		0.607	MIR3689A-201	KNOWN	basic	miRNA	miRNA		NR_037460	
TAAR8	83551	hgsc.bcm.edu	37	6	132874213	132874213	+	Missense_Mutation	SNP	G	G	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr6:132874213G>T	ENST00000275200.1	+	1	382	c.382G>T	c.(382-384)Gac>Tac	p.D128Y		NM_053278.1	NP_444508.1	Q969N4	TAAR8_HUMAN	trace amine associated receptor 8	128					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|trace-amine receptor activity (GO:0001594)			endometrium(3)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22	Breast(56;0.112)			OV - Ovarian serous cystadenocarcinoma(155;0.00412)|GBM - Glioblastoma multiforme(226;0.00792)		CATCTGCATCGACAGGTACAT	0.478																																					p.D128Y		.											TAAR8,colon,carcinoma,0,1	TAAR8	0	0			c.G382T						.						347.0	304.0	319.0					6																	132874213		2203	4300	6503	SO:0001583	missense	83551	exon1			TGCATCGACAGGT	AF380193	CCDS5154.1	6q23.2	2014-05-14	2005-02-23	2005-02-24	ENSG00000146385	ENSG00000146385		"""GPCR / Class A : Trace amine associated receptors"""	14964	protein-coding gene	gene with protein product		606927	"""trace amine receptor 5"""	GPR102, TRAR5		11574155, 15718104	Standard	NM_053278		Approved	TA5, TAR5	uc011ecj.2	Q969N4	OTTHUMG00000015586	ENST00000275200.1:c.382G>T	6.37:g.132874213G>T	ENSP00000275200:p.Asp128Tyr	Somatic	28	0		WXS	Illumina HiSeq	.	30	2	NM_053278	Q5VUQ0	Missense_Mutation	SNP	ENST00000275200.1	37	CCDS5154.1	.	.	.	.	.	.	.	.	.	.	G	14.67	2.603324	0.46423	.	.	ENSG00000146385	ENST00000275200	D	0.85861	-2.04	4.72	3.84	0.44239	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000016	D	0.95532	0.8548	H	0.99867	4.865	0.45962	D	0.99878	D	0.89917	1.0	D	0.91635	0.999	D	0.96923	0.9675	10	0.87932	D	0	-17.0667	13.4605	0.61225	0.0763:0.0:0.9237:0.0	.	128	Q969N4	TAAR8_HUMAN	Y	128	ENSP00000275200:D128Y	ENSP00000275200:D128Y	D	+	1	0	TAAR8	132915906	1.000000	0.71417	0.897000	0.35233	0.228000	0.25075	5.548000	0.67255	1.329000	0.45376	0.655000	0.94253	GAC	.		0.478	TAAR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042262.1	NM_053278	
WDR74	54663	hgsc.bcm.edu	37	11	62601270	62601270	+	Silent	SNP	C	C	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr11:62601270C>T	ENST00000525239.1	-	10	1452	c.915G>A	c.(913-915)gaG>gaA	p.E305E	STX5_ENST00000294179.3_5'Flank|WDR74_ENST00000525752.1_Silent_p.E248E|RP11-727F15.9_ENST00000535817.1_RNA|WDR74_ENST00000540620.1_5'Flank|WDR74_ENST00000529106.1_Silent_p.E305E|STX5_ENST00000377897.4_5'Flank|WDR74_ENST00000278856.4_Silent_p.E305E|RP11-727F15.9_ENST00000535867.1_RNA|WDR74_ENST00000311713.7_Silent_p.E305E|STX5_ENST00000394690.1_5'Flank|STX5_ENST00000541317.1_5'Flank			Q6RFH5	WDR74_HUMAN	WD repeat domain 74	305					blastocyst formation (GO:0001825)|RNA metabolic process (GO:0016070)	nucleolus (GO:0005730)|nucleus (GO:0005634)				kidney(2)|large_intestine(1)|liver(1)|lung(3)|ovary(1)	8						TTACCTTATGCTCCAGACCCC	0.567																																					p.E305E		.											WDR74_ENST00000525239,NS,carcinoma,0,2	WDR74_ENST00000525239	0	0			c.G915A						.						93.0	97.0	96.0					11																	62601270		1994	4170	6164	SO:0001819	synonymous_variant	54663	exon10			CTTATGCTCCAGA		CCDS44630.1	11q12.3	2013-01-09				ENSG00000133316		"""WD repeat domain containing"""	25529	protein-coding gene	gene with protein product							Standard	NM_018093		Approved	FLJ10439	uc001nvm.2	Q6RFH5		ENST00000525239.1:c.915G>A	11.37:g.62601270C>T		Somatic	34	0		WXS	Illumina HiSeq	.	47	2	NM_018093	A8K8G5|Q9BRC9|Q9H6X8|Q9NVY2	Silent	SNP	ENST00000525239.1	37	CCDS44630.1																																																																																			.		0.567	WDR74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395678.1	NM_018093	
SAMD9	54809	hgsc.bcm.edu	37	7	92734778	92734778	+	Silent	SNP	G	G	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr7:92734778G>T	ENST00000379958.2	-	3	902	c.633C>A	c.(631-633)gtC>gtA	p.V211V		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	211						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			ATTTCATCTTGACATCCTCTT	0.403																																					p.V211V		.											.	.	.	0			c.C633A						.						132.0	126.0	128.0					7																	92734778		2203	4300	6503	SO:0001819	synonymous_variant	54809	exon2			CATCTTGACATCC	AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"""Sterile alpha motif (SAM) domain containing"""	1348	protein-coding gene	gene with protein product		610456	"""chromosome 7 open reading frame 5"""	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.633C>A	7.37:g.92734778G>T		Somatic	45	0		WXS	Illumina HiSeq	.	77	4	NM_001193307	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Silent	SNP	ENST00000379958.2	37	CCDS34680.1																																																																																			.		0.403	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654	
DENND1C	79958	hgsc.bcm.edu	37	19	6476920	6476920	+	Missense_Mutation	SNP	G	G	A			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr19:6476920G>A	ENST00000381480.2	-	10	738	c.626C>T	c.(625-627)gCg>gTg	p.A209V	DENND1C_ENST00000591030.1_5'Flank|DENND1C_ENST00000543576.1_Missense_Mutation_p.A165V	NM_024898.2	NP_079174.2	Q8IV53	DEN1C_HUMAN	DENN/MADD domain containing 1C	209	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				positive regulation of Rab GTPase activity (GO:0032851)	cytoplasmic vesicle (GO:0031410)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			endometrium(3)|kidney(3)|large_intestine(1)|lung(3)	10						CAGGAGCGCCGCGAACAGCCC	0.692																																					p.A209V		.											DENND1C_ENST00000381480,colon,carcinoma,0,2	DENND1C_ENST00000381480	0	0			c.C626T						.						34.0	41.0	39.0					19																	6476920		1993	4158	6151	SO:0001583	missense	79958	exon10			AGCGCCGCGAACA	AL713770	CCDS45938.1	19p13.3	2014-02-06	2005-08-17	2005-08-17	ENSG00000205744	ENSG00000205744		"""DENN/MADD domain containing"""	26225	protein-coding gene	gene with protein product		613634	"""family with sequence similarity 31, member C"""	FAM31C		12477932	Standard	XM_005259646		Approved	FLJ22757	uc002mfe.3	Q8IV53	OTTHUMG00000180853	ENST00000381480.2:c.626C>T	19.37:g.6476920G>A	ENSP00000370889:p.Ala209Val	Somatic	31	0		WXS	Illumina HiSeq	.	42	2	NM_024898	B4E051|D3PFD4|Q8NDB1|Q9H5Z2	Missense_Mutation	SNP	ENST00000381480.2	37	CCDS45938.1	.	.	.	.	.	.	.	.	.	.	g	25.4	4.638749	0.87760	.	.	ENSG00000205744	ENST00000381480;ENST00000543576	T;T	0.11930	2.73;2.73	4.73	3.65	0.41850	DENN (3);	0.387112	0.25648	N	0.029223	T	0.36054	0.0953	M	0.77712	2.385	0.42608	D	0.9933	D	0.89917	1.0	D	0.79784	0.993	T	0.26087	-1.0113	10	0.87932	D	0	-9.7937	12.1118	0.53844	0.0:0.221:0.779:0.0	.	209	Q8IV53	DEN1C_HUMAN	V	209;165	ENSP00000370889:A209V;ENSP00000437805:A165V	ENSP00000370889:A209V	A	-	2	0	DENND1C	6427920	1.000000	0.71417	0.996000	0.52242	0.941000	0.58515	3.652000	0.54439	2.173000	0.68751	0.556000	0.70494	GCG	.		0.692	DENND1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453332.2	NM_024898	
ITPR2	3709	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	26755371	26755371	+	Nonsense_Mutation	SNP	G	G	A			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr12:26755371G>A	ENST00000381340.3	-	28	4026	c.3610C>T	c.(3610-3612)Caa>Taa	p.Q1204*		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	1204					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	AGTAATCGTTGATGTTGATTC	0.358																																					p.Q1204X		.											.	.	.	0			c.C3610T						.						101.0	95.0	97.0					12																	26755371		1824	4074	5898	SO:0001587	stop_gained	3709	exon28			ATCGTTGATGTTG	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"""Ion channels / Inositol triphosphate receptors"""	6181	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 48"""	600144	"""inositol 1,4,5-triphosphate receptor, type 2"""			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.3610C>T	12.37:g.26755371G>A	ENSP00000370744:p.Gln1204*	Somatic	97	0		WXS	Illumina HiSeq	.	116	34	NM_002223	O94773	Nonsense_Mutation	SNP	ENST00000381340.3	37	CCDS41764.1	.	.	.	.	.	.	.	.	.	.	G	47	13.526431	0.99747	.	.	ENSG00000123104	ENST00000381340	.	.	.	5.46	5.46	0.80206	.	0.119289	0.64402	D	0.000010	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.5125	0.95148	0.0:0.0:1.0:0.0	.	.	.	.	X	1204	.	ENSP00000370744:Q1204X	Q	-	1	0	ITPR2	26646638	1.000000	0.71417	0.944000	0.38274	0.982000	0.71751	9.463000	0.97652	2.840000	0.97914	0.655000	0.94253	CAA	.		0.358	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	
ITPR2	3709	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	26755405	26755405	+	Silent	SNP	G	G	A			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr12:26755405G>A	ENST00000381340.3	-	28	3992	c.3576C>T	c.(3574-3576)ctC>ctT	p.L1192L		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	1192					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	TCTGCACACAGAGTTTACTTA	0.333																																					p.L1192L		.											.	.	.	0			c.C3576T						.						87.0	81.0	83.0					12																	26755405		1813	4071	5884	SO:0001819	synonymous_variant	3709	exon28			CACACAGAGTTTA	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"""Ion channels / Inositol triphosphate receptors"""	6181	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 48"""	600144	"""inositol 1,4,5-triphosphate receptor, type 2"""			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.3576C>T	12.37:g.26755405G>A		Somatic	92	0		WXS	Illumina HiSeq	.	118	29	NM_002223	O94773	Silent	SNP	ENST00000381340.3	37	CCDS41764.1																																																																																			.		0.333	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	
INO80	54617	hgsc.bcm.edu	37	15	41297827	41297827	+	Nonsense_Mutation	SNP	G	G	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr15:41297827G>T	ENST00000361937.3	-	28	3885	c.3461C>A	c.(3460-3462)tCg>tAg	p.S1154*	INO80_ENST00000561244.1_5'Flank|INO80_ENST00000401393.3_Nonsense_Mutation_p.S1154*|RP11-540O11.6_ENST00000561388.1_RNA			Q9ULG1	INO80_HUMAN	INO80 complex subunit	1154	Assembles INO80 complex module consisting of conserved components INO80B, INO80C, ACTR5, RVBL1, RVBL2.|Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|mitotic sister chromatid segregation (GO:0000070)|positive regulation of cell growth (GO:0030307)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|spindle assembly (GO:0051225)|UV-damage excision repair (GO:0070914)	Ino80 complex (GO:0031011)|microtubule (GO:0005874)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)	p.S1154L(2)		NS(1)|breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						TCGCCTCTCCGAGATCTTGGA	0.398																																					p.S1154X		.											INOC1,face,carcinoma,0,2	INOC1	0	2	Substitution - Missense(2)	skin(2)	c.C3461A						.						95.0	82.0	86.0					15																	41297827		2203	4300	6503	SO:0001587	stop_gained	54617	exon28			CTCTCCGAGATCT	AB033085	CCDS10071.1	15q15.1	2013-08-21	2013-08-21	2008-08-07	ENSG00000128908	ENSG00000128908	3.6.1.3	"""INO80 complex subunits"""	26956	protein-coding gene	gene with protein product	"""INO80 complex subunit A"""	610169	"""INO80 complex homolog 1 (S. cerevisiae)"", ""INO80 homolog (S. cerevisiae)"""	INOC1		16298340, 16230350, 20237820	Standard	NM_017553		Approved	KIAA1259, Ino80, hINO80, INO80A	uc001zni.3	Q9ULG1	OTTHUMG00000130209	ENST00000361937.3:c.3461C>A	15.37:g.41297827G>T	ENSP00000355205:p.Ser1154*	Somatic	18	0		WXS	Illumina HiSeq	.	45	2	NM_017553	A6H8X4|Q9NTG6	Nonsense_Mutation	SNP	ENST00000361937.3	37	CCDS10071.1	.	.	.	.	.	.	.	.	.	.	G	46	12.577148	0.99679	.	.	ENSG00000128908	ENST00000361937;ENST00000401393	.	.	.	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10377	T	0.69	.	19.8931	0.96937	0.0:0.0:1.0:0.0	.	.	.	.	X	1154	.	ENSP00000355205:S1154X	S	-	2	0	INO80	39085119	1.000000	0.71417	0.993000	0.49108	0.985000	0.73830	9.022000	0.93678	2.873000	0.98535	0.563000	0.77884	TCG	.		0.398	INO80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252527.2	NM_017553	
ITPR2	3709	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	12	26755420	26755420	+	Missense_Mutation	SNP	G	G	C			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr12:26755420G>C	ENST00000381340.3	-	28	3977	c.3561C>G	c.(3559-3561)atC>atG	p.I1187M		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	1187					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	TACTTAGCCTGATCAAAATCT	0.328																																					p.I1187M		.											.	.	.	0			c.C3561G						.						73.0	68.0	70.0					12																	26755420		1802	4066	5868	SO:0001583	missense	3709	exon28			TAGCCTGATCAAA	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"""Ion channels / Inositol triphosphate receptors"""	6181	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 48"""	600144	"""inositol 1,4,5-triphosphate receptor, type 2"""			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.3561C>G	12.37:g.26755420G>C	ENSP00000370744:p.Ile1187Met	Somatic	92	0		WXS	Illumina HiSeq	.	115	25	NM_002223	O94773	Missense_Mutation	SNP	ENST00000381340.3	37	CCDS41764.1	.	.	.	.	.	.	.	.	.	.	G	10.55	1.380974	0.24944	.	.	ENSG00000123104	ENST00000381340	D	0.95412	-3.7	5.46	-2.82	0.05787	Intracellular calcium-release channel (1);	0.246503	0.41938	D	0.000782	D	0.89684	0.6786	N	0.19112	0.55	0.45087	D	0.998108	B	0.30193	0.272	B	0.37508	0.252	T	0.77088	-0.2717	10	0.20046	T	0.44	.	13.3263	0.60461	0.4888:0.0:0.5112:0.0	.	1187	Q14571	ITPR2_HUMAN	M	1187	ENSP00000370744:I1187M	ENSP00000370744:I1187M	I	-	3	3	ITPR2	26646687	0.560000	0.26570	0.966000	0.40874	0.976000	0.68499	-0.106000	0.10890	-0.352000	0.08237	-0.238000	0.12139	ATC	.		0.328	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	
ITPR2	3709	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	26755635	26755635	+	Nonsense_Mutation	SNP	G	G	C			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr12:26755635G>C	ENST00000381340.3	-	27	3883	c.3467C>G	c.(3466-3468)tCa>tGa	p.S1156*		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	1156					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	TAAAATGTTTGATTCCTAAAA	0.308																																					p.S1156X		.											.	.	.	0			c.C3467G						.						100.0	86.0	90.0					12																	26755635		1833	4095	5928	SO:0001587	stop_gained	3709	exon27			ATGTTTGATTCCT	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"""Ion channels / Inositol triphosphate receptors"""	6181	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 48"""	600144	"""inositol 1,4,5-triphosphate receptor, type 2"""			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.3467C>G	12.37:g.26755635G>C	ENSP00000370744:p.Ser1156*	Somatic	21	0		WXS	Illumina HiSeq	.	32	9	NM_002223	O94773	Nonsense_Mutation	SNP	ENST00000381340.3	37	CCDS41764.1	.	.	.	.	.	.	.	.	.	.	G	45	11.923358	0.99617	.	.	ENSG00000123104	ENST00000381340	.	.	.	4.58	4.58	0.56647	.	0.638191	0.15072	N	0.282149	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.24483	T	0.36	.	16.1956	0.82024	0.0:0.0:1.0:0.0	.	.	.	.	X	1156	.	ENSP00000370744:S1156X	S	-	2	0	ITPR2	26646902	0.997000	0.39634	0.847000	0.33407	0.910000	0.53928	3.817000	0.55668	2.542000	0.85734	0.650000	0.86243	TCA	.		0.308	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	
DNMBP	23268	hgsc.bcm.edu	37	10	101639890	101639890	+	Missense_Mutation	SNP	G	G	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr10:101639890G>T	ENST00000324109.4	-	16	4317	c.4226C>A	c.(4225-4227)cCg>cAg	p.P1409Q	DNMBP_ENST00000543621.1_Missense_Mutation_p.P655Q|DNMBP_ENST00000342239.3_Missense_Mutation_p.P1433Q|DNMBP_ENST00000540316.1_Missense_Mutation_p.P345Q	NM_015221.2	NP_056036.1	Q6XZF7	DNMBP_HUMAN	dynamin binding protein	1409	Ser-rich.				intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(4)|endometrium(9)|large_intestine(14)|lung(19)|ovary(5)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	61		Colorectal(252;0.234)		Epithelial(162;2.94e-10)|all cancers(201;3.15e-08)		TTCTTTTGGCGGAGGAGATGC	0.547																																					p.P1409Q		.											DNMBP,colon,carcinoma,0,1	DNMBP	0	0			c.C4226A						.						188.0	185.0	186.0					10																	101639890		2203	4300	6503	SO:0001583	missense	23268	exon16			TTTGGCGGAGGAG	AL833283	CCDS7485.1	10q24.31	2012-07-24			ENSG00000107554	ENSG00000107554		"""Rho guanine nucleotide exchange factors"""	30373	protein-coding gene	gene with protein product	"""scaffold protein TUBA"""	611282				10231032, 14506234	Standard	NM_015221		Approved	KIAA1010, Tuba, ARHGEF36	uc001kqj.2	Q6XZF7	OTTHUMG00000018897	ENST00000324109.4:c.4226C>A	10.37:g.101639890G>T	ENSP00000315659:p.Pro1409Gln	Somatic	24	1		WXS	Illumina HiSeq	.	31	2	NM_015221	Q8IVY3|Q9Y2L3	Missense_Mutation	SNP	ENST00000324109.4	37	CCDS7485.1	.	.	.	.	.	.	.	.	.	.	G	7.572	0.666896	0.14710	.	.	ENSG00000107554	ENST00000342239;ENST00000324109;ENST00000393570;ENST00000543621;ENST00000540316	T;T;T;T	0.34472	2.81;2.77;2.44;1.36	5.43	2.07	0.26955	.	2.398360	0.02512	N	0.091658	T	0.35566	0.0936	L	0.44542	1.39	0.09310	N	1	B;B;B	0.32893	0.389;0.302;0.389	B;B;B	0.36378	0.171;0.223;0.171	T	0.27226	-1.0080	10	0.27785	T	0.31	.	8.6413	0.33978	0.2039:0.1218:0.6743:0.0	.	1409;655;1433	Q6XZF7;Q6XZF7-2;Q5SVK8	DNMBP_HUMAN;.;.	Q	1433;1409;655;655;345	ENSP00000344914:P1433Q;ENSP00000315659:P1409Q;ENSP00000443657:P655Q;ENSP00000443573:P345Q	ENSP00000315659:P1409Q	P	-	2	0	DNMBP	101629880	0.023000	0.18921	0.000000	0.03702	0.001000	0.01503	2.033000	0.41136	0.653000	0.30826	0.561000	0.74099	CCG	.		0.547	DNMBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049832.2	NM_015221	
PLXNA4	91584	hgsc.bcm.edu	37	7	131887440	131887440	+	Missense_Mutation	SNP	C	C	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr7:131887440C>T	ENST00000359827.3	-	12	3513	c.2551G>A	c.(2551-2553)Gcc>Acc	p.A851T	PLXNA4_ENST00000321063.4_Missense_Mutation_p.A851T			Q9HCM2	PLXA4_HUMAN	plexin A4	851	PSI 3.				anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						TTGCTTTTGGCACCAGACAGC	0.657																																					p.A851T		.											.	.	.	0			c.G2551A						.						36.0	40.0	39.0					7																	131887440		2003	4172	6175	SO:0001583	missense	91584	exon12			TTTTGGCACCAGA	AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"""Plexins"""	9102	protein-coding gene	gene with protein product		604280	"""plexin A4, A"", ""plexin A4, B"""	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.2551G>A	7.37:g.131887440C>T	ENSP00000352882:p.Ala851Thr	Somatic	53	0		WXS	Illumina HiSeq	.	99	4	NM_020911	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	37	CCDS43646.1	.	.	.	.	.	.	.	.	.	.	C	7.167	0.586783	0.13749	.	.	ENSG00000221866	ENST00000321063;ENST00000359827	T;T	0.17528	2.27;2.27	4.5	-4.43	0.03568	.	0.308380	0.33938	N	0.004410	T	0.02848	0.0085	N	0.00471	-1.455	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.40683	-0.9550	10	0.11794	T	0.64	.	6.7981	0.23736	0.0:0.1341:0.3822:0.4837	.	851	Q9HCM2	PLXA4_HUMAN	T	851	ENSP00000323194:A851T;ENSP00000352882:A851T	ENSP00000323194:A851T	A	-	1	0	PLXNA4	131537980	0.018000	0.18449	0.002000	0.10522	0.778000	0.44026	0.234000	0.17930	-0.789000	0.04498	-0.304000	0.09214	GCC	.		0.657	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775	
NLGN1	22871	hgsc.bcm.edu	37	3	173322868	173322868	+	Silent	SNP	C	C	T	rs151237969		TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr3:173322868C>T	ENST00000457714.1	+	3	909	c.480C>T	c.(478-480)gtC>gtT	p.V160V	NLGN1_ENST00000361589.4_Silent_p.V160V|NLGN1_ENST00000401917.3_Silent_p.V160V|NLGN1_ENST00000545397.1_Silent_p.V160V	NM_014932.2	NP_055747.1	Q8N2Q7	NLGN1_HUMAN	neuroligin 1	160					alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|calcium-dependent cell-cell adhesion (GO:0016339)|cytoskeletal matrix organization at active zone (GO:0048789)|establishment of protein localization (GO:0045184)|heterophilic cell-cell adhesion (GO:0007157)|N-methyl-D-aspartate receptor clustering (GO:0097114)|nervous system development (GO:0007399)|neurexin clustering (GO:0097115)|neuron cell-cell adhesion (GO:0007158)|neuronal signal transduction (GO:0023041)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of ruffle assembly (GO:1900029)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of synaptic vesicle endocytosis (GO:1900244)|positive regulation of synaptic vesicle exocytosis (GO:2000302)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|protein homooligomerization (GO:0051260)|protein localization to synapse (GO:0035418)|protein targeting (GO:0006605)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuron differentiation (GO:0045664)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|synapse assembly (GO:0007416)|synaptic vesicle clustering (GO:0097091)|synaptic vesicle targeting (GO:0016080)|terminal button organization (GO:0072553)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|filopodium tip (GO:0032433)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|PDZ domain binding (GO:0030165)|protein dimerization activity (GO:0046983)|receptor activity (GO:0004872)	p.V160V(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(2)|lung(54)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	83	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			ATATATATGTCCCGACTGAGG	0.343																																					p.V160V		.											NLGN1,shoulder,malignant_melanoma,0,1	NLGN1	0	1	Substitution - coding silent(1)	skin(1)	c.C480T						.						74.0	78.0	77.0					3																	173322868		2203	4300	6503	SO:0001819	synonymous_variant	22871	exon3			ATATGTCCCGACT	AB028993	CCDS3222.1	3q26.32	2008-07-18			ENSG00000169760	ENSG00000169760			14291	protein-coding gene	gene with protein product		600568				10767552, 10819331	Standard	NM_014932		Approved	KIAA1070	uc003fio.1	Q8N2Q7	OTTHUMG00000157005	ENST00000457714.1:c.480C>T	3.37:g.173322868C>T		Somatic	11	0		WXS	Illumina HiSeq	.	26	2	NM_014932	Q9UPT2	Silent	SNP	ENST00000457714.1	37	CCDS3222.1																																																																																			.		0.343	NLGN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347054.3	NM_014932	
ASNS	440	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	7	97487633	97487633	+	Missense_Mutation	SNP	G	G	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr7:97487633G>T	ENST00000394309.3	-	7	1331	c.860C>A	c.(859-861)gCa>gAa	p.A287E	ASNS_ENST00000455086.1_Missense_Mutation_p.A204E|ASNS_ENST00000444334.1_Missense_Mutation_p.A266E|ASNS_ENST00000394308.3_Missense_Mutation_p.A287E|ASNS_ENST00000422745.1_Missense_Mutation_p.A266E|ASNS_ENST00000175506.4_Missense_Mutation_p.A287E|ASNS_ENST00000437628.1_Missense_Mutation_p.A204E	NM_133436.3	NP_597680.2	P08243	ASNS_HUMAN	asparagine synthetase (glutamine-hydrolyzing)	287	Asparagine synthetase.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|asparagine biosynthetic process (GO:0006529)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|cellular protein metabolic process (GO:0044267)|cellular response to glucose starvation (GO:0042149)|cellular response to hormone stimulus (GO:0032870)|endoplasmic reticulum unfolded protein response (GO:0030968)|glutamine metabolic process (GO:0006541)|L-asparagine biosynthetic process (GO:0070981)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|positive regulation of mitotic cell cycle (GO:0045931)|response to amino acid (GO:0043200)|response to follicle-stimulating hormone (GO:0032354)|response to light stimulus (GO:0009416)|response to mechanical stimulus (GO:0009612)|response to methotrexate (GO:0031427)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	asparagine synthase (glutamine-hydrolyzing) activity (GO:0004066)|ATP binding (GO:0005524)|cofactor binding (GO:0048037)			ovary(1)	1	all_cancers(62;6.64e-09)|all_epithelial(64;1.58e-09)|Esophageal squamous(72;0.00448)|Lung NSC(181;0.0342)|all_lung(186;0.0369)				Adenosine triphosphate(DB00171)|L-Asparagine(DB00174)|L-Aspartic Acid(DB00128)|L-Glutamine(DB00130)	CATGCCAATTGCAAATGTCTG	0.478																																					p.A287E	Melanoma(70;6 1280 3108 3799 51123)|GBM(6;275 291 425 9929 27738)	.											.	.	.	0			c.C860A						.						94.0	81.0	85.0					7																	97487633		2203	4300	6503	SO:0001583	missense	440	exon7			CCAATTGCAAATG	M27396	CCDS5652.1, CCDS55131.1, CCDS55132.1	7q21.3	2012-10-02	2010-05-07		ENSG00000070669	ENSG00000070669	6.3.5.4		753	protein-coding gene	gene with protein product		108370	"""asparagine synthetase"""				Standard	NM_001673		Approved		uc003uov.4	P08243	OTTHUMG00000022892	ENST00000394309.3:c.860C>A	7.37:g.97487633G>T	ENSP00000377846:p.Ala287Glu	Somatic	21	0		WXS	Illumina HiSeq	.	26	4	NM_133436	A4D1I8|B4DXZ1|B7ZAA9|D6W5R3|E9PCI3|E9PCX6|P08184|Q15666|Q549T9|Q96HD0	Missense_Mutation	SNP	ENST00000394309.3	37	CCDS5652.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.957408	0.92726	.	.	ENSG00000070669	ENST00000175506;ENST00000394309;ENST00000437628;ENST00000394308;ENST00000422745;ENST00000455086;ENST00000444334	T;T;T;T;T;T;T	0.45668	0.89;0.89;0.89;0.89;0.89;0.89;0.89	4.37	4.37	0.52481	Rossmann-like alpha/beta/alpha sandwich fold (1);Asparagine synthase (1);	0.110120	0.64402	D	0.000007	T	0.67429	0.2892	M	0.91406	3.205	0.58432	D	0.999995	D	0.52996	0.957	P	0.58660	0.843	T	0.76911	-0.2784	10	0.87932	D	0	-15.7215	15.2408	0.73468	0.0:0.0:1.0:0.0	.	287	P08243	ASNS_HUMAN	E	287;287;204;287;266;204;266	ENSP00000175506:A287E;ENSP00000377846:A287E;ENSP00000414379:A204E;ENSP00000377845:A287E;ENSP00000414901:A266E;ENSP00000408472:A204E;ENSP00000406994:A266E	ENSP00000175506:A287E	A	-	2	0	ASNS	97325569	1.000000	0.71417	0.917000	0.36280	0.989000	0.77384	8.521000	0.90569	2.368000	0.80403	0.557000	0.71058	GCA	.		0.478	ASNS-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333645.1	NM_001673, NM_183356	
KDM6B	23135	hgsc.bcm.edu	37	17	7750177	7750177	+	Missense_Mutation	SNP	T	T	C	rs375218857|rs61462443		TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr17:7750177T>C	ENST00000448097.2	+	9	1083	c.752T>C	c.(751-753)tTa>tCa	p.L251S	KDM6B_ENST00000254846.5_Missense_Mutation_p.L251S			O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	251	Pro-rich.				cardiac muscle cell differentiation (GO:0055007)|cellular response to hydrogen peroxide (GO:0070301)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|mesodermal cell differentiation (GO:0048333)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|skin(5)	37						ccaccaccattaccaccacca	0.612																																					p.L251S		.											.,2	.	95	0			c.T752C						.						30.0	27.0	28.0					17																	7750177		2195	4284	6479	SO:0001583	missense	23135	exon9			CACCATTACCACC	AB002344	CCDS32552.1	17p13.1	2011-07-01	2009-04-17	2009-04-17		ENSG00000132510		"""Chromatin-modifying enzymes / K-demethylases"""	29012	protein-coding gene	gene with protein product		611577	"""jumonji domain containing 3"", ""jumonji domain containing 3, histone lysine demethylase"""	JMJD3		10662545, 9205841	Standard	NM_001080424		Approved	KIAA0346	uc002giw.1	O15054		ENST00000448097.2:c.752T>C	17.37:g.7750177T>C	ENSP00000412513:p.Leu251Ser	Somatic	13	1		WXS	Illumina HiSeq	.	15	2	NM_001080424	C9IZ40|Q96G33	Missense_Mutation	SNP	ENST00000448097.2	37		.	.	.	.	.	.	.	.	.	.	T	5.427	0.264015	0.10294	.	.	ENSG00000132510	ENST00000254846;ENST00000448097	T;T	0.36520	1.25;1.25	5.23	3.0	0.34707	.	1.773790	0.04118	U	0.315852	T	0.18383	0.0441	N	0.08118	0	0.09310	N	1	B	0.25609	0.13	B	0.21917	0.037	T	0.25012	-1.0144	10	0.15499	T	0.54	0.3492	3.4931	0.07645	0.1653:0.1862:0.0:0.6486	.	251	O15054-1	.	S	251	ENSP00000254846:L251S;ENSP00000412513:L251S	ENSP00000254846:L251S	L	+	2	0	KDM6B	7690902	0.726000	0.28059	0.844000	0.33320	0.850000	0.48378	0.575000	0.23729	0.410000	0.25675	0.379000	0.24179	TTA	.		0.612	KDM6B-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000440248.1	XM_043272	
