#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_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_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_Start_position_hg18	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_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
SCRN1	9805	hgsc.bcm.edu	37	7	29980316	29980316	+	Missense_Mutation	SNP	T	T	C			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr7:29980316T>C	ENST00000426154.1	-	5	897	c.721A>G	c.(721-723)Agc>Ggc	p.S241G	SCRN1_ENST00000434476.2_Missense_Mutation_p.S261G|SCRN1_ENST00000409497.1_Missense_Mutation_p.S241G|SCRN1_ENST00000242059.5_Missense_Mutation_p.S241G|SCRN1_ENST00000425819.2_Missense_Mutation_p.S173G|SCRN1_ENST00000416113.2_Intron	NM_001145513.1	NP_001138985.1	Q12765	SCRN1_HUMAN	secernin 1	241					exocytosis (GO:0006887)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	dipeptidase activity (GO:0016805)	p.S241C(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(12)|ovary(2)|prostate(2)|skin(2)	25						TTTTCTAAGCTGTCTTTGCCA	0.473																																																	1	Substitution - Missense(1)	ovary(1)	7											131.0	122.0	125.0					7																	29980316		2203	4300	6503	29946841	SO:0001583	missense	9805			D83777	CCDS5422.1, CCDS47567.1, CCDS47568.1	7p14.3-p14.1	2006-09-06			ENSG00000136193	ENSG00000136193			22192	protein-coding gene	gene with protein product		614965				12221138	Standard	NM_014766		Approved	KIAA0193	uc011kaa.2	Q12765	OTTHUMG00000097093	ENST00000426154.1:c.721A>G	7.37:g.29980316T>C	ENSP00000409068:p.Ser241Gly	Somatic		Capture	Illumina HiSeq	Phase_I	29946841	A8K0E9|B4DHM0|B4DIP5|C9JPG0|Q25QX7|Q8IWD1	Missense_Mutation	SNP	ENST00000426154.1	37	CCDS5422.1	.	.	.	.	.	.	.	.	.	.	T	14.12	2.440997	0.43326	.	.	ENSG00000136193	ENST00000242059;ENST00000426154;ENST00000425819;ENST00000544388;ENST00000409497;ENST00000434476;ENST00000421434	T;T;T;T;T;T	0.18960	3.26;3.26;3.12;3.26;3.25;2.18	5.67	5.67	0.87782	.	0.272996	0.37261	N	0.002163	T	0.22820	0.0551	L	0.51422	1.61	0.80722	D	1	B;B;B	0.17268	0.021;0.021;0.008	B;B;B	0.25759	0.039;0.063;0.028	T	0.03524	-1.1028	9	.	.	.	-10.5716	14.7167	0.69275	0.0:0.0:0.0:1.0	.	261;261;241	C9JPG0;B4DHM0;Q12765	.;.;SCRN1_HUMAN	G	241;241;173;45;241;261;241	ENSP00000242059:S241G;ENSP00000409068:S241G;ENSP00000414245:S173G;ENSP00000386872:S241G;ENSP00000388942:S261G;ENSP00000413184:S241G	.	S	-	1	0	SCRN1	29946841	1.000000	0.71417	1.000000	0.80357	0.442000	0.32017	3.001000	0.49488	2.159000	0.67721	0.482000	0.46254	AGC		SCRN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214231.2	NM_014766	
GUSB	2990	hgsc.bcm.edu	37	7	65444800	65444800	+	Silent	SNP	C	C	A			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr7:65444800C>A	ENST00000304895.4	-	3	625	c.495G>T	c.(493-495)cgG>cgT	p.R165R	GUSB_ENST00000476486.1_Intron|GUSB_ENST00000421103.1_Intron|GUSB_ENST00000345660.6_Silent_p.R165R	NM_000181.3	NP_000172.2	P08236	BGLR_HUMAN	glucuronidase, beta	165					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	beta-glucuronidase activity (GO:0004566)			breast(1)|cervix(2)|kidney(2)|large_intestine(4)|lung(10)|skin(1)	20						TGATTCGGAGCCGGGAGGGCA	0.617																																																	0			7											137.0	138.0	138.0					7																	65444800		2203	4300	6503	65082235	SO:0001819	synonymous_variant	2990			M15182	CCDS5530.1, CCDS64665.1	7q11.21	2012-10-02			ENSG00000169919	ENSG00000169919	3.2.1.31		4696	protein-coding gene	gene with protein product		611499				3468507	Standard	NM_000181		Approved		uc003tun.3	P08236	OTTHUMG00000023735	ENST00000304895.4:c.495G>T	7.37:g.65444800C>A		Somatic		Capture	Illumina HiSeq	Phase_I	65082235	B4E1F6|E9PCV0|Q549U0|Q96CL9	Silent	SNP	ENST00000304895.4	37	CCDS5530.1																																																																																				GUSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251637.3	NM_000181	
PON3	5446	hgsc.bcm.edu	37	7	94993256	94993256	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr7:94993256A>G	ENST00000265627.5	-	6	624	c.614T>C	c.(613-615)cTt>cCt	p.L205P	PON3_ENST00000451904.1_Missense_Mutation_p.L205P|PON1_ENST00000542556.1_Intron|PON3_ENST00000427422.1_Missense_Mutation_p.L205P	NM_000940.2	NP_000931.1	Q15166	PON3_HUMAN	paraoxonase 3	205					aromatic compound catabolic process (GO:0019439)|carboxylic acid catabolic process (GO:0046395)|coumarin catabolic process (GO:0046226)|phenylacetate catabolic process (GO:0010124)|response to external stimulus (GO:0009605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	3,4-dihydrocoumarin hydrolase activity (GO:0018733)|aryldialkylphosphatase activity (GO:0004063)|arylesterase activity (GO:0004064)|dihydrocoumarin hydrolase activity (GO:0047856)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	24	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0151)		Edetic Acid(DB00974)|Lovastatin(DB00227)	GCTGTAGAAAAGAACATAAGT	0.443																																																	0			7											182.0	187.0	185.0					7																	94993256		2203	4300	6503	94831192	SO:0001583	missense	5446			L48516, AF320003	CCDS5639.1	7q21.3	2014-03-14			ENSG00000105852	ENSG00000105852	3.1.1.2	"""Paraoxonases"""	9206	protein-coding gene	gene with protein product	"""arylesterase 3"""	602720				8661009	Standard	NM_000940		Approved			Q15166	OTTHUMG00000153917	ENST00000265627.5:c.614T>C	7.37:g.94993256A>G	ENSP00000265627:p.Leu205Pro	Somatic		Capture	Illumina HiSeq	Phase_I	94831192	A4D1H8|O75855|O76060|Q6IRU9|Q8IX97|Q9BZH9	Missense_Mutation	SNP	ENST00000265627.5	37	CCDS5639.1	.	.	.	.	.	.	.	.	.	.	A	20.1	3.935290	0.73442	.	.	ENSG00000105852	ENST00000265627;ENST00000427422	T;T	0.47177	0.85;0.85	5.27	4.12	0.48240	Six-bladed beta-propeller, TolB-like (1);	0.387835	0.28442	N	0.015332	T	0.58032	0.2094	M	0.66939	2.045	0.28015	N	0.934745	D;P	0.54397	0.966;0.953	P;P	0.55161	0.77;0.74	T	0.56842	-0.7912	10	0.87932	D	0	-2.1494	10.806	0.46518	0.9247:0.0:0.0753:0.0	.	253;205	B4E2I0;Q15166	.;PON3_HUMAN	P	205	ENSP00000265627:L205P;ENSP00000413276:L205P	ENSP00000265627:L205P	L	-	2	0	PON3	94831192	0.999000	0.42202	0.022000	0.16811	0.325000	0.28411	6.606000	0.74159	0.958000	0.37956	0.533000	0.62120	CTT		PON3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333007.1	NM_000940	
MET	4233	hgsc.bcm.edu	37	7	116423473	116423473	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr7:116423473A>G	ENST00000318493.6	+	19	3989	c.3802A>G	c.(3802-3804)Atg>Gtg	p.M1268V	MET_ENST00000539704.1_Missense_Mutation_p.M120V|MET_ENST00000397752.3_Missense_Mutation_p.M1250V			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			AGTGAAGTGGATGGCTTTGGA	0.393			Mis		"""papillary renal, head-neck squamous cell """	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																															Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	0			7											94.0	92.0	93.0					7																	116423473		1873	4103	5976	116210709	SO:0001583	missense	8731	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"""hepatocyte growth factor receptor"""	164860	"""met proto-oncogene"""			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.3802A>G	7.37:g.116423473A>G	ENSP00000317272:p.Met1268Val	Somatic		Capture	Illumina HiSeq	Phase_I	116210709	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	37	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	A	19.79	3.893463	0.72639	.	.	ENSG00000105976	ENST00000397752;ENST00000318493;ENST00000539704	T;T;T	0.37058	1.22;1.22;1.22	5.68	5.68	0.88126	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.65133	0.2662	M	0.85373	2.75	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.79108	0.988;0.992	T	0.71300	-0.4634	10	0.87932	D	0	.	16.2225	0.82267	1.0:0.0:0.0:0.0	.	1268;1250	P08581-2;P08581	.;MET_HUMAN	V	1250;1268;120	ENSP00000380860:M1250V;ENSP00000317272:M1268V;ENSP00000445020:M120V	ENSP00000317272:M1268V	M	+	1	0	MET	116210709	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.287000	0.95975	2.289000	0.77006	0.460000	0.39030	ATG		MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3		
DPP6	1804	hgsc.bcm.edu	37	7	154684138	154684138	+	Missense_Mutation	SNP	T	T	C			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr7:154684138T>C	ENST00000377770.3	+	26	2687	c.2546T>C	c.(2545-2547)aTc>aCc	p.I849T	DPP6_ENST00000332007.3_Missense_Mutation_p.I787T|DPP6_ENST00000427557.1_Missense_Mutation_p.I742T|DPP6_ENST00000404039.1_Missense_Mutation_p.I785T			P42658	DPP6_HUMAN	dipeptidyl-peptidase 6	849					cell death (GO:0008219)|neuronal action potential (GO:0019228)|positive regulation of potassium ion transmembrane transport (GO:1901381)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			NS(3)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(35)|pancreas(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	71	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			TGCTTCAGGATCCAGGACAAA	0.502																																					NSCLC(125;1384 1783 2490 7422 34254)												0			7											135.0	145.0	142.0					7																	154684138		2132	4232	6364	154315071	SO:0001583	missense	1804			M96859	CCDS75682.1, CCDS75683.1, CCDS75684.1	7q36.2	2006-08-07	2006-01-12		ENSG00000130226	ENSG00000130226			3010	protein-coding gene	gene with protein product		126141	"""dipeptidylpeptidase VI"", ""dipeptidylpeptidase 6"""			1729689	Standard	XM_006715871		Approved	DPPX	uc003wlk.3	P42658	OTTHUMG00000151511	ENST00000377770.3:c.2546T>C	7.37:g.154684138T>C	ENSP00000367001:p.Ile849Thr	Somatic		Capture	Illumina HiSeq	Phase_I	154315071		Missense_Mutation	SNP	ENST00000377770.3	37		.	.	.	.	.	.	.	.	.	.	T	6.207	0.406277	0.11754	.	.	ENSG00000130226	ENST00000404039;ENST00000377770;ENST00000332007;ENST00000427557	T;T;T;T	0.29397	1.57;1.57;1.57;1.57	4.66	4.66	0.58398	Peptidase S9, prolyl oligopeptidase, catalytic domain (1);	0.559774	0.19698	N	0.108106	T	0.22003	0.0530	N	0.25647	0.755	0.09310	N	1	B;B;B;B	0.16603	0.011;0.004;0.018;0.005	B;B;B;B	0.25759	0.063;0.027;0.045;0.045	T	0.15263	-1.0443	10	0.27785	T	0.31	-3.9013	10.0964	0.42478	0.1499:0.0:0.0:0.8501	.	742;787;849;785	E9PDL2;P42658-2;P42658;E9PF59	.;.;DPP6_HUMAN;.	T	785;849;787;742	ENSP00000385578:I785T;ENSP00000367001:I849T;ENSP00000328226:I787T;ENSP00000397303:I742T	ENSP00000328226:I787T	I	+	2	0	DPP6	154315071	0.960000	0.32886	0.548000	0.28192	0.853000	0.48598	3.391000	0.52530	1.745000	0.51790	0.533000	0.62120	ATC		DPP6-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322932.1	NM_130797	