WFIKKN2	124857	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	17	48913377	48913377	+	Missense_Mutation	SNP	G	G	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr17:48913377G>T	ENST00000311378.4	+	1	607	c.79G>T	c.(79-81)Ggg>Tgg	p.G27W	WFIKKN2_ENST00000426127.1_Intron	NM_175575.5	NP_783165.1	Q8TEU8	WFKN2_HUMAN	WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 2	27					muscle fiber development (GO:0048747)|negative regulation of DNA binding (GO:0043392)|negative regulation of protein binding (GO:0032091)|palate development (GO:0060021)|skeletal system development (GO:0001501)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)	metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(13)|ovary(4)|skin(1)	29			BRCA - Breast invasive adenocarcinoma(22;1.09e-08)			gctactgctCGGGGTGCCCCC	0.682																																					p.G27W		.											.	.	.	0			c.G79T						.						15.0	15.0	15.0					17																	48913377		2194	4292	6486	SO:0001583	missense	124857	exon1			CTGCTCGGGGTGC	AY358142	CCDS11575.1	17q21.33	2013-01-21			ENSG00000173714	ENSG00000173714		"""Immunoglobulin superfamily / I-set domain containing"", ""WAP four-disulfide core domain containing"""	30916	protein-coding gene	gene with protein product	"""WAP four-disulfide core domain 20B"""	610895				11928817, 12709070	Standard	NM_175575		Approved	WFIKKNRP, WFDC20B	uc002isv.4	Q8TEU8	OTTHUMG00000162274	ENST00000311378.4:c.79G>T	17.37:g.48913377G>T	ENSP00000311184:p.Gly27Trp	Somatic	41	0		WXS	Illumina HiSeq	.	70	23	NM_175575	Q6UXZ9	Missense_Mutation	SNP	ENST00000311378.4	37	CCDS11575.1	.	.	.	.	.	.	.	.	.	.	G	8.980	0.975068	0.18736	.	.	ENSG00000173714	ENST00000311378	T	0.81078	-1.45	5.24	4.25	0.50352	.	0.536026	0.19882	N	0.103943	T	0.61148	0.2324	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.51044	-0.8755	10	0.37606	T	0.19	.	8.3184	0.32115	0.0786:0.0:0.7648:0.1567	.	27	Q8TEU8	WFKN2_HUMAN	W	27	ENSP00000311184:G27W	ENSP00000311184:G27W	G	+	1	0	WFIKKN2	46268376	0.391000	0.25221	0.327000	0.25402	0.117000	0.20001	0.897000	0.28390	1.172000	0.42781	0.655000	0.94253	GGG	.		0.682	WFIKKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368358.1	NM_175575	
ACTL7A	10881	hgsc.bcm.edu	37	9	111625685	111625685	+	Silent	SNP	C	C	T	rs371393958		TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr9:111625685C>T	ENST00000333999.3	+	1	1083	c.1083C>T	c.(1081-1083)tgC>tgT	p.C361C		NM_006687.2	NP_006678.1	Q9Y615	ACL7A_HUMAN	actin-like 7A	361						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|male germ cell nucleus (GO:0001673)|motile cilium (GO:0031514)|nucleus (GO:0005634)|protein complex (GO:0043234)	structural constituent of cytoskeleton (GO:0005200)			breast(1)|endometrium(2)|large_intestine(4)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						TCCTGCTCTGCGGGGGCAGCA	0.577																																					p.C361C	Esophageal Squamous(177;1480 3591 17554)	.											ACTL7A,NS,carcinoma,0,1	ACTL7A	0	0			c.C1083T						.						118.0	103.0	108.0					9																	111625685		2203	4300	6503	SO:0001819	synonymous_variant	10881	exon1			GCTCTGCGGGGGC	BC014610	CCDS6772.1	9q31	2008-02-05			ENSG00000187003	ENSG00000187003			161	protein-coding gene	gene with protein product		604303				10373328	Standard	NM_006687		Approved		uc004bdj.1	Q9Y615	OTTHUMG00000020461	ENST00000333999.3:c.1083C>T	9.37:g.111625685C>T		Somatic	22	0		WXS	Illumina HiSeq	.	33	3	NM_006687	B2RC83|Q5JSV0	Silent	SNP	ENST00000333999.3	37	CCDS6772.1																																																																																			.		0.577	ACTL7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053570.1	NM_006687	
TPR	7175	hgsc.bcm.edu	37	1	186281176	186281176	+	3'UTR	SNP	T	T	A			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr1:186281176T>A	ENST00000367478.4	-	0	9315				PRG4_ENST00000367483.4_Intron|PRG4_ENST00000445192.2_Intron|RNU6-1240P_ENST00000365155.1_RNA|PRG4_ENST00000367486.3_Intron|PRG4_ENST00000367485.4_Intron|PRG4_ENST00000367484.3_Intron	NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein						carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)			autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		ATAGCCATTATTAATATCAAT	0.224			T	NTRK1	papillary thyroid																																.		.		Dom	yes		1	1q25	7175	translocated promoter region		E	.	.	.	0			.						.																																			SO:0001624	3_prime_UTR_variant	7175	.			CCATTATTAATAT	U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"""translocated promoter region (to activated MET oncogene)"""			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.*1927A>T	1.37:g.186281176T>A		Somatic	98	0		WXS	Illumina HiSeq	.	171	8	.	Q15655|Q5SWY0|Q99968	RNA	SNP	ENST00000367478.4	37	CCDS41446.1																																																																																			.		0.224	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292	
LRRC55	219527	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	56949739	56949739	+	Silent	SNP	G	G	A			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr11:56949739G>A	ENST00000497933.1	+	1	519	c.372G>A	c.(370-372)ccG>ccA	p.P124P		NM_001005210.2	NP_001005210.1	Q6ZSA7	LRC55_HUMAN	leucine rich repeat containing 55	94					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(13)|ovary(2)|skin(2)	25						CAGCAGTGCCGCCTGGCTACC	0.602																																					p.P124P		.											.	.	.	0			c.G372A						.						59.0	59.0	59.0					11																	56949739		2201	4296	6497	SO:0001819	synonymous_variant	219527	exon1			AGTGCCGCCTGGC		CCDS31539.1	11q12.1	2008-02-05			ENSG00000183908	ENSG00000183908			32324	protein-coding gene	gene with protein product		615213					Standard	NM_001005210		Approved	FLJ45686	uc001njl.2	Q6ZSA7	OTTHUMG00000159309	ENST00000497933.1:c.372G>A	11.37:g.56949739G>A		Somatic	33	0		WXS	Illumina HiSeq	.	68	18	NM_001005210	A7E2U7|B2RN81	Silent	SNP	ENST00000497933.1	37	CCDS31539.1																																																																																			.		0.602	LRRC55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354503.2	NM_001005210	
PTPRD	5789	hgsc.bcm.edu	37	9	8331583	8331583	+	Splice_Site	SNP	T	T	A			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr9:8331583T>A	ENST00000381196.4	-	41	6076	c.5533A>T	c.(5533-5535)Agc>Tgc	p.S1845C	PTPRD_ENST00000486161.1_Splice_Site_p.S1438C|PTPRD_ENST00000540109.1_Splice_Site_p.S1845C|PTPRD_ENST00000356435.5_Splice_Site_p.S1845C|PTPRD_ENST00000397606.3_Splice_Site_p.S1438C|PTPRD_ENST00000397611.3_Splice_Site_p.S1435C|PTPRD_ENST00000537002.1_Splice_Site_p.S1435C|PTPRD_ENST00000397617.3_Splice_Site_p.S1438C|PTPRD_ENST00000360074.4_Splice_Site_p.S1832C|PTPRD_ENST00000358503.5_Splice_Site_p.S1823C|PTPRD_ENST00000355233.5_Splice_Site_p.S1439C	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	1845	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.S1845C(1)|p.S1316C(1)		NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		GAAACTTACCTGCAATGGACT	0.373										TSP Lung(15;0.13)																											p.S1845C		.											PTPRD_ENST00000346816,NS,carcinoma,0,2	PTPRD_ENST00000346816	0	2	Substitution - Missense(2)	lung(2)	c.A5533T						.						120.0	135.0	130.0					9																	8331583		2203	4299	6502	SO:0001630	splice_region_variant	5789	exon44			CTTACCTGCAATG	X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.5534+1A>T	9.37:g.8331583T>A		Somatic	27	1		WXS	Illumina HiSeq	.	25	4	NM_002839	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Missense_Mutation	SNP	ENST00000381196.4	37	CCDS43786.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.468046	0.84533	.	.	ENSG00000153707	ENST00000381196;ENST00000356435;ENST00000360074;ENST00000358503;ENST00000355233;ENST00000397617;ENST00000397611;ENST00000537002;ENST00000346816;ENST00000540109;ENST00000486161;ENST00000397606	T;T;T;T;T;T;T;T;T;T;T	0.15603	2.41;2.41;2.41;2.41;2.41;2.41;2.41;2.41;2.41;2.41;2.41	5.72	5.72	0.89469	Protein-tyrosine phosphatase, receptor/non-receptor type (3);Protein-tyrosine/Dual-specificity phosphatase (1);	0.000000	0.85682	D	0.000000	T	0.57007	0.2024	H	0.95884	3.735	0.80722	D	1	D;D;D;D;D;D;D;D;D	0.89917	1.0;0.999;0.998;0.969;0.999;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D	0.91635	0.997;0.997;0.961;0.914;0.979;0.994;0.996;0.999;0.995	T	0.72077	-0.4399	9	.	.	.	.	16.2962	0.82776	0.0:0.0:0.0:1.0	.	1438;1429;1438;1439;1435;1435;1832;1845;1845	Q3KPJ2;Q3KPI9;Q3KPJ0;Q3KPJ1;F5GWT7;F5GWY7;G3XAE2;Q2HXI4;P23468	.;.;.;.;.;.;.;.;PTPRD_HUMAN	C	1845;1845;1832;1823;1439;1438;1435;1435;1316;1845;1438;1438	ENSP00000370593:S1845C;ENSP00000348812:S1845C;ENSP00000353187:S1832C;ENSP00000351293:S1823C;ENSP00000347373:S1439C;ENSP00000380741:S1438C;ENSP00000380735:S1435C;ENSP00000440515:S1435C;ENSP00000438164:S1845C;ENSP00000417093:S1438C;ENSP00000380731:S1438C	.	S	-	1	0	PTPRD	8321583	1.000000	0.71417	1.000000	0.80357	0.863000	0.49368	7.641000	0.83368	2.304000	0.77564	0.528000	0.53228	AGC	.		0.373	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3		Missense_Mutation
OR8B3	390271	hgsc.bcm.edu	37	11	124266927	124266927	+	Silent	SNP	A	A	G	rs142812088		TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr11:124266927A>G	ENST00000354597.3	-	1	337	c.321T>C	c.(319-321)ttT>ttC	p.F107F		NM_001005467.1	NP_001005467.1	Q8NGG8	OR8B3_HUMAN	olfactory receptor, family 8, subfamily B, member 3	107						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	14		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		CAGAGATGACAAAAAAGAGAA	0.388																																					p.F107F		.											OR8B3,NS,carcinoma,0,1	OR8B3	0	0			c.T321C						.						78.0	76.0	77.0					11																	124266927		2201	4299	6500	SO:0001819	synonymous_variant	390271	exon1			GATGACAAAAAAG	AB065827	CCDS31709.1	11q24.1	2012-08-09			ENSG00000196661	ENSG00000196661		"""GPCR / Class A : Olfactory receptors"""	8472	protein-coding gene	gene with protein product							Standard	NM_001005467		Approved		uc010saj.2	Q8NGG8	OTTHUMG00000165983	ENST00000354597.3:c.321T>C	11.37:g.124266927A>G		Somatic	45	1		WXS	Illumina HiSeq	.	56	5	NM_001005467	Q6IFQ8|Q8NGH1	Silent	SNP	ENST00000354597.3	37	CCDS31709.1																																																																																			0.000		0.388	OR8B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387291.1	NM_001005467	
LEO1	123169	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	52252121	52252121	+	Missense_Mutation	SNP	G	G	A			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr15:52252121G>A	ENST00000299601.5	-	5	1195	c.1135C>T	c.(1135-1137)Ccc>Tcc	p.P379S	LEO1_ENST00000315141.5_Missense_Mutation_p.P379S	NM_138792.2	NP_620147.1	Q8WVC0	LEO1_HUMAN	Leo1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)	379					endodermal cell fate commitment (GO:0001711)|histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|mRNA polyadenylation (GO:0006378)|negative regulation of myeloid cell differentiation (GO:0045638)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|skin(1)	14				all cancers(107;0.00264)		AGAAAGTTGGGCAGTTTAACA	0.343																																					p.P379S	Esophageal Squamous(40;229 896 18505 32465 43844)|Ovarian(53;886 1123 14462 18432 23189)	.											.	.	.	0			c.C1135T						.						166.0	169.0	168.0					15																	52252121		2195	4293	6488	SO:0001583	missense	123169	exon5			AGTTGGGCAGTTT	AY302186	CCDS10146.1, CCDS66767.1	15q21.2	2008-02-05			ENSG00000166477	ENSG00000166477			30401	protein-coding gene	gene with protein product		610507				15632063	Standard	NM_001286430		Approved		uc002abo.3	Q8WVC0	OTTHUMG00000131843	ENST00000299601.5:c.1135C>T	15.37:g.52252121G>A	ENSP00000299601:p.Pro379Ser	Somatic	48	0		WXS	Illumina HiSeq	.	87	28	NM_138792	Q96N99	Missense_Mutation	SNP	ENST00000299601.5	37	CCDS10146.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.827460	0.90955	.	.	ENSG00000166477	ENST00000299601;ENST00000538386;ENST00000315141	.	.	.	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.75620	0.3874	L	0.49513	1.565	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.74463	-0.3657	9	0.44086	T	0.13	.	19.1638	0.93546	0.0:0.0:1.0:0.0	.	379;379	Q8WVC0-2;Q8WVC0	.;LEO1_HUMAN	S	379;357;379	.	ENSP00000299601:P379S	P	-	1	0	LEO1	50039413	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.429000	0.97481	2.597000	0.87782	0.650000	0.86243	CCC	.		0.343	LEO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254791.2	NM_138792	
MVD	4597	hgsc.bcm.edu	37	16	88721779	88721779	+	Missense_Mutation	SNP	C	C	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr16:88721779C>T	ENST00000301012.3	-	7	754	c.725G>A	c.(724-726)cGc>cAc	p.R242H	MVD_ENST00000568709.1_5'Flank	NM_002461.1	NP_002452.1	P53602	MVD1_HUMAN	mevalonate (diphospho) decarboxylase	242					cellular protein metabolic process (GO:0044267)|cholesterol biosynthetic process (GO:0006695)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|dolichyl diphosphate biosynthetic process (GO:0006489)|isopentenyl diphosphate biosynthetic process, mevalonate pathway (GO:0019287)|isoprenoid biosynthetic process (GO:0008299)|positive regulation of cell proliferation (GO:0008284)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|diphosphomevalonate decarboxylase activity (GO:0004163)|Hsp70 protein binding (GO:0030544)|protein homodimerization activity (GO:0042803)			endometrium(3)|large_intestine(1)|lung(7)|ovary(1)	12				BRCA - Breast invasive adenocarcinoma(80;0.0478)		CCGGATGCAGCGGGCCATCTC	0.667																																					p.R242H		.											MVD,NS,carcinoma,0,1	MVD	0	0			c.G725A						.						163.0	124.0	137.0					16																	88721779		2184	4295	6479	SO:0001583	missense	4597	exon7			ATGCAGCGGGCCA	U49260	CCDS10968.1	16q24.3	2010-04-29			ENSG00000167508	ENSG00000167508	4.1.1.33		7529	protein-coding gene	gene with protein product	"""mevalonate pyrophosphate decarboxylase"""	603236				8626466	Standard	NM_002461		Approved	MPD	uc002flg.1	P53602	OTTHUMG00000137865	ENST00000301012.3:c.725G>A	16.37:g.88721779C>T	ENSP00000301012:p.Arg242His	Somatic	23	0		WXS	Illumina HiSeq	.	48	3	NM_002461	Q53Y65	Missense_Mutation	SNP	ENST00000301012.3	37	CCDS10968.1	.	.	.	.	.	.	.	.	.	.	C	8.703	0.910219	0.17833	.	.	ENSG00000167508	ENST00000301012	T	0.43294	0.95	4.53	-2.71	0.05986	.	0.583782	0.19499	N	0.112791	T	0.40498	0.1119	M	0.77820	2.39	0.09310	N	1	B	0.18013	0.025	B	0.10450	0.005	T	0.41752	-0.9491	10	0.59425	D	0.04	-12.2247	11.6986	0.51558	0.0:0.452:0.0:0.548	.	242	P53602	MVD1_HUMAN	H	242	ENSP00000301012:R242H	ENSP00000301012:R242H	R	-	2	0	MVD	87249280	0.000000	0.05858	0.000000	0.03702	0.053000	0.15095	-0.171000	0.09883	-0.739000	0.04809	-0.339000	0.08088	CGC	.		0.667	MVD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269547.2	NM_002461	
KIF2B	84643	hgsc.bcm.edu	37	17	51902198	51902198	+	Missense_Mutation	SNP	C	C	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr17:51902198C>T	ENST00000268919.4	+	1	1960	c.1804C>T	c.(1804-1806)Ccc>Tcc	p.P602S		NM_032559.4	NP_115948.4	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	602					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of chromosome segregation (GO:0051983)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.P602S(1)		NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(15)|lung(58)|ovary(5)|prostate(4)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						TGAAACATTACCCACTCTGTT	0.423																																					p.P602S		.											KIF2B,NS,carcinoma,0,1	KIF2B	0	1	Substitution - Missense(1)	lung(1)	c.C1804T						.						161.0	152.0	155.0					17																	51902198		2203	4300	6503	SO:0001583	missense	84643	exon1			ACATTACCCACTC	AF333335	CCDS32685.1	17q22	2014-08-12			ENSG00000141200	ENSG00000141200		"""Kinesins"""	29443	protein-coding gene	gene with protein product		615142				11416179	Standard	NM_032559		Approved		uc002iua.2	Q8N4N8	OTTHUMG00000177756	ENST00000268919.4:c.1804C>T	17.37:g.51902198C>T	ENSP00000268919:p.Pro602Ser	Somatic	23	0		WXS	Illumina HiSeq	.	33	2	NM_032559	Q96MA2|Q9BXG6	Missense_Mutation	SNP	ENST00000268919.4	37	CCDS32685.1	.	.	.	.	.	.	.	.	.	.	C	0	-2.870922	0.00062	.	.	ENSG00000141200	ENST00000268919;ENST00000416491	T	0.72167	-0.63	5.14	-7.98	0.01135	.	6.653280	0.00357	N	0.000026	T	0.43612	0.1255	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34229	-0.9837	10	0.21540	T	0.41	.	4.9708	0.14115	0.0976:0.1842:0.4985:0.2197	.	602	Q8N4N8	KIF2B_HUMAN	S	602;490	ENSP00000268919:P602S	ENSP00000268919:P602S	P	+	1	0	KIF2B	49257197	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.212000	0.02994	-1.989000	0.00979	-3.555000	0.00030	CCC	.		0.423	KIF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438854.1	NM_032559	
SPATA31D5P	347127	hgsc.bcm.edu	37	9	84529888	84529888	+	RNA	SNP	T	T	A			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr9:84529888T>A	ENST00000527857.1	+	0	267					NR_026851.1				SPATA31 subfamily D, member 5, pseudogene																		CCCAAGGGTCTTCCACAGAGT	0.413																																					.		.											.	.	.	0			.						.																																					347127	.			AGGGTCTTCCACA			9q21.32	2012-10-12	2012-10-12	2012-10-12	ENSG00000240632	ENSG00000240632			38602	pseudogene	pseudogene			"""family with sequence similarity 75, member D5"", ""family with sequence similarity 75, member D5, pseudogene"""	FAM75D5			Standard	NR_026851		Approved	FLJ43950, FAM75D5P	uc011lst.2		OTTHUMG00000020087		9.37:g.84529888T>A		Somatic	49	0		WXS	Illumina HiSeq	.	46	16	.		RNA	SNP	ENST00000527857.1	37																																																																																				.		0.413	SPATA31D5P-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000052810.2	NR_026851	
LCE2B	26239	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	152659372	152659372	+	Missense_Mutation	SNP	C	C	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr1:152659372C>T	ENST00000368780.3	+	2	107	c.53C>T	c.(52-54)cCc>cTc	p.P18L	LCE2B_ENST00000417924.2_Missense_Mutation_p.P18L	NM_014357.4	NP_055172.1	O14633	LCE2B_HUMAN	late cornified envelope 2B	18	Cys-rich.|Pro-rich.				epidermis development (GO:0008544)|keratinization (GO:0031424)			p.P18H(1)		endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	11	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			AAGTGTCCTCCCAAGTGTACC	0.517																																					p.P18L		.											LCE2B,NS,carcinoma,0,1	LCE2B	0	1	Substitution - Missense(1)	lung(1)	c.C53T						.						112.0	113.0	112.0					1																	152659372		2203	4300	6503	SO:0001583	missense	26239	exon2			GTCCTCCCAAGTG	BI670514	CCDS1020.1	1q21	2008-02-05	2004-10-11	2004-10-15	ENSG00000159455	ENSG00000159455		"""Late cornified envelopes"""	16610	protein-coding gene	gene with protein product		612610	"""small proline rich-like (epidermal differentiation complex) 1B"""	SPRL1B		11698679, 9344646	Standard	NM_014357		Approved	LEP10, XP5	uc001fai.3	O14633	OTTHUMG00000012404	ENST00000368780.3:c.53C>T	1.37:g.152659372C>T	ENSP00000357769:p.Pro18Leu	Somatic	77	0		WXS	Illumina HiSeq	.	96	33	NM_014357	Q5TA80	Missense_Mutation	SNP	ENST00000368780.3	37	CCDS1020.1	.	.	.	.	.	.	.	.	.	.	C	7.324	0.617646	0.14129	.	.	ENSG00000159455	ENST00000417924;ENST00000368780	T;T	0.06294	3.32;3.32	2.1	2.1	0.27182	.	.	.	.	.	T	0.12732	0.0309	M	0.83483	2.645	0.33005	D	0.526737	D	0.69078	0.997	D	0.68483	0.958	T	0.02059	-1.1221	9	0.87932	D	0	.	7.5681	0.27892	0.0:1.0:0.0:0.0	.	18	O14633	LCE2B_HUMAN	L	18	ENSP00000414043:P18L;ENSP00000357769:P18L	ENSP00000357769:P18L	P	+	2	0	LCE2B	150925996	0.631000	0.27164	0.956000	0.39512	0.705000	0.40729	1.682000	0.37628	1.154000	0.42482	0.313000	0.20887	CCC	.		0.517	LCE2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034524.1	NM_014357	
ITPR2	3709	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	26755574	26755574	+	Missense_Mutation	SNP	G	G	C			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr12:26755574G>C	ENST00000381340.3	-	27	3944	c.3528C>G	c.(3526-3528)agC>agG	p.S1176R		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	1176					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	GGTAGTTATTGCTCTTGTTGC	0.323																																					p.S1176R		.											.	.	.	0			c.C3528G						.						122.0	103.0	109.0					12																	26755574		1839	4097	5936	SO:0001583	missense	3709	exon27			GTTATTGCTCTTG	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"""Ion channels / Inositol triphosphate receptors"""	6181	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 48"""	600144	"""inositol 1,4,5-triphosphate receptor, type 2"""			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.3528C>G	12.37:g.26755574G>C	ENSP00000370744:p.Ser1176Arg	Somatic	27	0		WXS	Illumina HiSeq	.	54	11	NM_002223	O94773	Missense_Mutation	SNP	ENST00000381340.3	37	CCDS41764.1	.	.	.	.	.	.	.	.	.	.	G	12.60	1.987740	0.35036	.	.	ENSG00000123104	ENST00000381340	D	0.89123	-2.47	4.83	2.98	0.34508	.	0.529785	0.22464	N	0.059704	T	0.81370	0.4808	L	0.35542	1.07	0.80722	D	1	B	0.33135	0.399	B	0.36289	0.221	T	0.72408	-0.4303	10	0.22109	T	0.4	.	7.9062	0.29763	0.1471:0.1339:0.7189:0.0	.	1176	Q14571	ITPR2_HUMAN	R	1176	ENSP00000370744:S1176R	ENSP00000370744:S1176R	S	-	3	2	ITPR2	26646841	1.000000	0.71417	0.998000	0.56505	0.975000	0.68041	1.899000	0.39818	0.732000	0.32470	0.655000	0.94253	AGC	.		0.323	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	
ADAMTS20	80070	hgsc.bcm.edu	37	12	43925997	43925997	+	Splice_Site	SNP	G	G	T	rs141043529		TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr12:43925997G>T	ENST00000389420.3	-	3	454	c.455C>A	c.(454-456)aCg>aAg	p.T152K	ADAMTS20_ENST00000553158.1_Splice_Site_p.T152K	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	152				T -> V (in Ref. 2; CAD56159/CAD56160). {ECO:0000305}.	extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.T152M(1)|p.?(1)		breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		AAATGTTCCCGTCTGAAAATA	0.358																																					p.T152K		.											ADAMTS20_ENST00000389420,NS,carcinoma,0,6	ADAMTS20_ENST00000389420	0	2	Substitution - Missense(1)|Unknown(1)	pancreas(2)	c.C455A						.						100.0	105.0	103.0					12																	43925997		2202	4300	6502	SO:0001630	splice_region_variant	80070	exon3			GTTCCCGTCTGAA	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17178	protein-coding gene	gene with protein product		611681	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"""			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.454-1C>A	12.37:g.43925997G>T		Somatic	37	0		WXS	Illumina HiSeq	.	45	2	NM_025003	A6NNC9|J3QT00	Missense_Mutation	SNP	ENST00000389420.3	37	CCDS31778.2	.	.	.	.	.	.	.	.	.	.	G	13.30	2.195859	0.38806	.	.	ENSG00000173157	ENST00000389420;ENST00000553158;ENST00000389417	T;T	0.05580	3.42;3.42	4.74	3.6	0.41247	Peptidase M12B, propeptide (1);	0.117171	0.36628	N	0.002492	T	0.04363	0.0120	N	0.05012	-0.13	0.80722	D	1	B	0.31931	0.347	B	0.39094	0.29	T	0.52548	-0.8561	10	0.44086	T	0.13	.	9.3807	0.38311	0.9089:0.0:0.0911:0.0	.	152	P59510	ATS20_HUMAN	K	152	ENSP00000374071:T152K;ENSP00000448341:T152K	ENSP00000374068:T152K	T	-	2	0	ADAMTS20	42212264	1.000000	0.71417	1.000000	0.80357	0.875000	0.50365	4.804000	0.62554	0.914000	0.36822	-0.482000	0.04802	ACG	.		0.358	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003	Missense_Mutation
MAP1A	4130	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	43818646	43818646	+	Missense_Mutation	SNP	G	G	A			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr15:43818646G>A	ENST00000300231.5	+	4	5425	c.4975G>A	c.(4975-4977)Gag>Aag	p.E1659K	MAP1A_ENST00000399453.1_Missense_Mutation_p.E1659K|MAP1A_ENST00000382031.1_Missense_Mutation_p.E1897K			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	1659					microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	TACCAGAGAGGAGCCGGCTGG	0.582																																					p.E1659K		.											.	.	.	0			c.G4975A						.						41.0	54.0	50.0					15																	43818646		1978	4141	6119	SO:0001583	missense	4130	exon4			AGAGAGGAGCCGG	U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.4975G>A	15.37:g.43818646G>A	ENSP00000300231:p.Glu1659Lys	Somatic	47	0		WXS	Illumina HiSeq	.	83	24	NM_002373	O95643|Q12973|Q15882|Q9UJT4	Missense_Mutation	SNP	ENST00000300231.5	37	CCDS42031.1	.	.	.	.	.	.	.	.	.	.	G	0.942	-0.709347	0.03230	.	.	ENSG00000166963	ENST00000382031;ENST00000399453;ENST00000300231	T;T;T	0.01745	4.66;4.66;4.66	4.19	1.09	0.20402	.	.	.	.	.	T	0.01489	0.0048	N	0.20986	0.625	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.46119	-0.9214	9	0.39692	T	0.17	-6.2385	6.4759	0.22034	0.177:0.1487:0.6743:0.0	.	1659	P78559	MAP1A_HUMAN	K	1897;1659;1659	ENSP00000371462:E1897K;ENSP00000382380:E1659K;ENSP00000300231:E1659K	ENSP00000300231:E1659K	E	+	1	0	MAP1A	41605938	0.033000	0.19621	0.312000	0.25196	0.022000	0.10575	1.562000	0.36353	0.424000	0.26061	-0.253000	0.11424	GAG	.		0.582	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373	
SEMA6D	80031	hgsc.bcm.edu	37	15	48056069	48056069	+	Missense_Mutation	SNP	G	G	A			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr15:48056069G>A	ENST00000316364.5	+	10	1209	c.770G>A	c.(769-771)cGc>cAc	p.R257H	SEMA6D_ENST00000389433.2_Missense_Mutation_p.R257H|SEMA6D_ENST00000558014.1_Missense_Mutation_p.R257H|SEMA6D_ENST00000354744.4_Missense_Mutation_p.R257H|SEMA6D_ENST00000558816.1_Missense_Mutation_p.R257H|SEMA6D_ENST00000358066.4_Missense_Mutation_p.R257H|SEMA6D_ENST00000389428.3_Missense_Mutation_p.R257H|SEMA6D_ENST00000537942.1_Missense_Mutation_p.R257H|SEMA6D_ENST00000389425.3_Missense_Mutation_p.R257H|SEMA6D_ENST00000536845.2_Missense_Mutation_p.R257H|SEMA6D_ENST00000355997.3_Missense_Mutation_p.R257H|SEMA6D_ENST00000389432.2_Missense_Mutation_p.R257H	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	257	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|negative regulation of smooth muscle cell migration (GO:0014912)|positive regulation of smooth muscle cell migration (GO:0014911)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	77		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		CGCGTGGCCCGCATATGTAAA	0.493																																					p.R257H		.											SEMA6D_ENST00000558014,NS,carcinoma,0,2	SEMA6D_ENST00000558014	0	0			c.G770A						.						145.0	141.0	142.0					15																	48056069		2198	4297	6495	SO:0001583	missense	80031	exon10			TGGCCCGCATATG	AF389430	CCDS32224.1, CCDS32225.1, CCDS32226.1, CCDS32227.1, CCDS32228.1, CCDS32229.1	15q21.1	2006-09-18				ENSG00000137872		"""Semaphorins"""	16770	protein-coding gene	gene with protein product		609295				12110693, 14977921	Standard	NM_020858		Approved	KIAA1479, FLJ11598	uc001zvy.3	Q8NFY4		ENST00000316364.5:c.770G>A	15.37:g.48056069G>A	ENSP00000324857:p.Arg257His	Somatic	29	0		WXS	Illumina HiSeq	.	54	3	NM_153617	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Missense_Mutation	SNP	ENST00000316364.5	37	CCDS32225.1	.	.	.	.	.	.	.	.	.	.	G	36	5.755662	0.96898	.	.	ENSG00000137872	ENST00000537942;ENST00000536845;ENST00000316364;ENST00000389433;ENST00000389432;ENST00000354744;ENST00000358066;ENST00000389428;ENST00000355997;ENST00000389425	T;T;T;T;T;T;T;T;T;T	0.49139	0.79;0.79;0.79;0.79;0.79;0.79;0.79;0.79;0.79;0.79	5.87	5.87	0.94306	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.81083	0.4749	H	0.96691	3.865	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;0.998;1.0	D	0.86618	0.1877	10	0.87932	D	0	.	20.206	0.98277	0.0:0.0:1.0:0.0	.	257;257;257;257;257	Q8NFY4-3;A6NM95;Q8NFY4-4;Q8NFY4;Q8NFY4-2	.;.;.;SEM6D_HUMAN;.	H	257	ENSP00000442040:R257H;ENSP00000446152:R257H;ENSP00000324857:R257H;ENSP00000374084:R257H;ENSP00000374083:R257H;ENSP00000346786:R257H;ENSP00000350770:R257H;ENSP00000374079:R257H;ENSP00000348276:R257H;ENSP00000374076:R257H	ENSP00000324857:R257H	R	+	2	0	SEMA6D	45843361	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	9.869000	0.99810	2.785000	0.95823	0.655000	0.94253	CGC	.		0.493	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966	
JAKMIP2	9832	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	147040819	147040819	+	Missense_Mutation	SNP	G	G	A			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr5:147040819G>A	ENST00000265272.5	-	3	786	c.319C>T	c.(319-321)Cgt>Tgt	p.R107C	JAKMIP2_ENST00000333010.6_Missense_Mutation_p.R65C|JAKMIP2_ENST00000507386.1_Missense_Mutation_p.R107C	NM_001270941.1|NM_014790.4	NP_001257870.1|NP_055605.2	Q96AA8	JKIP2_HUMAN	janus kinase and microtubule interacting protein 2	107						Golgi apparatus (GO:0005794)				NS(1)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(22)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCTCCATCACGTACCTTCACC	0.557																																					p.R107C		.											.	.	.	0			c.C319T						.						187.0	176.0	180.0					5																	147040819		2203	4300	6503	SO:0001583	missense	9832	exon3			CATCACGTACCTT	AB011127	CCDS4285.1, CCDS59495.1, CCDS64284.1, CCDS75352.1	5q32	2009-08-13	2009-08-13		ENSG00000176049	ENSG00000176049			29067	protein-coding gene	gene with protein product		611197				9628581	Standard	NM_001270941		Approved	JAMIP2, KIAA0555	uc010jgo.2	Q96AA8	OTTHUMG00000129731	ENST00000265272.5:c.319C>T	5.37:g.147040819G>A	ENSP00000265272:p.Arg107Cys	Somatic	14	0		WXS	Illumina HiSeq	.	16	5	NM_001270941	A4ZZA7|A8K5G5|B4DSG0|G5E9Y0|O60302|Q548S1	Missense_Mutation	SNP	ENST00000265272.5	37	CCDS4285.1	.	.	.	.	.	.	.	.	.	.	G	11.95	1.792878	0.31685	.	.	ENSG00000176049	ENST00000507386;ENST00000265272;ENST00000333010;ENST00000539401	T;T;T	0.35973	1.28;1.28;1.28	4.67	3.71	0.42584	.	0.059973	0.64402	D	0.000003	T	0.30448	0.0765	N	0.24115	0.695	0.50313	D	0.999865	D;D;D;D	0.67145	0.987;0.996;0.996;0.993	B;P;P;P	0.47744	0.432;0.556;0.556;0.556	T	0.12811	-1.0533	10	0.87932	D	0	.	12.4034	0.55426	0.0:0.0:0.6863:0.3137	.	65;107;107;107	B4DSG0;Q96AA8-3;G5E9Y0;Q96AA8	.;.;.;JKIP2_HUMAN	C	107;107;65;107	ENSP00000421398:R107C;ENSP00000265272:R107C;ENSP00000328989:R65C	ENSP00000265272:R107C	R	-	1	0	JAKMIP2	147021012	1.000000	0.71417	1.000000	0.80357	0.068000	0.16541	4.826000	0.62715	2.529000	0.85273	0.563000	0.77884	CGT	.		0.557	JAKMIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251941.1	NM_014790	
CEP68	23177	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	65309725	65309725	+	Silent	SNP	C	C	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr2:65309725C>T	ENST00000377990.2	+	6	2363	c.2160C>T	c.(2158-2160)caC>caT	p.H720H	CEP68_ENST00000546106.1_3'UTR|CEP68_ENST00000260569.4_Silent_p.H583H|RAB1A_ENST00000494188.1_Intron	NM_015147.2	NP_055962.2	Q76N32	CEP68_HUMAN	centrosomal protein 68kDa	720					centriole-centriole cohesion (GO:0010457)|centrosome organization (GO:0051297)|protein localization to organelle (GO:0033365)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|endometrium(6)|kidney(8)|large_intestine(5)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32						TGGAGAGCCACGCAGATCGCC	0.498																																					p.H720H		.											CEP68,NS,carcinoma,0,1	CEP68	0	0			c.C2160T						.						165.0	152.0	157.0					2																	65309725		2203	4300	6503	SO:0001819	synonymous_variant	23177	exon6			GAGCCACGCAGAT	BC004873	CCDS1880.2	2p14	2014-02-20	2005-12-01	2005-12-01	ENSG00000011523	ENSG00000011523			29076	protein-coding gene	gene with protein product			"""KIAA0582"""	KIAA0582		9628581, 9847074, 14654843	Standard	NM_015147		Approved		uc002sdl.4	Q76N32	OTTHUMG00000129538	ENST00000377990.2:c.2160C>T	2.37:g.65309725C>T		Somatic	30	0		WXS	Illumina HiSeq	.	27	16	NM_015147	B4DRQ1|D6W5F1|D6W5F2|O60326|Q9BQ18|Q9UDM9	Silent	SNP	ENST00000377990.2	37	CCDS1880.2																																																																																			.		0.498	CEP68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251727.2	NM_015147	
DDX5	1655	hgsc.bcm.edu	37	17	62496866	62496866	+	Silent	SNP	G	G	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr17:62496866G>T	ENST00000225792.5	-	12	1643	c.1242C>A	c.(1240-1242)atC>atA	p.I414I	DDX5_ENST00000580026.1_5'UTR|MIR3064_ENST00000581130.1_RNA|MIR5047_ENST00000579212.1_RNA|DDX5_ENST00000578804.1_Silent_p.I414I|DDX5_ENST00000450599.2_Silent_p.I335I	NM_004396.3	NP_004387.1	P17844	DDX5_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 5	414	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				cell growth (GO:0016049)|circadian rhythm (GO:0007623)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of osteoblast differentiation (GO:0045667)|regulation of skeletal muscle cell differentiation (GO:2001014)|regulation of viral genome replication (GO:0045069)|transcription, DNA-templated (GO:0006351)	catalytic step 2 spliceosome (GO:0071013)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|pre-mRNA binding (GO:0036002)|RNA helicase activity (GO:0003724)|transcription coactivator activity (GO:0003713)			breast(3)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)	19	Breast(5;2.15e-14)		BRCA - Breast invasive adenocarcinoma(8;8.6e-12)			AGTCATAATTGATGACAAATT	0.403			T	ETV4	prostate																																p.I414I	NSCLC(22;406 813 4871 19580 40307)	.		Dom	yes		17	17q21	1655	DEAD (Asp-Glu-Ala-Asp) box polypeptide 5		E	DDX5_ENST00000540698,NS,carcinoma,0,2	DDX5_ENST00000540698	0	0			c.C1242A						.						120.0	106.0	111.0					17																	62496866		2203	4300	6503	SO:0001819	synonymous_variant	1655	exon12			ATAATTGATGACA	AF015812	CCDS11659.1	17q21	2012-07-27	2012-02-23		ENSG00000108654	ENSG00000108654		"""DEAD-boxes"""	2746	protein-coding gene	gene with protein product		180630	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 5 (RNA helicase, 68kD)"", ""DEAD (Asp-Glu-Ala-Asp) box polypeptide 5"""	HLR1, G17P1		22156369, 18698352	Standard	NM_004396		Approved	p68	uc002jek.2	P17844	OTTHUMG00000178936	ENST00000225792.5:c.1242C>A	17.37:g.62496866G>T		Somatic	29	0		WXS	Illumina HiSeq	.	38	2	NM_004396	B4DLW8|B5BU21|D3DU32|E7ETL9|O75681|Q53Y61	Silent	SNP	ENST00000225792.5	37	CCDS11659.1																																																																																			.		0.403	DDX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444030.1	NM_004396	
NAV3	89795	hgsc.bcm.edu	37	12	78520946	78520946	+	Splice_Site	SNP	G	G	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr12:78520946G>T	ENST00000397909.2	+	17	4411		c.e17-1		NAV3_ENST00000536525.2_Splice_Site|NAV3_ENST00000266692.7_Intron|NAV3_ENST00000228327.6_Splice_Site			Q8IVL0	NAV3_HUMAN	neuron navigator 3							membrane (GO:0016020)|nuclear envelope (GO:0005635)				NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						TGTTTTAACAGCATGCAGCTT	0.333										HNSCC(70;0.22)																											.		.											NAV3,NS,carcinoma,0,1	NAV3	0	0			c.4239-1G>T						.						173.0	159.0	163.0					12																	78520946		1845	4085	5930	SO:0001630	splice_region_variant	89795	exon17			TTAACAGCATGCA	AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 1"", ""steerin 3"""	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.4239-1G>T	12.37:g.78520946G>T		Somatic	38	0		WXS	Illumina HiSeq	.	53	3	NM_014903	Q8NFW7|Q9Y2E7	Splice_Site	SNP	ENST00000397909.2	37		.	.	.	.	.	.	.	.	.	.	G	24.5	4.536285	0.85812	.	.	ENSG00000067798	ENST00000536525;ENST00000397909;ENST00000228327	.	.	.	5.86	5.86	0.93980	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.1726	0.98160	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NAV3	77045077	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.183000	0.94887	2.763000	0.94921	0.650000	0.86243	.	.		0.333	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383	Intron
TCHH	7062	hgsc.bcm.edu	37	1	152084531	152084531	+	Missense_Mutation	SNP	G	G	C	rs530429479	byFrequency	TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr1:152084531G>C	ENST00000368804.1	-	2	1161	c.1162C>G	c.(1162-1164)Cag>Gag	p.Q388E		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	388	8 X 6 AA tandem repeats of R-R-E-Q-Q-L.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			cgcctcagctgctgctcgcgc	0.721													-|||	107	0.0213658	0.003	0.1023	5008	,	,		16197	0.0298		0.001	False		,,,				2504	0.001				p.Q388E		.											.	.	.	0			c.C1162G						.						2.0	4.0	3.0					1																	152084531		541	1723	2264	SO:0001583	missense	7062	exon3			TCAGCTGCTGCTC	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"""EF-hand domain containing"""	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.1162C>G	1.37:g.152084531G>C	ENSP00000357794:p.Gln388Glu	Somatic	10	0		WXS	Illumina HiSeq	.	25	6	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	37	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	N	5.805	0.332821	0.11013	.	.	ENSG00000159450	ENST00000368804	T	0.04275	3.66	3.35	-0.432	0.12291	.	.	.	.	.	T	0.00695	0.0023	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.45571	-0.9252	9	0.02654	T	1	.	16.3773	0.83410	0.0:0.2058:0.7942:0.0	.	388	Q07283	TRHY_HUMAN	E	388	ENSP00000357794:Q388E	ENSP00000357794:Q388E	Q	-	1	0	TCHH	150351155	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.503000	0.00965	-0.501000	0.06605	-1.947000	0.00488	CAG	.		0.721	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113	
MPDZ	8777	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	13222402	13222402	+	Missense_Mutation	SNP	C	C	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr9:13222402C>T	ENST00000319217.7	-	6	824	c.577G>A	c.(577-579)Gga>Aga	p.G193R	MPDZ_ENST00000541718.1_Missense_Mutation_p.G193R|MPDZ_ENST00000381015.4_Missense_Mutation_p.G193R|MPDZ_ENST00000447879.1_Missense_Mutation_p.G193R|MPDZ_ENST00000546205.1_Missense_Mutation_p.G193R|MPDZ_ENST00000536827.1_Missense_Mutation_p.G193R|MPDZ_ENST00000381022.2_Missense_Mutation_p.G193R	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	193	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell adhesion (GO:0007155)|myelination (GO:0042552)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein C-terminus binding (GO:0008022)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61				GBM - Glioblastoma multiforme(50;2.03e-06)		AGAGCCTGTCCATTGATAGCA	0.418																																					p.G193R		.											.	.	.	0			c.G577A						.						222.0	205.0	210.0					9																	13222402		1904	4123	6027	SO:0001583	missense	8777	exon6			CCTGTCCATTGAT	AF093419	CCDS47951.1, CCDS59119.1, CCDS59120.1	9p23	2008-05-15			ENSG00000107186	ENSG00000107186			7208	protein-coding gene	gene with protein product		603785					Standard	NM_003829		Approved	MUPP1	uc003zlb.4	O75970	OTTHUMG00000021031	ENST00000319217.7:c.577G>A	9.37:g.13222402C>T	ENSP00000320006:p.Gly193Arg	Somatic	25	0		WXS	Illumina HiSeq	.	37	12	NM_003829	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Missense_Mutation	SNP	ENST00000319217.7	37		.	.	.	.	.	.	.	.	.	.	C	32	5.108766	0.94292	.	.	ENSG00000107186	ENST00000319217;ENST00000541718;ENST00000381022;ENST00000536827;ENST00000447879;ENST00000381015;ENST00000399902;ENST00000546205	T;T;T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97;0.97;0.97	6.07	6.07	0.98685	.	0.000000	0.45126	D	0.000398	T	0.74306	0.3699	M	0.91090	3.175	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.77749	-0.2471	10	0.62326	D	0.03	.	20.6525	0.99598	0.0:1.0:0.0:0.0	.	193;193;193	B7ZMI4;O75970-3;O75970-2	.;.;.	R	193	ENSP00000320006:G193R;ENSP00000439807:G193R;ENSP00000370410:G193R;ENSP00000444151:G193R;ENSP00000415208:G193R;ENSP00000370403:G193R;ENSP00000446358:G193R	ENSP00000320006:G193R	G	-	1	0	MPDZ	13212402	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.440000	0.80464	2.890000	0.99128	0.585000	0.79938	GGA	.		0.418	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829	
CCNB3	85417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	X	50085219	50085219	+	Missense_Mutation	SNP	C	C	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chrX:50085219C>T	ENST00000376042.1	+	9	3833	c.3535C>T	c.(3535-3537)Cat>Tat	p.H1179Y	CCNB3_ENST00000348603.2_Missense_Mutation_p.H75Y|CCNB3_ENST00000376038.1_Missense_Mutation_p.H75Y|CCNB3_ENST00000276014.7_Missense_Mutation_p.H1179Y			Q8WWL7	CCNB3_HUMAN	cyclin B3	1179					meiotic nuclear division (GO:0007126)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)	nucleus (GO:0005634)				breast(3)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Ovarian(276;0.236)					TGAGATGACCCATGAGACCCT	0.488																																					p.H1179Y		.											.	.	.	0			c.C3535T						.						220.0	178.0	192.0					X																	50085219		2203	4300	6503	SO:0001583	missense	85417	exon8			ATGACCCATGAGA	AJ314764	CCDS14331.1, CCDS14332.1	Xp11	2008-07-03			ENSG00000147082	ENSG00000147082			18709	protein-coding gene	gene with protein product		300456				11846420, 12185076	Standard	XM_006724610		Approved		uc004doy.3	Q8WWL7	OTTHUMG00000021519	ENST00000376042.1:c.3535C>T	X.37:g.50085219C>T	ENSP00000365210:p.His1179Tyr	Somatic	37	0		WXS	Illumina HiSeq	.	49	15	NM_033031	B1AQI5|B1AQI6|Q96SB5|Q96SB6|Q96SB7|Q9NT38	Missense_Mutation	SNP	ENST00000376042.1	37	CCDS14331.1	.	.	.	.	.	.	.	.	.	.	C	17.58	3.426158	0.62733	.	.	ENSG00000147082	ENST00000376042;ENST00000376038;ENST00000348603;ENST00000276014	T;T;T;T	0.11495	2.77;2.77;2.77;2.77	5.11	5.11	0.69529	Cyclin, N-terminal (1);Cyclin-like (3);	0.109289	0.64402	D	0.000009	T	0.39462	0.1079	M	0.86864	2.845	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.87578	0.994;0.997;0.998	T	0.41052	-0.9530	9	.	.	.	.	16.5859	0.84727	0.0:1.0:0.0:0.0	.	1179;75;1179	A8K8T9;Q8WWL7-2;Q8WWL7	.;.;CCNB3_HUMAN	Y	1179;75;75;1179	ENSP00000365210:H1179Y;ENSP00000365206:H75Y;ENSP00000338682:H75Y;ENSP00000276014:H1179Y	.	H	+	1	0	CCNB3	50101959	1.000000	0.71417	0.434000	0.26772	0.500000	0.33767	4.944000	0.63561	2.261000	0.74972	0.436000	0.28706	CAT	.		0.488	CCNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056558.1		
USP47	55031	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	11969496	11969496	+	Missense_Mutation	SNP	G	G	C			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr11:11969496G>C	ENST00000399455.2	+	22	3276	c.3156G>C	c.(3154-3156)ttG>ttC	p.L1052F	USP47_ENST00000527733.1_Missense_Mutation_p.L1032F|USP47_ENST00000339865.5_Missense_Mutation_p.L964F|USP47_ENST00000539466.1_5'UTR	NM_001282659.1	NP_001269588.1	Q96K76	UBP47_HUMAN	ubiquitin specific peptidase 47	1052					base-excision repair (GO:0006284)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of G2/M transition of mitotic cell cycle (GO:0010972)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell growth (GO:0030307)|response to drug (GO:0042493)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	ubiquitin-specific protease activity (GO:0004843)|WD40-repeat domain binding (GO:0071987)			breast(4)|endometrium(7)|kidney(2)|large_intestine(8)|liver(2)|lung(14)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46				Epithelial(150;0.000339)		GCTTAGGGTTGATGGTGCATG	0.338																																					p.L964F		.											.	.	.	0			c.G2892C						.						118.0	111.0	113.0					11																	11969496		1810	4070	5880	SO:0001583	missense	55031	exon20			AGGGTTGATGGTG	AK027362	CCDS41619.1, CCDS60725.1	11p15.2	2008-02-05	2005-08-08		ENSG00000170242	ENSG00000170242		"""Ubiquitin-specific peptidases"""	20076	protein-coding gene	gene with protein product		614460	"""Trf (TATA binding protein-related factor)-proximal homolog (Drosophila)"", ""ubiquitin specific protease 47"""			12838346	Standard	XM_005252997		Approved		uc001mjr.3	Q96K76	OTTHUMG00000165685	ENST00000399455.2:c.3156G>C	11.37:g.11969496G>C	ENSP00000382382:p.Leu1052Phe	Somatic	37	0		WXS	Illumina HiSeq	.	50	25	NM_017944	B3KXF5|E9PM46|Q658U0|Q86Y73|Q8TEP6|Q9BWI0|Q9NWN1	Missense_Mutation	SNP	ENST00000399455.2	37		.	.	.	.	.	.	.	.	.	.	G	17.60	3.430457	0.62844	.	.	ENSG00000170242	ENST00000339865;ENST00000527733;ENST00000399455	D;D;D	0.95622	-3.76;-3.76;-3.76	5.46	4.55	0.56014	.	0.000000	0.85682	D	0.000000	D	0.96210	0.8764	L	0.58101	1.795	0.80722	D	1	D;D	0.69078	0.995;0.997	D;D	0.75484	0.969;0.986	D	0.94550	0.7753	10	0.31617	T	0.26	.	9.359	0.38184	0.0766:0.1446:0.7788:0.0	.	1032;964	E9PM46;Q96K76-2	.;.	F	964;1032;1052	ENSP00000339957:L964F;ENSP00000433146:L1032F;ENSP00000382382:L1052F	ENSP00000339957:L964F	L	+	3	2	USP47	11926072	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	4.474000	0.60203	1.283000	0.44513	0.591000	0.81541	TTG	.		0.338	USP47-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000385853.2	NM_017944	
TRAF4	9618	hgsc.bcm.edu;broad.mit.edu	37	17	27071215	27071215	+	Missense_Mutation	SNP	G	G	A			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr17:27071215G>A	ENST00000262395.5	+	1	214	c.85G>A	c.(85-87)Gtg>Atg	p.V29M	TRAF4_ENST00000262396.6_Missense_Mutation_p.V29M|AC010761.6_ENST00000582536.1_RNA|TRAF4_ENST00000444415.3_Missense_Mutation_p.V29M|AC010761.9_ENST00000577325.1_RNA|AC010761.6_ENST00000584779.1_RNA	NM_004295.3	NP_004286.2	Q9BUZ4	TRAF4_HUMAN	TNF receptor-associated factor 4	29					activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of protein kinase activity (GO:0045860)|regulation of apoptotic process (GO:0042981)|respiratory gaseous exchange (GO:0007585)|respiratory tube development (GO:0030323)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	DNA binding (GO:0003677)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|WW domain binding (GO:0050699)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	10	Lung NSC(42;0.01)		Epithelial(11;3.26e-05)|all cancers(11;0.000272)|OV - Ovarian serous cystadenocarcinoma(11;0.235)			GCGCGAGCCTGTGCAGGTTTC	0.697																																					p.V29M		.											.	.	.	0			c.G85A						.						21.0	24.0	23.0					17																	27071215		2203	4298	6501	SO:0001583	missense	9618	exon1			GAGCCTGTGCAGG	X80200	CCDS11243.1	17q11-q21.3	2013-01-09			ENSG00000076604	ENSG00000076604		"""RING-type (C3HC4) zinc fingers"""	12034	protein-coding gene	gene with protein product		602464				7592751, 7490069	Standard	NM_004295		Approved	CART1, MLN62, RNF83	uc002hcs.3	Q9BUZ4	OTTHUMG00000132677	ENST00000262395.5:c.85G>A	17.37:g.27071215G>A	ENSP00000262395:p.Val29Met	Somatic	16	0		WXS	Illumina HiSeq	.	11	6	NM_004295	O75615|Q14848|Q2KJU4|Q2PJN8	Missense_Mutation	SNP	ENST00000262395.5	37	CCDS11243.1	.	.	.	.	.	.	.	.	.	.	g	16.28	3.079523	0.55753	.	.	ENSG00000076604	ENST00000262395;ENST00000454852;ENST00000422344;ENST00000444415;ENST00000262396;ENST00000394924;ENST00000394925	D;T;D;D	0.86432	-2.12;1.85;-2.12;-2.12	4.61	2.62	0.31277	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.074205	0.53938	D	0.000047	D	0.91640	0.7358	M	0.77406	2.37	0.35382	D	0.789984	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.961	D	0.91897	0.5528	10	0.62326	D	0.03	.	7.9367	0.29933	0.1937:0.0:0.8063:0.0	.	29;29	Q9BUZ4;Q9BUZ4-2	TRAF4_HUMAN;.	M	29	ENSP00000262395:V29M;ENSP00000415789:V29M;ENSP00000438154:V29M;ENSP00000262396:V29M	ENSP00000262395:V29M	V	+	1	0	TRAF4	24095342	1.000000	0.71417	0.989000	0.46669	0.121000	0.20230	5.444000	0.66587	0.399000	0.25367	0.538000	0.68166	GTG	.		0.697	TRAF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255944.2	NM_145751	
KCNQ5	56479	hgsc.bcm.edu	37	6	73834220	73834220	+	Missense_Mutation	SNP	G	G	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr6:73834220G>T	ENST00000370398.1	+	9	1341	c.1232G>T	c.(1231-1233)gGg>gTg	p.G411V	KCNQ5_ENST00000342056.2_Missense_Mutation_p.G411V|KCNQ5_ENST00000403813.2_Intron|KCNQ5_ENST00000402622.2_Intron|KCNQ5_ENST00000355635.3_Intron|KCNQ5_ENST00000355194.4_Missense_Mutation_p.G411V|KCNQ5_ENST00000414165.2_Missense_Mutation_p.G411V|KCNQ5_ENST00000370392.1_Missense_Mutation_p.G411V	NM_019842.3	NP_062816.2	Q9NR82	KCNQ5_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 5	411					protein complex assembly (GO:0006461)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|inward rectifier potassium channel activity (GO:0005242)			breast(1)|cervix(1)|endometrium(6)|kidney(7)|large_intestine(13)|lung(15)|ovary(4)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	57		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)	Ezogabine(DB04953)	AAAGAACAAGGGGAAGCATCA	0.383																																					p.G411V	GBM(142;1375 1859 14391 23261 44706)	.											KCNQ5,NS,malignant_melanoma,0,1	KCNQ5	0	0			c.G1232T						.						182.0	166.0	172.0					6																	73834220		2203	4300	6503	SO:0001583	missense	56479	exon9			AACAAGGGGAAGC	AF202977	CCDS4976.1, CCDS55034.1	6q14	2012-07-05			ENSG00000185760	ENSG00000185760		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6299	protein-coding gene	gene with protein product		607357				10787416, 10816588, 16382104	Standard	NM_019842		Approved	Kv7.5	uc011dyh.2	Q9NR82	OTTHUMG00000015020	ENST00000370398.1:c.1232G>T	6.37:g.73834220G>T	ENSP00000359425:p.Gly411Val	Somatic	24	0		WXS	Illumina HiSeq	.	37	2	NM_001160133	A6NKT6|A6PVT6|A8MSQ5|B4DS33|B5MC83|B7ZL37|F5GZV0|Q17RE1|Q5VVP3|Q86W40|Q9NRN0|Q9NYA6	Missense_Mutation	SNP	ENST00000370398.1	37	CCDS4976.1	.	.	.	.	.	.	.	.	.	.	G	16.16	3.043799	0.55003	.	.	ENSG00000185760	ENST00000342056;ENST00000451840;ENST00000355194;ENST00000370398;ENST00000370392;ENST00000414165	D;D;D;D;D	0.99270	-5.6;-5.6;-5.6;-5.41;-5.66	5.44	5.44	0.79542	.	7739.210000	0.00166	N	0.000000	D	0.98356	0.9454	L	0.47716	1.5	0.80722	D	1	B;B;B;P	0.50617	0.111;0.015;0.134;0.937	B;B;B;P	0.47915	0.041;0.011;0.034;0.561	D	0.90114	0.4194	10	0.17832	T	0.49	.	19.6178	0.95640	0.0:0.0:1.0:0.0	.	411;411;411;411	F5GZV0;A6PVT6;Q9NR82;Q9NR82-4	.;.;KCNQ5_HUMAN;.	V	411	ENSP00000345055:G411V;ENSP00000347326:G411V;ENSP00000359425:G411V;ENSP00000359419:G411V;ENSP00000409861:G411V	ENSP00000345055:G411V	G	+	2	0	KCNQ5	73890941	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.539000	0.90637	2.709000	0.92574	0.655000	0.94253	GGG	.		0.383	KCNQ5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041198.3	NM_019842	
AKAP13	11214	hgsc.bcm.edu	37	15	86284600	86284600	+	Missense_Mutation	SNP	G	G	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr15:86284600G>T	ENST00000394518.2	+	35	8027	c.7932G>T	c.(7930-7932)aaG>aaT	p.K2644N	AKAP13_ENST00000394510.2_Missense_Mutation_p.K889N|RP11-158M2.3_ENST00000558375.1_RNA|AKAP13_ENST00000560579.1_3'UTR|AKAP13_ENST00000361243.2_Missense_Mutation_p.K2648N	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	2644	Interaction with ESR1.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)	p.K2648K(1)		NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						AGCAGAAGAAGGGCACATACC	0.667																																					p.K2648N	Melanoma(94;603 1453 3280 32295 32951)	.											AKAP13,brain,glioma,0,1	AKAP13	0	1	Substitution - coding silent(1)	central_nervous_system(1)	c.G7944T						.						50.0	46.0	47.0					15																	86284600		2199	4299	6498	SO:0001583	missense	11214	exon35			GAAGAAGGGCACA	M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"""A-kinase anchor proteins"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	371	protein-coding gene	gene with protein product		604686	"""lymphoid blast crisis oncogene"""	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.7932G>T	15.37:g.86284600G>T	ENSP00000378026:p.Lys2644Asn	Somatic	35	0		WXS	Illumina HiSeq	.	46	2	NM_006738	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Missense_Mutation	SNP	ENST00000394518.2	37	CCDS32319.1	.	.	.	.	.	.	.	.	.	.	G	11.63	1.694479	0.30052	.	.	ENSG00000170776	ENST00000361243;ENST00000394518;ENST00000394516;ENST00000458540;ENST00000394510	T;T;T	0.22743	1.94;1.94;1.94	5.47	2.53	0.30540	.	.	.	.	.	T	0.22166	0.0534	M	0.65975	2.015	0.09310	N	0.999999	B;B	0.32382	0.252;0.368	B;B	0.32677	0.071;0.15	T	0.15694	-1.0428	9	0.48119	T	0.1	.	7.0348	0.24987	0.2036:0.0:0.6735:0.1229	.	2644;2648	Q12802;Q12802-2	AKP13_HUMAN;.	N	2648;2644;2647;2623;889	ENSP00000354718:K2648N;ENSP00000378026:K2644N;ENSP00000378018:K889N	ENSP00000354718:K2648N	K	+	3	2	AKAP13	84085604	1.000000	0.71417	0.080000	0.20451	0.626000	0.37791	1.154000	0.31688	0.664000	0.31047	-0.140000	0.14226	AAG	.		0.667	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200	
MYO3B	140469	hgsc.bcm.edu;bcgsc.ca	37	2	171371510	171371510	+	Silent	SNP	C	C	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr2:171371510C>T	ENST00000408978.4	+	29	3593	c.3450C>T	c.(3448-3450)tgC>tgT	p.C1150C	MYO3B_ENST00000602629.1_3'UTR|MYO3B_ENST00000334231.6_Silent_p.C1159C|MYO3B_ENST00000409044.3_Silent_p.C1123C	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	1150					peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium bundle tip (GO:0032426)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	59						TTCAAGACTGCAGCGAGCCTG	0.502																																					p.C1150C		.											.	.	.	0			c.C3450T						.						79.0	81.0	80.0					2																	171371510		1929	4137	6066	SO:0001819	synonymous_variant	140469	exon29			AGACTGCAGCGAG		CCDS42773.1, CCDS46446.1	2q31.1-q31.2	2011-09-27			ENSG00000071909	ENSG00000071909		"""Myosins / Myosin superfamily : Class III"""	15576	protein-coding gene	gene with protein product		610040					Standard	NM_001083615		Approved		uc002ufy.3	Q8WXR4	OTTHUMG00000154002	ENST00000408978.4:c.3450C>T	2.37:g.171371510C>T		Somatic	46	0		WXS	Illumina HiSeq	.	60	4	NM_138995	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Silent	SNP	ENST00000408978.4	37	CCDS42773.1																																																																																			.		0.502	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1		
MSS51	118490	hgsc.bcm.edu	37	10	75184905	75184905	+	Missense_Mutation	SNP	G	G	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr10:75184905G>T	ENST00000372912.1	-	5	1116	c.1114C>A	c.(1114-1116)Ctg>Atg	p.L372M	MSS51_ENST00000299432.2_Missense_Mutation_p.L372M			Q4VC12	MSS51_HUMAN	MSS51 mitochondrial translational activator	372					social behavior (GO:0035176)		metal ion binding (GO:0046872)										AGTAGCAGCAGGGTGGGCAGC	0.428																																					p.L372M		.											.	.	.	0			c.C1114A						.						88.0	92.0	91.0					10																	75184905		2203	4300	6503	SO:0001583	missense	118490	exon6			GCAGCAGGGTGGG	AK096884	CCDS31221.1	10q22.3	2013-01-10	2013-01-10	2012-02-24	ENSG00000166343	ENSG00000166343		"""Zinc fingers, MYND-type"""	21000	protein-coding gene	gene with protein product		614773	"""zinc finger, MYND-type containing 17"", ""MSS51 mitochondrial translational activator homolog (S. cerevisiae)"""	ZMYND17		19710419	Standard	NM_001024593		Approved	FLJ39565	uc001jud.3	Q4VC12	OTTHUMG00000018464	ENST00000372912.1:c.1114C>A	10.37:g.75184905G>T	ENSP00000362003:p.Leu372Met	Somatic	37	0		WXS	Illumina HiSeq	.	61	2	NM_001024593	A6NGH6|Q2VP95|Q5F2H5|Q7Z3M9|Q8N8G0	Missense_Mutation	SNP	ENST00000372912.1	37	CCDS31221.1	.	.	.	.	.	.	.	.	.	.	G	17.11	3.305718	0.60305	.	.	ENSG00000166343	ENST00000299432;ENST00000372912	T;T	0.58060	0.36;0.36	5.21	1.25	0.21368	.	0.000000	0.85682	D	0.000000	T	0.59676	0.2211	M	0.66939	2.045	0.35412	D	0.792558	D;D	0.71674	0.998;0.996	P;P	0.60173	0.87;0.745	T	0.64188	-0.6466	10	0.56958	D	0.05	-4.7815	5.4887	0.16763	0.2351:0.0:0.6249:0.14	.	151;372	Q4VC12-2;Q4VC12	.;ZMY17_HUMAN	M	372	ENSP00000299432:L372M;ENSP00000362003:L372M	ENSP00000299432:L372M	L	-	1	2	ZMYND17	74854911	1.000000	0.71417	0.991000	0.47740	0.928000	0.56348	2.778000	0.47726	0.071000	0.16664	-0.157000	0.13467	CTG	.		0.428	MSS51-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048652.3	NM_178451	