NCOA6	23054	hgsc.bcm.edu	37	20	33328653	33328653	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr20:33328653A>G	ENST00000374796.2	-	12	7977	c.5407T>C	c.(5407-5409)Tcc>Ccc	p.S1803P	NCOA6_ENST00000359003.2_Missense_Mutation_p.S1803P			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	1803	EP300/CRSP3-binding region.				brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						TTGCCAGAGGACCCTGGACTA	0.488																																																	0			20											79.0	78.0	78.0					20																	33328653		2203	4300	6503	32792314	SO:0001583	missense	23054			AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"""nuclear receptor coactivator RAP250"", ""activating signal cointegrator-2"", ""peroxisome proliferator-activated receptor interacting protein"""	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.5407T>C	20.37:g.33328653A>G	ENSP00000363929:p.Ser1803Pro	Somatic		Capture	Illumina HiSeq	Phase_I	32792314	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Missense_Mutation	SNP	ENST00000374796.2	37	CCDS13241.1	.	.	.	.	.	.	.	.	.	.	A	16.76	3.211721	0.58452	.	.	ENSG00000198646	ENST00000374796;ENST00000359003	T;T	0.25085	1.82;1.82	5.65	5.65	0.86999	.	0.280434	0.31531	N	0.007485	T	0.14657	0.0354	N	0.12182	0.205	0.31858	N	0.621315	P	0.44090	0.826	B	0.41860	0.368	T	0.08146	-1.0736	10	0.25751	T	0.34	-7.4797	9.077	0.36527	0.8369:0.0:0.0:0.1631	.	1803	Q14686	NCOA6_HUMAN	P	1803	ENSP00000363929:S1803P;ENSP00000351894:S1803P	ENSP00000351894:S1803P	S	-	1	0	NCOA6	32792314	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	3.196000	0.51020	2.371000	0.80710	0.533000	0.62120	TCC		NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071	
RBM12	10137	hgsc.bcm.edu	37	20	34242050	34242050	+	Nonsense_Mutation	SNP	C	C	A			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr20:34242050C>A	ENST00000374114.3	-	3	1458	c.1195G>T	c.(1195-1197)Gga>Tga	p.G399*	RP1-309K20.6_ENST00000541176.2_Intron|CPNE1_ENST00000397446.1_Intron|CPNE1_ENST00000397443.1_Intron|CPNE1_ENST00000397445.1_Intron|RBM12_ENST00000359646.1_Nonsense_Mutation_p.G399*|RBM12_ENST00000374104.3_Nonsense_Mutation_p.G399*|CPNE1_ENST00000317619.3_Intron|CPNE1_ENST00000397442.1_Intron|CPNE1_ENST00000317677.5_5'Flank|CPNE1_ENST00000352393.4_Intron	NM_001198838.1|NM_001198840.1|NM_006047.5	NP_001185767.1|NP_001185769.1|NP_006038.2	Q9NTZ6	RBM12_HUMAN	RNA binding motif protein 12	399						nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(7)|kidney(1)|large_intestine(3)|lung(14)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36	Lung NSC(9;0.00608)|all_lung(11;0.00918)		BRCA - Breast invasive adenocarcinoma(18;0.00953)			TGAGTTTGTCCAGAAGGTCCC	0.488											OREG0004044	type=REGULATORY REGION|Gene=CPNE1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																																					0			20											137.0	134.0	135.0					20																	34242050		2203	4300	6503	33705464	SO:0001587	stop_gained	10137			AJ289772	CCDS13261.1	20q11.21	2013-02-12			ENSG00000244462	ENSG00000244462		"""RNA binding motif (RRM) containing"""	9898	protein-coding gene	gene with protein product		607179				11435693	Standard	NM_006047		Approved	HRIHFB2091, KIAA0765, SWAN	uc021wcq.1	Q9NTZ6	OTTHUMG00000032350	ENST00000374114.3:c.1195G>T	20.37:g.34242050C>A	ENSP00000363228:p.Gly399*	Somatic	846	Capture	Illumina HiSeq	Phase_I	33705464	B3KRU2|E1P5R6|O94865|Q8N3B1|Q9H196	Nonsense_Mutation	SNP	ENST00000374114.3	37	CCDS13261.1	.	.	.	.	.	.	.	.	.	.	C	35	5.495324	0.96355	.	.	ENSG00000244462	ENST00000374114;ENST00000359646;ENST00000374104;ENST00000349942	.	.	.	4.77	3.83	0.44106	.	0.503823	0.18724	N	0.132929	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-5.8808	13.2267	0.59919	0.0:0.9236:0.0:0.0764	.	.	.	.	X	399;399;399;198	.	ENSP00000339879:G198X	G	-	1	0	RBM12	33705464	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	3.609000	0.54117	1.251000	0.43983	0.549000	0.68633	GGA		RBM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078894.1	NM_006047	
COL9A3	1299	hgsc.bcm.edu	37	20	61461027	61461027	+	Silent	SNP	C	C	T			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr20:61461027C>T	ENST00000343916.3	+	21	1104	c.1101C>T	c.(1099-1101)ggC>ggT	p.G367G		NM_001853.3	NP_001844.3	Q14050	CO9A3_HUMAN	collagen, type IX, alpha 3	367	Triple-helical region 3 (COL3).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female gonad development (GO:0008585)|male gonad development (GO:0008584)	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)			breast(1)|endometrium(3)|large_intestine(1)|lung(18)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	28	Breast(26;5.68e-08)					GAGAGCCAGGCGTCCCTGTGA	0.662																																																	0			20											29.0	37.0	34.0					20																	61461027		2193	4292	6485	60931472	SO:0001819	synonymous_variant	1299			AK075240	CCDS13505.1	20q13.3	2013-01-16			ENSG00000092758	ENSG00000092758		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2219	protein-coding gene	gene with protein product	"""collagen type IX proteoglycan"""	120270				8586434, 1429648	Standard	NM_001853		Approved	IDD, MED, EDM3, FLJ90759, DJ885L7.4.1	uc002ydm.3	Q14050	OTTHUMG00000032938	ENST00000343916.3:c.1101C>T	20.37:g.61461027C>T		Somatic		Capture	Illumina HiSeq	Phase_I	60931472	Q13681|Q9H4G9|Q9UPE2	Silent	SNP	ENST00000343916.3	37	CCDS13505.1																																																																																				COL9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080071.2	NM_001853	
TTC38	55020	hgsc.bcm.edu	37	22	46677512	46677512	+	Missense_Mutation	SNP	C	C	T			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr22:46677512C>T	ENST00000381031.3	+	7	708	c.632C>T	c.(631-633)cCg>cTg	p.P211L	TTC38_ENST00000445282.2_Missense_Mutation_p.P153L	NM_017931.2	NP_060401	Q5R3I4	TTC38_HUMAN	tetratricopeptide repeat domain 38	211						extracellular vesicular exosome (GO:0070062)				endometrium(4)|large_intestine(3)|lung(4)|ovary(1)	12						TCTATTAACCCGACAGACGCA	0.562																																																	0			22											112.0	112.0	112.0					22																	46677512		2000	4182	6182	45056176	SO:0001583	missense	55020				CCDS43030.1	22q13	2013-01-11			ENSG00000075234	ENSG00000075234		"""Tetratricopeptide (TTC) repeat domain containing"""	26082	protein-coding gene	gene with protein product							Standard	NM_017931		Approved	FLJ20699	uc003bhi.3	Q5R3I4	OTTHUMG00000150494	ENST00000381031.3:c.632C>T	22.37:g.46677512C>T	ENSP00000370419:p.Pro211Leu	Somatic		Capture	Illumina HiSeq	Phase_I	45056176	Q8WV27|Q9NWP8	Missense_Mutation	SNP	ENST00000381031.3	37	CCDS43030.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.121353	0.77436	.	.	ENSG00000075234	ENST00000381031;ENST00000445282	T;T	0.78246	0.67;-1.16	5.79	4.72	0.59763	Tetratricopeptide-like helical (1);	0.158344	0.64402	D	0.000020	T	0.81039	0.4740	M	0.68593	2.085	0.53005	D	0.999961	D;D	0.65815	0.995;0.995	P;P	0.55087	0.768;0.768	T	0.80890	-0.1180	10	0.51188	T	0.08	-9.3532	8.7618	0.34678	0.3362:0.5357:0.1281:0.0	.	153;211	E7ES35;Q5R3I4	.;TTC38_HUMAN	L	211;153	ENSP00000370419:P211L;ENSP00000393960:P153L	ENSP00000370419:P211L	P	+	2	0	TTC38	45056176	0.237000	0.23815	0.221000	0.23827	0.301000	0.27625	0.717000	0.25851	2.733000	0.93635	0.655000	0.94253	CCG		TTC38-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000318469.1	NM_017931	