LIG3	3980	hgsc.bcm.edu	37	17	33310393	33310393	+	Silent	SNP	G	G	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr17:33310393G>T	ENST00000378526.4	+	2	502	c.369G>T	c.(367-369)gtG>gtT	p.V123V	LIG3_ENST00000586407.1_Intron|LIG3_ENST00000262327.5_Silent_p.V123V	NM_013975.3	NP_039269.2	P49916	DNLI3_HUMAN	ligase III, DNA, ATP-dependent	123					base-excision repair (GO:0006284)|base-excision repair, DNA ligation (GO:0006288)|DNA biosynthetic process (GO:0071897)|DNA repair (GO:0006281)|double-strand break repair via nonhomologous end joining (GO:0006303)|lagging strand elongation (GO:0006273)|mitochondrial DNA repair (GO:0043504)|negative regulation of DNA recombination (GO:0045910)|nucleotide-excision repair (GO:0006289)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|zinc ion binding (GO:0008270)			endometrium(4)|large_intestine(8)|lung(9)|ovary(3)|pancreas(2)|prostate(1)|skin(3)|stomach(1)	31		Ovarian(249;0.17)			Bleomycin(DB00290)	GCAAAGTGGTGCCCAATCCCT	0.493								Other BER factors																													p.V123V		.											.	.	.	0			c.G369T						.						74.0	69.0	71.0					17																	33310393		2203	4300	6503	SO:0001819	synonymous_variant	3980	exon2			AGTGGTGCCCAAT		CCDS11284.2, CCDS11285.2	17q11.2-q12	2008-10-29			ENSG00000005156	ENSG00000005156			6600	protein-coding gene	gene with protein product		600940	"""ligase II, DNA, ATP-dependent"""	LIG2		7760816	Standard	NM_002311		Approved		uc002hik.2	P49916	OTTHUMG00000128519	ENST00000378526.4:c.369G>T	17.37:g.33310393G>T		Somatic	45	0		WXS	Illumina HiSeq	.	87	4	NM_013975	Q16714|Q6NVK3	Silent	SNP	ENST00000378526.4	37	CCDS11284.2																																																																																			.		0.493	LIG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250330.3	NM_013975	
LAMA4	3910	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	112450203	112450203	+	Missense_Mutation	SNP	G	G	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr6:112450203G>T	ENST00000230538.7	-	31	4605	c.4208C>A	c.(4207-4209)cCc>cAc	p.P1403H	LAMA4_ENST00000522006.1_Missense_Mutation_p.P1396H|LAMA4_ENST00000389463.4_Missense_Mutation_p.P1396H|LAMA4_ENST00000424408.2_Missense_Mutation_p.P1396H	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4	1403					blood vessel development (GO:0001568)|brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(42)|ovary(4)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(8)	100		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		AGACTCAATGGGACACTCATA	0.373																																					p.P1403H		.											.	.	.	0			c.C4208A						.						109.0	105.0	106.0					6																	112450203		2203	4300	6503	SO:0001583	missense	3910	exon31			TCAATGGGACACT		CCDS34514.1, CCDS43491.1, CCDS43492.1	6q21	2014-09-17			ENSG00000112769	ENSG00000112769		"""Laminins"""	6484	protein-coding gene	gene with protein product		600133				7959779	Standard	NM_001105206		Approved	LAMA3	uc003pvu.3	Q16363	OTTHUMG00000015386	ENST00000230538.7:c.4208C>A	6.37:g.112450203G>T	ENSP00000230538:p.Pro1403His	Somatic	55	0		WXS	Illumina HiSeq	.	50	29	NM_001105206	Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	Missense_Mutation	SNP	ENST00000230538.7	37	CCDS43491.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.671785	0.88348	.	.	ENSG00000112769	ENST00000230538;ENST00000522006;ENST00000389463;ENST00000424408	T;T;T;T	0.14144	2.54;2.53;2.53;2.53	5.59	5.59	0.84812	.	0.048249	0.85682	D	0.000000	T	0.20618	0.0496	L	0.34521	1.04	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.01484	-1.1343	10	0.40728	T	0.16	.	19.5844	0.95485	0.0:0.0:1.0:0.0	.	1403;1396	Q16363;Q16363-2	LAMA4_HUMAN;.	H	1403;1396;1396;1396	ENSP00000230538:P1403H;ENSP00000429488:P1396H;ENSP00000374114:P1396H;ENSP00000416470:P1396H	ENSP00000230538:P1403H	P	-	2	0	LAMA4	112556896	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.188000	0.89710	2.638000	0.89438	0.585000	0.79938	CCC	.		0.373	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041876.2	NM_001105206	
MT-ND2	4536	hgsc.bcm.edu;broad.mit.edu	37	M	2410	2410	+	5'Flank	SNP	T	T	C			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chrM:2410T>C	ENST00000361453.3	+	0	0				MT-TV_ENST00000387342.1_RNA|MT-TL1_ENST00000386347.1_RNA|MT-TM_ENST00000387377.1_RNA|MT-TQ_ENST00000387372.1_RNA|MT-ND1_ENST00000361390.2_5'Flank|MT-TI_ENST00000387365.1_RNA|MT-RNR1_ENST00000389680.2_RNA|MT-RNR2_ENST00000387347.2_RNA|MT-TF_ENST00000387314.1_RNA			P03891	NU2M_HUMAN	mitochondrially encoded NADH dehydrogenase 2						cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|reactive oxygen species metabolic process (GO:0072593)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|lung(1)	3						AACAAGTCATTATTACCCTCA	0.408																																					.		.											.	.	.	0			.						.																																			SO:0001631	upstream_gene_variant	6053	.			TCATTATTACCCT			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198763	ENSG00000198763	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7456	protein-coding gene	gene with protein product	"""complex I ND2 subunit"", ""NADH-ubiquinone oxidoreductase chain 2"""	516001	"""NADH dehydrogenase 2"""	MTND2			Standard			Approved	ND2, NAD2		P03891			M.37:g.2410T>C	Exception_encountered	Somatic	217	0		WXS	Illumina HiSeq	.	713	29	.	Q34769|Q9TGI0|Q9TGI1|Q9TGI2|Q9TGI3|Q9TGI4	RNA	SNP	ENST00000361453.3	37																																																																																				.		0.408	MT-ND2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024027	
PIH1D2	120379	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	111942424	111942424	+	Missense_Mutation	SNP	G	G	A			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr11:111942424G>A	ENST00000280350.4	-	3	458	c.236C>T	c.(235-237)cCc>cTc	p.P79L	PIH1D2_ENST00000532211.1_Missense_Mutation_p.P79L|PIH1D2_ENST00000530641.1_Missense_Mutation_p.P79L|C11orf57_ENST00000530104.1_5'Flank|C11orf57_ENST00000532163.1_5'Flank|C11orf57_ENST00000280352.9_5'Flank|PIH1D2_ENST00000431456.1_Missense_Mutation_p.P79L|C11orf57_ENST00000393047.3_5'Flank|PIH1D2_ENST00000521853.2_5'UTR|C11orf57_ENST00000420986.2_5'Flank|PIH1D2_ENST00000528775.1_Missense_Mutation_p.P79L	NM_138789.3	NP_620144.1	Q8WWB5	PIHD2_HUMAN	PIH1 domain containing 2	79										endometrium(2)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	11		all_cancers(61;1.09e-14)|all_epithelial(67;7.64e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;3.19e-07)|BRCA - Breast invasive adenocarcinoma(274;6.17e-07)|all cancers(92;6.18e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0508)		GGTTGATTGGGGAGCTGGGAT	0.363																																					p.P79L		.											.	.	.	0			c.C236T						.						146.0	144.0	145.0					11																	111942424		2201	4297	6498	SO:0001583	missense	120379	exon3			GATTGGGGAGCTG	BC019238	CCDS8355.1, CCDS44730.1	11q23.1	2007-01-31			ENSG00000150773	ENSG00000150773			25210	protein-coding gene	gene with protein product						12477932	Standard	NM_138789		Approved		uc001pmp.4	Q8WWB5	OTTHUMG00000166925	ENST00000280350.4:c.236C>T	11.37:g.111942424G>A	ENSP00000280350:p.Pro79Leu	Somatic	56	0		WXS	Illumina HiSeq	.	66	22	NM_001082619	B4DU48|E9PD82	Missense_Mutation	SNP	ENST00000280350.4	37	CCDS8355.1	.	.	.	.	.	.	.	.	.	.	G	18.97	3.736317	0.69189	.	.	ENSG00000150773	ENST00000528775;ENST00000431456;ENST00000532211;ENST00000280350;ENST00000530641;ENST00000525744	T;T;T;T;T;T	0.54866	0.55;0.55;0.55;0.55;0.55;0.55	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	T	0.75228	0.3821	M	0.86028	2.79	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.78560	-0.2157	10	0.62326	D	0.03	-10.2927	15.7104	0.77623	0.0:0.0:1.0:0.0	.	79;79;79	B4DU48;E9PD82;Q8WWB5	.;.;PIHD2_HUMAN	L	79;79;79;79;79;44	ENSP00000434275:P79L;ENSP00000388209:P79L;ENSP00000431841:P79L;ENSP00000280350:P79L;ENSP00000431147:P79L;ENSP00000433297:P44L	ENSP00000280350:P79L	P	-	2	0	PIH1D2	111447634	1.000000	0.71417	0.975000	0.42487	0.839000	0.47603	3.643000	0.54374	2.695000	0.91970	0.561000	0.74099	CCC	.		0.363	PIH1D2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391916.1	NM_138789	
SPATA5L1	79029	hgsc.bcm.edu	37	15	45697670	45697670	+	Missense_Mutation	SNP	G	G	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr15:45697670G>T	ENST00000305560.6	+	2	1341	c.1242G>T	c.(1240-1242)gaG>gaT	p.E414D	SPATA5L1_ENST00000559860.1_Missense_Mutation_p.E414D	NM_024063.2	NP_076968.2	Q9BVQ7	SPA5L_HUMAN	spermatogenesis associated 5-like 1	414						cytoplasm (GO:0005737)	ATP binding (GO:0005524)	p.E414D(1)		kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	14		Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;7.31e-17)|GBM - Glioblastoma multiforme(94;6.28e-07)		TCTGTAGGGAGGCTGCCATGC	0.428																																					p.E414D		.											SPATA5L1,NS,carcinoma,0,1	SPATA5L1	0	1	Substitution - Missense(1)	lung(1)	c.G1242T						.						105.0	88.0	94.0					15																	45697670		2198	4298	6496	SO:0001583	missense	79029	exon2			TAGGGAGGCTGCC	AK023232	CCDS10123.1	15q15.1	2010-04-21			ENSG00000171763	ENSG00000171763		"""ATPases / AAA-type"""	28762	protein-coding gene	gene with protein product						12477932	Standard	NM_024063		Approved	MGC5347, FLJ12286	uc001zve.3	Q9BVQ7	OTTHUMG00000131425	ENST00000305560.6:c.1242G>T	15.37:g.45697670G>T	ENSP00000305494:p.Glu414Asp	Somatic	31	0		WXS	Illumina HiSeq	.	49	2	NM_024063	C9JHR5|Q9H8W7|Q9HA41	Missense_Mutation	SNP	ENST00000305560.6	37	CCDS10123.1	.	.	.	.	.	.	.	.	.	.	G	14.18	2.457023	0.43634	.	.	ENSG00000171763	ENST00000305560	D	0.95205	-3.64	5.47	1.55	0.23275	.	0.000000	0.85682	D	0.000000	D	0.92358	0.7575	M	0.77486	2.375	0.37470	D	0.915579	B	0.28584	0.216	B	0.32342	0.144	D	0.87693	0.2555	10	0.87932	D	0	-27.3202	4.708	0.12858	0.3788:0.0:0.4835:0.1377	.	414	Q9BVQ7	SPA5L_HUMAN	D	414	ENSP00000305494:E414D	ENSP00000305494:E414D	E	+	3	2	SPATA5L1	43484962	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	0.975000	0.29449	0.039000	0.15632	-0.122000	0.15005	GAG	.		0.428	SPATA5L1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254218.1	NM_024063	
ADAMTS7	11173	hgsc.bcm.edu	37	15	79051846	79051846	+	Missense_Mutation	SNP	T	T	C	rs199524707		TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr15:79051846T>C	ENST00000388820.4	-	24	5188	c.4978A>G	c.(4978-4980)Atc>Gtc	p.I1660V		NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	1660	PLAC. {ECO:0000255|PROSITE- ProRule:PRU00233}.				cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						TGGGTGCGGATGGTGGGCAGC	0.721																																					p.I1660V		.											ADAMTS7,NS,neuroblastoma,0,1	ADAMTS7	0	0			c.A4978G						.						9.0	11.0	10.0					15																	79051846		2122	4204	6326	SO:0001583	missense	11173	exon24			TGCGGATGGTGGG	AF140675	CCDS32303.1	15q25.1	2012-05-16	2005-08-19		ENSG00000136378	ENSG00000136378		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	223	protein-coding gene	gene with protein product	"""COMPase"", ""a disintegrin and metalloprotease with thrombospondin motifs-7 preproprotein"""	605009	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 7"""			10464288	Standard	NM_014272		Approved	ADAM-TS7, DKFZp434H204	uc002bej.4	Q9UKP4	OTTHUMG00000172907	ENST00000388820.4:c.4978A>G	15.37:g.79051846T>C	ENSP00000373472:p.Ile1660Val	Somatic	12	2		WXS	Illumina HiSeq	.	21	3	NM_014272	Q14F51|Q6P7J9	Missense_Mutation	SNP	ENST00000388820.4	37	CCDS32303.1	.	.	.	.	.	.	.	.	.	.	t	0.003	-2.471801	0.00167	.	.	ENSG00000136378	ENST00000388820	T	0.56941	0.43	2.92	-0.818	0.10833	PLAC (1);	0.176997	0.36002	N	0.002857	T	0.17066	0.0410	N	0.01874	-0.695	0.24807	N	0.992664	B	0.02656	0.0	B	0.01281	0.0	T	0.33292	-0.9874	10	0.02654	T	1	.	7.4446	0.27203	0.0:0.6997:0.0:0.3003	.	1660	Q9UKP4	ATS7_HUMAN	V	1660	ENSP00000373472:I1660V	ENSP00000373472:I1660V	I	-	1	0	ADAMTS7	76838901	0.463000	0.25799	0.157000	0.22605	0.002000	0.02628	0.822000	0.27352	-0.289000	0.09038	-0.830000	0.03078	ATC	.		0.721	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272	
SLC28A1	9154	hgsc.bcm.edu	37	15	85438311	85438311	+	Missense_Mutation	SNP	C	C	G	rs151038463	byFrequency	TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr15:85438311C>G	ENST00000286749.3	+	5	508	c.418C>G	c.(418-420)Ctc>Gtc	p.L140V	SLC28A1_ENST00000537216.1_Missense_Mutation_p.L140V|SLC28A1_ENST00000338602.2_Missense_Mutation_p.L140V|SLC28A1_ENST00000394573.1_Missense_Mutation_p.L140V|SLC28A1_ENST00000537624.1_Missense_Mutation_p.L140V|SLC28A1_ENST00000537703.1_Missense_Mutation_p.L62V|SLC28A1_ENST00000538177.1_Missense_Mutation_p.L140V			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1	140			L -> LV (in A). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9124315}.		nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside transmembrane transporter activity (GO:0005337)|nucleoside:sodium symporter activity (GO:0005415)	p.L140_K141insV(2)		breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	41			BRCA - Breast invasive adenocarcinoma(143;0.0587)		Gemcitabine(DB00441)|Stavudine(DB00649)|Zidovudine(DB00495)	GAGGAGGTTTCTCAAGCCTCA	0.637																																					p.L140V		.											.,4	.	118	2	Insertion - In frame(2)	lung(2)	c.C418G						.						45.0	47.0	46.0					15																	85438311		2203	4298	6501	SO:0001583	missense	9154	exon6			AGGTTTCTCAAGC	U62967	CCDS10334.1, CCDS10335.1, CCDS73777.1	15q25.3	2013-07-17	2013-07-17		ENSG00000156222	ENSG00000156222		"""Solute carriers"""	11001	protein-coding gene	gene with protein product		606207	"""solute carrier family 28 (sodium-coupled nucleoside transporter), member 1"""			9124315	Standard	NM_004213		Approved	CNT1	uc002blg.3	O00337	OTTHUMG00000148668	ENST00000286749.3:c.418C>G	15.37:g.85438311C>G	ENSP00000286749:p.Leu140Val	Somatic	42	0		WXS	Illumina HiSeq	.	69	2	NM_201651	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	Missense_Mutation	SNP	ENST00000286749.3	37	CCDS10334.1	.	.	.	.	.	.	.	.	.	.	C	1.612	-0.523846	0.04141	.	.	ENSG00000156222	ENST00000338602;ENST00000537216;ENST00000538177;ENST00000537624;ENST00000286749;ENST00000394573;ENST00000537703	D;D;D;D;D;D;D	0.81739	-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53	4.58	-2.54	0.06307	.	0.777035	0.12231	N	0.487478	T	0.53110	0.1776	N	0.05158	-0.105	0.09310	N	1	B;B;B;B;B;B	0.18013	0.001;0.01;0.025;0.002;0.001;0.008	B;B;B;B;B;B	0.21360	0.008;0.024;0.034;0.002;0.008;0.002	T	0.39623	-0.9605	10	0.38643	T	0.18	0.0017	1.2716	0.02022	0.2759:0.3261:0.2631:0.1349	.	140;140;140;62;140;140	B7Z533;F5H560;B7Z3L6;B7Z3M4;O00337;O00337-2	.;.;.;.;S28A1_HUMAN;.	V	140;140;140;140;140;140;62	ENSP00000341629:L140V;ENSP00000440546:L140V;ENSP00000443752:L140V;ENSP00000444700:L140V;ENSP00000286749:L140V;ENSP00000378074:L140V;ENSP00000443764:L62V	ENSP00000286749:L140V	L	+	1	0	SLC28A1	83239315	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.742000	0.04850	-0.243000	0.09653	-0.868000	0.02995	CTC	.		0.637	SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2		
CLCN5	1184	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	X	49851058	49851058	+	Missense_Mutation	SNP	G	G	A			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chrX:49851058G>A	ENST00000307367.2	+	8	1169	c.878G>A	c.(877-879)cGc>cAc	p.R293H	CLCN5_ENST00000376088.3_Missense_Mutation_p.R363H|CLCN5_ENST00000376108.3_Missense_Mutation_p.R293H|CLCN5_ENST00000376091.3_Missense_Mutation_p.R363H			P51795	CLCN5_HUMAN	chloride channel, voltage-sensitive 5	293					chloride transmembrane transport (GO:1902476)|endocytosis (GO:0006897)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical part of cell (GO:0045177)|endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(8)|ovary(2)|skin(1)	30	Ovarian(276;0.236)					TTCACTCTACGCTCCATCAAT	0.473																																					p.R363H		.											.	.	.	0			c.G1088A						.						101.0	79.0	87.0					X																	49851058		2203	4300	6503	SO:0001583	missense	1184	exon11			CTCTACGCTCCAT	X91906	CCDS14328.1, CCDS48115.1, CCDS69763.1	Xp11.23-p11.22	2012-09-26	2012-02-23		ENSG00000171365	ENSG00000171365		"""Ion channels / Chloride channels : Voltage-sensitive"""	2023	protein-coding gene	gene with protein product	"""Dent disease"""	300008	"""nephrolithiasis 2, X-linked"", ""nephrolithiasis 1 (X-linked)"", ""chloride channel 5"""	NPHL2, NPHL1		7874126, 8111383, 8099916, 8559248, 9602200	Standard	NM_001272102		Approved	DENTS, XLRH, hClC-K2, hCIC-K2, CLC5, XRN, ClC-5	uc004doq.1	P51795	OTTHUMG00000021514	ENST00000307367.2:c.878G>A	X.37:g.49851058G>A	ENSP00000304257:p.Arg293His	Somatic	30	0		WXS	Illumina HiSeq	.	63	28	NM_001127898	A1L475|B3KPN6|Q5JQD5|Q7RTN8	Missense_Mutation	SNP	ENST00000307367.2	37	CCDS14328.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.855876	0.91355	.	.	ENSG00000171365	ENST00000376088;ENST00000450422;ENST00000376091;ENST00000376108;ENST00000307367	D;D;D;D	0.94650	-3.48;-3.48;-3.48;-3.48	5.83	5.83	0.93111	Chloride channel, core (2);	0.000000	0.85682	D	0.000000	D	0.97222	0.9092	M	0.79926	2.475	0.80722	D	1	D;D	0.76494	0.958;0.999	P;D	0.80764	0.531;0.994	D	0.97028	0.9748	10	0.46703	T	0.11	-9.8095	17.7786	0.88517	0.0:0.0:1.0:0.0	.	293;363	P51795;P51795-2	CLCN5_HUMAN;.	H	363;195;363;293;293	ENSP00000365256:R363H;ENSP00000365259:R363H;ENSP00000365276:R293H;ENSP00000304257:R293H	ENSP00000304257:R293H	R	+	2	0	CLCN5	49737798	1.000000	0.71417	0.837000	0.33122	0.954000	0.61252	9.705000	0.98719	2.472000	0.83506	0.529000	0.55759	CGC	.		0.473	CLCN5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056544.1		
ANKRD30BP2	149992	hgsc.bcm.edu;broad.mit.edu	37	21	14417481	14417481	+	RNA	SNP	C	C	G			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr21:14417481C>G	ENST00000507941.1	+	0	95				RNU6-614P_ENST00000384369.1_RNA					ankyrin repeat domain 30B pseudogene 2																		TGCTGTTTTACAGGCTGGCCA	0.303																																					.		.											.	.	.	0			.						.																																					149992	.			GTTTTACAGGCTG	AF427490		21q11.2	2010-06-14	2010-06-14	2010-06-14	ENSG00000224309	ENSG00000224309			16620	pseudogene	pseudogene	"""cancer/testis antigen 85"""		"""chromosome 21 open reading frame 99"""	C21orf99		12036297, 17114284	Standard	NR_026916		Approved	CT85, CTSP-1	uc002yja.4		OTTHUMG00000074164		21.37:g.14417481C>G		Somatic	264	0		WXS	Illumina HiSeq	.	273	59	.		RNA	SNP	ENST00000507941.1	37																																																																																				.		0.303	ANKRD30BP2-004	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000372094.1	NR_026916	
SF3B1	23451	hgsc.bcm.edu	37	2	198273209	198273209	+	Missense_Mutation	SNP	C	C	A			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr2:198273209C>A	ENST00000335508.6	-	8	1092	c.1001G>T	c.(1000-1002)aGa>aTa	p.R334I		NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	334	Interaction with PPP1R8.|U2AF homology region; mediates interaction with RMB39.				anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)			NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			CCGTGATTTTCTTTTACTGGC	0.507			Mis		myelodysplastic syndrome																																p.R334I		.		Dom	yes		2	2q33.1	23451	"""splicing factor 3b, subunit 1, 155kDa"""		L	SF3B1,NS,carcinoma,0,1	SF3B1	0	0			c.G1001T						.						97.0	98.0	97.0					2																	198273209		2203	4300	6503	SO:0001583	missense	23451	exon8			GATTTTCTTTTAC	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"""splicing factor 3b, subunit 1, 155kD"""			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.1001G>T	2.37:g.198273209C>A	ENSP00000335321:p.Arg334Ile	Somatic	44	0		WXS	Illumina HiSeq	.	45	2	NM_012433	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	37	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	C	34	5.319847	0.95682	.	.	ENSG00000115524	ENST00000335508	.	.	.	4.67	4.67	0.58626	Splicing factor 3B subunit 1 (1);	0.000000	0.85682	D	0.000000	T	0.77745	0.4176	M	0.81497	2.545	0.80722	D	1	B	0.28760	0.221	B	0.42959	0.403	T	0.80086	-0.1529	9	0.87932	D	0	.	18.1137	0.89543	0.0:1.0:0.0:0.0	.	334	O75533	SF3B1_HUMAN	I	334	.	ENSP00000335321:R334I	R	-	2	0	SF3B1	197981454	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.440000	0.80464	2.582000	0.87167	0.561000	0.74099	AGA	.		0.507	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2		
ACAP3	116983	hgsc.bcm.edu	37	1	1237394	1237394	+	Silent	SNP	C	C	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr1:1237394C>T	ENST00000354700.5	-	5	514	c.312G>A	c.(310-312)cgG>cgA	p.R104R	ACAP3_ENST00000353662.3_Silent_p.R62R	NM_030649.2	NP_085152.2	Q96P50	ACAP3_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 3	104					regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)	p.R104R(1)|p.R62R(1)		endometrium(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	14						GGAGCTGCTGCCGCACGGACC	0.652																																					p.R104R		.											ACAP3_ENST00000354700,NS,carcinoma,0,2	ACAP3_ENST00000354700	0	2	Substitution - coding silent(2)	lung(2)	c.G312A						.						47.0	53.0	51.0					1																	1237394		2198	4295	6493	SO:0001819	synonymous_variant	116983	exon5			CTGCTGCCGCACG	AF411981	CCDS19.2	1p36	2013-01-10	2008-09-22	2008-09-22	ENSG00000131584	ENSG00000131584		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16754	protein-coding gene	gene with protein product			"""centaurin, beta 5"""	CENTB5			Standard	NM_030649		Approved	KIAA1716	uc001aeb.2	Q96P50	OTTHUMG00000002235	ENST00000354700.5:c.312G>A	1.37:g.1237394C>T		Somatic	32	1		WXS	Illumina HiSeq	.	44	2	NM_030649	B1AMF5|Q5TA42|Q5TA43|Q86UT3|Q9BSR9|Q9C0E7	Silent	SNP	ENST00000354700.5	37	CCDS19.2																																																																																			.		0.652	ACAP3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006366.2	NM_030649	
MAP3K3	4215	hgsc.bcm.edu;bcgsc.ca	37	17	61767703	61767703	+	Silent	SNP	C	C	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr17:61767703C>T	ENST00000361733.3	+	12	1463	c.1143C>T	c.(1141-1143)gaC>gaT	p.D381D	MAP3K3_ENST00000584573.1_Silent_p.D408D|MAP3K3_ENST00000577395.1_Silent_p.D377D|MAP3K3_ENST00000579585.1_Silent_p.D412D|MAP3K3_ENST00000361357.3_Silent_p.D412D	NM_002401.3	NP_002392.2	Q99759	M3K3_HUMAN	mitogen-activated protein kinase kinase kinase 3	381	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein autophosphorylation (GO:0046777)	cytosol (GO:0005829)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)			breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	28						TGTGCTATGACGTGGACACGG	0.557																																					p.D412D		.											.	.	.	0			c.C1236T						.						95.0	84.0	88.0					17																	61767703		2203	4300	6503	SO:0001819	synonymous_variant	4215	exon13			CTATGACGTGGAC	U78876	CCDS32701.1, CCDS32702.1	17q	2011-06-09				ENSG00000198909		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6855	protein-coding gene	gene with protein product	"""MAP/ERK kinase kinase 3"", ""MAPK/ERK kinase kinase 3"""	602539		MEKK3		9006902	Standard	NM_002401		Approved	MAPKKK3	uc002jbf.3	Q99759		ENST00000361733.3:c.1143C>T	17.37:g.61767703C>T		Somatic	31	0		WXS	Illumina HiSeq	.	47	4	NM_203351	B2RCW2|D3DU15|Q5BKZ6|Q8N3I9	Silent	SNP	ENST00000361733.3	37	CCDS32702.1																																																																																			.		0.557	MAP3K3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000443867.1	NM_002401	
THOC7	80145	hgsc.bcm.edu	37	3	63825392	63825392	+	Missense_Mutation	SNP	C	C	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr3:63825392C>T	ENST00000295899.5	-	2	189	c.77G>A	c.(76-78)aGa>aAa	p.R26K	C3orf49_ENST00000295896.8_Intron|THOC7_ENST00000498422.1_5'UTR	NM_025075.2	NP_079351.2	Q6I9Y2	THOC7_HUMAN	THO complex 7 homolog (Drosophila)	26					mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)			central_nervous_system(1)|large_intestine(1)|ovary(1)|pancreas(1)	4				BRCA - Breast invasive adenocarcinoma(55;0.000439)|Kidney(15;0.00194)|KIRC - Kidney renal clear cell carcinoma(15;0.00218)		CAGATTAATTCTCCGATCATC	0.448																																					p.R26K	Colon(48;665 1127 6720 18651)	.											THOC7,NS,carcinoma,0,1	THOC7	0	0			c.G77A						.						104.0	95.0	98.0					3																	63825392		2203	4300	6503	SO:0001583	missense	80145	exon2			TTAATTCTCCGAT	BC020599	CCDS2900.1, CCDS74957.1	3p14.1	2013-02-11			ENSG00000163634	ENSG00000163634		"""THO complex subunits"""	29874	protein-coding gene	gene with protein product	"""Ngg1 interacting factor 3 like 1 binding protein 1"", ""functional spliceosome-associated protein 24"""	611965				12951069	Standard	NM_001285404		Approved	NIF3L1BP1, FLJ23445, fSAP24	uc003dlt.4	Q6I9Y2	OTTHUMG00000158767	ENST00000295899.5:c.77G>A	3.37:g.63825392C>T	ENSP00000295899:p.Arg26Lys	Somatic	42	1		WXS	Illumina HiSeq	.	37	2	NM_025075	Q6P1L3|Q8WUF2|Q9H5H0	Missense_Mutation	SNP	ENST00000295899.5	37	CCDS2900.1	.	.	.	.	.	.	.	.	.	.	C	36	5.958274	0.97145	.	.	ENSG00000163634	ENST00000295899	.	.	.	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	T	0.82033	0.4949	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.76358	-0.2988	9	0.17832	T	0.49	-5.1792	20.1951	0.98241	0.0:1.0:0.0:0.0	.	26	Q6I9Y2	THOC7_HUMAN	K	26	.	ENSP00000295899:R26K	R	-	2	0	THOC7	63800432	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.766000	0.85320	2.780000	0.95670	0.585000	0.79938	AGA	.		0.448	THOC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352096.1	NM_025075	
ATP11A	23250	hgsc.bcm.edu	37	13	113530136	113530136	+	Silent	SNP	C	C	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr13:113530136C>T	ENST00000487903.1	+	28	3296	c.3208C>T	c.(3208-3210)Ctg>Ttg	p.L1070L	ATP11A_ENST00000283558.8_Silent_p.L1070L|ATP11A_ENST00000375630.2_Silent_p.L1070L|ATP11A_ENST00000375645.3_Silent_p.L1070L			P98196	AT11A_HUMAN	ATPase, class VI, type 11A	1070					phospholipid translocation (GO:0045332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(12)|lung(17)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	51	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.134)|all_epithelial(44;0.141)				CATCCAGATGCTGTCCAGCGG	0.627																																					p.L1070L		.											.	.	.	0			c.C3208T						.						83.0	78.0	79.0					13																	113530136		2203	4300	6503	SO:0001819	synonymous_variant	23250	exon28			CAGATGCTGTCCA	AB028944	CCDS32011.1	13q34	2010-04-20	2007-09-19		ENSG00000068650	ENSG00000068650	3.6.3.1	"""ATPases / P-type"""	13552	protein-coding gene	gene with protein product	"""potential phospholipid-transporting ATPase IH"", ""phospholipid-translocating ATPase"""	605868	"""ATPase, Class VI, type 11A"""			11015572	Standard	NM_032189		Approved	ATPIH, ATPIS, KIAA1021	uc001vsj.4	P98196	OTTHUMG00000017371	ENST00000487903.1:c.3208C>T	13.37:g.113530136C>T		Somatic	67	0		WXS	Illumina HiSeq	.	109	4	NM_032189	Q5VXT2	Silent	SNP	ENST00000487903.1	37	CCDS32011.1	.	.	.	.	.	.	.	.	.	.	C	1.874	-0.459518	0.04508	.	.	ENSG00000068650	ENST00000415301	.	.	.	4.79	1.48	0.22813	.	.	.	.	.	T	0.61009	0.2313	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56866	-0.7908	4	.	.	.	.	11.8153	0.52207	0.0:0.8645:0.0:0.1355	.	.	.	.	V	5	.	.	A	+	2	0	ATP11A	112578137	0.880000	0.30214	0.992000	0.48379	0.053000	0.15095	-0.011000	0.12721	0.304000	0.22809	0.561000	0.74099	GCT	.		0.627	ATP11A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045834.3	NM_015205	
LPP	4026	hgsc.bcm.edu	37	3	187896873	187896873	+	5'UTR	SNP	G	G	A	rs201695497		TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr3:187896873G>A	ENST00000392468.2	+	0	543				LPP_ENST00000448637.1_Intron																kidney(1)	1						agagagggagggagagagaca	0.507																																					.		.											.	.	.	0			.						.																																			SO:0001623	5_prime_UTR_variant	0	.			AGGGAGGGAGAGA																												ENST00000392468.2:c.-99G>A	3.37:g.187896873G>A		Somatic	15	0		WXS	Illumina HiSeq	.	43	7	.		RNA	SNP	ENST00000392468.2	37																																																																																				.		0.507	AC022498.1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			
AQP12B	653437	hgsc.bcm.edu	37	2	241621970	241621970	+	Silent	SNP	G	G	A	rs370087461		TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr2:241621970G>A	ENST00000407834.3	-	1	347	c.285C>T	c.(283-285)acC>acT	p.T95T		NM_001102467.1	NP_001095937.1	A6NM10	AQ12B_HUMAN	aquaporin 12B	83						integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|lung(8)|ovary(1)	13		all_epithelial(40;1.71e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|all_neural(83;0.0459)|Lung NSC(271;0.094)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;2.2e-31)|all cancers(36;1.08e-28)|OV - Ovarian serous cystadenocarcinoma(60;2.13e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.52e-06)|Lung(119;0.00163)|LUSC - Lung squamous cell carcinoma(224;0.008)|Colorectal(34;0.0124)|COAD - Colon adenocarcinoma(134;0.0757)		GCAGGGACACGGTGGGGTTGG	0.687																																					p.T95T		.											AQP12B,NS,carcinoma,0,1	AQP12B	0	0			c.C285T						.			0,4406		0,0,2203	52.0	53.0	53.0		285	-5.3	0.0	2	dbSNP_134	53	1,8599		0,1,4299	no	coding-synonymous	AQP12B	NM_001102467.1		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		95/308	241621970	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	653437	exon1			GGACACGGTGGGG	BC041460	CCDS46560.1	2q37.3	2007-12-14	2005-05-26	2005-05-26	ENSG00000185176	ENSG00000185176		"""Ion channels / Aquaporins"""	6096	protein-coding gene	gene with protein product			"""insulin synthesis associated 3"""	INSSA3			Standard	NM_001102467		Approved		uc010fzj.3	A6NM10	OTTHUMG00000152263	ENST00000407834.3:c.285C>T	2.37:g.241621970G>A		Somatic	46	1		WXS	Illumina HiSeq	.	68	5	NM_001102467	A4QPB9	Silent	SNP	ENST00000407834.3	37	CCDS46560.1																																																																																			.		0.687	AQP12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325625.1		
HERC4	26091	hgsc.bcm.edu	37	10	69785435	69785435	+	Splice_Site	SNP	T	T	A	rs397840935|rs3834396	byFrequency	TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr10:69785435T>A	ENST00000395198.3	-	8	1025		c.e8-2		HERC4_ENST00000395187.2_Splice_Site|HERC4_ENST00000412272.2_Splice_Site|HERC4_ENST00000373700.4_Splice_Site|HERC4_ENST00000277817.6_Splice_Site	NM_022079.2	NP_071362.1	Q5GLZ8	HERC4_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 4						cell differentiation (GO:0030154)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.?(1)		NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	27						TCCACCTTCCTAAAAAAAGAC	0.338																																					.		.											.,1	.	78	1	Unknown(1)	pancreas(1)	c.778-2A>T						.						84.0	91.0	89.0					10																	69785435		2203	4300	6503	SO:0001630	splice_region_variant	26091	exon9			CCTTCCTAAAAAA	AY221963	CCDS7274.1, CCDS41533.1, CCDS60541.1, CCDS60542.1	10q21.3	2013-09-20	2012-02-23		ENSG00000148634	ENSG00000148634			24521	protein-coding gene	gene with protein product		609248	"""hect domain and RLD 4"""			10997877	Standard	NM_022079		Approved	DKFZP564G092, KIAA1593	uc001jng.4	Q5GLZ8	OTTHUMG00000018343	ENST00000395198.3:c.778-2A>T	10.37:g.69785435T>A		Somatic	85	0		WXS	Illumina HiSeq	.	144	0	NM_022079	Q5GC98|Q5GC99|Q5GCA0|Q8IXP9|Q9HCH9	Splice_Site	SNP	ENST00000395198.3	37	CCDS41533.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.411748	0.83340	.	.	ENSG00000148634	ENST00000277817;ENST00000412272;ENST00000395198;ENST00000373700	.	.	.	5.22	5.22	0.72569	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.084	0.72135	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	HERC4	69455441	1.000000	0.71417	0.961000	0.40146	0.956000	0.61745	7.991000	0.88244	1.962000	0.57031	0.482000	0.46254	.	.		0.338	HERC4-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359262.1	NM_015601	Intron
COL27A1	85301	hgsc.bcm.edu	37	9	117070033	117070033	+	Missense_Mutation	SNP	G	G	A			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr9:117070033G>A	ENST00000356083.3	+	59	5583	c.5192G>A	c.(5191-5193)tGt>tAt	p.C1731Y		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	1731	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)	p.C1731F(1)		central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						GGACAGACGTGTCTCAAGCCC	0.612																																					p.C1731Y		.											COL27A1,colon,carcinoma,-1,1	COL27A1	-1	1	Substitution - Missense(1)	ovary(1)	c.G5192A						.						210.0	155.0	174.0					9																	117070033		2203	4300	6503	SO:0001583	missense	85301	exon59			AGACGTGTCTCAA	AB058773	CCDS6802.1	9q33.1	2013-01-16			ENSG00000196739	ENSG00000196739		"""Collagens"""	22986	protein-coding gene	gene with protein product		608461				12766169	Standard	NM_032888		Approved	KIAA1870, MGC11337, FLJ11895	uc011lxl.2	Q8IZC6	OTTHUMG00000020537	ENST00000356083.3:c.5192G>A	9.37:g.117070033G>A	ENSP00000348385:p.Cys1731Tyr	Somatic	23	0		WXS	Illumina HiSeq	.	20	2	NM_032888	Q66K43|Q96JF7	Missense_Mutation	SNP	ENST00000356083.3	37	CCDS6802.1	.	.	.	.	.	.	.	.	.	.	G	19.69	3.874341	0.72180	.	.	ENSG00000196739	ENST00000356083;ENST00000357257	D	0.88124	-2.34	5.6	5.6	0.85130	Fibrillar collagen, C-terminal (3);	.	.	.	.	D	0.95934	0.8676	H	0.96633	3.855	0.80722	D	1	D;D	0.89917	1.0;0.994	D;D	0.97110	1.0;0.947	D	0.97044	0.9759	9	0.72032	D	0.01	.	17.1167	0.86690	0.0:0.0:1.0:0.0	.	46;1731	Q9HAA3;Q8IZC6	.;CORA1_HUMAN	Y	1731;1738	ENSP00000348385:C1731Y	ENSP00000348385:C1731Y	C	+	2	0	COL27A1	116109854	1.000000	0.71417	0.987000	0.45799	0.958000	0.62258	9.869000	0.99810	2.648000	0.89879	0.561000	0.74099	TGT	.		0.612	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888	
SOX5	6660	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	23757376	23757376	+	Missense_Mutation	SNP	G	G	A			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr12:23757376G>A	ENST00000451604.2	-	9	1210	c.1109C>T	c.(1108-1110)tCt>tTt	p.S370F	SOX5_ENST00000541536.1_Missense_Mutation_p.S357F|SOX5_ENST00000545921.1_Missense_Mutation_p.S360F|SOX5_ENST00000309359.1_Missense_Mutation_p.S357F|SOX5_ENST00000381381.2_Missense_Mutation_p.S357F|SOX5_ENST00000537393.1_Missense_Mutation_p.S335F|SOX5_ENST00000546136.1_Missense_Mutation_p.S357F			P35711	SOX5_HUMAN	SRY (sex determining region Y)-box 5	370					cartilage development (GO:0051216)|cell fate commitment (GO:0045165)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system neuron differentiation (GO:0021953)|in utero embryonic development (GO:0001701)|negative regulation of transcription, DNA-templated (GO:0045892)|oligodendrocyte differentiation (GO:0048709)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of timing of neuron differentiation (GO:0060164)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear transcription factor complex (GO:0044798)	sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.S370F(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(25)|ovary(5)|skin(2)|upper_aerodigestive_tract(3)	57						GCTGGTAGGAGATACAGCAGC	0.502																																					p.S370F		.											SOX5,colon,carcinoma,-1,1	SOX5	-1	1	Substitution - Missense(1)	ovary(1)	c.C1109T						.						163.0	133.0	143.0					12																	23757376		2203	4300	6503	SO:0001583	missense	6660	exon9			GTAGGAGATACAG	AB081589	CCDS8699.1, CCDS41761.1, CCDS44844.1, CCDS58216.1, CCDS58217.1	12p12.1	2010-04-20			ENSG00000134532	ENSG00000134532		"""SRY (sex determining region Y)-boxes"""	11201	protein-coding gene	gene with protein product		604975				8812465	Standard	NM_006940		Approved	L-SOX5, MGC35153	uc001rfw.3	P35711	OTTHUMG00000169026	ENST00000451604.2:c.1109C>T	12.37:g.23757376G>A	ENSP00000398273:p.Ser370Phe	Somatic	24	0		WXS	Illumina HiSeq	.	43	19	NM_006940	B7Z8V0|F5H5B0|Q86UK8|Q8J017|Q8J018|Q8J019|Q8J020|Q8N1D9|Q8N7E0|Q8TEA4	Missense_Mutation	SNP	ENST00000451604.2	37	CCDS8699.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.657444	0.88154	.	.	ENSG00000134532	ENST00000546136;ENST00000309359;ENST00000381381;ENST00000451604;ENST00000435266;ENST00000537393;ENST00000541536;ENST00000545921	D;D;D;D;D;D;D	0.98105	-4.7;-4.7;-4.34;-4.71;-4.72;-4.34;-4.71	6.16	6.16	0.99307	.	0.171135	0.53938	D	0.000045	D	0.98526	0.9508	M	0.76170	2.325	0.58432	D	0.999998	D;D;D	0.67145	0.996;0.984;0.993	D;D;P	0.74348	0.956;0.983;0.904	D	0.97379	0.9981	10	0.20046	T	0.44	.	20.8598	0.99761	0.0:0.0:1.0:0.0	.	335;357;370	F5H0I3;P35711-4;P35711	.;.;SOX5_HUMAN	F	357;357;357;370;322;335;357;360	ENSP00000437487:S357F;ENSP00000308927:S357F;ENSP00000370788:S357F;ENSP00000398273:S370F;ENSP00000439832:S335F;ENSP00000441973:S357F;ENSP00000443520:S360F	ENSP00000308927:S357F	S	-	2	0	SOX5	23648643	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.241000	0.89816	2.937000	0.99478	0.650000	0.86243	TCT	.		0.502	SOX5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402006.2	NM_006940	
ZCCHC14	23174	hgsc.bcm.edu	37	16	87443922	87443922	+	Silent	SNP	G	G	A			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr16:87443922G>A	ENST00000268616.4	-	13	3031	c.2814C>T	c.(2812-2814)taC>taT	p.Y938Y		NM_015144.2	NP_055959.1	Q8WYQ9	ZCH14_HUMAN	zinc finger, CCHC domain containing 14	938							nucleic acid binding (GO:0003676)|phosphatidylinositol binding (GO:0035091)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	36				BRCA - Breast invasive adenocarcinoma(80;0.0285)		CTGGAGGGGCGTATTTCAACC	0.408																																					p.Y938Y		.											.	.	.	0			c.C2814T						.						120.0	126.0	124.0					16																	87443922		2198	4300	6498	SO:0001819	synonymous_variant	23174	exon13			AGGGGCGTATTTC	AB011151	CCDS10961.1	16q24.2	2013-01-10			ENSG00000140948	ENSG00000140948		"""Zinc fingers, CCHC domain containing"", ""Sterile alpha motif (SAM) domain containing"""	24134	protein-coding gene	gene with protein product						9628581	Standard	XM_005255858		Approved	BDG29, MGC14139	uc002fjz.1	Q8WYQ9	OTTHUMG00000137655	ENST00000268616.4:c.2814C>T	16.37:g.87443922G>A		Somatic	67	0		WXS	Illumina HiSeq	.	98	4	NM_015144	D3DUN1|O60324|Q3MJD8|Q9UFP0	Silent	SNP	ENST00000268616.4	37	CCDS10961.1																																																																																			.		0.408	ZCCHC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269107.1	NM_015144	
JAKMIP2	9832	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	147029994	147029994	+	Silent	SNP	G	G	C			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr5:147029994G>C	ENST00000265272.5	-	4	1211	c.744C>G	c.(742-744)ctC>ctG	p.L248L	JAKMIP2_ENST00000333010.6_Silent_p.L206L|JAKMIP2_ENST00000507386.1_Silent_p.L248L	NM_001270941.1|NM_014790.4	NP_001257870.1|NP_055605.2	Q96AA8	JKIP2_HUMAN	janus kinase and microtubule interacting protein 2	248						Golgi apparatus (GO:0005794)				NS(1)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(22)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGACCAGAAAGAGTTGTTCGT	0.502																																					p.L248L		.											.	.	.	0			c.C744G						.						145.0	132.0	136.0					5																	147029994		2203	4300	6503	SO:0001819	synonymous_variant	9832	exon4			CAGAAAGAGTTGT	AB011127	CCDS4285.1, CCDS59495.1, CCDS64284.1, CCDS75352.1	5q32	2009-08-13	2009-08-13		ENSG00000176049	ENSG00000176049			29067	protein-coding gene	gene with protein product		611197				9628581	Standard	NM_001270941		Approved	JAMIP2, KIAA0555	uc010jgo.2	Q96AA8	OTTHUMG00000129731	ENST00000265272.5:c.744C>G	5.37:g.147029994G>C		Somatic	47	0		WXS	Illumina HiSeq	.	92	41	NM_001270941	A4ZZA7|A8K5G5|B4DSG0|G5E9Y0|O60302|Q548S1	Silent	SNP	ENST00000265272.5	37	CCDS4285.1																																																																																			.		0.502	JAKMIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251941.1	NM_014790	
TFG	10342	hgsc.bcm.edu	37	3	100467371	100467371	+	Missense_Mutation	SNP	G	G	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr3:100467371G>T	ENST00000240851.4	+	8	1539	c.1199G>T	c.(1198-1200)cGa>cTa	p.R400L	TFG_ENST00000476228.1_Missense_Mutation_p.R396L|TFG_ENST00000481203.1_3'UTR|TFG_ENST00000490574.1_Missense_Mutation_p.R400L|TFG_ENST00000418917.2_Missense_Mutation_p.R396L	NM_001195478.1|NM_001195479.1|NM_006070.5	NP_001182407.1|NP_001182408.1|NP_006061.2	Q92734	TFG_HUMAN	TRK-fused gene	400					cell death (GO:0008219)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	signal transducer activity (GO:0004871)		TFG/NR4A3(2)|TFG/NTRK1_ENST00000392302(5)|TFG/ALK(9)	large_intestine(4)|lung(2)|prostate(1)|stomach(1)	8						CCTGGTTATCGATAAGGAGGC	0.468			T	"""NTRK1, ALK"""	"""papillary thyroid, ALCL, NSCLC"""																																p.R400L		.		Dom	yes		3	3q11-q12	10342	TRK-fused gene		"""E, L"""	TFG_ENST00000240851,colon,carcinoma,0,1	TFG_ENST00000240851	0	0			c.G1199T						.						55.0	51.0	52.0					3																	100467371		2202	4297	6499	SO:0001583	missense	10342	exon8			GTTATCGATAAGG	BC009241	CCDS2939.1, CCDS56266.1	3q12.2	2013-03-13	2001-12-04		ENSG00000114354	ENSG00000114354			11758	protein-coding gene	gene with protein product		602498				9169129, 23479643	Standard	NM_001007565		Approved	TF6, FLJ36137, SPG57	uc003dui.3	Q92734	OTTHUMG00000159085	ENST00000240851.4:c.1199G>T	3.37:g.100467371G>T	ENSP00000240851:p.Arg400Leu	Somatic	24	0		WXS	Illumina HiSeq	.	39	2	NM_006070	D3DN49|G5E9V1|Q15656|Q969I2	Missense_Mutation	SNP	ENST00000240851.4	37	CCDS2939.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.077600	0.76528	.	.	ENSG00000114354	ENST00000418917;ENST00000490574;ENST00000240851;ENST00000476228	T;T;T;T	0.59906	0.23;0.25;0.25;0.23	6.16	5.28	0.74379	.	0.062835	0.64402	D	0.000004	T	0.50188	0.1601	N	0.19112	0.55	0.80722	D	1	P;P	0.42620	0.785;0.68	B;B	0.43508	0.422;0.241	T	0.56974	-0.7890	10	0.72032	D	0.01	.	17.5775	0.87955	0.0:0.1235:0.8765:0.0	.	396;400	G5E9V1;Q92734	.;TFG_HUMAN	L	396;400;400;396	ENSP00000397182:R396L;ENSP00000419960:R400L;ENSP00000240851:R400L;ENSP00000417952:R396L	ENSP00000240851:R400L	R	+	2	0	TFG	101950061	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.947000	0.93000	1.600000	0.50102	0.650000	0.86243	CGA	.		0.468	TFG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353242.1	NM_006070	
PLA2G4E	123745	hgsc.bcm.edu	37	15	42292455	42292455	+	Silent	SNP	G	G	A			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr15:42292455G>A	ENST00000399518.3	-	8	1185	c.699C>T	c.(697-699)aaC>aaT	p.N233N	PLA2G4E_ENST00000413860.2_Silent_p.N204N|CTD-2382E5.1_ENST00000499478.2_RNA	NM_001206670.1	NP_001193599.1	Q3MJ16	PA24E_HUMAN	phospholipase A2, group IVE	226					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phospholipase A2 activity (GO:0004623)	p.N204N(1)		NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|stomach(1)	16		all_cancers(109;8.09e-13)|all_epithelial(112;2.03e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.0273)		OV - Ovarian serous cystadenocarcinoma(18;7.61e-18)|GBM - Glioblastoma multiforme(94;3.07e-06)		CAAAGGATTCGTTCACCATCA	0.582																																					p.N233N		.											PLA2G4E,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	PLA2G4E	0	1	Substitution - coding silent(1)	central_nervous_system(1)	c.C699T						.						40.0	46.0	44.0					15																	42292455		2031	4183	6214	SO:0001819	synonymous_variant	123745	exon8			GGATTCGTTCACC		CCDS55962.1	15q15.1	2008-09-19			ENSG00000188089	ENSG00000188089	3.1.1.4		24791	protein-coding gene	gene with protein product						15866882	Standard	NM_001206670		Approved	FLJ45651	uc021sjp.1	Q3MJ16	OTTHUMG00000130371	ENST00000399518.3:c.699C>T	15.37:g.42292455G>A		Somatic	29	0		WXS	Illumina HiSeq	.	46	3	NM_001206670	Q6ZSC0	Silent	SNP	ENST00000399518.3	37	CCDS55962.1																																																																																			.		0.582	PLA2G4E-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252738.2	NM_198442	
OSBPL3	26031	hgsc.bcm.edu	37	7	24849546	24849546	+	Missense_Mutation	SNP	G	G	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr7:24849546G>T	ENST00000313367.2	-	20	2648	c.2197C>A	c.(2197-2199)Cat>Aat	p.H733N	OSBPL3_ENST00000409069.1_Missense_Mutation_p.H666N|OSBPL3_ENST00000487020.1_5'UTR|OSBPL3_ENST00000396431.1_Missense_Mutation_p.H702N|OSBPL3_ENST00000353930.1_Missense_Mutation_p.H697N|OSBPL3_ENST00000431825.2_Missense_Mutation_p.H666N|OSBPL3_ENST00000396429.1_Missense_Mutation_p.H697N|OSBPL3_ENST00000352860.1_Missense_Mutation_p.H702N	NM_015550.2	NP_056365.1	Q9H4L5	OSBL3_HUMAN	oxysterol binding protein-like 3	733					lipid transport (GO:0006869)	cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)	p.H733N(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(19)|prostate(1)|skin(3)|urinary_tract(1)	43						TCAATCTCATGGGCATTAGTG	0.438																																					p.H733N		.											OSBPL3,NS,malignant_melanoma,0,1	OSBPL3	0	1	Substitution - Missense(1)	lung(1)	c.C2197A						.						212.0	186.0	194.0					7																	24849546		2203	4300	6503	SO:0001583	missense	26031	exon20			TCTCATGGGCATT	AB014604	CCDS5390.1, CCDS5391.1, CCDS5392.1, CCDS47564.1	7p15.3	2013-01-10			ENSG00000070882	ENSG00000070882		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16370	protein-coding gene	gene with protein product		606732		OSBP3		9734811	Standard	XM_005249698		Approved	ORP-3, ORP3, KIAA0704	uc003sxf.3	Q9H4L5	OTTHUMG00000023277	ENST00000313367.2:c.2197C>A	7.37:g.24849546G>T	ENSP00000315410:p.His733Asn	Somatic	31	0		WXS	Illumina HiSeq	.	44	2	NM_015550	A4D167|A4D168|A4D169|A4D170|A4D171|A4D172|B8ZZ79|B8ZZP0|O14591|O43357|O43358|Q8N702|Q8N703|Q8N704|Q8NFH0|Q8NFH1|Q8NI12|Q8NI13|Q9BZF4|Q9UED6	Missense_Mutation	SNP	ENST00000313367.2	37	CCDS5390.1	.	.	.	.	.	.	.	.	.	.	G	6.036	0.375085	0.11409	.	.	ENSG00000070882	ENST00000313367;ENST00000352860;ENST00000353930;ENST00000431825;ENST00000396431;ENST00000396429;ENST00000409069	T;T;T;T;T;T;T	0.25912	1.77;1.77;1.77;1.77;1.77;1.77;1.77	5.25	5.25	0.73442	.	0.200391	0.52532	D	0.000077	T	0.16300	0.0392	N	0.12831	0.26	0.44843	D	0.997851	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.002;0.001;0.001;0.001	T	0.09662	-1.0664	10	0.12103	T	0.63	-13.1469	19.2157	0.93776	0.0:0.0:1.0:0.0	.	666;702;697;733	Q9H4L5-4;Q9H4L5-2;Q9H4L5-3;Q9H4L5	.;.;.;OSBL3_HUMAN	N	733;702;697;666;702;697;666	ENSP00000315410:H733N;ENSP00000315331:H702N;ENSP00000315277:H697N;ENSP00000389779:H666N;ENSP00000379708:H702N;ENSP00000379706:H697N;ENSP00000386953:H666N	ENSP00000315410:H733N	H	-	1	0	OSBPL3	24816071	1.000000	0.71417	0.645000	0.29479	0.963000	0.63663	6.972000	0.76110	2.610000	0.88304	0.557000	0.71058	CAT	.		0.438	OSBPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214085.2		
NF2	4771	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	22	30064437	30064437	+	Splice_Site	SNP	T	T	G			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr22:30064437T>G	ENST00000338641.4	+	10	1440		c.e10+2		NF2_ENST00000403435.1_Splice_Site|NF2_ENST00000361452.4_Splice_Site|NF2_ENST00000413209.2_Intron|NF2_ENST00000361166.4_Splice_Site|NF2_ENST00000334961.7_Splice_Site|NF2_ENST00000353887.4_Splice_Site|NF2_ENST00000397789.3_Splice_Site|NF2_ENST00000347330.5_Splice_Site|NF2_ENST00000361676.4_Splice_Site|NF2_ENST00000403999.3_Splice_Site	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)						actin cytoskeleton organization (GO:0030036)|cell-cell junction organization (GO:0045216)|ectoderm development (GO:0007398)|hippocampus development (GO:0021766)|lens fiber cell differentiation (GO:0070306)|mesoderm formation (GO:0001707)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of DNA replication (GO:0008156)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell differentiation (GO:0045597)|positive regulation of stress fiber assembly (GO:0051496)|regulation of hippo signaling (GO:0035330)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of protein localization to nucleus (GO:1900180)|regulation of protein stability (GO:0031647)|Schwann cell proliferation (GO:0014010)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|cleavage furrow (GO:0032154)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome (GO:0005769)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)		p.?(4)		NS(1)|bone(2)|breast(5)|central_nervous_system(21)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(17)|large_intestine(9)|liver(1)|lung(9)|meninges(372)|ovary(2)|pituitary(1)|pleura(9)|prostate(1)|skin(7)|soft_tissue(303)|stomach(2)|thyroid(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	776						AGAAAGCAGGTGAGCACAACC	0.522			"""D, Mis, N, F, S, O"""		"""meningioma, acoustic neuroma, renal """	"""meningioma, acoustic neuroma"""			Neurofibromatosis, type 2																												.		.	yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	.	.	.	4	Unknown(4)	large_intestine(1)|stomach(1)|soft_tissue(1)|central_nervous_system(1)	c.999+2T>G						.						109.0	95.0	99.0					22																	30064437		2203	4300	6503	SO:0001630	splice_region_variant	4771	exon10	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	AGCAGGTGAGCAC	L11353	CCDS13861.1, CCDS13862.1, CCDS13863.1, CCDS13864.1, CCDS13865.1, CCDS54516.1	22q12.2	2014-09-17	2007-12-17		ENSG00000186575	ENSG00000186575		"""A-kinase anchor proteins"""	7773	protein-coding gene	gene with protein product	"""moesin-ezrin-radixin like"", ""schwannomin"""	607379	"""neurofibromin 2 (bilateral acoustic neuroma)"""			10591208	Standard	NM_000268		Approved	merlin	uc003age.4	P35240	OTTHUMG00000030727	ENST00000338641.4:c.999+2T>G	22.37:g.30064437T>G		Somatic	41	0		WXS	Illumina HiSeq	.	25	6	NM_016418	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Splice_Site	SNP	ENST00000338641.4	37	CCDS13861.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.476772	0.84640	.	.	ENSG00000186575	ENST00000347330;ENST00000338641;ENST00000403435;ENST00000361452;ENST00000397822;ENST00000403999;ENST00000334961;ENST00000353887;ENST00000397789;ENST00000361676;ENST00000361166	.	.	.	5.81	4.77	0.60923	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.4643	0.55749	0.0:0.0:0.14:0.86	.	.	.	.	.	-1	.	.	.	+	.	.	NF2	28394437	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.060000	0.71141	0.995000	0.38917	0.533000	0.62120	.	.		0.522	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3	NM_000268	Intron
GPR179	440435	hgsc.bcm.edu	37	17	36495366	36495366	+	Silent	SNP	G	G	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr17:36495366G>T	ENST00000342292.4	-	2	857	c.837C>A	c.(835-837)atC>atA	p.I279I		NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	279					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.I279M(1)		breast(4)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(16)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				CACACTGATTGATGTCCACAC	0.542																																					p.I279I		.											GPR179,rectum,carcinoma,-1,1	GPR179	-1	1	Substitution - Missense(1)	ovary(1)	c.C837A						.						126.0	127.0	127.0					17																	36495366		2133	4229	6362	SO:0001819	synonymous_variant	440435	exon2			CTGATTGATGTCC		CCDS42308.1	17q21.1	2014-05-06	2006-02-16	2006-02-16	ENSG00000188888	ENSG00000277399		"""GPCR / Class C : Orphans"""	31371	protein-coding gene	gene with protein product		614515	"""GPR158-like 1"", ""GPR179"""	GPR158L1			Standard	NM_001004334		Approved	CSNB1E	uc002hpz.3	Q6PRD1	OTTHUMG00000188545	ENST00000342292.4:c.837C>A	17.37:g.36495366G>T		Somatic	34	0		WXS	Illumina HiSeq	.	45	2	NM_001004334		Silent	SNP	ENST00000342292.4	37	CCDS42308.1																																																																																			.		0.542	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2		
IDH2	3418	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	90631838	90631838	+	Missense_Mutation	SNP	C	C	T	rs121913503		TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr15:90631838C>T	ENST00000330062.3	-	4	628	c.515G>A	c.(514-516)aGg>aAg	p.R172K	IDH2_ENST00000559482.1_Intron|IDH2_ENST00000539790.1_Missense_Mutation_p.R42K|IDH2_ENST00000540499.2_Missense_Mutation_p.R120K	NM_002168.2	NP_002159.2	P48735	IDHP_HUMAN	isocitrate dehydrogenase 2 (NADP+), mitochondrial	172					2-oxoglutarate metabolic process (GO:0006103)|carbohydrate metabolic process (GO:0005975)|cellular metabolic process (GO:0044237)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)	p.R172K(116)|p.R172M(21)|p.R172N(1)		biliary_tract(11)|bone(19)|central_nervous_system(107)|endometrium(1)|haematopoietic_and_lymphoid_tissue(953)|large_intestine(8)|lung(5)|skin(5)	1109	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.106)			ATGGGCGTGCCTGCCAATGGT	0.632			M		GBM																																p.R172K		.		Dom	yes		15	15q26.1	3418	"""socitrate dehydrogenase 2 (NADP+), mitochondrial """		M	IDH2,NS,haematopoietic_neoplasm,0,179	IDH2	0	138	Substitution - Missense(138)	haematopoietic_and_lymphoid_tissue(67)|central_nervous_system(65)|biliary_tract(6)	c.G515A						.						85.0	81.0	82.0					15																	90631838		2200	4298	6498	SO:0001583	missense	3418	exon4			GCGTGCCTGCCAA		CCDS10359.1	15q26.1	2014-09-17			ENSG00000182054	ENSG00000182054	1.1.1.42		5383	protein-coding gene	gene with protein product		147650					Standard	NM_001289910		Approved		uc002box.3	P48735	OTTHUMG00000149815	ENST00000330062.3:c.515G>A	15.37:g.90631838C>T	ENSP00000331897:p.Arg172Lys	Somatic	37	0		WXS	Illumina HiSeq	.	39	11	NM_002168	B2R6L6|B4DFL2|Q96GT3	Missense_Mutation	SNP	ENST00000330062.3	37	CCDS10359.1	.	.	.	.	.	.	.	.	.	.	C	15.86	2.957149	0.53293	.	.	ENSG00000182054	ENST00000330062;ENST00000539790;ENST00000540499	D;D;D	0.86432	-2.12;-2.12;-2.12	5.93	4.07	0.47477	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.95217	0.8449	H	0.96889	3.9	0.49687	D	0.999812	D	0.89917	1.0	D	0.91635	0.999	D	0.95096	0.8226	10	0.87932	D	0	.	10.781	0.46377	0.0:0.8464:0.0:0.1536	.	172	P48735	IDHP_HUMAN	K	172;42;120	ENSP00000331897:R172K;ENSP00000438457:R42K;ENSP00000446147:R120K	ENSP00000331897:R172K	R	-	2	0	IDH2	88432842	1.000000	0.71417	0.025000	0.17156	0.001000	0.01503	7.797000	0.85911	0.862000	0.35528	-0.258000	0.10820	AGG	.		0.632	IDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313426.1		