SMARCA4	6597	hgsc.bcm.edu	37	19	11096909	11096909	+	Missense_Mutation	SNP	G	G	A			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr19:11096909G>A	ENST00000429416.3	+	5	681	c.400G>A	c.(400-402)Gtt>Att	p.V134I	SMARCA4_ENST00000450717.3_Missense_Mutation_p.V134I|SMARCA4_ENST00000589677.1_Missense_Mutation_p.V134I|SMARCA4_ENST00000413806.3_Missense_Mutation_p.V134I|SMARCA4_ENST00000358026.2_Missense_Mutation_p.V134I|SMARCA4_ENST00000444061.3_Missense_Mutation_p.V134I|SMARCA4_ENST00000541122.2_Missense_Mutation_p.V134I|SMARCA4_ENST00000344626.4_Missense_Mutation_p.V134I|SMARCA4_ENST00000590574.1_Missense_Mutation_p.V134I	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	134	Necessary for interaction with SS18L1/CREST. {ECO:0000250}.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				CTCTAGTCCAGTTCCAGCCAG	0.632			"""F, N, Mis"""		NSCLC																																			Rec	yes		19	19p13.2	6597	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"""		E	1	Unknown(1)	lung(1)	19											42.0	44.0	43.0					19																	11096909		2203	4300	6503	10957909	SO:0001583	missense	6597			D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"""SNF2-like 4"", ""global transcription activator homologous sequence"", ""sucrose nonfermenting-like 4"", ""mitotic growth and transcription activator"", ""BRM/SWI2-related gene 1"", ""homeotic gene regulator"", ""nuclear protein GRB1"", ""brahma protein-like 1"", ""ATP-dependent helicase SMARCA4"""	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.400G>A	19.37:g.11096909G>A	ENSP00000395654:p.Val134Ile	Somatic		Capture	Illumina HiSeq	Phase_I	10957909	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	37	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	G	6.020	0.372017	0.11409	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	D;D;D;D;D;D;D	0.86627	-2.14;-2.15;-2.14;-2.13;-2.13;-2.13;-2.13	4.44	3.4	0.38934	.	0.000000	0.64402	D	0.000001	D	0.84365	0.5456	N	0.24115	0.695	0.34269	D	0.680781	B;B;B;P;B;B;B	0.44690	0.02;0.02;0.02;0.841;0.02;0.02;0.02	B;B;B;P;B;B;B	0.55824	0.018;0.011;0.011;0.785;0.018;0.018;0.018	D	0.83565	0.0109	10	0.16896	T	0.51	-16.0935	11.369	0.49690	0.09:0.0:0.91:0.0	.	134;134;134;134;134;134;134	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;A7E2E1;P51532	.;.;.;.;.;.;SMCA4_HUMAN	I	134	ENSP00000395654:V134I;ENSP00000350720:V134I;ENSP00000343896:V134I;ENSP00000445036:V134I;ENSP00000392837:V134I;ENSP00000397783:V134I;ENSP00000414727:V134I	ENSP00000343896:V134I	V	+	1	0	SMARCA4	10957909	0.995000	0.38212	0.963000	0.40424	0.002000	0.02628	2.282000	0.43461	1.100000	0.41517	-0.373000	0.07131	GTT		SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072	
ZNF208	7757	hgsc.bcm.edu	37	19	22155167	22155167	+	Missense_Mutation	SNP	T	T	A			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr19:22155167T>A	ENST00000397126.4	-	4	2817	c.2669A>T	c.(2668-2670)aAa>aTa	p.K890I	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	890					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				TTCTTCACATTTGTAGGGTTT	0.388																																																	0			19											44.0	47.0	46.0					19																	22155167		2074	4229	6303	21947007	SO:0001583	missense	7757			BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"""Zinc fingers, C2H2-type"", ""-"""	12999	protein-coding gene	gene with protein product	"""zinc finger protein 95"""	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.2669A>T	19.37:g.22155167T>A	ENSP00000380315:p.Lys890Ile	Somatic		Capture	Illumina HiSeq	Phase_I	21947007		Missense_Mutation	SNP	ENST00000397126.4	37	CCDS54240.1	.	.	.	.	.	.	.	.	.	.	T	11.79	1.744421	0.30865	.	.	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.20881	2.04	2.58	-1.91	0.07641	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.35451	0.0932	.	.	.	0.09310	N	1	D	0.64830	0.994	D	0.91635	0.999	T	0.25882	-1.0119	8	0.62326	D	0.03	.	2.7988	0.05409	0.1885:0.2494:0.0:0.5621	.	790	O43345	ZN208_HUMAN	I	890;790	ENSP00000380315:K890I	ENSP00000380315:K890I	K	-	2	0	ZNF208	21947007	0.000000	0.05858	0.000000	0.03702	0.094000	0.18550	-1.260000	0.02858	-1.490000	0.01842	-0.804000	0.03201	AAA		ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153	
ZNF257	113835	hgsc.bcm.edu	37	19	22271739	22271739	+	Missense_Mutation	SNP	G	G	C			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr19:22271739G>C	ENST00000594947.1	+	4	1331	c.1187G>C	c.(1186-1188)aGa>aCa	p.R396T		NM_033468.2	NP_258429.2	Q9Y2Q1	ZN257_HUMAN	zinc finger protein 257	396					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(2)|lung(4)	6		all_lung(12;0.0961)|Lung NSC(12;0.103)				ATTCATACTAGAGAGAAGGCC	0.363																																																	0			19											43.0	49.0	47.0					19																	22271739		2103	4244	6347	22063579	SO:0001583	missense	113835			AF070651	CCDS46030.1	19p12	2014-02-14			ENSG00000197134	ENSG00000197134		"""Zinc fingers, C2H2-type"", ""-"""	13498	protein-coding gene	gene with protein product		606957				10585455	Standard	NM_033468		Approved	BMZF-4	uc010ecx.3	Q9Y2Q1	OTTHUMG00000182927	ENST00000594947.1:c.1187G>C	19.37:g.22271739G>C	ENSP00000470209:p.Arg396Thr	Somatic		Capture	Illumina HiSeq	Phase_I	22063579	B3KPS4|E9PG34|Q8NE34	Missense_Mutation	SNP	ENST00000594947.1	37	CCDS46030.1	.	.	.	.	.	.	.	.	.	.	G	4.470	0.087172	0.08583	.	.	ENSG00000197134	ENST00000435820;ENST00000397123	.	.	.	1.11	1.11	0.20524	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.36386	0.0965	L	0.37750	1.13	0.24261	N	0.995283	B	0.13594	0.008	B	0.08055	0.003	T	0.36212	-0.9757	8	0.87932	D	0	.	9.0461	0.36347	0.0:0.0:1.0:0.0	.	396	Q9Y2Q1	ZN257_HUMAN	T	396;368	.	ENSP00000380312:R368T	R	+	2	0	ZNF257	22063579	0.023000	0.18921	0.288000	0.24862	0.339000	0.28857	2.047000	0.41269	0.518000	0.28383	0.313000	0.20887	AGA		ZNF257-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464382.1		
ZNF461	92283	hgsc.bcm.edu	37	19	37129789	37129789	+	Silent	SNP	T	T	C			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr19:37129789T>C	ENST00000588268.1	-	6	1685	c.1458A>G	c.(1456-1458)caA>caG	p.Q486Q	ZNF461_ENST00000360357.4_Silent_p.Q463Q|ZNF461_ENST00000540605.2_5'UTR	NM_153257.2	NP_694989.2	Q8TAF7	ZN461_HUMAN	zinc finger protein 461	486					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)			endometrium(4)|kidney(1)|large_intestine(4)|lung(17)|prostate(1)|urinary_tract(2)	29	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			TTCTTTGATGTTGAATAAGGT	0.388																																																	0			19											70.0	74.0	73.0					19																	37129789		2201	4299	6500	41821629	SO:0001819	synonymous_variant	92283			BX649031	CCDS54257.1, CCDS74348.1	19q13.13	2013-01-08				ENSG00000197808		"""Zinc fingers, C2H2-type"", ""-"""	21629	protein-coding gene	gene with protein product		608640				11579202, 15004467	Standard	XM_005259402		Approved	GIOT-1, MGC33911	uc002oem.3	Q8TAF7		ENST00000588268.1:c.1458A>G	19.37:g.37129789T>C		Somatic		Capture	Illumina HiSeq	Phase_I	41821629	A8K9W9|Q6VSF7|Q9ULZ8	Silent	SNP	ENST00000588268.1	37	CCDS54257.1																																																																																				ZNF461-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453202.1	NM_153257	
SUPT5H	6829	hgsc.bcm.edu	37	19	39965265	39965265	+	Silent	SNP	C	C	T			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr19:39965265C>T	ENST00000599117.1	+	29	3298	c.2931C>T	c.(2929-2931)agC>agT	p.S977S	SUPT5H_ENST00000432763.2_Silent_p.S977S|SUPT5H_ENST00000359191.6_Silent_p.S973S|SUPT5H_ENST00000402194.2_Silent_p.S973S|SUPT5H_ENST00000598725.1_Silent_p.S977S			O00267	SPT5H_HUMAN	suppressor of Ty 5 homolog (S. cerevisiae)	977					7-methylguanosine mRNA capping (GO:0006370)|cell cycle (GO:0007049)|chromatin remodeling (GO:0006338)|DNA-templated transcription, elongation (GO:0006354)|gene expression (GO:0010467)|negative regulation of DNA-templated transcription, elongation (GO:0032785)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of macroautophagy (GO:0016239)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|response to organic substance (GO:0010033)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	DSIF complex (GO:0032044)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)			breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(13)|lung(12)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	51	all_cancers(60;6.69e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;1.57e-06)|Ovarian(47;0.159)		Epithelial(26;3.9e-26)|all cancers(26;1.35e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			AGAACTCCAGCGACTGGGTAA	0.607																																																	0			19											74.0	61.0	65.0					19																	39965265		2203	4300	6503	44657105	SO:0001819	synonymous_variant	6829			U56402	CCDS12536.1, CCDS46072.1	19q13	2008-07-22	2001-11-28			ENSG00000196235			11469	protein-coding gene	gene with protein product		602102	"""suppressor of Ty (S.cerevisiae) 5 homolog"""			8975720	Standard	NM_003169		Approved	SPT5H, SPT5, FLJ34157	uc002olp.4	O00267		ENST00000599117.1:c.2931C>T	19.37:g.39965265C>T		Somatic		Capture	Illumina HiSeq	Phase_I	44657105	O43279|Q59G52|Q99639	Silent	SNP	ENST00000599117.1	37	CCDS12536.1																																																																																				SUPT5H-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464918.1	NM_003169	
ZNF347	84671	hgsc.bcm.edu	37	19	53644067	53644067	+	Missense_Mutation	SNP	G	G	A	rs138912076	byFrequency	TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr19:53644067G>A	ENST00000334197.7	-	5	2082	c.2014C>T	c.(2014-2016)Cgg>Tgg	p.R672W	ZNF347_ENST00000601469.2_Missense_Mutation_p.R673W|ZNF347_ENST00000601804.1_Intron|ZNF347_ENST00000452676.2_Missense_Mutation_p.R673W	NM_032584.2	NP_115973.2	Q96SE7	ZN347_HUMAN	zinc finger protein 347	672					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|prostate(3)|skin(1)	23				GBM - Glioblastoma multiforme(134;0.0179)		TGAACTCTCCGATGTCTTGCA	0.423																																					Melanoma(64;205 1597 17324 45721)												0			19											164.0	148.0	154.0					19																	53644067		2203	4300	6503	58335879	SO:0001583	missense	84671			AY029765	CCDS33097.1, CCDS54314.1	19q13.3	2013-01-08				ENSG00000197937		"""Zinc fingers, C2H2-type"", ""-"""	16447	protein-coding gene	gene with protein product							Standard	NM_032584		Approved	ZNF1111	uc010eql.2	Q96SE7		ENST00000334197.7:c.2014C>T	19.37:g.53644067G>A	ENSP00000334146:p.Arg672Trp	Somatic		Capture	Illumina HiSeq	Phase_I	58335879	B3KU77|B9EG59|G5E9N4|Q8TCN1	Missense_Mutation	SNP	ENST00000334197.7	37	CCDS33097.1	.	.	.	.	.	.	.	.	.	.	G	9.937	1.216547	0.22373	.	.	ENSG00000197937	ENST00000334197;ENST00000452676	T;T	0.07688	3.17;3.17	2.94	0.565	0.17309	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.19644	0.0472	M	0.63208	1.945	0.22811	N	0.998705	D;B	0.76494	0.999;0.009	P;B	0.59948	0.866;0.008	T	0.07868	-1.0750	9	0.87932	D	0	.	9.9088	0.41392	0.0:0.0:0.6326:0.3674	.	673;672	G5E9N4;Q96SE7	.;ZN347_HUMAN	W	672;673	ENSP00000334146:R672W;ENSP00000405218:R673W	ENSP00000334146:R672W	R	-	1	2	ZNF347	58335879	0.000000	0.05858	0.002000	0.10522	0.007000	0.05969	-2.901000	0.00704	0.087000	0.17167	0.655000	0.94253	CGG		ZNF347-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464170.1	NM_032584	
NLRP12	91662	hgsc.bcm.edu	37	19	54301646	54301646	+	Silent	SNP	G	G	A			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr19:54301646G>A	ENST00000324134.6	-	8	2946	c.2778C>T	c.(2776-2778)ggC>ggT	p.G926G	NLRP12_ENST00000391773.1_Silent_p.G927G|NLRP12_ENST00000535162.1_Silent_p.G926G|NLRP12_ENST00000391775.3_Intron|NLRP12_ENST00000345770.5_Silent_p.G927G|NLRP12_ENST00000391772.1_Intron|NLRP12_ENST00000354278.3_Intron|NLRP12_ENST00000351894.4_Intron	NM_001277126.1|NM_144687.2	NP_001264055.1|NP_653288.1	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12	926					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to cytokine stimulus (GO:0071345)|dendritic cell migration (GO:0036336)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 secretion (GO:0050711)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of signal transduction (GO:0009968)|negative regulation of Toll signaling pathway (GO:0045751)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of MHC class I biosynthetic process (GO:0045345)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of interleukin-18 biosynthetic process (GO:0045381)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)			NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(36)|ovary(5)|pancreas(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	80	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)		AGGCGGCAGAGCCCAGCCGGC	0.622																																																	0			19											36.0	35.0	35.0					19																	54301646		2203	4300	6503	58993458	SO:0001819	synonymous_variant	91662			AY095146	CCDS12864.1, CCDS62784.1, CCDS62785.1	19q13.42	2014-09-17	2006-12-08	2006-12-08	ENSG00000142405	ENSG00000142405		"""Nucleotide-binding domain and leucine rich repeat containing"""	22938	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 12"""	609648	"""NACHT, leucine rich repeat and PYD containing 12"""	NALP12		12563287, 12019269	Standard	NM_001277129		Approved	RNO2, PYPAF7, Monarch1, PAN6, CLR19.3	uc002qcj.5	P59046	OTTHUMG00000060776	ENST00000324134.6:c.2778C>T	19.37:g.54301646G>A		Somatic		Capture	Illumina HiSeq	Phase_I	58993458	A8MTQ2|B3KTE7|Q8NEU4|Q9BY26	Silent	SNP	ENST00000324134.6	37	CCDS12864.1																																																																																				NLRP12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000134340.1	NM_144687	
LENG8	114823	hgsc.bcm.edu	37	19	54967586	54967586	+	Missense_Mutation	SNP	C	C	T			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr19:54967586C>T	ENST00000326764.5	+	10	1866	c.1387C>T	c.(1387-1389)Cgg>Tgg	p.R463W	LENG8_ENST00000376514.2_Intron	NM_052925.2	NP_443157.1	Q96PV6	LENG8_HUMAN	leukocyte receptor cluster (LRC) member 8	426										breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.139)		CCCTAAGGGCCGGGGCGGTCG	0.667																																																	0			19											25.0	31.0	29.0					19																	54967586		2201	4295	6496	59659398	SO:0001583	missense	114823			AF211975	CCDS12894.1	19q13.4	2008-02-05			ENSG00000167615	ENSG00000167615			15500	protein-coding gene	gene with protein product						10941842	Standard	XM_005278248		Approved	KIAA1932, MGC40108, pp13842	uc002qfw.2	Q96PV6	OTTHUMG00000065548	ENST00000326764.5:c.1387C>T	19.37:g.54967586C>T	ENSP00000318374:p.Arg463Trp	Somatic		Capture	Illumina HiSeq	Phase_I	59659398	B0VJY9|Q8IZ27|Q8NCX6	Missense_Mutation	SNP	ENST00000326764.5	37	CCDS12894.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.592606	0.86953	.	.	ENSG00000167615	ENST00000326764;ENST00000301196;ENST00000376526;ENST00000431846	T;T;T	0.34859	1.38;1.35;1.34	4.52	4.52	0.55395	.	0.247523	0.33382	N	0.004976	T	0.45975	0.1369	L	0.27053	0.805	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.67548	0.952;0.952	T	0.49082	-0.8976	10	0.72032	D	0.01	-8.8628	15.6069	0.76679	0.0:1.0:0.0:0.0	.	463;426	Q96PV6-2;F8W9Q9	.;.	W	463;426;426;463	ENSP00000318374:R463W;ENSP00000365709:R426W;ENSP00000388053:R463W	ENSP00000301196:R426W	R	+	1	2	LENG8	59659398	1.000000	0.71417	0.997000	0.53966	0.905000	0.53344	4.289000	0.59013	2.466000	0.83321	0.555000	0.69702	CGG		LENG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140523.2	NM_052925	
BRSK1	84446	hgsc.bcm.edu	37	19	55815067	55815067	+	Silent	SNP	C	C	T			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr19:55815067C>T	ENST00000309383.1	+	12	1436	c.1159C>T	c.(1159-1161)Ctg>Ttg	p.L387L	BRSK1_ENST00000590333.1_Silent_p.L403L|BRSK1_ENST00000326848.7_Silent_p.L82L	NM_032430.1	NP_115806.1	Q8TDC3	BRSK1_HUMAN	BR serine/threonine kinase 1	387					axonogenesis (GO:0007409)|cellular response to DNA damage stimulus (GO:0006974)|centrosome duplication (GO:0051298)|establishment of cell polarity (GO:0030010)|G2 DNA damage checkpoint (GO:0031572)|neuron differentiation (GO:0030182)|neurotransmitter secretion (GO:0007269)|protein phosphorylation (GO:0006468)|response to UV (GO:0009411)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|gamma-tubulin binding (GO:0043015)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(15)|ovary(2)|prostate(2)|skin(6)|stomach(1)	48		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0474)		TTCTCCCATGCTGAGCCGTCA	0.607																																																	0			19											62.0	72.0	69.0					19																	55815067		2203	4300	6503	60506879	SO:0001819	synonymous_variant	84446			AB058714	CCDS12921.1	19q13.4	2008-02-05				ENSG00000160469			18994	protein-coding gene	gene with protein product		609235				14976552	Standard	NM_032430		Approved	KIAA1811	uc002qkg.3	Q8TDC3		ENST00000309383.1:c.1159C>T	19.37:g.55815067C>T		Somatic		Capture	Illumina HiSeq	Phase_I	60506879	F1DG44|Q5J5B5|Q8NDD0|Q8NDR4|Q8TDC2|Q96AV4|Q96JL4	Silent	SNP	ENST00000309383.1	37	CCDS12921.1																																																																																				BRSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452787.1	NM_032430	
ZNF628	89887	hgsc.bcm.edu	37	19	55994762	55994762	+	Silent	SNP	G	G	A			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr19:55994762G>A	ENST00000598519.1	+	3	2755	c.2202G>A	c.(2200-2202)ccG>ccA	p.P734P	NAT14_ENST00000587400.1_5'Flank|NAT14_ENST00000591590.1_5'Flank|ZNF628_ENST00000391718.2_Silent_p.P730P|NAT14_ENST00000205194.4_5'Flank			Q5EBL2	ZN628_HUMAN	zinc finger protein 628	734	Pro-rich.				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)			endometrium(4)|kidney(1)|lung(2)	7	Breast(117;0.155)		BRCA - Breast invasive adenocarcinoma(297;0.18)|LUSC - Lung squamous cell carcinoma(43;0.193)	GBM - Glioblastoma multiforme(193;0.0531)		CTACACCTCCGCCCCCTCCCG	0.711																																																	0			19											8.0	7.0	7.0					19																	55994762		2071	4125	6196	60686574	SO:0001819	synonymous_variant	89887			AF367249	CCDS33116.3	19q13.43	2013-01-08			ENSG00000197483	ENSG00000197483		"""Zinc fingers, C2H2-type"""	28054	protein-coding gene	gene with protein product	"""Zinc finger expressed in Embryonal cells and Certain adult organs"""	610671					Standard	NM_033113		Approved	ZEC, Zfp628	uc002qld.3	Q5EBL2	OTTHUMG00000150396	ENST00000598519.1:c.2202G>A	19.37:g.55994762G>A		Somatic		Capture	Illumina HiSeq	Phase_I	60686574	Q86X34	Silent	SNP	ENST00000598519.1	37	CCDS33116.3																																																																																				ZNF628-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317934.2	XM_058964	
NLRP13	126204	hgsc.bcm.edu	37	19	56407363	56407363	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr19:56407363A>G	ENST00000342929.3	-	11	3079	c.3080T>C	c.(3079-3081)aTg>aCg	p.M1027T	NLRP13_ENST00000588751.1_Missense_Mutation_p.M1027T	NM_176810.2	NP_789780.2	Q86W25	NAL13_HUMAN	NLR family, pyrin domain containing 13	1027							ATP binding (GO:0005524)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(58)|ovary(4)|pancreas(2)|prostate(2)|skin(13)|stomach(2)|urinary_tract(1)	109		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)		GBM - Glioblastoma multiforme(193;0.0642)		CTTACATAGCATCTTGACACC	0.473																																																	0			19											196.0	183.0	188.0					19																	56407363		2203	4300	6503	61099175	SO:0001583	missense	126204			AY154468	CCDS33119.1	19q13.43	2008-02-05	2006-12-08	2006-12-08	ENSG00000173572	ENSG00000173572		"""Nucleotide-binding domain and leucine rich repeat containing"""	22937	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 13"""	609660	"""NACHT, leucine rich repeat and PYD containing 13"""	NALP13		12563287	Standard	NM_176810		Approved	NOD14, PAN13, CLR19.7	uc010ygg.2	Q86W25	OTTHUMG00000167839	ENST00000342929.3:c.3080T>C	19.37:g.56407363A>G	ENSP00000343891:p.Met1027Thr	Somatic		Capture	Illumina HiSeq	Phase_I	61099175	Q7RTR5	Missense_Mutation	SNP	ENST00000342929.3	37	CCDS33119.1	.	.	.	.	.	.	.	.	.	.	A	0.007	-1.990810	0.00439	.	.	ENSG00000173572	ENST00000342929	T	0.51817	0.69	2.85	-5.69	0.02428	.	.	.	.	.	T	0.25938	0.0632	N	0.16833	0.445	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.13415	-1.0510	9	0.26408	T	0.33	.	9.1146	0.36750	0.7081:0.1102:0.1817:0.0	.	1027	Q86W25	NAL13_HUMAN	T	1027	ENSP00000343891:M1027T	ENSP00000343891:M1027T	M	-	2	0	NLRP13	61099175	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.581000	0.05820	-3.136000	0.00234	-1.317000	0.01298	ATG		NLRP13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396560.1	NM_176810	