NLGN1	22871	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	173999084	173999084	+	Silent	SNP	C	C	A			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr3:173999084C>A	ENST00000457714.1	+	7	2892	c.2463C>A	c.(2461-2463)acC>acA	p.T821T	NLGN1_ENST00000361589.4_Silent_p.T821T|NLGN1_ENST00000401917.3_Silent_p.T861T|NLGN1_ENST00000545397.1_Silent_p.T821T	NM_014932.2	NP_055747.1	Q8N2Q7	NLGN1_HUMAN	neuroligin 1	838					alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|calcium-dependent cell-cell adhesion (GO:0016339)|cytoskeletal matrix organization at active zone (GO:0048789)|establishment of protein localization (GO:0045184)|heterophilic cell-cell adhesion (GO:0007157)|N-methyl-D-aspartate receptor clustering (GO:0097114)|nervous system development (GO:0007399)|neurexin clustering (GO:0097115)|neuron cell-cell adhesion (GO:0007158)|neuronal signal transduction (GO:0023041)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of ruffle assembly (GO:1900029)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of synaptic vesicle endocytosis (GO:1900244)|positive regulation of synaptic vesicle exocytosis (GO:2000302)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|protein homooligomerization (GO:0051260)|protein localization to synapse (GO:0035418)|protein targeting (GO:0006605)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuron differentiation (GO:0045664)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|synapse assembly (GO:0007416)|synaptic vesicle clustering (GO:0097091)|synaptic vesicle targeting (GO:0016080)|terminal button organization (GO:0072553)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|filopodium tip (GO:0032433)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|PDZ domain binding (GO:0030165)|protein dimerization activity (GO:0046983)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(2)|lung(54)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	83	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			ATTCAACAACCAGGGTATAGC	0.418																																					p.T821T		.											.	.	.	0			c.C2463A						.						44.0	43.0	43.0					3																	173999084		2203	4300	6503	SO:0001819	synonymous_variant	22871	exon7			AACAACCAGGGTA	AB028993	CCDS3222.1	3q26.32	2008-07-18			ENSG00000169760	ENSG00000169760			14291	protein-coding gene	gene with protein product		600568				10767552, 10819331	Standard	NM_014932		Approved	KIAA1070	uc003fio.1	Q8N2Q7	OTTHUMG00000157005	ENST00000457714.1:c.2463C>A	3.37:g.173999084C>A		Somatic	40	0		WXS	Illumina HiSeq	.	87	22	NM_014932	Q9UPT2	Silent	SNP	ENST00000457714.1	37	CCDS3222.1																																																																																			.		0.418	NLGN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347054.3	NM_014932	
Unknown	0	hgsc.bcm.edu	37	16	33524803	33524803	+	IGR	SNP	C	C	T	rs61143183	byFrequency	TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr16:33524803C>T								BMS1P8 (25711 upstream) : IGHV3OR16-12 (80427 downstream)																							ACAGGTGGCACGGTGTCTGAC	0.493													c|||	111	0.0221645	0.084	0.0	5008	,	,		26296	0.0		0.0	False		,,,				2504	0.0				.		.											.	.	.	0			.						.																																			SO:0001628	intergenic_variant	100873777	.			GTGGCACGGTGTC																													16.37:g.33524803C>T		Somatic	41	0		WXS	Illumina HiSeq	.	81	4	.		RNA	SNP		37																																																																																				.	0	0.493								
ITPR3	3710	hgsc.bcm.edu	37	6	33661448	33661448	+	Missense_Mutation	SNP	C	C	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr6:33661448C>T	ENST00000374316.5	+	57	8811	c.7751C>T	c.(7750-7752)aCg>aTg	p.T2584M	ITPR3_ENST00000605930.1_Missense_Mutation_p.T2584M			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	2584					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	ACCGACTACACGGGCCCTGAG	0.537																																					p.T2584M		.											ITPR3_ENST00000374316,NS,adenocarcinoma,0,2	ITPR3_ENST00000374316	0	0			c.C7751T						.						117.0	93.0	101.0					6																	33661448		2203	4300	6503	SO:0001583	missense	3710	exon56			ACTACACGGGCCC	D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"""Ion channels / Inositol triphosphate receptors"""	6182	protein-coding gene	gene with protein product		147267	"""inositol 1,4,5-triphosphate receptor, type 3"""			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.7751C>T	6.37:g.33661448C>T	ENSP00000363435:p.Thr2584Met	Somatic	34	0		WXS	Illumina HiSeq	.	39	2	NM_002224	Q14649|Q5TAQ2	Missense_Mutation	SNP	ENST00000374316.5	37	CCDS4783.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.744345	0.89663	.	.	ENSG00000096433	ENST00000374316	T	0.45276	0.9	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.73697	0.3620	H	0.95917	3.74	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.82991	-0.0182	10	0.87932	D	0	-25.5971	19.1089	0.93309	0.0:1.0:0.0:0.0	.	2584;2254	Q14573;Q59ES2	ITPR3_HUMAN;.	M	2584	ENSP00000363435:T2584M	ENSP00000363435:T2584M	T	+	2	0	ITPR3	33769426	1.000000	0.71417	0.955000	0.39395	0.633000	0.38033	7.818000	0.86416	2.527000	0.85204	0.462000	0.41574	ACG	.		0.537	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224	
PTCH1	5727	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	98242716	98242716	+	Missense_Mutation	SNP	C	C	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr9:98242716C>T	ENST00000331920.6	-	6	1200	c.901G>A	c.(901-903)Gat>Aat	p.D301N	PTCH1_ENST00000548379.1_5'Flank|PTCH1_ENST00000429896.2_Missense_Mutation_p.D150N|PTCH1_ENST00000437951.1_Missense_Mutation_p.D235N|PTCH1_ENST00000375274.2_Missense_Mutation_p.D300N|PTCH1_ENST00000430669.2_Missense_Mutation_p.D235N|PTCH1_ENST00000418258.1_Missense_Mutation_p.D150N|PTCH1_ENST00000421141.1_Missense_Mutation_p.D150N	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	301					brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)			NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				CAGTCTGGATCGGCCGGATTG	0.502																																					p.D301N		.											.	.	.	0			c.G901A						.						85.0	90.0	88.0					9																	98242716		2203	4300	6503	SO:0001583	missense	5727	exon6			CTGGATCGGCCGG	AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"""patched (Drosophila) homolog"", ""patched homolog (Drosophila)"", ""patched homolog 1 (Drosophila)"""	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.901G>A	9.37:g.98242716C>T	ENSP00000332353:p.Asp301Asn	Somatic	21	0		WXS	Illumina HiSeq	.	28	12	NM_000264	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Missense_Mutation	SNP	ENST00000331920.6	37	CCDS6714.1	.	.	.	.	.	.	.	.	.	.	C	35	5.436985	0.96168	.	.	ENSG00000185920	ENST00000331920;ENST00000437951;ENST00000421141;ENST00000418258;ENST00000430669;ENST00000429896;ENST00000375274;ENST00000375271;ENST00000548420;ENST00000553011;ENST00000551845;ENST00000547672;ENST00000546820	D;D;D;D;D;D;D;D;D;D;D;D;D	0.95171	-3.62;-3.56;-3.56;-3.56;-3.56;-3.56;-3.63;-3.3;-1.6;-2.49;-2.49;-2.49;-2.49	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	D	0.96824	0.8963	M	0.64676	1.99	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;0.999	D;D;D;P	0.97110	0.999;0.947;1.0;0.886	D	0.95811	0.8841	10	0.41790	T	0.15	-27.136	20.2187	0.98312	0.0:1.0:0.0:0.0	.	150;235;300;301	Q13635-4;Q13635-3;Q13635-2;Q13635	.;.;.;PTC1_HUMAN	N	301;235;150;150;235;150;300;18;21;150;150;150;150	ENSP00000332353:D301N;ENSP00000389744:D235N;ENSP00000399981:D150N;ENSP00000396135:D150N;ENSP00000410287:D235N;ENSP00000414823:D150N;ENSP00000364423:D300N;ENSP00000364420:D18N;ENSP00000449078:D21N;ENSP00000447797:D150N;ENSP00000447008:D150N;ENSP00000447878:D150N;ENSP00000448843:D150N	ENSP00000332353:D301N	D	-	1	0	PTCH1	97282537	1.000000	0.71417	0.924000	0.36721	0.886000	0.51366	7.487000	0.81328	2.780000	0.95670	0.655000	0.94253	GAT	.		0.502	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264	
SMG7	9887	hgsc.bcm.edu;broad.mit.edu	37	1	183514431	183514431	+	Missense_Mutation	SNP	A	A	G			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr1:183514431A>G	ENST00000347615.2	+	16	2473	c.2354A>G	c.(2353-2355)cAc>cGc	p.H785R	SMG7_ENST00000367537.3_Missense_Mutation_p.H768R|SMG7_ENST00000456731.2_Missense_Mutation_p.H697R|SMG7_ENST00000508461.1_Missense_Mutation_p.H743R|SMG7_ENST00000507469.1_Missense_Mutation_p.H739R|SMG7_ENST00000515829.2_Missense_Mutation_p.H739R	NM_173156.2	NP_775179.1	Q92540	SMG7_HUMAN	SMG7 nonsense mediated mRNA decay factor	785	Gln/Pro-rich.				gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	protein phosphatase 2A binding (GO:0051721)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(16)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	46						CCGCCTCACCACTCTGGATTC	0.458																																					p.H785R		.											.	.	.	0			c.A2354G						.						70.0	76.0	74.0					1																	183514431		2203	4300	6503	SO:0001583	missense	9887	exon16			CTCACCACTCTGG	D87437	CCDS1355.1, CCDS41445.1, CCDS41445.2, CCDS53444.1, CCDS53445.1	1q25	2013-07-02	2013-07-02	2006-02-16	ENSG00000116698	ENSG00000116698			16792	protein-coding gene	gene with protein product	"""EST1 telomerase component homolog C (S. cerevisiae)"""	610964	"""chromosome 1 open reading frame 16"", ""smg-7 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	C1orf16		14636577, 15721257	Standard	NM_173156		Approved	KIAA0250, EST1C, SGA56M, SMG-7	uc001gqf.3	Q92540	OTTHUMG00000035221	ENST00000347615.2:c.2354A>G	1.37:g.183514431A>G	ENSP00000340766:p.His785Arg	Somatic	12	0		WXS	Illumina HiSeq	.	22	4	NM_173156	B4DRB2|E9PCI0|E9PEH2|Q5T1Q0|Q6PIE0|Q7Z7H9|Q8IXC1|Q8IXC2	Missense_Mutation	SNP	ENST00000347615.2	37	CCDS1355.1	.	.	.	.	.	.	.	.	.	.	A	19.26	3.792840	0.70452	.	.	ENSG00000116698	ENST00000456731;ENST00000367537;ENST00000508461;ENST00000419169;ENST00000347615;ENST00000507469;ENST00000515829	T;T;T;T;T;T;T	0.52057	0.68;0.68;0.68;0.68;0.68;0.68;0.68	5.69	5.69	0.88448	.	0.362376	0.32952	N	0.005448	T	0.57740	0.2074	L	0.29908	0.895	0.80722	D	1	D;D;D;D;D;D	0.63880	0.993;0.981;0.993;0.989;0.993;0.981	D;D;D;D;D;D	0.75020	0.977;0.966;0.977;0.985;0.977;0.966	T	0.60919	-0.7167	10	0.62326	D	0.03	-14.9073	15.6154	0.76764	1.0:0.0:0.0:0.0	.	743;768;697;739;785;739	E9PCI0;E9PD50;E9PCE5;Q92540-2;Q92540;E9PEH2	.;.;.;.;SMG7_HUMAN;.	R	697;768;743;697;785;739;739	ENSP00000407629:H697R;ENSP00000356507:H768R;ENSP00000426915:H743R;ENSP00000388390:H697R;ENSP00000340766:H785R;ENSP00000425133:H739R;ENSP00000421358:H739R	ENSP00000340766:H785R	H	+	2	0	SMG7	181781054	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.454000	0.90352	2.162000	0.67917	0.533000	0.62120	CAC	.		0.458	SMG7-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000085432.1	NM_014837	
YAP1	10413	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	102100578	102100578	+	Silent	SNP	G	G	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr11:102100578G>T	ENST00000282441.5	+	9	1810	c.1422G>T	c.(1420-1422)ctG>ctT	p.L474L	YAP1_ENST00000345877.2_Silent_p.L424L|YAP1_ENST00000528834.1_3'UTR|YAP1_ENST00000537274.1_Silent_p.L462L|YAP1_ENST00000524575.1_Silent_p.L296L|YAP1_ENST00000526343.1_Silent_p.L420L|RP11-864G5.3_ENST00000526310.1_RNA|YAP1_ENST00000531439.1_Silent_p.L458L	NM_001130145.2|NM_001282101.1	NP_001123617.1|NP_001269030.1	P46937	YAP1_HUMAN	Yes-associated protein 1	474	Transactivation domain.				cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|contact inhibition (GO:0060242)|embryonic heart tube morphogenesis (GO:0003143)|gene expression (GO:0010467)|hippo signaling (GO:0035329)|keratinocyte differentiation (GO:0030216)|lateral mesoderm development (GO:0048368)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|notochord development (GO:0030903)|paraxial mesoderm development (GO:0048339)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|positive regulation of organ growth (GO:0046622)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of keratinocyte proliferation (GO:0010837)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of stem cell proliferation (GO:0072091)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)	4	all_cancers(8;0.000575)|all_epithelial(12;0.00564)	Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.00936)	Lung(13;0.245)	BRCA - Breast invasive adenocarcinoma(274;0.0189)		TGCCAAGTCTGCAGGAAGCTT	0.463																																					p.L474L	Colon(50;247 1103 7861 28956)	.											.	.	.	0			c.G1422T						.						130.0	127.0	128.0					11																	102100578		2203	4299	6502	SO:0001819	synonymous_variant	10413	exon9			AAGTCTGCAGGAA		CCDS8314.1, CCDS44716.1, CCDS8314.2, CCDS53699.1, CCDS53700.1, CCDS60944.1, CCDS73373.1, CCDS73374.1	11q13	2010-03-19	2010-03-19		ENSG00000137693	ENSG00000137693			16262	protein-coding gene	gene with protein product		606608	"""Yes-associated protein 1, 65kDa"""			7782338	Standard	NM_001130145		Approved	YAP65	uc001pgt.3	P46937	OTTHUMG00000167322	ENST00000282441.5:c.1422G>T	11.37:g.102100578G>T		Somatic	43	0		WXS	Illumina HiSeq	.	60	14	NM_001130145	B4DTY1|B7ZA01|E3WEB5|E3WEB6|E9PRV2|F5H202|K0KQ18|K0KYZ8|K0L195|K0L1G3|Q7Z574|Q8IUY9	Silent	SNP	ENST00000282441.5	37	CCDS44716.1	.	.	.	.	.	.	.	.	.	.	G	7.355	0.623638	0.14193	.	.	ENSG00000137693	ENST00000529029	.	.	.	6.17	0.382	0.16234	.	.	.	.	.	T	0.53318	0.1789	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43032	-0.9416	4	.	.	.	.	6.8983	0.24269	0.18:0.0:0.4347:0.3853	.	.	.	.	F	228	.	.	C	+	2	0	YAP1	101605788	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	0.967000	0.29344	0.155000	0.19261	0.655000	0.94253	TGC	.		0.463	YAP1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394151.1	NM_006106	
EXOC1	55763	hgsc.bcm.edu	37	4	56756490	56756490	+	Missense_Mutation	SNP	T	T	G			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr4:56756490T>G	ENST00000381295.2	+	12	1825	c.1477T>G	c.(1477-1479)Ttg>Gtg	p.L493V	EXOC1_ENST00000349598.6_Missense_Mutation_p.L478V|EXOC1_ENST00000346134.7_Missense_Mutation_p.L493V	NM_001024924.1	NP_001020095.1	Q9NV70	EXOC1_HUMAN	exocyst complex component 1	493					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	exocyst (GO:0000145)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	35	Glioma(25;0.08)|all_neural(26;0.101)					ATCTTCCCTGTTGGATATGGG	0.388																																					p.L493V		.											.	.	.	0			c.T1477G						.						163.0	146.0	152.0					4																	56756490		2203	4300	6503	SO:0001583	missense	55763	exon12			TCCCTGTTGGATA	AK027047	CCDS3502.1, CCDS3503.1	4q12	2013-01-22	2005-11-01	2005-11-01	ENSG00000090989	ENSG00000090989			30380	protein-coding gene	gene with protein product		607879	"""SEC3-like 1 (S. cerevisiae)"""	SEC3L1		11042152, 11406615	Standard	XM_005265747		Approved	SEC3, FLJ10893, BM-102, Sec3p	uc003hbf.1	Q9NV70	OTTHUMG00000102165	ENST00000381295.2:c.1477T>G	4.37:g.56756490T>G	ENSP00000370695:p.Leu493Val	Somatic	49	0		WXS	Illumina HiSeq	.	53	15	NM_018261	Q504V4|Q8WUE7|Q96T15|Q9NZE4	Missense_Mutation	SNP	ENST00000381295.2	37	CCDS3502.1	.	.	.	.	.	.	.	.	.	.	T	15.62	2.888621	0.52014	.	.	ENSG00000090989	ENST00000381295;ENST00000346134;ENST00000349598	.	.	.	5.45	-1.12	0.09808	.	0.000000	0.85682	D	0.000000	T	0.63616	0.2526	L	0.51422	1.61	0.54753	D	0.999989	D;P	0.56035	0.974;0.948	D;P	0.70487	0.969;0.718	T	0.57470	-0.7806	9	0.24483	T	0.36	.	11.5936	0.50959	0.0:0.4307:0.0:0.5693	.	478;493	Q9NV70-2;Q9NV70	.;EXOC1_HUMAN	V	493;493;478	.	ENSP00000326514:L493V	L	+	1	2	EXOC1	56451247	0.998000	0.40836	0.986000	0.45419	0.948000	0.59901	0.522000	0.22909	-0.412000	0.07519	-1.179000	0.01719	TTG	.		0.388	EXOC1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361799.1	NM_018261	
CAP1	10487	broad.mit.edu	37	1	40530008	40530008	+	Missense_Mutation	SNP	G	G	A			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr1:40530008G>A	ENST00000372797.3	+	5	965	c.404G>A	c.(403-405)aGc>aAc	p.S135N	CAP1_ENST00000372798.1_Missense_Mutation_p.S134N|CAP1_ENST00000340450.3_Missense_Mutation_p.S134N|CAP1_ENST00000372792.2_Missense_Mutation_p.S135N|CAP1_ENST00000372805.3_Missense_Mutation_p.S135N|CAP1_ENST00000372802.1_Missense_Mutation_p.S134N	NM_001105530.1|NM_006367.3	NP_001099000|NP_006358	Q13114	TRAF3_HUMAN	CAP, adenylate cyclase-associated protein 1 (yeast)	0					apoptotic process (GO:0006915)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|regulation of apoptotic process (GO:0042981)|regulation of cytokine production (GO:0001817)|regulation of defense response to virus (GO:0050688)|regulation of interferon-beta production (GO:0032648)|regulation of proteolysis (GO:0030162)|signal transduction (GO:0007165)|Toll signaling pathway (GO:0008063)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	CD40 receptor complex (GO:0035631)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endosome (GO:0005768)|mitochondrion (GO:0005739)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.S135N(1)		endometrium(3)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(1)	12	Lung NSC(20;5.03e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;4.63e-18)|Epithelial(16;1.27e-16)|all cancers(16;2.3e-15)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			TCAGCTGTCAGCGAAAGTATC	0.512																																					p.S135N													CAP1,NS,carcinoma,0,1	CAP1	38	1	Substitution - Missense(1)	endometrium(1)	c.G404A						.						72.0	69.0	70.0					1																	40530008		1944	4130	6074	SO:0001583	missense	10487	exon5			CTGTCAGCGAAAG	L12168	CCDS41309.1	1p34.3	2010-07-13			ENSG00000131236	ENSG00000131236			20040	protein-coding gene	gene with protein product						1406678, 8761950	Standard	NM_006367		Approved	CAP	uc001cey.4	Q01518	OTTHUMG00000004493	ENST00000372797.3:c.404G>A	1.37:g.40530008G>A	ENSP00000361883:p.Ser135Asn	Somatic	64	1		WXS	Illumina GAIIx	Phase_I	53	5	NM_006367	B7Z8C4|Q12990|Q13076|Q13947|Q6AZX1|Q9UNL1	Missense_Mutation	SNP	ENST00000372797.3	37	CCDS41309.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.040033	0.93630	.	.	ENSG00000131236	ENST00000372797;ENST00000372802;ENST00000449311;ENST00000421589;ENST00000414281;ENST00000420216;ENST00000372792;ENST00000538246;ENST00000372798;ENST00000340450;ENST00000372805;ENST00000435719;ENST00000427843;ENST00000424977;ENST00000417287	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.15372	2.43;2.43;2.43;2.43;2.43;2.43;2.43;2.43;2.43;2.43;2.43;2.43;2.43;2.43	5.39	5.39	0.77823	Adenylate cyclase-associated CAP, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.41650	0.1168	M	0.88377	2.95	0.80722	D	1	P;P	0.35944	0.529;0.529	P;P	0.46585	0.521;0.521	T	0.44360	-0.9333	10	0.66056	D	0.02	-14.0802	18.1414	0.89641	0.0:0.0:1.0:0.0	.	82;135	E7ENY9;Q01518	.;CAP1_HUMAN	N	135;134;135;135;135;135;135;112;134;134;135;134;135;135;135	ENSP00000361883:S135N;ENSP00000361888:S134N;ENSP00000398475:S135N;ENSP00000403198:S135N;ENSP00000408561:S135N;ENSP00000410586:S135N;ENSP00000361878:S135N;ENSP00000361884:S134N;ENSP00000344832:S134N;ENSP00000361891:S135N;ENSP00000412859:S134N;ENSP00000413656:S135N;ENSP00000413383:S135N;ENSP00000400943:S135N	ENSP00000344832:S134N	S	+	2	0	CAP1	40302595	1.000000	0.71417	0.999000	0.59377	0.981000	0.71138	9.869000	0.99810	2.522000	0.85027	0.650000	0.86243	AGC	.		0.512	CAP1-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000013109.1	NM_006367	
LOC100288069	100288069	broad.mit.edu	37	1	700532	700532	+	lincRNA	SNP	T	T	A			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr1:700532T>A	ENST00000428504.1	-	0	1021				RP11-206L10.5_ENST00000417659.1_lincRNA	NR_033908.1																						aaaaaaaaaaTTCCTTTGGGA	0.453																																					.													.	.	.	0			.						.																																					0	.			AAAAAATTCCTTT																													1.37:g.700532T>A		Somatic	13	0		WXS	Illumina GAIIx	Phase_I	23	5	.		RNA	SNP	ENST00000428504.1	37																																																																																				.		0.453	RP11-206L10.2-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000006889.1		
NBPF8	728841	broad.mit.edu	37	1	144220816	144220816	+	Missense_Mutation	SNP	A	A	G	rs587673408	byFrequency	TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr1:144220816A>G	ENST00000369373.5	+	2	83	c.83A>G	c.(82-84)gAg>gGg	p.E28G				Q3BBV2	NBPF8_HUMAN	neuroblastoma breakpoint family, member 8	668						cytoplasm (GO:0005737)											GATGAGAAAGAGCCTGAAGTC	0.483													.|||	167	0.0333466	0.1097	0.0115	5008	,	,		50002	0.001		0.006	False		,,,				2504	0.0072				.													ENSG00000162825,bladder,carcinoma,0,2	.	.	0			.						.																																			SO:0001583	missense	728841	.			AGAAAGAGCCTGA	AY894572		1q21.1	2014-04-01	2013-04-24	2013-04-24	ENSG00000162825	ENSG00000162825		"""neuroblastoma breakpoint family"""	31990	protein-coding gene	gene with protein product		613998	"""neuroblastoma breakpoint family, member 8, pseudogene"""	NBPF8P		16079250	Standard	NM_001037501		Approved			Q3BBV2	OTTHUMG00000074805	ENST00000369373.5:c.83A>G	1.37:g.144220816A>G	ENSP00000358380:p.Glu28Gly	Somatic	37	1		WXS	Illumina GAIIx	Phase_I	62	9	.		Missense_Mutation	SNP	ENST00000369373.5	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	8.213|8.213	0.800676|0.800676	0.16397|0.16397	.|.	.|.	ENSG00000162825|ENSG00000162825	ENST00000369373|ENST00000369365	T|.	0.15603|.	2.41|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.39835|.	0.1093|.	.|.	.|.	.|.	.|.	.|.	.|.	B;B;.;B;B|.	0.23316|.	0.0;0.001;.;0.083;0.002|.	B;B;.;B;B|.	0.34038|.	0.0;0.003;.;0.174;0.011|.	T|.	0.29610|.	-1.0006|.	3|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	434;30;601;376;443|.	Q5VTG8;A8K9F1;B4DG53;Q8IX72;Q5TB04|.	.;.;.;.;.|.	G|G	28|3579	ENSP00000358380:E28G|.	.|.	E|S	+|+	2|1	0|0	RP3-377D14.1|RP3-377D14.1	142932173|142932173	0.724000|0.724000	0.28038|0.28038	.|.	.|.	.|.	.|.	0.868000|0.868000	0.27982|0.27982	.|.	.|.	.|.	.|.	GAG|AGC	.		0.483	NBPF8-204	KNOWN	basic|appris_candidate	protein_coding	protein_coding			
LINC00264	645528	broad.mit.edu	37	10	26880266	26880266	+	lincRNA	SNP	G	G	A			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr10:26880266G>A	ENST00000412114.1	+	0	501					NR_026793.1				long intergenic non-protein coding RNA 264																		ACCAAGCCCAGTGGACAGATG	0.443																																					.													.	.	.	0			.						.																																					0	.			AGCCCAGTGGACA			10p12.1	2012-10-12	2011-08-11	2011-08-11	ENSG00000233261	ENSG00000233261		"""Long non-coding RNAs"""	17776	non-coding RNA	RNA, long non-coding			"""chromosome 10 open reading frame 50"", ""non-protein coding RNA 264"""	C10orf50, NCRNA00264			Standard	NR_026793		Approved	bA128B16.2	uc001ist.3		OTTHUMG00000017839		10.37:g.26880266G>A		Somatic	32	0		WXS	Illumina GAIIx	Phase_I	37	6	.		RNA	SNP	ENST00000412114.1	37																																																																																				.		0.443	LINC00264-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000047265.1	XR_040540	
AGAP6	414189	broad.mit.edu	37	10	51768543	51768543	+	Missense_Mutation	SNP	T	T	C	rs368970869		TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr10:51768543T>C	ENST00000374056.4	+	7	987	c.589T>C	c.(589-591)Tcg>Ccg	p.S197P	AGAP6_ENST00000412531.3_Missense_Mutation_p.S220P			Q5VW22	AGAP6_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 6	197					regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)	p.S220P(3)		NS(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(1)|lung(8)|prostate(3)|skin(1)|stomach(2)	29						CTCCATTCCATCGACTCCCAG	0.532																																					p.S220P													AGAP6,NS,carcinoma,0,3	AGAP6	53	3	Substitution - Missense(3)	endometrium(2)|NS(1)	c.T658C						.																																			SO:0001583	missense	414189	exon8			ATTCCATCGACTC		CCDS44397.1	10q11.23	2013-01-10	2008-09-22	2008-09-22	ENSG00000204149	ENSG00000204149		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	23466	protein-coding gene	gene with protein product			"""centaurin, gamma-like family, member 3"""	CTGLF3			Standard	NM_001077665		Approved	bA324H6.1	uc001jix.4	Q5VW22	OTTHUMG00000018220	ENST00000374056.4:c.589T>C	10.37:g.51768543T>C	ENSP00000363168:p.Ser197Pro	Somatic	198	1		WXS	Illumina GAIIx	Phase_I	302	4	NM_001077665		Missense_Mutation	SNP	ENST00000374056.4	37		.	.	.	.	.	.	.	.	.	.	.	7.332	0.619129	0.14129	.	.	ENSG00000204149	ENST00000374056;ENST00000412531	T	0.56776	0.44	0.0465	0.0465	0.14256	.	0.149774	0.46145	D	0.000318	T	0.42314	0.1197	M	0.65498	2.005	0.37828	D	0.92861	B	0.14012	0.009	B	0.13407	0.009	T	0.20140	-1.0284	10	0.31617	T	0.26	.	4.565	0.12180	0.0:6.0E-4:0.0:0.9994	.	220	C9IYN2	.	P	220;197	ENSP00000400972:S197P	ENSP00000363168:S220P	S	+	1	0	AGAP6	51438549	1.000000	0.71417	0.059000	0.19551	0.060000	0.15804	3.691000	0.54720	0.115000	0.18071	0.113000	0.15668	TCG	T|0.500;C|0.500		0.532	AGAP6-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_001077665	
TPTE2P5	100616668	broad.mit.edu	37	13	41400911	41400922	+	RNA	DEL	TGTGTGTGTGTG	TGTGTGTGTGTG	-	rs200635743|rs201964730|rs370213099|rs71200140|rs562745957|rs34743508		TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr13:41400911_41400922delTGTGTGTGTGTG	ENST00000432905.1	-	0	500									transmembrane phosphoinositide 3-phosphatase and tensin homolog 2 pseudogene 5																		tatgtatgtatgtgtgtgtgtgtgtgtgtgtg	0.406																																					.													.	.	.	0			.						.																																					0	.			TATGTATGTGTGT			13q14.11	2012-06-20			ENSG00000168852	ENSG00000168852			42356	pseudogene	pseudogene							Standard	NR_038258		Approved		uc001uxo.2		OTTHUMG00000016779		13.37:g.41400911_41400922delTGTGTGTGTGTG		Somatic	4	0		WXS	Illumina GAIIx	Phase_I	8	4	.		RNA	DEL	ENST00000432905.1	37																																																																																				.		0.406	TPTE2P5-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000044650.1		
RP11-252A24.2	0	broad.mit.edu	37	16	74372644	74372644	+	RNA	SNP	A	A	G			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr16:74372644A>G	ENST00000429810.2	-	0	1552																											TACCCTTGTCAGGGGGAACAA	0.443																																					.													.	.	.	0			.						.																																					0	.			CTTGTCAGGGGGA																													16.37:g.74372644A>G		Somatic	65	1		WXS	Illumina GAIIx	Phase_I	155	6	.		RNA	SNP	ENST00000429810.2	37																																																																																				.		0.443	RP11-252A24.2-003	KNOWN	basic	retained_intron	pseudogene	OTTHUMT00000434683.1		