DLC1	10395	hgsc.bcm.edu	37	8	12957877	12957877	+	Missense_Mutation	SNP	C	C	T			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr8:12957877C>T	ENST00000276297.4	-	9	2378	c.1969G>A	c.(1969-1971)Gaa>Aaa	p.E657K	DLC1_ENST00000520226.1_Missense_Mutation_p.E146K|DLC1_ENST00000358919.2_Missense_Mutation_p.E220K|DLC1_ENST00000512044.2_Missense_Mutation_p.E254K	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	657					actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						GCAGTTTTTTCGTGGCCTTTC	0.552																																																	0			8											118.0	109.0	112.0					8																	12957877		2203	4300	6503	13002248	SO:0001583	missense	10395			AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"""Rho GTPase activating proteins"", ""StAR-related lipid transfer (START) domain containing"""	2897	protein-coding gene	gene with protein product	"""StAR-related lipid transfer (START) domain containing 12"""	604258	"""deleted in liver cancer 1"""			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.1969G>A	8.37:g.12957877C>T	ENSP00000276297:p.Glu657Lys	Somatic		Capture	Illumina HiSeq	Phase_I	13002248	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Missense_Mutation	SNP	ENST00000276297.4	37	CCDS5989.1	.	.	.	.	.	.	.	.	.	.	C	10.66	1.412427	0.25465	.	.	ENSG00000164741	ENST00000276297;ENST00000358919;ENST00000512044;ENST00000520226	T;T;T;T	0.07216	3.43;3.25;3.24;3.21	4.74	4.74	0.60224	.	0.326661	0.35179	N	0.003389	T	0.10035	0.0246	M	0.69358	2.11	0.80722	D	1	P;B;P	0.51933	0.949;0.188;0.68	B;B;B	0.35039	0.194;0.042;0.119	T	0.05209	-1.0899	10	0.72032	D	0.01	.	13.988	0.64348	0.0:0.8485:0.1515:0.0	.	657;254;220	Q96QB1;E9PDZ8;Q96QB1-1	RHG07_HUMAN;.;.	K	657;220;254;146	ENSP00000276297:E657K;ENSP00000351797:E220K;ENSP00000422595:E254K;ENSP00000428028:E146K	ENSP00000276297:E657K	E	-	1	0	DLC1	13002248	0.989000	0.36119	0.985000	0.45067	0.128000	0.20619	2.135000	0.42112	2.624000	0.88883	0.655000	0.94253	GAA		DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094	
DLC1	10395	hgsc.bcm.edu	37	8	13259111	13259111	+	Silent	SNP	T	T	C			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr8:13259111T>C	ENST00000276297.4	-	3	1450	c.1041A>G	c.(1039-1041)cgA>cgG	p.R347R	DLC1_ENST00000511869.1_Silent_p.R347R|DLC1_ENST00000316609.5_Silent_p.R347R	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	347					actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						GCGCCCTATCTCGATCTTCTC	0.438																																																	0			8											132.0	118.0	123.0					8																	13259111		2203	4300	6503	13303482	SO:0001819	synonymous_variant	10395			AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"""Rho GTPase activating proteins"", ""StAR-related lipid transfer (START) domain containing"""	2897	protein-coding gene	gene with protein product	"""StAR-related lipid transfer (START) domain containing 12"""	604258	"""deleted in liver cancer 1"""			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.1041A>G	8.37:g.13259111T>C		Somatic		Capture	Illumina HiSeq	Phase_I	13303482	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Silent	SNP	ENST00000276297.4	37	CCDS5989.1																																																																																				DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094	
CYP7B1	9420	hgsc.bcm.edu	37	8	65527669	65527669	+	Missense_Mutation	SNP	C	C	T	rs59035258	byFrequency	TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr8:65527669C>T	ENST00000310193.3	-	4	1144	c.971G>A	c.(970-972)cGt>cAt	p.R324H	CYP7B1_ENST00000523954.1_5'UTR	NM_004820.3	NP_004811.1	O75881	CP7B1_HUMAN	cytochrome P450, family 7, subfamily B, polypeptide 1	324				R -> H (in Ref. 1; AAC95426). {ECO:0000305}.	bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cell death (GO:0008219)|cholesterol metabolic process (GO:0008203)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|positive regulation of epithelial cell proliferation (GO:0050679)|prostate gland epithelium morphogenesis (GO:0060740)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	25-hydroxycholesterol 7alpha-hydroxylase activity (GO:0033783)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxysterol 7-alpha-hydroxylase activity (GO:0008396)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(11)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28		all_cancers(86;0.217)|Lung NSC(129;0.0521)|all_lung(136;0.0906)|all_epithelial(80;0.215)				CTGCAGCAAACGGTCAATTTC	0.463													C|||	89	0.0177716	0.0015	0.0115	5008	,	,		18048	0.001		0.0427	False		,,,				2504	0.0358																0			8						C	HIS/ARG	40,4366	43.8+/-77.6	0,40,2163	115.0	107.0	110.0		971	-4.4	0.8	8	dbSNP_129	110	344,8256	118.3+/-177.8	8,328,3964	yes	missense	CYP7B1	NM_004820.3	29	8,368,6127	TT,TC,CC		4.0,0.9079,2.9525	benign	324/507	65527669	384,12622	2203	4300	6503	65690223	SO:0001583	missense	9420			AF029403	CCDS6180.1	8q21.3	2008-07-04	2003-01-14		ENSG00000172817	ENSG00000172817		"""Cytochrome P450s"""	2652	protein-coding gene	gene with protein product		603711	"""cytochrome P450, subfamily VIIB (oxysterol 7 alpha-hydroxylase), polypeptide 1"", ""spastic paraplegia 5A (autosomal recessive)"""	SPG5A		9802883, 18252231	Standard	NM_004820		Approved		uc003xvj.2	O75881	OTTHUMG00000164387	ENST00000310193.3:c.971G>A	8.37:g.65527669C>T	ENSP00000310721:p.Arg324His	Somatic		Capture	Illumina HiSeq	Phase_I	65690223	B2RN07|Q9UNF5	Missense_Mutation	SNP	ENST00000310193.3	37	CCDS6180.1	42	0.019230769230769232	0	0.0	6	0.016574585635359115	0	0.0	36	0.047493403693931395	C	2.435	-0.329922	0.05314	0.009079	0.04	ENSG00000172817	ENST00000310193	T	0.69926	-0.44	5.93	-4.44	0.03557	.	0.617158	0.19131	N	0.121927	T	0.07593	0.0191	N	0.04018	-0.295	0.22112	N	0.999356	B	0.13145	0.007	B	0.11329	0.006	T	0.09100	-1.0690	10	0.11182	T	0.66	-19.8849	14.5279	0.67902	0.0:0.2062:0.0:0.7938	rs59035258;rs61729537	324	O75881	CP7B1_HUMAN	H	324	ENSP00000310721:R324H	ENSP00000310721:R324H	R	-	2	0	CYP7B1	65690223	1.000000	0.71417	0.763000	0.31416	0.995000	0.86356	0.783000	0.26802	-1.137000	0.02888	-0.140000	0.14226	CGT		CYP7B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378550.1		
TRIM55	84675	hgsc.bcm.edu	37	8	67062025	67062025	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr8:67062025A>G	ENST00000315962.4	+	5	1122	c.749A>G	c.(748-750)aAg>aGg	p.K250R	TRIM55_ENST00000353317.5_Missense_Mutation_p.K250R|TRIM55_ENST00000350034.4_Intron|TRIM55_ENST00000276573.7_Missense_Mutation_p.K250R	NM_184085.1	NP_908973.1	Q9BYV6	TRI55_HUMAN	tripartite motif containing 55	250					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(2)	39		Lung NSC(129;0.138)|all_lung(136;0.221)	Epithelial(68;0.0136)|all cancers(69;0.0582)|BRCA - Breast invasive adenocarcinoma(89;0.0628)|OV - Ovarian serous cystadenocarcinoma(28;0.0904)			CTGATCAAAAAGTATTCTGAT	0.428																																																	0			8											133.0	131.0	131.0					8																	67062025		2203	4300	6503	67224579	SO:0001583	missense	84675			AJ291712	CCDS6184.1, CCDS6185.1, CCDS6186.1, CCDS6187.1	8q13.1	2013-01-09	2011-01-25	2004-11-17	ENSG00000147573	ENSG00000147573		"""RING-type (C3HC4) zinc fingers"", ""Tripartite motif containing / Tripartite motif containing"""	14215	protein-coding gene	gene with protein product		606469	"""ring finger protein 29"", ""tripartite motif-containing 55"""	RNF29		11243782	Standard	NM_033058		Approved	MURF-2	uc003xvv.3	Q9BYV6	OTTHUMG00000164473	ENST00000315962.4:c.749A>G	8.37:g.67062025A>G	ENSP00000323913:p.Lys250Arg	Somatic		Capture	Illumina HiSeq	Phase_I	67224579	B3KRC0|B3KRJ3|Q53XX3|Q8IUD9|Q8IUE4|Q96DV2|Q96DV3|Q9BYV5	Missense_Mutation	SNP	ENST00000315962.4	37	CCDS6184.1	.	.	.	.	.	.	.	.	.	.	A	14.31	2.496600	0.44352	.	.	ENSG00000147573	ENST00000315962;ENST00000353317;ENST00000276573	T;T;T	0.31247	1.5;1.55;1.5	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.27832	0.0685	L	0.38649	1.16	0.80722	D	1	B;B;B	0.21520	0.012;0.057;0.02	B;B;B	0.24006	0.018;0.05;0.032	T	0.03403	-1.1040	10	0.31617	T	0.26	.	15.898	0.79350	1.0:0.0:0.0:0.0	.	250;250;250	Q9BYV6-2;Q9BYV6;Q9BYV6-3	.;TRI55_HUMAN;.	R	250	ENSP00000323913:K250R;ENSP00000297348:K250R;ENSP00000276573:K250R	ENSP00000276573:K250R	K	+	2	0	TRIM55	67224579	1.000000	0.71417	1.000000	0.80357	0.790000	0.44656	6.248000	0.72418	2.150000	0.67090	0.528000	0.53228	AAG		TRIM55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378921.1	NM_184085	
PEX2	5828	hgsc.bcm.edu	37	8	77896008	77896008	+	Missense_Mutation	SNP	T	T	C			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr8:77896008T>C	ENST00000419564.2	-	4	871	c.407A>G	c.(406-408)aAg>aGg	p.K136R	PEX2_ENST00000357039.4_Missense_Mutation_p.K136R|PEX2_ENST00000520103.1_Missense_Mutation_p.K136R|PEX2_ENST00000522527.1_Missense_Mutation_p.K136R	NM_001172087.1	NP_001165558.1	P28328	PEX2_HUMAN	peroxisomal biogenesis factor 2	136					bile acid biosynthetic process (GO:0006699)|cholesterol homeostasis (GO:0042632)|fatty acid beta-oxidation (GO:0006635)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|peroxisome organization (GO:0007031)|protein destabilization (GO:0031648)|protein import into peroxisome matrix (GO:0016558)|regulation of cholesterol biosynthetic process (GO:0045540)|very long-chain fatty acid metabolic process (GO:0000038)	Cdc73/Paf1 complex (GO:0016593)|integral component of peroxisomal membrane (GO:0005779)|membrane (GO:0016020)|peroxisomal membrane (GO:0005778)	zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)	14						CACACACTGCTTGACTTTCCC	0.373																																																	0			8											98.0	95.0	96.0					8																	77896008		2203	4300	6503	78058563	SO:0001583	missense	5828			M86852	CCDS6221.1	8q21.11	2010-02-09	2010-01-25	2010-01-25		ENSG00000164751		"""RING-type (C3HC4) zinc fingers"""	9717	protein-coding gene	gene with protein product	"""Zellweger syndrome"", ""peroxin 2"""	170993	"""peroxisomal membrane protein 3 (35kD, Zellweger syndrome)"", ""peroxisomal membrane protein 3, 35kDa"""	PXMP3		1546315, 8858157	Standard	NM_000318		Approved	PMP35, PAF-1, RNF72, ZWS3	uc022awf.1	P28328		ENST00000419564.2:c.407A>G	8.37:g.77896008T>C	ENSP00000400984:p.Lys136Arg	Somatic		Capture	Illumina HiSeq	Phase_I	78058563	Q567S6|Q9BW41	Missense_Mutation	SNP	ENST00000419564.2	37	CCDS6221.1	.	.	.	.	.	.	.	.	.	.	T	8.396	0.840839	0.16891	.	.	ENSG00000164751	ENST00000357039;ENST00000419564;ENST00000520103;ENST00000522527;ENST00000518986	D;D;D;D;D	0.82167	-1.58;-1.58;-1.58;-1.58;-1.58	5.18	4.02	0.46733	Pex, N-terminal (1);	0.115856	0.56097	N	0.000027	T	0.68778	0.3038	N	0.22421	0.69	0.38453	D	0.947001	B	0.02656	0.0	B	0.04013	0.001	T	0.60510	-0.7249	10	0.12103	T	0.63	-16.6691	10.3466	0.43909	0.0:0.08:0.0:0.92	.	136	P28328	PEX2_HUMAN	R	136	ENSP00000349543:K136R;ENSP00000400984:K136R;ENSP00000428590:K136R;ENSP00000428638:K136R;ENSP00000429304:K136R	ENSP00000349543:K136R	K	-	2	0	PEX2	78058563	0.990000	0.36364	0.996000	0.52242	0.953000	0.61014	2.282000	0.43461	0.981000	0.38548	0.456000	0.33151	AAG		PEX2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379122.1	NM_000318	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110457743	110457743	+	Missense_Mutation	SNP	G	G	A			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr8:110457743G>A	ENST00000378402.5	+	38	5749	c.5645G>A	c.(5644-5646)tGc>tAc	p.C1882Y		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	1882	IPT/TIG 11.				immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.C1884Y(1)		NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			GAAGTCTACTGCCGCACTCCC	0.438										HNSCC(38;0.096)																																							1	Substitution - Missense(1)	ovary(1)	8											48.0	48.0	48.0					8																	110457743		1918	4142	6060	110526919	SO:0001583	missense	93035			AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.5645G>A	8.37:g.110457743G>A	ENSP00000367655:p.Cys1882Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	110526919	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	G	15.89	2.967065	0.53507	.	.	ENSG00000205038	ENST00000378402	D	0.83163	-1.69	5.91	5.91	0.95273	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.94476	0.8222	H	0.96633	3.855	0.50632	D	0.999887	D	0.89917	1.0	D	0.97110	1.0	D	0.95736	0.8779	10	0.87932	D	0	.	17.7921	0.88555	0.0:0.0:1.0:0.0	.	1882	Q86WI1	PKHL1_HUMAN	Y	1882	ENSP00000367655:C1882Y	ENSP00000367655:C1882Y	C	+	2	0	PKHD1L1	110526919	1.000000	0.71417	0.523000	0.27875	0.129000	0.20672	7.560000	0.82277	2.802000	0.96397	0.655000	0.94253	TGC		PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
CASP9	842	hgsc.bcm.edu	37	1	15844623	15844623	+	Missense_Mutation	SNP	C	C	T			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr1:15844623C>T	ENST00000333868.5	-	2	494	c.400G>A	c.(400-402)Gga>Aga	p.G134R	CASP9_ENST00000375890.4_Missense_Mutation_p.G51R|CASP9_ENST00000348549.5_Missense_Mutation_p.G134R|CASP9_ENST00000546424.1_Missense_Mutation_p.G134R|CASP9_ENST00000469637.1_5'Flank	NM_001229.3	NP_001220.2	P55211	CASP9_HUMAN	caspase 9, apoptosis-related cysteine peptidase	134					activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|aging (GO:0007568)|apoptotic process (GO:0006915)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell apoptotic process (GO:0034349)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of apoptotic process (GO:0043065)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of apoptotic process (GO:0042981)|regulation of response to DNA damage stimulus (GO:2001020)|response to antibiotic (GO:0046677)|response to cobalt ion (GO:0032025)|response to estradiol (GO:0032355)|response to lipopolysaccharide (GO:0032496)|signal transduction in response to DNA damage (GO:0042770)	apoptosome (GO:0043293)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|enzyme activator activity (GO:0008047)|peptidase activity (GO:0008233)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|stomach(1)	18		Breast(348;0.000207)|all_lung(284;0.000211)|Colorectal(325;0.000259)|Lung NSC(340;0.000269)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;8.49e-07)|COAD - Colon adenocarcinoma(227;4.36e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00013)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00763)|READ - Rectum adenocarcinoma(331;0.0655)		CCAAATCCTCCAGAACCAATG	0.522																																																	0			1											112.0	100.0	104.0					1																	15844623		2203	4300	6503	15717210	SO:0001583	missense	842			U60521	CCDS158.1, CCDS159.1, CCDS159.2, CCDS59995.1	1p36.21	2012-04-17	2005-08-17		ENSG00000132906	ENSG00000132906		"""Caspases"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1511	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 56"""	602234	"""caspase 9, apoptosis-related cysteine protease"""			8663294, 9390557	Standard	NM_001229		Approved	MCH6, ICE-LAP6, APAF-3, PPP1R56	uc001awn.4	P55211	OTTHUMG00000002256	ENST00000333868.5:c.400G>A	1.37:g.15844623C>T	ENSP00000330237:p.Gly134Arg	Somatic		Capture	Illumina HiSeq	Phase_I	15717210	B4E1A3|O95348|Q53Y70|Q5JRU9|Q5UGI1|Q92852|Q9BQ62|Q9UEQ3|Q9UIJ8	Missense_Mutation	SNP	ENST00000333868.5	37	CCDS158.1	.	.	.	.	.	.	.	.	.	.	C	8.144	0.785883	0.16189	.	.	ENSG00000132906	ENST00000546424;ENST00000333868;ENST00000348549;ENST00000375890;ENST00000447522;ENST00000440484	T;T;T;T;T;T	0.10099	4.64;4.67;2.91;4.6;3.93;3.58	4.77	2.88	0.33553	.	1.735820	0.02593	N	0.100170	T	0.11922	0.0290	L	0.50333	1.59	0.09310	N	1	B;P;B	0.44521	0.033;0.837;0.037	B;B;B	0.39876	0.027;0.312;0.067	T	0.25187	-1.0139	10	0.16896	T	0.51	.	6.4847	0.22083	0.0:0.787:0.0:0.213	.	134;134;134	P55211-2;P55211;F8VVS7	.;CASP9_HUMAN;.	R	134;134;134;51;51;134	ENSP00000449584:G134R;ENSP00000330237:G134R;ENSP00000255256:G134R;ENSP00000365051:G51R;ENSP00000396540:G51R;ENSP00000411304:G134R	ENSP00000330237:G134R	G	-	1	0	CASP9	15717210	0.001000	0.12720	0.136000	0.22124	0.093000	0.18481	-0.019000	0.12546	1.365000	0.46057	0.563000	0.77884	GGA		CASP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006438.1	NM_032996	
PADI1	29943	hgsc.bcm.edu	37	1	17556621	17556621	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr1:17556621A>G	ENST00000375471.4	+	9	1063	c.971A>G	c.(970-972)gAc>gGc	p.D324G		NM_013358.2	NP_037490.2	Q9ULC6	PADI1_HUMAN	peptidyl arginine deiminase, type I	324					protein citrullination (GO:0018101)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)	p.D324G(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|skin(1)|stomach(1)|urinary_tract(1)	28		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00054)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00522)|BRCA - Breast invasive adenocarcinoma(304;1.3e-05)|COAD - Colon adenocarcinoma(227;1.31e-05)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(196;0.0069)|READ - Rectum adenocarcinoma(331;0.0681)|Lung(427;0.197)	L-Citrulline(DB00155)	TTCCTGGAGGACATGTCTTAT	0.517																																					Esophageal Squamous(80;414 1257 4580 27746 50832)												1	Substitution - Missense(1)	lung(1)	1											107.0	98.0	101.0					1																	17556621		2203	4300	6503	17429208	SO:0001583	missense	29943			AB033768	CCDS178.1	1p36.13	2008-07-18			ENSG00000142623	ENSG00000142623	3.5.3.15	"""Peptidyl arginine deiminases"""	18367	protein-coding gene	gene with protein product	"""peptidylarginine deiminase type I"", ""protein-arginine deiminase type-1"", ""hPAD-colony 10"""	607934				12416996	Standard	NM_013358		Approved	HPAD10, PDI1, PDI, PAD1	uc001bah.1	Q9ULC6	OTTHUMG00000002294	ENST00000375471.4:c.971A>G	1.37:g.17556621A>G	ENSP00000364620:p.Asp324Gly	Somatic		Capture	Illumina HiSeq	Phase_I	17429208	A1L4K6|Q70SX6	Missense_Mutation	SNP	ENST00000375471.4	37	CCDS178.1	.	.	.	.	.	.	.	.	.	.	A	8.880	0.951330	0.18431	.	.	ENSG00000142623	ENST00000375471	T	0.23950	1.88	4.99	3.8	0.43715	Protein-arginine deiminase, C-terminal (1);	0.545977	0.19466	N	0.113591	T	0.23886	0.0578	L	0.43923	1.385	0.37424	D	0.913756	P	0.36712	0.566	B	0.40702	0.338	T	0.10428	-1.0630	10	0.25106	T	0.35	-30.0529	10.614	0.45439	0.7244:0.2756:0.0:0.0	.	324	Q9ULC6	PADI1_HUMAN	G	324	ENSP00000364620:D324G	ENSP00000364620:D324G	D	+	2	0	PADI1	17429208	0.034000	0.19679	0.995000	0.50966	0.204000	0.24138	0.356000	0.20181	2.009000	0.58944	0.383000	0.25322	GAC		PADI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006621.1	NM_013358	