PABPN1L	390748	broad.mit.edu	37	16	88930645	88930645	+	Splice_Site	SNP	C	C	T	rs545706965	byFrequency	TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr16:88930645C>T	ENST00000419291.2	-	6	808	c.797G>A	c.(796-798)cGg>cAg	p.R266Q	PABPN1L_ENST00000411789.2_Splice_Site_p.G237R|PABPN1L_ENST00000427766.1_Splice_Site_p.P230P|PABPN1L_ENST00000378358.4_Splice_Site_p.R266Q	NM_001080487.2	NP_001073956.2	A6NDY0	EPAB2_HUMAN	poly(A) binding protein, nuclear 1-like (cytoplasmic)	266						cytoplasm (GO:0005737)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			kidney(1)	1						ACCCACTCACCGGTTCTGCCC	0.726													.|||	3	0.000599042	0.0	0.0	5008	,	,		11772	0.0		0.0	False		,,,				2504	0.0031				p.R266Q													.	PABPN1L	25	0			c.G797A						.						12.0	15.0	14.0					16																	88930645		1854	4027	5881	SO:0001630	splice_region_variant	390748	exon6			ACTCACCGGTTCT		CCDS45547.1, CCDS45547.2, CCDS73925.1	16q24.3	2013-02-12	2009-12-17		ENSG00000205022	ENSG00000205022		"""RNA binding motif (RRM) containing"""	37237	protein-coding gene	gene with protein product	"""embryonic poly(A) binding protein 2"""					18483763	Standard	NM_001080487		Approved	ePABP2	uc010vpe.2	A6NDY0		ENST00000419291.2:c.797+1G>A	16.37:g.88930645C>T		Somatic	19	0		WXS	Illumina GAIIx	Phase_I	35	3	NM_001080487	A1L3B3|A2VDI2	Splice_Site	SNP	ENST00000419291.2	37	CCDS45547.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.7|20.7	4.032220|4.032220	0.75504|0.75504	.|.	.|.	ENSG00000205022|ENSG00000205022	ENST00000411789|ENST00000378358;ENST00000419291	.|T;T	.|0.15718	.|2.4;2.52	4.52|4.52	1.31|1.31	0.21738|0.21738	.|.	.|0.078134	.|0.48286	.|D	.|0.000186	T|T	0.22322|0.22322	0.0538|0.0538	M|M	0.85542|0.85542	2.76|2.76	0.80722|0.80722	D|D	1|1	B|P;P	0.27791|0.48589	0.189|0.513;0.912	B|B;B	0.25884|0.44108	0.064|0.018;0.441	T|T	0.02126|0.02126	-1.1209|-1.1209	7|9	.|.	.|.	.|.	.|.	4.3021|4.3021	0.10930|0.10930	0.16:0.5969:0.1548:0.0883|0.16:0.5969:0.1548:0.0883	.|.	237|266;266	A6NDY0-2|A6NDY0;A6NDY0-4	.|EPAB2_HUMAN;.	R|Q	237|266	.|ENSP00000367609:R266Q;ENSP00000408598:R266Q	.|.	G|R	-|-	1|2	0|0	PABPN1L|PABPN1L	87458146|87458146	0.031000|0.031000	0.19500|0.19500	0.049000|0.049000	0.19019|0.19019	0.132000|0.132000	0.20833|0.20833	0.408000|0.408000	0.21065|0.21065	0.089000|0.089000	0.17243|0.17243	-1.473000|-1.473000	0.01005|0.01005	GGG|CGG	.		0.726	PABPN1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407502.1	NM_001080487	Missense_Mutation
LRRC37A11P	342666	broad.mit.edu	37	17	37190747	37190747	+	RNA	DEL	T	T	-			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr17:37190747delT	ENST00000425901.2	+	0	2604					NR_033753.2				leucine rich repeat containing 37, member A11, pseudogene																		ttcttttttcttttttttttt	0.343																																					.													.	.	.	0			.						.																																					0	.			TTTTTCTTTTTTT			17q12	2013-05-14			ENSG00000214553	ENSG00000214553			43815	pseudogene	pseudogene							Standard	NR_033753		Approved		uc002hrd.1		OTTHUMG00000133184		17.37:g.37190747delT		Somatic	5	0		WXS	Illumina GAIIx	Phase_I	17	3	.		RNA	DEL	ENST00000425901.2	37																																																																																				.		0.343	LRRC37A11P-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000444105.1	NR_033753	
KRTAP4-11	653240	broad.mit.edu	37	17	39274087	39274087	+	Missense_Mutation	SNP	G	G	C	rs141357429		TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr17:39274087G>C	ENST00000391413.2	-	1	519	c.481C>G	c.(481-483)Ctg>Gtg	p.L161V		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	161	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].					keratin filament (GO:0045095)		p.L161V(1)		endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			ACTGGACGCAGGcagcagcag	0.657																																					p.L161V													KRTAP4-11,NS,carcinoma,0,7	KRTAP4-11	94	1	Substitution - Missense(1)	prostate(1)	c.C481G						.						17.0	21.0	20.0					17																	39274087		692	1589	2281	SO:0001583	missense	653240	exon1			GACGCAGGCAGCA	AC025904	CCDS45675.1	17q21.2	2013-06-25			ENSG00000212721	ENSG00000212721		"""Keratin associated proteins"""	18911	protein-coding gene	gene with protein product			"""keratin associated protein 4-14"""	KRTAP4-14			Standard	NM_033059		Approved	KAP4.11, KAP4.14	uc002hvz.3	Q9BYQ6	OTTHUMG00000133586	ENST00000391413.2:c.481C>G	17.37:g.39274087G>C	ENSP00000375232:p.Leu161Val	Somatic	57	1		WXS	Illumina GAIIx	Phase_I	105	14	NM_033059	A0AUY2	Missense_Mutation	SNP	ENST00000391413.2	37	CCDS45675.1	249	0.11401098901098901	67	0.13617886178861788	40	0.11049723756906077	104	0.18181818181818182	38	0.05013192612137203	.	1.347	-0.592411	0.03799	.	.	ENSG00000212721	ENST00000391413	T	0.00614	6.21	4.35	0.986	0.19784	.	.	.	.	.	T	0.00012	0.0000	L	0.31752	0.955	0.80722	P	0.0	B	0.30068	0.267	B	0.18871	0.023	T	0.19063	-1.0317	8	0.11794	T	0.64	.	5.8913	0.18915	0.1751:0.0:0.6569:0.168	.	161	Q9BYQ6	KR411_HUMAN	V	161	ENSP00000375232:L161V	ENSP00000375232:L161V	L	-	1	2	KRTAP4-11	36527613	0.671000	0.27521	0.912000	0.35992	0.970000	0.65996	0.971000	0.29396	0.348000	0.23949	0.609000	0.83330	CTG	G|0.500;C|0.500		0.657	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1		
AMZ2P1	201283	broad.mit.edu	37	17	62968690	62968690	+	RNA	SNP	A	A	G			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr17:62968690A>G	ENST00000430983.1	-	0	1554					NR_026903.1				archaelysin family metallopeptidase 2 pseudogene 1																		AAAATTCCACAAGTCTCTTGG	0.373																																					.													.	.	.	0			.						.																																					0	.			TTCCACAAGTCTC	AK056627		17q24.1	2012-10-16	2010-04-08		ENSG00000214174	ENSG00000214174			26491	pseudogene	pseudogene							Standard	NR_026903		Approved	FLJ32065	uc002jfb.3		OTTHUMG00000132075		17.37:g.62968690A>G		Somatic	68	1		WXS	Illumina GAIIx	Phase_I	93	4	.		RNA	SNP	ENST00000430983.1	37																																																																																				.		0.373	AMZ2P1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000255102.1	NM_153032	
LRRC37A16P	651250	broad.mit.edu	37	17	66141017	66141017	+	RNA	DEL	C	C	-	rs376314569|rs368840037		TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr17:66141017delC	ENST00000590019.1	-	0	70									leucine rich repeat containing 37, member A16, pseudogene																		AAGATTTCTACAAAAAAAAAA	0.323																																					.													.	.	.	0			.						.																																					0	.			TTTCTACAAAAAA			17q24.2	2012-10-18				ENSG00000267023			43820	pseudogene	pseudogene							Standard	NG_023507		Approved				OTTHUMG00000180160		17.37:g.66141017delC		Somatic	94	0		WXS	Illumina GAIIx	Phase_I	131	8	.		RNA	DEL	ENST00000590019.1	37																																																																																				.		0.323	LRRC37A16P-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000450078.1		
KIAA1683	80726	broad.mit.edu	37	19	18377943	18377943	+	Missense_Mutation	SNP	G	G	T	rs531584807		TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr19:18377943G>T	ENST00000600328.3	-	3	600	c.407C>A	c.(406-408)gCc>gAc	p.A136D	KIAA1683_ENST00000392413.4_Missense_Mutation_p.A136D|KIAA1683_ENST00000600359.3_Missense_Mutation_p.A90D			Q9H0B3	K1683_HUMAN	KIAA1683	136						mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						GCGCCGCCAGGCCTCCTGGAT	0.597																																					p.A136D													.	KIAA1683	190	0			c.C407A						.						57.0	56.0	56.0					19																	18377943		2203	4300	6503	SO:0001583	missense	80726	exon3			CGCCAGGCCTCCT	AB051470	CCDS32958.1, CCDS46017.1, CCDS46018.1	19p13.1	2008-02-05				ENSG00000130518			29350	protein-coding gene	gene with protein product						11214970, 11230166	Standard	NM_025249		Approved		uc010ebn.2	Q9H0B3		ENST00000600328.3:c.407C>A	19.37:g.18377943G>T	ENSP00000470780:p.Ala136Asp	Somatic	20	0		WXS	Illumina GAIIx	Phase_I	36	5	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Missense_Mutation	SNP	ENST00000600328.3	37	CCDS32958.1	.	.	.	.	.	.	.	.	.	.	G	13.39	2.223893	0.39300	.	.	ENSG00000130518	ENST00000392413;ENST00000359737;ENST00000427634;ENST00000358422;ENST00000411671	T;T;T	0.73152	-0.72;-0.72;-0.72	4.06	1.89	0.25635	.	0.243684	0.21342	N	0.076120	T	0.67776	0.2929	L	0.32530	0.975	0.23266	N	0.998013	D;D	0.69078	0.997;0.997	P;P	0.59115	0.852;0.852	T	0.55995	-0.8052	10	0.87932	D	0	-12.346	6.0576	0.19820	0.2231:0.0:0.7769:0.0	.	136;136	E9PDE0;Q9H0B3	.;K1683_HUMAN	D	136;136;90;135;136	ENSP00000376213:A136D;ENSP00000352774:A136D;ENSP00000404501:A90D	ENSP00000351198:A135D	A	-	2	0	KIAA1683	18238943	0.997000	0.39634	0.997000	0.53966	0.095000	0.18619	1.167000	0.31847	1.821000	0.53095	0.313000	0.20887	GCC	.		0.597	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3		
ANKRD36C	400986	broad.mit.edu	37	2	96628278	96628278	+	Missense_Mutation	SNP	G	G	C	rs182453827		TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr2:96628278G>C	ENST00000456556.1	-	7	901	c.817C>G	c.(817-819)Cca>Gca	p.P273A				Q5JPF3	AN36C_HUMAN	ankyrin repeat domain 36C	273							ion channel inhibitor activity (GO:0008200)			breast(1)|endometrium(8)|kidney(5)|lung(4)	18						TTCAAGGCTGGTTGTTTCTGA	0.313																																					.													ENSG00000174501,NS,malignant_melanoma,0,1	.	.	0			.						.																																			SO:0001583	missense	400986	.			AGGCTGGTTGTTT	AL832836		2q11.1	2013-01-10			ENSG00000174501	ENSG00000174501		"""Ankyrin repeat domain containing"""	32946	protein-coding gene	gene with protein product	"""protein immuno-reactive with anti-PTH polyclonal antibodies"""						Standard	XR_251121		Approved	DKFZp667P0924	uc002suz.1	Q5JPF3	OTTHUMG00000155211	ENST00000456556.1:c.817C>G	2.37:g.96628278G>C	ENSP00000403302:p.Pro273Ala	Somatic	69	1		WXS	Illumina GAIIx	Phase_I	106	11	.	C9JZ08|Q15694|Q53S06|Q658V2	Missense_Mutation	SNP	ENST00000456556.1	37		.	.	.	.	.	.	.	.	.	.	N	2.583	-0.296876	0.05532	.	.	ENSG00000174501	ENST00000456556	T	0.76578	-1.03	1.25	0.315	0.15852	.	.	.	.	.	T	0.64864	0.2637	L	0.39898	1.24	0.09310	N	1	.	.	.	.	.	.	T	0.50825	-0.8782	7	0.19590	T	0.45	.	3.5052	0.07688	0.2753:0.0:0.7247:0.0	.	.	.	.	A	273	ENSP00000403302:P273A	ENSP00000403302:P273A	P	-	1	0	AC073995.2	95992005	0.000000	0.05858	0.001000	0.08648	0.023000	0.10783	-0.369000	0.07533	0.100000	0.17581	0.291000	0.19559	CCA	.		0.313	ANKRD36C-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000338799.2	NM_001010914	
RANBP2	5903	broad.mit.edu	37	2	109367844	109367844	+	Missense_Mutation	SNP	T	T	G			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr2:109367844T>G	ENST00000283195.6	+	10	1524	c.1398T>G	c.(1396-1398)caT>caG	p.H466Q		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	466					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.H466Q(6)	RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						ATTTGCCCCATGAAACCTCAA	0.358																																					p.H466Q													RANBP2_ENST00000283195,NS,carcinoma,0,6	RANBP2	488	6	Substitution - Missense(6)	endometrium(6)	c.T1398G						.						69.0	78.0	75.0					2																	109367844		1510	2703	4213	SO:0001583	missense	5903	exon10			GCCCCATGAAACC	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"""Tetratricopeptide (TTC) repeat domain containing"""	9848	protein-coding gene	gene with protein product		601181	"""acute necrotizing encephalopathy 1 (autosomal dominant)"""	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.1398T>G	2.37:g.109367844T>G	ENSP00000283195:p.His466Gln	Somatic	297	1		WXS	Illumina GAIIx	Phase_I	428	5	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	37	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	G	2.180	-0.387877	0.04932	.	.	ENSG00000153201	ENST00000409491;ENST00000283195	D	0.82526	-1.62	5.25	2.44	0.29823	.	.	.	.	.	T	0.43545	0.1252	N	0.00197	-1.87	0.20563	N	0.999888	B	0.02656	0.0	B	0.01281	0.0	T	0.50039	-0.8874	9	0.02654	T	1	-0.0972	5.4961	0.16804	0.3195:0.0:0.5396:0.1409	.	466	P49792	RBP2_HUMAN	Q	466	ENSP00000283195:H466Q	ENSP00000283195:H466Q	H	+	3	2	RANBP2	108734276	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.307000	0.43682	0.319000	0.23209	-0.127000	0.14921	CAT	.		0.358	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267	
AC017002.1	0	broad.mit.edu	37	2	112252464	112252464	+	lincRNA	SNP	G	G	A	rs1128295		TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr2:112252464G>A	ENST00000455309.1	+	0	390				AC017002.2_ENST00000432268.1_lincRNA																							ATACTCACCAGGGAGAGGCTG	0.537																																					.													.	.	.	0			.						.																																					0	.			TCACCAGGGAGAG																													2.37:g.112252464G>A		Somatic	58	1		WXS	Illumina GAIIx	Phase_I	79	4	.		RNA	SNP	ENST00000455309.1	37																																																																																				G|0.500;A|0.500		0.537	AC017002.1-001	KNOWN	basic|exp_conf	lincRNA	lincRNA	OTTHUMT00000332149.1		
BAGE2	85319	broad.mit.edu	37	21	11078137	11078137	+	RNA	DEL	C	C	-	rs111912474		TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr21:11078137delC	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2							extracellular region (GO:0005576)								Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		caaaaattagccaggcgtggt	0.547																																					.													.	.	.	0			.						.																																					85319	.			AATTAGCCAGGCG	AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172			15723	protein-coding gene	gene with protein product	"""cancer/testis antigen family 2, member 2"""					12461691	Standard	NM_182482		Approved	CT2.2		Q86Y30	OTTHUMG00000074128		21.37:g.11078137delC		Somatic	12	0		WXS	Illumina GAIIx	Phase_I	9	4	.	A8K925|Q08ER0	RNA	DEL	ENST00000470054.1	37																																																																																				C|0.500;-|0.500		0.547	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	NM_182482	
SYNJ1	8867	broad.mit.edu	37	21	34045776	34045776	+	Silent	SNP	G	G	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr21:34045776G>T	ENST00000322229.7	-	13	1599	c.1600C>A	c.(1600-1602)Cga>Aga	p.R534R	SYNJ1_ENST00000433931.2_Silent_p.R573R|SYNJ1_ENST00000357345.3_Silent_p.R534R|SYNJ1_ENST00000382491.3_Silent_p.R529R|SYNJ1_ENST00000382499.2_Silent_p.R573R			O43426	SYNJ1_HUMAN	synaptojanin 1	534	Catalytic. {ECO:0000255}.				cell death (GO:0008219)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of synaptic vesicle uncoating (GO:1903390)|regulation of synaptic vesicle membrane organization (GO:1901632)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)	cytosol (GO:0005829)	inositol-polyphosphate 5-phosphatase activity (GO:0004445)|nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)	p.R534*(2)		breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|lung(11)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	57						ACACATACTCGAATTTTCTTA	0.388																																					p.R573R													SYNJ1,colon,carcinoma,0,2	SYNJ1	253	2	Substitution - Nonsense(2)	large_intestine(2)	c.C1717A						.						95.0	91.0	92.0					21																	34045776		2203	4300	6503	SO:0001819	synonymous_variant	8867	exon14			ATACTCGAATTTT	AF009040	CCDS33539.1, CCDS33540.1, CCDS33539.2, CCDS33540.2, CCDS54483.1	21q22.2	2008-06-23			ENSG00000159082	ENSG00000159082			11503	protein-coding gene	gene with protein product		604297				9428629, 10773674	Standard	NM_203446		Approved	INPP5G	uc002yqh.2	O43426	OTTHUMG00000064926	ENST00000322229.7:c.1600C>A	21.37:g.34045776G>T		Somatic	42	0		WXS	Illumina GAIIx	Phase_I	38	3	NM_203446	O43425|O94984|Q4KMR1	Silent	SNP	ENST00000322229.7	37	CCDS54484.1																																																																																			.		0.388	SYNJ1-201	KNOWN	basic|CCDS	protein_coding	protein_coding			
PCDHGA9	56107	broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	140783658	140783658	+	Missense_Mutation	SNP	G	G	C			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr5:140783658G>C	ENST00000573521.1	+	1	1139	c.1139G>C	c.(1138-1140)gGt>gCt	p.G380A	PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron	NM_018921.2|NM_032089.1	NP_061744.1|NP_114478.1	Q9Y5G4	PCDG9_HUMAN	protocadherin gamma subfamily A, 9	380	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGGAAGAATGGTCAAGTTGTC	0.413																																					p.G380A													.	PCDHGA9	110	0			c.G1139C						.						38.0	38.0	38.0					5																	140783658		1913	4135	6048	SO:0001583	missense	0	exon1			AGAATGGTCAAGT	AF152516	CCDS58981.1, CCDS75341.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8707	other	protocadherin		606296				10380929	Standard	NM_018921		Approved	PCDH-GAMMA-A9		Q9Y5G4		ENST00000573521.1:c.1139G>C	5.37:g.140783658G>C	ENSP00000460274:p.Gly380Ala	Somatic	37	1		WXS	Illumina GAIIx	Phase_I	56	17	NM_032089	A2RU65|Q9Y5C9	Missense_Mutation	SNP	ENST00000573521.1	37	CCDS58981.1																																																																																			.		0.413	PCDHGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437105.1	NM_018921	
COL9A1	1297	broad.mit.edu	37	6	70990553	70990553	+	Missense_Mutation	SNP	G	G	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr6:70990553G>T	ENST00000357250.6	-	10	1095	c.937C>A	c.(937-939)Cca>Aca	p.P313T	COL9A1_ENST00000370496.3_Missense_Mutation_p.P313T|COL9A1_ENST00000370499.4_Missense_Mutation_p.P70T|COL9A1_ENST00000320755.7_Missense_Mutation_p.P70T|COL9A1_ENST00000489611.1_5'Flank	NM_001851.4	NP_001842.3	P20849	CO9A1_HUMAN	collagen, type IX, alpha 1	313	Collagen-like 1.|Triple-helical region (COL3).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|organ morphogenesis (GO:0009887)|tissue homeostasis (GO:0001894)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)	p.P313T(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(44)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)	80						GGAGCTCCTGGCTTTCCCGGT	0.627																																					p.P313T													COL9A1,NS,carcinoma,0,1	COL9A1	228	1	Substitution - Missense(1)	prostate(1)	c.C937A						.																																			SO:0001583	missense	1297	exon10			CTCCTGGCTTTCC		CCDS4971.1, CCDS47447.1	6q13	2013-05-07			ENSG00000112280	ENSG00000112280		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2217	protein-coding gene	gene with protein product		120210				1429648	Standard	NM_001851		Approved		uc003pfg.4	P20849	OTTHUMG00000014988	ENST00000357250.6:c.937C>A	6.37:g.70990553G>T	ENSP00000349790:p.Pro313Thr	Somatic	37	1		WXS	Illumina GAIIx	Phase_I	36	5	NM_001851	Q13699|Q13700|Q5TF52|Q6P467|Q96BM8|Q99225|Q9H151|Q9H152|Q9Y6P2|Q9Y6P3	Missense_Mutation	SNP	ENST00000357250.6	37	CCDS4971.1	.	.	.	.	.	.	.	.	.	.	G	8.030	0.761439	0.15914	.	.	ENSG00000112280	ENST00000357250;ENST00000320755;ENST00000370499;ENST00000370496	D;D;D;D	0.95588	-3.75;-3.75;-3.75;-3.73	5.73	3.95	0.45737	.	0.239072	0.50627	D	0.000120	D	0.84392	0.5462	L	0.45051	1.395	0.40273	D	0.978311	B;B	0.11235	0.004;0.001	B;B	0.12156	0.007;0.003	T	0.77542	-0.2549	10	0.22109	T	0.4	.	3.7236	0.08466	0.143:0.1328:0.5866:0.1376	.	313;70	P20849;P20849-2	CO9A1_HUMAN;.	T	313;70;70;313	ENSP00000349790:P313T;ENSP00000315252:P70T;ENSP00000359530:P70T;ENSP00000359527:P313T	ENSP00000315252:P70T	P	-	1	0	COL9A1	71047274	1.000000	0.71417	0.876000	0.34364	0.000000	0.00434	2.069000	0.41481	0.779000	0.33543	-0.897000	0.02905	CCA	.		0.627	COL9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041131.2		
TAS2R3	50831	broad.mit.edu	37	7	141464042	141464042	+	Missense_Mutation	SNP	G	G	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr7:141464042G>T	ENST00000247879.2	+	1	146	c.84G>T	c.(82-84)gaG>gaT	p.E28D	SSBP1_ENST00000465582.1_Intron	NM_016943.2	NP_058639.1	Q9NYW6	TA2R3_HUMAN	taste receptor, type 2, member 3	28					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|sensory perception of taste (GO:0050909)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)	14	Melanoma(164;0.0171)					GTTTCATTGAGTTGGTCAATG	0.473																																					p.E28D													.	TAS2R3	40	0			c.G84T						.						245.0	238.0	241.0					7																	141464042		2203	4300	6503	SO:0001583	missense	50831	exon1			CATTGAGTTGGTC	AF227130	CCDS5867.1	7q31.3-q32	2012-08-22			ENSG00000127362	ENSG00000127362		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14910	protein-coding gene	gene with protein product		604868					Standard	NM_016943		Approved	T2R3	uc003vwp.1	Q9NYW6	OTTHUMG00000157637	ENST00000247879.2:c.84G>T	7.37:g.141464042G>T	ENSP00000247879:p.Glu28Asp	Somatic	26	0		WXS	Illumina GAIIx	Phase_I	37	3	NM_016943	A4D1U2|Q645W2|Q75MV6	Missense_Mutation	SNP	ENST00000247879.2	37	CCDS5867.1	.	.	.	.	.	.	.	.	.	.	g	9.435	1.086586	0.20390	.	.	ENSG00000127362	ENST00000247879	T	0.37058	1.22	6.17	0.113	0.14631	.	1.168210	0.06286	N	0.698341	T	0.24661	0.0598	N	0.22421	0.69	0.09310	N	1	B	0.14438	0.01	B	0.19946	0.027	T	0.30387	-0.9980	10	0.56958	D	0.05	.	4.9511	0.14015	0.0972:0.1903:0.5151:0.1974	.	28	Q9NYW6	TA2R3_HUMAN	D	28	ENSP00000247879:E28D	ENSP00000247879:E28D	E	+	3	2	TAS2R3	141110511	0.000000	0.05858	0.000000	0.03702	0.466000	0.32739	-0.022000	0.12480	-0.517000	0.06461	-2.416000	0.00220	GAG	.		0.473	TAS2R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349288.1		
KMT2C	58508	broad.mit.edu	37	7	151962255	151962255	+	Missense_Mutation	SNP	C	C	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr7:151962255C>T	ENST00000262189.6	-	8	1270	c.1052G>A	c.(1051-1053)gGa>gAa	p.G351E	KMT2C_ENST00000355193.2_Missense_Mutation_p.G351E	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	351					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										TAAGAGGTCTCCCGGGCTGTC	0.393																																					p.G351E													.	MLL3	1564	0			c.G1052A						.						154.0	142.0	146.0					7																	151962255		2203	4296	6499	SO:0001583	missense	58508	exon8			AGGTCTCCCGGGC	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.1052G>A	7.37:g.151962255C>T	ENSP00000262189:p.Gly351Glu	Somatic	116	0		WXS	Illumina GAIIx	Phase_I	118	7	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	C	13.85	2.361625	0.41801	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.99226	-5.59;-5.59	4.65	4.65	0.58169	Zinc finger, PHD-finger (1);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, PHD-type (1);Protein kinase C-like, phorbol ester/diacylglycerol binding (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.40640	U	0.001053	D	0.99336	0.9767	M	0.74546	2.27	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99143	1.0856	10	0.87932	D	0	.	17.9157	0.88950	0.0:1.0:0.0:0.0	.	351	Q8NEZ4	MLL3_HUMAN	E	351	ENSP00000262189:G351E;ENSP00000347325:G351E	ENSP00000262189:G351E	G	-	2	0	MLL3	151593188	1.000000	0.71417	1.000000	0.80357	0.050000	0.14768	7.772000	0.85439	2.271000	0.75665	0.557000	0.71058	GGA	.		0.393	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
RP11-162D16.2	0	broad.mit.edu	37	9	124170937	124170937	+	RNA	DEL	A	A	-	rs373702406|rs60249110|rs558133861|rs34883987|rs112905846	byFrequency	TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr9:124170937delA	ENST00000440807.1	+	0	85																											acaaagatttaaaaaaaaaaa	0.373													|||unknown(HR)	2810	0.561102	0.559	0.5043	5008	,	,		16574	0.5198		0.6143	False		,,,				2504	0.592				.													.	.	.	0			.						.																																					0	.			AGATTTAAAAAAA																													9.37:g.124170937delA		Somatic	5	0		WXS	Illumina GAIIx	Phase_I	10	3	.		RNA	DEL	ENST00000440807.1	37																																																																																				-|1.000;|0.000		0.373	RP11-162D16.2-001	KNOWN	basic	antisense	antisense	OTTHUMT00000053891.1		
TUBBP5	643224	broad.mit.edu	37	9	141069844	141069844	+	RNA	SNP	T	T	C	rs62581042		TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr9:141069844T>C	ENST00000503395.1	+	0	1053									tubulin, beta pseudogene 5									p.A29A(1)									ATGAACATGCTATCGACTCCG	0.667																																					.													.	.	.	1	Substitution - coding silent(1)	endometrium(1)	.						.																																					0	.			ACATGCTATCGAC	AF355123		9q34.3	2012-03-06	2005-11-15		ENSG00000159247	ENSG00000159247			23674	pseudogene	pseudogene			"""tubulin, beta polypeptide pseudogene 5"""			11731935	Standard	NR_027156		Approved		uc010ncq.3		OTTHUMG00000021001		9.37:g.141069844T>C		Somatic	35	0		WXS	Illumina GAIIx	Phase_I	52	4	.		RNA	SNP	ENST00000503395.1	37																																																																																				T|0.500;C|0.500		0.667	TUBBP5-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000373087.1	NR_027156	
MT-ND2	4536	broad.mit.edu	37	M	2555	2555	+	5'Flank	SNP	C	C	A			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chrM:2555C>A	ENST00000361453.3	+	0	0				MT-TV_ENST00000387342.1_RNA|MT-TL1_ENST00000386347.1_RNA|MT-TM_ENST00000387377.1_RNA|MT-TQ_ENST00000387372.1_RNA|MT-ND1_ENST00000361390.2_5'Flank|MT-TI_ENST00000387365.1_RNA|MT-RNR1_ENST00000389680.2_RNA|MT-RNR2_ENST00000387347.2_RNA|MT-TW_ENST00000387382.1_RNA|MT-TF_ENST00000387314.1_RNA			P03891	NU2M_HUMAN	mitochondrially encoded NADH dehydrogenase 2						cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|reactive oxygen species metabolic process (GO:0072593)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|lung(1)	3						CCTGCCCAGTGACACATGTTT	0.483																																					.													.	.	.	0			.						.																																			SO:0001631	upstream_gene_variant	0	.			CAGTGACACATGT			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198763	ENSG00000198763	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7456	protein-coding gene	gene with protein product	"""complex I ND2 subunit"", ""NADH-ubiquinone oxidoreductase chain 2"""	516001	"""NADH dehydrogenase 2"""	MTND2			Standard			Approved	ND2, NAD2		P03891			M.37:g.2555C>A	Exception_encountered	Somatic	588	1		WXS	Illumina GAIIx	Phase_I	2026	12	.	Q34769|Q9TGI0|Q9TGI1|Q9TGI2|Q9TGI3|Q9TGI4	RNA	SNP	ENST00000361453.3	37																																																																																				.		0.483	MT-ND2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024027	
ZNF157	7712	broad.mit.edu	37	X	47272699	47272699	+	Silent	SNP	A	A	G			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chrX:47272699A>G	ENST00000377073.3	+	4	1313	c.1227A>G	c.(1225-1227)tcA>tcG	p.S409S		NM_003446.3	NP_003437.2	P51786	ZN157_HUMAN	zinc finger protein 157	409					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	11						GGATGCATTCAGGAGAGAAAC	0.413																																					p.S409S													.	ZNF157	46	0			c.A1227G						.						66.0	60.0	62.0					X																	47272699		2203	4300	6503	SO:0001819	synonymous_variant	7712	exon4			GCATTCAGGAGAG	U28687	CCDS14278.1	Xp11.2	2013-01-08	2006-08-22		ENSG00000147117	ENSG00000147117		"""Zinc fingers, C2H2-type"", ""-"""	12942	protein-coding gene	gene with protein product		300024	"""zinc finger protein 157 (HZF22)"""			8586441	Standard	NM_003446		Approved	HZF22	uc004dhr.1	P51786	OTTHUMG00000021443	ENST00000377073.3:c.1227A>G	X.37:g.47272699A>G		Somatic	32	0		WXS	Illumina GAIIx	Phase_I	58	3	NM_003446	Q96LE9	Silent	SNP	ENST00000377073.3	37	CCDS14278.1																																																																																			.		0.413	ZNF157-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056415.1	NM_003446	
FAM205B	389715	ucsc.edu	37	9	34834103	34834103	+	RNA	SNP	T	T	C	rs200572923	byFrequency	TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr9:34834103T>C	ENST00000455647.2	-	0	2290							Q63HN1	F205B_HUMAN	family with sequence similarity 205, member B																		CTTTGTGATGTAGGTCTGGGT	0.542													C|||	1956	0.390575	0.4297	0.2363	5008	,	,		14315	0.5188		0.2197	False		,,,				2504	0.4908				.													.	FAM205B	10	0			.						.																																					389715	.			GTGATGTAGGTCT			9p13.3	2013-05-22	2011-08-15	2011-08-15	ENSG00000257198	ENSG00000257198			24504	other	unknown			"""chromosome 9 open reading frame 144"""	C9orf144			Standard	NR_024481		Approved	DKFZp434J193, C9orf144A	uc003zvp.4	Q63HN1	OTTHUMG00000019839		9.37:g.34834103T>C		Somatic	30	7		WXS	Illumina HiSeq		39	16	.	Q6ZRJ7	Silent	SNP	ENST00000455647.2	37																																																																																				.		0.542	FAM205B-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000052246.5	NR_024481	