USP48	84196	hgsc.bcm.edu	37	1	22021622	22021622	+	Silent	SNP	T	T	C			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr1:22021622T>C	ENST00000308271.9	-	23	3468	c.2820A>G	c.(2818-2820)aaA>aaG	p.K940K	USP48_ENST00000374732.3_Intron|USP48_ENST00000529637.1_Silent_p.K952K|USP48_ENST00000400301.1_Intron	NM_032236.5	NP_115612.4	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 48	940	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)	p.K940N(1)		NS(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(14)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)		CACCACGAACTTTTCTATGTC	0.378																																																	1	Substitution - Missense(1)	ovary(1)	1											162.0	154.0	157.0					1																	22021622		2203	4299	6502	21894209	SO:0001819	synonymous_variant	84196			AF502942	CCDS30623.1, CCDS44084.1	1p36.12	2008-02-05	2005-08-08	2004-04-07	ENSG00000090686	ENSG00000090686		"""Ubiquitin-specific peptidases"""	18533	protein-coding gene	gene with protein product			"""ubiquitin specific protease 31"", ""ubiquitin specific protease 48"""	USP31		12838346	Standard	XM_005246009		Approved	FLJ23277, FLJ11328, FLJ20103, FLJ23054, MGC14879	uc001bfb.3	Q86UV5	OTTHUMG00000007798	ENST00000308271.9:c.2820A>G	1.37:g.22021622T>C		Somatic		Capture	Illumina HiSeq	Phase_I	21894209	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Silent	SNP	ENST00000308271.9	37	CCDS30623.1																																																																																				USP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021372.1	NM_032236	
ARID1A	8289	hgsc.bcm.edu	37	1	27057980	27057980	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr1:27057980A>G	ENST00000324856.7	+	3	2059	c.1688A>G	c.(1687-1689)cAg>cGg	p.Q563R	ARID1A_ENST00000374152.2_Missense_Mutation_p.Q180R|ARID1A_ENST00000457599.2_Missense_Mutation_p.Q563R	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	563	Poly-Gln.				androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		TACCAGCAGCAGCAACCTCAG	0.647			"""Mis, N, F, S, D"""		"""clear cell ovarian carcinoma, RCC"""																																			Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	0			1											162.0	165.0	164.0					1																	27057980		2203	4300	6503	26930567	SO:0001583	missense	8289			AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"""-"""	11110	protein-coding gene	gene with protein product		603024	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1"", ""AT rich interactive domain 1A (SWI- like)"""	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.1688A>G	1.37:g.27057980A>G	ENSP00000320485:p.Gln563Arg	Somatic		Capture	Illumina HiSeq	Phase_I	26930567	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Missense_Mutation	SNP	ENST00000324856.7	37	CCDS285.1	.	.	.	.	.	.	.	.	.	.	A	13.88	2.367684	0.42003	.	.	ENSG00000117713	ENST00000324856;ENST00000457599;ENST00000374152	T;T;T	0.02656	4.37;4.21;4.27	5.44	4.31	0.51392	.	0.185795	0.47455	D	0.000221	T	0.02342	0.0072	N	0.24115	0.695	0.80722	D	1	P;P;P	0.42409	0.534;0.779;0.671	B;B;B	0.38500	0.142;0.275;0.142	T	0.64635	-0.6361	10	0.15066	T	0.55	-2.009	11.5642	0.50796	0.8508:0.1492:0.0:0.0	.	563;563;217	O14497;O14497-2;Q4LE49	ARI1A_HUMAN;.;.	R	563;563;180	ENSP00000320485:Q563R;ENSP00000387636:Q563R;ENSP00000363267:Q180R	ENSP00000320485:Q563R	Q	+	2	0	ARID1A	26930567	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	6.450000	0.73477	1.063000	0.40649	0.533000	0.62120	CAG		ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135	
MACF1	23499	hgsc.bcm.edu	37	1	39905073	39905073	+	Silent	SNP	T	T	C			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr1:39905073T>C	ENST00000372915.3	+	71	18132	c.18045T>C	c.(18043-18045)gcT>gcC	p.A6015A	MACF1_ENST00000545844.1_Silent_p.A4057A|MACF1_ENST00000539005.1_Silent_p.A3927A|MACF1_ENST00000317713.7_Silent_p.A4057A|MACF1_ENST00000567887.1_Silent_p.A6153A|MACF1_ENST00000289893.4_Silent_p.A4559A|MACF1_ENST00000564288.1_Silent_p.A6116A|MACF1_ENST00000361689.2_Silent_p.A4057A			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	6015					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			ACATGGCAGCTCTCCTGACCA	0.458																																																	0			1											86.0	80.0	82.0					1																	39905073		2203	4300	6503	39677660	SO:0001819	synonymous_variant	23499			AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"""EF-hand domain containing"""	13664	protein-coding gene	gene with protein product	"""actin cross-linking factor"", ""620 kDa actin binding protein"", ""macrophin 1"", ""trabeculin-alpha"", ""actin cross-linking family protein 7"""	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.18045T>C	1.37:g.39905073T>C		Somatic		Capture	Illumina HiSeq	Phase_I	39677660	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Silent	SNP	ENST00000372915.3	37		.	.	.	.	.	.	.	.	.	.	T	10.95	1.494532	0.26774	.	.	ENSG00000127603	ENST00000372925	.	.	.	5.77	-0.902	0.10537	.	.	.	.	.	T	0.54398	0.1856	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48210	-0.9055	4	.	.	.	.	8.6957	0.34293	0.0:0.6008:0.154:0.2453	.	.	.	.	P	3061	.	.	S	+	1	0	MACF1	39677660	0.460000	0.25776	0.998000	0.56505	0.997000	0.91878	-0.254000	0.08781	-0.108000	0.12066	0.528000	0.53228	TCT		MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044	
FAM212B	55924	hgsc.bcm.edu	37	1	112269921	112269921	+	Missense_Mutation	SNP	C	C	T	rs371956554		TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr1:112269921C>T	ENST00000357260.5	-	2	744	c.563G>A	c.(562-564)cGt>cAt	p.R188H	FAM212B_ENST00000534365.1_Intron|FAM212B_ENST00000444059.2_Missense_Mutation_p.R173H	NM_019099.4	NP_061972.1	Q9NTI7	F212B_HUMAN	family with sequence similarity 212, member B	188										cervix(1)|endometrium(1)	2						TTTGGGTTCACGTGCCCCCCC	0.577																																																	0			1						C	HIS/ARG,HIS/ARG	0,4406		0,0,2203	67.0	66.0	66.0		563,518	1.2	0.0	1		66	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	C1orf183	NM_019099.4,NM_198926.2	29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	188/298,173/283	112269921	1,13005	2203	4300	6503	112071444	SO:0001583	missense	55924			AK055667	CCDS841.1, CCDS44195.1	1p13.2	2011-11-24	2011-11-24	2011-11-24	ENSG00000197852	ENSG00000197852			28045	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 183"""	C1orf183			Standard	NM_019099		Approved	FLJ31105	uc001ebo.2	Q9NTI7	OTTHUMG00000011953	ENST00000357260.5:c.563G>A	1.37:g.112269921C>T	ENSP00000349805:p.Arg188His	Somatic		Capture	Illumina HiSeq	Phase_I	112071444	B3KP38|B4DF94|Q9NTI6	Missense_Mutation	SNP	ENST00000357260.5	37	CCDS841.1	.	.	.	.	.	.	.	.	.	.	C	7.342	0.621032	0.14193	0.0	1.16E-4	ENSG00000197852	ENST00000357260;ENST00000444059	.	.	.	5.3	1.19	0.21007	.	0.898267	0.09763	N	0.759003	T	0.02888	0.0086	N	0.08118	0	0.09310	N	1	P;P	0.43024	0.798;0.798	B;B	0.35550	0.205;0.205	T	0.26292	-1.0107	9	0.38643	T	0.18	-37.0073	1.7452	0.02961	0.1681:0.4877:0.163:0.1812	.	173;188	Q9NTI7-2;Q9NTI7	.;CA183_HUMAN	H	188;173	.	ENSP00000349805:R188H	R	-	2	0	C1orf183	112071444	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-0.255000	0.08769	0.198000	0.20407	0.484000	0.47621	CGT		FAM212B-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000033060.2	NM_019099	
NOTCH2	4853	hgsc.bcm.edu	37	1	120506311	120506311	+	Missense_Mutation	SNP	C	C	A			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr1:120506311C>A	ENST00000256646.2	-	11	2020	c.1801G>T	c.(1801-1803)Ggc>Tgc	p.G601C		NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	601	EGF-like 15; calcium-binding. {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)	p.G601C(1)		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)		CAGATGGCGCCCATGTACCCG	0.527			"""N, F, Mis"""		"""marginal zone lymphoma, DLBCL"""				Alagille Syndrome																															Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	1	Substitution - Missense(1)	central_nervous_system(1)	1											231.0	204.0	213.0					1																	120506311		2203	4300	6503	120307834	SO:0001583	missense	4853	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	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.1801G>T	1.37:g.120506311C>A	ENSP00000256646:p.Gly601Cys	Somatic		Capture	Illumina HiSeq	Phase_I	120307834	Q5T3X7|Q99734|Q9H240	Missense_Mutation	SNP	ENST00000256646.2	37	CCDS908.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.830727	0.91036	.	.	ENSG00000134250	ENST00000256646;ENST00000539617	T	0.34072	1.38	5.73	5.73	0.89815	EGF-like region, conserved site (2);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.38164	U	0.001799	T	0.77370	0.4120	H	0.99764	4.76	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.997;0.997;1.0	D	0.87234	0.2262	10	0.87932	D	0	.	19.248	0.93909	0.0:1.0:0.0:0.0	.	562;601;601	D2WEZ3;Q6IQ50;Q04721	.;.;NOTC2_HUMAN	C	601;562	ENSP00000256646:G601C	ENSP00000256646:G601C	G	-	1	0	NOTCH2	120307834	1.000000	0.71417	1.000000	0.80357	0.741000	0.42261	7.729000	0.84864	2.861000	0.98227	0.655000	0.94253	GGC		NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408	
INSRR	3645	hgsc.bcm.edu	37	1	156815492	156815492	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr1:156815492A>G	ENST00000368195.3	-	10	2489	c.2093T>C	c.(2092-2094)gTt>gCt	p.V698A	NTRK1_ENST00000392302.2_Intron	NM_014215.2	NP_055030.1	P14616	INSRR_HUMAN	insulin receptor-related receptor	698	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton reorganization (GO:0031532)|cellular response to alkaline pH (GO:0071469)|male sex determination (GO:0030238)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(7)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	42	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					CGGGGGCAGAACCTGACCAGG	0.617																																																	0			1											46.0	45.0	45.0					1																	156815492		2203	4300	6503	155082116	SO:0001583	missense	3645			J05046	CCDS1160.1	1q21-q23	2013-02-11			ENSG00000027644	ENSG00000027644		"""Fibronectin type III domain containing"""	6093	protein-coding gene	gene with protein product		147671				2768234, 2249481	Standard	NM_014215		Approved	IRR	uc010pht.2	P14616	OTTHUMG00000041291	ENST00000368195.3:c.2093T>C	1.37:g.156815492A>G	ENSP00000357178:p.Val698Ala	Somatic		Capture	Illumina HiSeq	Phase_I	155082116	O60724|Q5VZS3	Missense_Mutation	SNP	ENST00000368195.3	37	CCDS1160.1	.	.	.	.	.	.	.	.	.	.	A	0.034	-1.316804	0.01331	.	.	ENSG00000027644	ENST00000368195	T	0.73152	-0.72	4.58	-3.43	0.04810	Fibronectin, type III (2);	1.122080	0.06836	N	0.794908	T	0.14313	0.0346	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.05767	-1.0865	9	0.06757	T	0.87	.	1.473	0.02420	0.2116:0.1416:0.37:0.2769	.	698	P14616	INSRR_HUMAN	A	698	ENSP00000357178:V698A	ENSP00000357178:V698A	V	-	2	0	INSRR	155082116	0.241000	0.23857	0.119000	0.21687	0.606000	0.37113	-0.463000	0.06696	-0.502000	0.06596	0.459000	0.35465	GTT		INSRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098929.1	NM_014215	