ADCY4	196883	ucsc.edu;bcgsc.ca	37	14	24787682	24787682	+	Silent	SNP	G	G	A			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr14:24787682G>A	ENST00000310677.4	-	26	3287	c.3174C>T	c.(3172-3174)tgC>tgT	p.C1058C	ADCY4_ENST00000554068.2_Silent_p.C1058C|ADCY4_ENST00000418030.2_Silent_p.C1058C	NM_001198568.1|NM_001198592.1|NM_139247.3	NP_001185497.1|NP_001185521.1|NP_640340.2	Q8NFM4	ADCY4_HUMAN	adenylate cyclase 4	1058					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(265;0.0192)		GGAAGTAGGTGCAGAGCTGCC	0.527																																					p.C1058C													ADCY4,NS,carcinoma,-1,1	ADCY4	86	0			c.C3174T						.						147.0	131.0	137.0					14																	24787682		2203	4300	6503	SO:0001819	synonymous_variant	196883	exon26			GTAGGTGCAGAGC	AF497516	CCDS9627.1	14q11.2	2013-02-04			ENSG00000129467	ENSG00000129467	4.6.1.1	"""Adenylate cyclases"""	235	protein-coding gene	gene with protein product		600292				7766992	Standard	NM_001198592		Approved	AC4	uc001woy.3	Q8NFM4	OTTHUMG00000029347	ENST00000310677.4:c.3174C>T	14.37:g.24787682G>A		Somatic	30	0		WXS	Illumina HiSeq		40	4	NM_139247	B3KV74|D3DS75|Q17R40|Q6ZTM6|Q96ML7	Silent	SNP	ENST00000310677.4	37	CCDS9627.1																																																																																			.		0.527	ADCY4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073200.4		
LINC00970	101978719	bcgsc.ca	37	1	168907806	168907806	+	RNA	SNP	G	G	A			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr1:168907806G>A	ENST00000366408.3	-	0	209					NR_104091.1				long intergenic non-protein coding RNA 970																		TAAGGGGGTGGACCCCAAGTT	0.502																																					.													.	.	.	0			.						.																																					0	.			GGGGTGGACCCCA	BC041008		1q24.2	2013-06-07			ENSG00000203601	ENSG00000203601		"""Long non-coding RNAs"""	48730	non-coding RNA	RNA, long non-coding						23741487	Standard	NR_104091		Approved				OTTHUMG00000034588		1.37:g.168907806G>A		Somatic	17	0		WXS	Illumina HiSeq	Phase_1	19	6	.		RNA	SNP	ENST00000366408.3	37																																																																																				.		0.502	LINC00970-001	KNOWN	basic	antisense	antisense	OTTHUMT00000083693.1		
AC018804.7	0	bcgsc.ca	37	2	130988166	130988166	+	RNA	SNP	A	A	G	rs201275727		TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	A	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr2:130988166A>G	ENST00000450578.1	+	0	0																											CTGGCAGTACATGCACTGCCT	0.602																																					.													.	.	.	0			.						.																																					0	.			CAGTACATGCACT																													2.37:g.130988166A>G		Somatic	25	0		WXS	Illumina HiSeq	Phase_1	47	11	.		RNA	SNP	ENST00000450578.1	37																																																																																				.		0.602	AC018804.7-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000332326.2		
LOC401010	401010	bcgsc.ca	37	2	132200652	132200652	+	IGR	SNP	C	C	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr2:132200652C>T								AC073869.19 (34030 upstream) : RP11-109E12.1 (18741 downstream)																							TCAGCTTCTGCCAGGCTTCCA	0.602																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			CTTCTGCCAGGCT																													2.37:g.132200652C>T		Somatic	31	0		WXS	Illumina HiSeq	Phase_1	53	4	.		RNA	SNP		37																																																																																				.	0	0.602								
GUSBP1	728411	bcgsc.ca	37	5	21481681	21481681	+	RNA	SNP	C	C	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr5:21481681C>T	ENST00000607545.1	+	0	179					NR_027026.1		Q15486	GUSP1_HUMAN	glucuronidase, beta pseudogene 1						carbohydrate metabolic process (GO:0005975)|nervous system development (GO:0007399)|skeletal system development (GO:0001501)		hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)										TTCCCAGACACGGGAGCTGTA	0.612																																					.													.	.	.	0			.						.																																					0	.			CAGACACGGGAGC	BC064850, X75940		5p14.3	2012-10-04			ENSG00000183666	ENSG00000183666			13670	pseudogene	pseudogene						8565635	Standard	NR_027026		Approved		uc010iub.3	Q15486	OTTHUMG00000162474		5.37:g.21481681C>T		Somatic	272	0		WXS	Illumina HiSeq	Phase_1	451	35	.	A6NLY8|A8K1B7|Q969T8|Q9BUH2	RNA	SNP	ENST00000607545.1	37																																																																																				.		0.612	GUSBP1-006	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000470546.1	NG_008324	
MTO1	25821	bcgsc.ca	37	6	74176311	74176311	+	Missense_Mutation	SNP	G	G	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr6:74176311G>T	ENST00000370300.4	+	3	607	c.517G>T	c.(517-519)Gtc>Ttc	p.V173F	MTO1_ENST00000518210.1_3'UTR|RNU6-975P_ENST00000384296.1_RNA|MTO1_ENST00000415954.2_Missense_Mutation_p.V173F|MTO1_ENST00000370305.1_Missense_Mutation_p.V99F|MTO1_ENST00000498286.1_Missense_Mutation_p.V173F	NM_012123.3|NM_133645.2	NP_036255.2|NP_598400.1	Q9Y2Z2	MTO1_HUMAN	mitochondrial tRNA translation optimization 1	173					mitochondrial tRNA wobble uridine modification (GO:0070899)|oxidation-reduction process (GO:0055114)	mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|stomach(1)	27						GAAATGCCGTGTCAGTGGGGT	0.403																																					p.V173F													.	MTO1	59	0			c.G517T						.						160.0	141.0	148.0					6																	74176311		2203	4300	6503	SO:0001583	missense	25821	exon3			TGCCGTGTCAGTG	AF132937	CCDS4979.1, CCDS34485.1, CCDS47452.1	6q14.1	2013-05-07	2013-05-07		ENSG00000135297	ENSG00000135297			19261	protein-coding gene	gene with protein product		614667	"""mitochondrial translation optimization 1 homolog (S. cerevisiae)"""			12011058, 22608499	Standard	NM_012123		Approved		uc003pgy.4	Q9Y2Z2	OTTHUMG00000015032	ENST00000370300.4:c.517G>T	6.37:g.74176311G>T	ENSP00000359323:p.Val173Phe	Somatic	51	0		WXS	Illumina HiSeq	Phase_1	52	4	NM_133645	B3KQB5|Q5SWL2|Q5SWL3|Q5SWL4|Q8NDN7|Q8WZ57|Q96FE6|Q9BS06	Missense_Mutation	SNP	ENST00000370300.4	37	CCDS4979.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.789589	0.90367	.	.	ENSG00000135297	ENST00000415954;ENST00000498286;ENST00000357845;ENST00000370305;ENST00000370300	T;T;T;T	0.80214	-1.35;-1.35;-1.35;-1.35	5.68	5.68	0.88126	.	0.123536	0.56097	D	0.000040	D	0.83115	0.5184	M	0.83312	2.635	0.58432	D	0.999999	P;P;P	0.44877	0.845;0.534;0.785	P;P;P	0.57057	0.805;0.715;0.812	T	0.81998	-0.0675	10	0.02654	T	1	-11.7518	18.3213	0.90239	0.0:0.0:1.0:0.0	.	173;173;173	Q9Y2Z2-6;Q9Y2Z2-4;Q9Y2Z2	.;.;MTO1_HUMAN	F	173;173;173;99;173	ENSP00000402038:V173F;ENSP00000419561:V173F;ENSP00000359328:V99F;ENSP00000359323:V173F	ENSP00000350506:V173F	V	+	1	0	MTO1	74233032	1.000000	0.71417	0.998000	0.56505	0.738000	0.42128	8.060000	0.89464	2.838000	0.97847	0.585000	0.79938	GTC	.		0.403	MTO1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041215.2	NM_012123	
LOC100128317	100128317	bcgsc.ca	37	7	81213697	81213697	+	lincRNA	SNP	G	G	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr7:81213697G>T	ENST00000413944.2	-	0	803																											TTTTACTCTTGCTATAATTTC	0.318																																					.													.	.	.	0			.						.																																					0	.			ACTCTTGCTATAA																													7.37:g.81213697G>T		Somatic	62	0		WXS	Illumina HiSeq	Phase_1	89	4	.		RNA	SNP	ENST00000413944.2	37																																																																																				.		0.318	AC010091.1-002	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000339912.2		
TAF6	6878	bcgsc.ca	37	7	99707848	99707848	+	Missense_Mutation	SNP	G	G	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr7:99707848G>T	ENST00000344095.4	-	11	1658	c.1133C>A	c.(1132-1134)gCa>gAa	p.A378E	TAF6_ENST00000453269.2_Missense_Mutation_p.A378E|TAF6_ENST00000418432.2_Missense_Mutation_p.A302E|AP4M1_ENST00000421755.1_3'UTR|TAF6_ENST00000472509.1_Missense_Mutation_p.A435E|TAF6_ENST00000452041.1_Missense_Mutation_p.A378E|TAF6_ENST00000437822.2_Missense_Mutation_p.A415E	NM_005641.3	NP_005632.1	P49848	TAF6_HUMAN	TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 80kDa	378					DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(2)	26	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					AGCCAAGCCTGCGATGGAGCC	0.542																																					p.A415E													.	TAF6	55	0			c.C1244A						.						201.0	205.0	203.0					7																	99707848		2203	4300	6503	SO:0001583	missense	9179	exon11			AAGCCTGCGATGG		CCDS5686.1, CCDS55135.1	7q	2010-02-26	2002-08-29	2001-12-07	ENSG00000106290	ENSG00000106290			11540	protein-coding gene	gene with protein product	"""TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 80 kD"", ""transcription initiation factor TFIID 70 kD subunit"""	602955	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, E, 70/85kD"""	TAF2E		826207	Standard	NM_139315		Approved	TAFII70, TAFII80, MGC:8964, TAFII85	uc011kji.2	P49848	OTTHUMG00000154771	ENST00000344095.4:c.1133C>A	7.37:g.99707848G>T	ENSP00000344537:p.Ala378Glu	Somatic	37	0		WXS	Illumina HiSeq	Phase_1	45	4	NM_001190415	A4D2B2|A4D2B3|B4DT11|D6W5U2|Q6AI29	Missense_Mutation	SNP	ENST00000344095.4	37	CCDS5686.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	14.11|14.11	2.437508|2.437508	0.43224|0.43224	.|.	.|.	ENSG00000106290|ENSG00000221838	ENST00000453269;ENST00000472509;ENST00000452041;ENST00000344095;ENST00000418432;ENST00000437822|ENST00000450807	T;T;T;T;T;T|.	0.67171|.	-0.25;-0.25;-0.25;-0.25;-0.25;-0.25|.	5.24|5.24	5.24|5.24	0.73138|0.73138	Domain of unknown function DUF1546 (1);|.	0.103098|.	0.64402|.	D|.	0.000003|.	T|T	0.57666|0.57666	0.2069|0.2069	L|L	0.31065|0.31065	0.9|0.9	0.80722|0.80722	D|D	1|1	P;B;P;B;B|.	0.35944|.	0.529;0.274;0.529;0.387;0.321|.	B;B;B;B;B|.	0.35039|.	0.194;0.122;0.194;0.09;0.194|.	T|T	0.55166|0.55166	-0.8183|-0.8183	10|6	0.25106|0.38643	T|T	0.35|0.18	-11.5068|-11.5068	16.3666|16.3666	0.83331|0.83331	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	415;378;368;378;302|.	B4DT11;P49848-2;A4D299;P49848;B3KUR4|.	.;.;.;TAF6_HUMAN;.|.	E|F	378;435;378;378;302;415|143	ENSP00000389575:A378E;ENSP00000419760:A435E;ENSP00000416396:A378E;ENSP00000344537:A378E;ENSP00000407980:A302E;ENSP00000399982:A415E|.	ENSP00000344537:A378E|ENSP00000391585:C143F	A|C	-|+	2|2	0|0	TAF6|AP4M1	99545784|99545784	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.983000|0.983000	0.72400|0.72400	8.424000|8.424000	0.90267|0.90267	2.720000|2.720000	0.93068|0.93068	0.556000|0.556000	0.70494|0.70494	GCA|TGC	.		0.542	TAF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337024.2	NM_005641	
MUC6	4588	bcgsc.ca	37	11	1017988	1017988	+	Missense_Mutation	SNP	G	G	T	rs112579249		TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr11:1017988G>T	ENST00000421673.2	-	31	4863	c.4813C>A	c.(4813-4815)Cca>Aca	p.P1605T		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1605	Pro-rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GGGTGTGATGGGGTTGGATAG	0.547																																					p.P1605T													.	MUC6	408	0			c.C4813A						.						440.0	415.0	424.0					11																	1017988		2181	4271	6452	SO:0001583	missense	4588	exon31			GTGATGGGGTTGG	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.4813C>A	11.37:g.1017988G>T	ENSP00000406861:p.Pro1605Thr	Somatic	49	1		WXS	Illumina HiSeq	Phase_1	68	13	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	G	1.148	-0.647618	0.03506	.	.	ENSG00000184956	ENST00000421673	T	0.25579	1.79	2.39	-0.213	0.13165	.	.	.	.	.	T	0.28333	0.0700	L	0.35341	1.055	0.09310	N	1	D	0.71674	0.998	D	0.73708	0.981	T	0.18209	-1.0344	9	0.29301	T	0.29	.	0.7847	0.01046	0.1618:0.2393:0.3558:0.2431	.	1605	Q6W4X9	MUC6_HUMAN	T	1605	ENSP00000406861:P1605T	ENSP00000406861:P1605T	P	-	1	0	MUC6	1007988	0.001000	0.12720	0.002000	0.10522	0.020000	0.10135	0.017000	0.13399	0.255000	0.21593	0.297000	0.19635	CCA	G|0.500;T|0.500		0.547	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
STAT6	6778	bcgsc.ca	37	12	57499001	57499001	+	Missense_Mutation	SNP	T	T	A			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr12:57499001T>A	ENST00000300134.3	-	9	1259	c.934A>T	c.(934-936)Agg>Tgg	p.R312W	STAT6_ENST00000537215.2_Missense_Mutation_p.R202W|STAT6_ENST00000556155.1_Missense_Mutation_p.R312W|STAT6_ENST00000454075.3_Missense_Mutation_p.R312W|STAT6_ENST00000543873.2_Missense_Mutation_p.R312W|STAT6_ENST00000538913.2_Missense_Mutation_p.R202W	NM_001178078.1|NM_003153.4	NP_001171549.1|NP_003144.3	P42226	STAT6_HUMAN	signal transducer and activator of transcription 6, interleukin-4 induced	312					cellular response to hydrogen peroxide (GO:0070301)|cellular response to reactive nitrogen species (GO:1902170)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|mammary gland epithelial cell proliferation (GO:0033598)|mammary gland morphogenesis (GO:0060443)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of isotype switching to IgE isotypes (GO:0048295)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|T-helper 1 cell lineage commitment (GO:0002296)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane raft (GO:0045121)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|protein phosphatase binding (GO:0019903)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(2)|lung(8)|ovary(4)|skin(1)	28						ATGTCGGCCCTGACCAGCGGA	0.637																																					p.R312W													.	STAT6	69	0			c.A934T						.						44.0	46.0	45.0					12																	57499001		2203	4300	6503	SO:0001583	missense	6778	exon9			CGGCCCTGACCAG	BC005823, BQ028928	CCDS8931.1, CCDS53804.1	12q13	2013-02-14				ENSG00000166888		"""SH2 domain containing"""	11368	protein-coding gene	gene with protein product		601512				9605853, 8085155	Standard	NM_003153		Approved	D12S1644, IL-4-STAT	uc001sna.3	P42226		ENST00000300134.3:c.934A>T	12.37:g.57499001T>A	ENSP00000300134:p.Arg312Trp	Somatic	59	0		WXS	Illumina HiSeq	Phase_1	48	4	NM_001178079	A8K316|B7ZA27|F5GXI9|Q5FBW5|Q71UP4	Missense_Mutation	SNP	ENST00000300134.3	37	CCDS8931.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.97|19.97	3.924721|3.924721	0.73213|0.73213	.|.	.|.	ENSG00000166888|ENSG00000166888	ENST00000553533|ENST00000300134;ENST00000535201;ENST00000538913;ENST00000543873;ENST00000556155;ENST00000537215;ENST00000454075;ENST00000542721;ENST00000542516	.|T;T;T;T;T;T	.|0.77489	.|-1.1;-1.1;-1.1;-1.1;-1.1;-1.1	4.37|4.37	3.2|3.2	0.36748|0.36748	.|STAT transcription factor, DNA-binding, subdomain (1);STAT transcription factor, DNA-binding (1);p53-like transcription factor, DNA-binding (1);	.|0.055499	.|0.64402	.|D	.|0.000001	T|T	0.81361|0.81361	0.4806|0.4806	L|L	0.43923|0.43923	1.385|1.385	0.42896|0.42896	D|D	0.994217|0.994217	.|D;D	.|0.76494	.|0.999;0.999	.|D;D	.|0.73380	.|0.98;0.98	T|T	0.80993|0.80993	-0.1134|-0.1134	5|10	.|0.87932	.|D	.|0	-19.9088|-19.9088	9.2243|9.2243	0.37395|0.37395	0.0:0.0:0.1831:0.8169|0.0:0.0:0.1831:0.8169	.|.	.|312;312	.|A8K4S9;P42226	.|.;STAT6_HUMAN	L|W	12|312;202;202;312;312;202;312;202;312	.|ENSP00000300134:R312W;ENSP00000445409:R202W;ENSP00000438451:R312W;ENSP00000451742:R312W;ENSP00000444530:R202W;ENSP00000401486:R312W	.|ENSP00000300134:R312W	Q|R	-|-	2|1	0|2	STAT6|STAT6	55785268|55785268	0.998000|0.998000	0.40836|0.40836	1.000000|1.000000	0.80357|0.80357	0.954000|0.954000	0.61252|0.61252	1.066000|1.066000	0.30604|0.30604	0.699000|0.699000	0.31761|0.31761	-0.466000|-0.466000	0.05196|0.05196	CAG|AGG	.		0.637	STAT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412248.3	NM_003153	
MED15P1	326615	bcgsc.ca	37	14	19500335	19500335	+	RNA	SNP	C	C	T	rs371871636		TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr14:19500335C>T	ENST00000552968.1	-	0	488									mediator complex subunit 15 pseudogene 1																		AGCGGGCTGGCGGTAGGATGC	0.622																																					.													.	.	.	0			.						.																																					0	.			GGCTGGCGGTAGG			14q11.2	2013-06-03	2010-02-25	2010-02-25	ENSG00000257853	ENSG00000257853			19271	pseudogene	pseudogene			"""PCQAP pseudogene"", ""mediator complex subunit 15 pseudogene"""	PCQAPP, MED15P			Standard	NG_002605		Approved				OTTHUMG00000170337		14.37:g.19500335C>T		Somatic	70	1		WXS	Illumina HiSeq	Phase_1	120	16	.		RNA	SNP	ENST00000552968.1	37																																																																																				.		0.622	MED15P1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000408573.1	NG_002605	
POTEG	404785	bcgsc.ca	37	14	19553530	19553530	+	Silent	SNP	C	C	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr14:19553530C>T	ENST00000409832.3	+	1	166	c.114C>T	c.(112-114)agC>agT	p.S38S		NM_001005356.2	NP_001005356.1	Q6S5H5	POTEG_HUMAN	POTE ankyrin domain family, member G	38										cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(31)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	47						GCAGGGGGAGCGGCAAGAGCA	0.592																																					p.S38S													.	POTEG	118	0			c.C114T						.						19.0	29.0	26.0					14																	19553530		1586	3339	4925	SO:0001819	synonymous_variant	404785	exon1			GGGGAGCGGCAAG		CCDS73610.1	14q11.2	2013-01-10	2008-11-26	2008-11-26	ENSG00000222036	ENSG00000222036		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33896	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 4"""	608916	"""ANKRD26-like family C, member 2"""	A26C2			Standard	NR_027480		Approved	POTE14, POTE-14, POTE14alpha, CT104.4	uc001vuz.1	Q6S5H5	OTTHUMG00000170340	ENST00000409832.3:c.114C>T	14.37:g.19553530C>T		Somatic	302	10		WXS	Illumina HiSeq	Phase_1	463	39	NM_001005356	A1L153|A6NMI9|Q6S5H6|Q6S8J2	Silent	SNP	ENST00000409832.3	37	CCDS32018.1																																																																																			.		0.592	POTEG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408579.1	NM_001005356	
RP11-848P1.9	0	bcgsc.ca	37	17	29349145	29349145	+	RNA	SNP	G	G	A	rs564994527	byFrequency	TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr17:29349145G>A	ENST00000579692.1	+	0	525																		p.?(1)									atatacatatgtgtgtgtgta	0.299													-|||	6	0.00119808	0.0045	0.0	5008	,	,		16024	0.0		0.0	False		,,,				2504	0.0				.													.	.	.	1	Unknown(1)	central_nervous_system(1)	.						.																																					0	.			ACATATGTGTGTG																													17.37:g.29349145G>A		Somatic	21	1		WXS	Illumina HiSeq	Phase_1	40	9	.		RNA	SNP	ENST00000579692.1	37																																																																																				.		0.299	RP11-848P1.9-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000445165.1		
ZNF849P	100130108	bcgsc.ca	37	19	22868275	22868275	+	RNA	SNP	C	C	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr19:22868275C>T	ENST00000601860.1	-	0	340																											TGGAAAGAAACCTTTCAAATG	0.289																																					.													.	.	.	0			.						.																																					0	.			AAGAAACCTTTCA																													19.37:g.22868275C>T		Somatic	70	0		WXS	Illumina HiSeq	Phase_1	107	9	.		Missense_Mutation	SNP	ENST00000601860.1	37		.	.	.	.	.	.	.	.	.	.	.	6.699	0.497705	0.12762	.	.	ENSG00000198153	ENST00000340708	.	.	.	1.01	1.01	0.19927	.	.	.	.	.	T	0.47002	0.1422	.	.	.	.	.	.	.	.	.	.	.	.	T	0.57165	-0.7858	4	0.54805	T	0.06	.	7.5874	0.28002	0.0:1.0:0.0:0.0	.	.	.	.	S	103	.	ENSP00000342595:P103S	P	+	1	0	AC011467.1	22660115	0.000000	0.05858	0.017000	0.16124	0.027000	0.11550	0.126000	0.15769	0.518000	0.28383	0.289000	0.19496	CCT	.		0.289	CTC-457E21.9-001	KNOWN	basic	antisense	antisense	OTTHUMT00000464586.1		
TPTE	7179	bcgsc.ca	37	21	11021153	11021153	+	5'UTR	SNP	G	G	A			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr21:11021153G>A	ENST00000415664.2	-	0	297				BAGE2_ENST00000470054.1_RNA			P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology						peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		CAACACAACCGTAGTGTGCAT	0.343																																					.													.	.	.	0			.						.																																			SO:0001623	5_prime_UTR_variant	7179	.			ACAACCGTAGTGT	AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	12023	protein-coding gene	gene with protein product	"""PTEN-related tyrosine phosphatase"", ""cancer/testis antigen 44"""	604336				10830953, 14659893	Standard	NM_001290224		Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000415664.2:c.-3039C>T	21.37:g.11021153G>A		Somatic	252	2		WXS	Illumina HiSeq	Phase_1	337	32	.	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	RNA	SNP	ENST00000415664.2	37																																																																																				GTAGTGT|0.500;ATATCGA|0.500		0.343	TPTE-006	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000340030.1		
HMGXB4	10042	bcgsc.ca	37	22	35683427	35683427	+	Missense_Mutation	SNP	G	G	T			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr22:35683427G>T	ENST00000216106.5	+	8	1578	c.1450G>T	c.(1450-1452)Ggt>Tgt	p.G484C	HMGXB4_ENST00000444518.2_Missense_Mutation_p.G375C	NM_001003681.2	NP_001003681.1	Q9UGU5	HMGX4_HUMAN	HMG box domain containing 4	484					endosome to lysosome transport (GO:0008333)|negative regulation of Wnt signaling pathway (GO:0030178)|Wnt signaling pathway (GO:0016055)	NURF complex (GO:0016589)	DNA binding (GO:0003677)			breast(1)|endometrium(1)|large_intestine(6)|liver(1)|lung(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						CAGCTCAGAAGGTTCCATGAA	0.438																																					p.G484C													.	HMGXB4	52	0			c.G1450T						.						122.0	104.0	110.0					22																	35683427		2203	4300	6503	SO:0001583	missense	10042	exon8			TCAGAAGGTTCCA	AJ010069	CCDS33641.1	22q13	2011-07-01	2009-01-05	2009-01-05	ENSG00000100281	ENSG00000100281		"""High mobility group / Non-canonical"""	5003	protein-coding gene	gene with protein product		604702	"""high-mobility group protein 2-like 1"""	HMG2L1		10329004, 10591208, 20511232	Standard	NM_001003681		Approved	THC211630	uc003anl.3	Q9UGU5	OTTHUMG00000150439	ENST00000216106.5:c.1450G>T	22.37:g.35683427G>T	ENSP00000216106:p.Gly484Cys	Somatic	25	0		WXS	Illumina HiSeq	Phase_1	18	3	NM_001003681	O75672|O75673|Q9UMT5	Missense_Mutation	SNP	ENST00000216106.5	37	CCDS33641.1	.	.	.	.	.	.	.	.	.	.	G	17.09	3.300608	0.60195	.	.	ENSG00000100281	ENST00000444518;ENST00000216106	T;T	0.20738	2.05;2.06	5.41	4.4	0.53042	.	0.472911	0.25114	N	0.033029	T	0.33352	0.0860	L	0.40543	1.245	0.37907	D	0.931246	D	0.89917	1.0	D	0.71184	0.972	T	0.22626	-1.0211	10	0.72032	D	0.01	-5.6943	9.1645	0.37043	0.0729:0.0:0.7819:0.1452	.	484	Q9UGU5	HMGX4_HUMAN	C	375;484	ENSP00000398302:G375C;ENSP00000216106:G484C	ENSP00000216106:G484C	G	+	1	0	HMGXB4	34013427	1.000000	0.71417	0.979000	0.43373	0.971000	0.66376	2.490000	0.45294	1.511000	0.48818	0.655000	0.94253	GGT	.		0.438	HMGXB4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318104.2	NM_005487	
LPIN1	23175	hgsc.bcm.edu	37	2	11943082	11943082	+	Missense_Mutation	SNP	C	C	A	rs4669781	byFrequency	TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr2:11943082C>A	ENST00000256720.2	+	14	1921	c.1828C>A	c.(1828-1830)Cca>Aca	p.P610T	LPIN1_ENST00000396097.1_Missense_Mutation_p.P340T|LPIN1_ENST00000449576.2_Missense_Mutation_p.P695T|LPIN1_ENST00000396099.1_Missense_Mutation_p.P652T|LPIN1_ENST00000404113.2_Missense_Mutation_p.P111T|LPIN1_ENST00000425416.2_Missense_Mutation_p.P616T	NM_145693.2	NP_663731.1	Q14693	LPIN1_HUMAN	lipin 1	610			P -> S (in dbSNP:rs4669781). {ECO:0000269|PubMed:12111372}.		cellular lipid metabolic process (GO:0044255)|fatty acid catabolic process (GO:0009062)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)|triglyceride mobilization (GO:0006642)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(15)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	45	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)		AGCTGCCAAGCCATCAAACGC	0.537																																					p.P695T		.											LPIN1_ENST00000404113,NS,carcinoma,-2,1	LPIN1_ENST00000404113	-2	0			c.C2083A						.						182.0	160.0	167.0					2																	11943082		2203	4300	6503	SO:0001583	missense	23175	exon16			GCCAAGCCATCAA	D80010	CCDS1682.1, CCDS58699.1, CCDS58700.1, CCDS58701.1	2p25.1	2008-05-23			ENSG00000134324	ENSG00000134324			13345	protein-coding gene	gene with protein product		605518				11138012, 8724849, 16950137	Standard	NM_145693		Approved	KIAA0188	uc010yjm.3	Q14693	OTTHUMG00000119082	ENST00000256720.2:c.1828C>A	2.37:g.11943082C>A	ENSP00000256720:p.Pro610Thr	Somatic	16	0		WXS	Illumina HiSeq	.	30	2	NM_001261428	A8MU38|B4DET9|B4DGS4|B4DGZ6|B5MC18|B7Z858|D6W506|E7ESE7|F5GY24|Q53T25	Missense_Mutation	SNP	ENST00000256720.2	37	CCDS1682.1	.	.	.	.	.	.	.	.	.	.	C	7.596	0.671746	0.14776	.	.	ENSG00000134324	ENST00000449576;ENST00000396099;ENST00000425416;ENST00000256720;ENST00000396097;ENST00000404113;ENST00000454151	T;T;T;T;T;T;T	0.80909	-1.43;-1.41;-1.4;-1.4;-1.24;-0.38;0.48	4.56	4.56	0.56223	.	0.053133	0.85682	D	0.000000	T	0.73853	0.3640	L	0.35644	1.08	0.36084	D	0.842985	B;B;B	0.31705	0.0;0.336;0.002	B;B;B	0.38500	0.007;0.275;0.008	T	0.73279	-0.4033	10	0.14656	T	0.56	-19.8574	13.5335	0.61635	0.1567:0.8433:0.0:0.0	.	111;695;610	B4DET9;F5GY24;Q14693	.;.;LPIN1_HUMAN	T	695;652;616;610;340;111;137	ENSP00000397908:P695T;ENSP00000379406:P652T;ENSP00000401522:P616T;ENSP00000256720:P610T;ENSP00000379404:P340T;ENSP00000386120:P111T;ENSP00000413714:P137T	ENSP00000256720:P610T	P	+	1	0	LPIN1	11860533	1.000000	0.71417	0.984000	0.44739	0.046000	0.14306	2.155000	0.42301	2.240000	0.73641	0.462000	0.41574	CCA	.		0.537	LPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239296.3	NM_145693	
SMG1	23049	broad.mit.edu	37	16	18882689	18882690	+	Missense_Mutation	DNP	TG	TG	CA			TCGA-W6-AA0S-01A-11D-A417-09	TCGA-W6-AA0S-10A-01D-A41A-09	TG	TG						Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67fd4351-eff3-4ce8-87c8-d33cf1120c4b	3ed583ee-0f5b-475f-8401-f7e7d1679df3	g.chr16:18882689_18882690TG>CA	ENST00000446231.2	-	16	2710_2711	c.2298_2299CA>TG	c.(2296-2301)gcCAac>gcTGac	p.N767D	snoU13_ENST00000459248.1_RNA|SMG1_ENST00000389467.3_Missense_Mutation_p.N767D			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	767	Interaction with SMG8 and SMG9.				DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						GTCTTACTGTTGGCTAAAAGGC	0.366																																					p.N767D													.	SMG1	401	0			c.C2298T						.																																			SO:0001583	missense	23049	exon16			ACTGTTGGCTAAA	AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"""phosphatidylinositol 3-kinase-related kinase"""	607032	"""smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"""			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.2298_2299delinsCA	16.37:g.18882689_18882690delinsCA	ENSP00000402515:p.Asn767Asp	Somatic	177	0		WXS	Illumina GAIIx	Phase_I	277	12	NM_015092	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Missense_Mutation	DNP	ENST00000446231.2	37	CCDS45430.1																																																																																			.		0.366	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092	