ASPM	259266	hgsc.bcm.edu	37	1	197070657	197070657	+	Missense_Mutation	SNP	T	T	C			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr1:197070657T>C	ENST00000367409.4	-	18	7980	c.7724A>G	c.(7723-7725)aAg>aGg	p.K2575R	ASPM_ENST00000367408.1_Intron|ASPM_ENST00000294732.7_Intron	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	2575					developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)				breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						CCACTGAAGCTTTTGGTAGAA	0.318																																																	0			1											55.0	50.0	52.0					1																	197070657		2202	4297	6499	195337280	SO:0001583	missense	259266			AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"""microcephaly, primary autosomal recessive 5"", ""asp (abnormal spindle)-like, microcephaly associated (Drosophila)"""	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.7724A>G	1.37:g.197070657T>C	ENSP00000356379:p.Lys2575Arg	Somatic		Capture	Illumina HiSeq	Phase_I	195337280	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Missense_Mutation	SNP	ENST00000367409.4	37	CCDS1389.1	.	.	.	.	.	.	.	.	.	.	T	11.05	1.523694	0.27299	.	.	ENSG00000066279	ENST00000367409;ENST00000367406	T	0.71817	-0.6	5.15	4.03	0.46877	.	0.766419	0.12705	N	0.446024	T	0.72439	0.3460	M	0.70903	2.155	0.09310	N	1	P;B	0.40875	0.731;0.017	P;B	0.49752	0.621;0.013	T	0.58999	-0.7536	10	0.15952	T	0.53	.	5.1767	0.15139	0.1325:0.148:0.0:0.7194	.	561;2575	E7EQ84;Q8IZT6	.;ASPM_HUMAN	R	2575;561	ENSP00000356379:K2575R	ENSP00000356376:K561R	K	-	2	0	ASPM	195337280	0.000000	0.05858	0.047000	0.18901	0.969000	0.65631	0.510000	0.22723	0.900000	0.36469	-0.385000	0.06624	AAG		ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136	
DNAH14	127602	hgsc.bcm.edu	37	1	225341465	225341465	+	Missense_Mutation	SNP	T	T	A			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr1:225341465T>A	ENST00000445597.2	+	21	3929	c.3929T>A	c.(3928-3930)tTt>tAt	p.F1310Y	DNAH14_ENST00000430092.1_Missense_Mutation_p.F1720Y|DNAH14_ENST00000439375.2_Missense_Mutation_p.F1720Y			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	1310					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						CATTATAATTTTGGCTTGAGA	0.284																																																	0			1											78.0	68.0	71.0					1																	225341465		692	1589	2281	223408088	SO:0001583	missense	127602			U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.3929T>A	1.37:g.225341465T>A	ENSP00000409472:p.Phe1310Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	223408088	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		.	.	.	.	.	.	.	.	.	.	T	20.7	4.031894	0.75504	.	.	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375;ENST00000328556	T;T;T;T	0.09255	3.0;3.0;3.0;3.0	4.69	4.69	0.59074	.	0.000000	0.49305	U	0.000146	T	0.20981	0.0505	L	0.41906	1.305	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.05321	-1.0892	10	0.12430	T	0.62	.	13.4162	0.60970	0.0:0.0:0.0:1.0	.	1720	Q0VDD8-4	.	Y	1310;1720;1720;817	ENSP00000409472:F1310Y;ENSP00000414402:F1720Y;ENSP00000392061:F1720Y;ENSP00000332424:F817Y	ENSP00000332424:F817Y	F	+	2	0	DNAH14	223408088	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	6.223000	0.72257	1.867000	0.54127	0.352000	0.21897	TTT		DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
ABCB10	23456	hgsc.bcm.edu	37	1	229667428	229667428	+	Missense_Mutation	SNP	G	G	A			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr1:229667428G>A	ENST00000344517.4	-	7	1432	c.1390C>T	c.(1390-1392)Cgc>Tgc	p.R464C		NM_012089.2	NP_036221.2	Q9NRK6	ABCBA_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 10	464					transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of mitochondrial membrane (GO:0032592)|mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(2)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)	31	Breast(184;0.143)|Ovarian(103;0.249)	Prostate(94;0.167)				TCCCAGAGGCGCCCCCCTGCA	0.512																																																	0			1											75.0	83.0	80.0					1																	229667428		2203	4300	6503	227734051	SO:0001583	missense	23456			U18237	CCDS1580.1	1q32	2012-03-14			ENSG00000135776	ENSG00000135776		"""ATP binding cassette transporters / subfamily B"""	41	protein-coding gene	gene with protein product	"""ATP-binding cassette sub-family B member 10, mitochondrial"", ""ATP-binding cassette transporter 10"", ""ABC transporter 10 protein"", ""mitochondrial ATP-binding cassette 2"""	605454				7766993	Standard	NM_012089		Approved	EST20237, M-ABC2, MTABC2	uc001htp.4	Q9NRK6	OTTHUMG00000039471	ENST00000344517.4:c.1390C>T	1.37:g.229667428G>A	ENSP00000355637:p.Arg464Cys	Somatic		Capture	Illumina HiSeq	Phase_I	227734051	Q13040|Q6P1Q8|Q9H3V0	Missense_Mutation	SNP	ENST00000344517.4	37	CCDS1580.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.183300	0.78677	.	.	ENSG00000135776	ENST00000344517	D	0.87179	-2.22	5.96	5.03	0.67393	ABC transporter, transmembrane domain, type 1 (1);	0.000000	0.85682	D	0.000000	D	0.93759	0.8005	H	0.96460	3.825	0.80722	D	1	D	0.61697	0.99	P	0.51079	0.658	D	0.95430	0.8515	10	0.72032	D	0.01	-19.3968	16.4122	0.83722	0.0:0.0:0.8674:0.1326	.	464	Q9NRK6	ABCBA_HUMAN	C	464	ENSP00000355637:R464C	ENSP00000355637:R464C	R	-	1	0	ABCB10	227734051	1.000000	0.71417	0.961000	0.40146	0.977000	0.68977	5.920000	0.70017	1.482000	0.48325	0.650000	0.86243	CGC		ABCB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095240.1	NM_012089	
GALNT2	2590	hgsc.bcm.edu	37	1	230338901	230338901	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr1:230338901A>G	ENST00000366672.4	+	3	311	c.239A>G	c.(238-240)gAc>gGc	p.D80G	GALNT2_ENST00000541865.1_5'UTR|GALNT2_ENST00000543760.1_Missense_Mutation_p.D42G	NM_004481.3	NP_004472.1	Q10471	GALT2_HUMAN	polypeptide N-acetylgalactosaminyltransferase 2	80					cellular protein metabolic process (GO:0044267)|immunoglobulin biosynthetic process (GO:0002378)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|protein O-linked glycosylation via serine (GO:0018242)|protein O-linked glycosylation via threonine (GO:0018243)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|manganese ion binding (GO:0030145)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(5)|skin(2)	32	Breast(184;0.193)|Ovarian(103;0.249)	all_cancers(173;0.156)|Prostate(94;0.179)				CGGTGGCCAGACTTTAACCAG	0.517																																																	0			1											147.0	147.0	147.0					1																	230338901		2203	4300	6503	228405524	SO:0001583	missense	2590			BC041120	CCDS1582.1	1q41-q42	2014-03-13	2014-03-13		ENSG00000143641	ENSG00000143641	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4124	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 2"""	602274	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2 (GalNAc-T2)"""			9592121, 7592619	Standard	NM_004481		Approved	GalNAc-T2	uc010pwa.1	Q10471	OTTHUMG00000037771	ENST00000366672.4:c.239A>G	1.37:g.230338901A>G	ENSP00000355632:p.Asp80Gly	Somatic		Capture	Illumina HiSeq	Phase_I	228405524	A8K1Y3|B7Z8V8|C5HU00|Q9NPY4	Missense_Mutation	SNP	ENST00000366672.4	37	CCDS1582.1	.	.	.	.	.	.	.	.	.	.	A	17.44	3.389350	0.61956	.	.	ENSG00000143641	ENST00000543760;ENST00000366672	T;T	0.55234	0.54;0.53	5.77	5.77	0.91146	.	1.713610	0.05220	U	0.508464	T	0.46560	0.1399	L	0.34521	1.04	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.09377	0.004;0.004	T	0.15350	-1.0440	10	0.07644	T	0.81	.	16.383	0.83481	1.0:0.0:0.0:0.0	.	80;42	Q10471;G3V1S6	GALT2_HUMAN;.	G	42;80	ENSP00000445017:D42G;ENSP00000355632:D80G	ENSP00000355632:D80G	D	+	2	0	GALNT2	228405524	1.000000	0.71417	1.000000	0.80357	0.855000	0.48748	7.125000	0.77193	2.326000	0.78906	0.533000	0.62120	GAC		GALNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092158.1	NM_004481	
GNG4	2786	hgsc.bcm.edu	37	1	235715439	235715439	+	Silent	SNP	G	G	A			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr1:235715439G>A	ENST00000366598.4	-	3	413	c.198C>T	c.(196-198)cgC>cgT	p.R66R	GNG4_ENST00000391854.2_Silent_p.R66R|GNG4_ENST00000450593.1_Silent_p.R66R|GNG4_ENST00000484517.1_5'UTR|GNG4_ENST00000366597.1_Silent_p.R66R			P50150	GBG4_HUMAN	guanine nucleotide binding protein (G protein), gamma 4	66					cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of cell growth (GO:0030308)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			NS(1)|endometrium(2)|large_intestine(1)|lung(3)|prostate(1)	8	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00168)|Prostate(94;0.0776)|Acute lymphoblastic leukemia(190;0.23)	OV - Ovarian serous cystadenocarcinoma(106;0.000882)			ACTTCTTCTCGCGAAAGGGGT	0.512																																																	0			1											170.0	168.0	169.0					1																	235715439		2203	4300	6503	233782062	SO:0001819	synonymous_variant	2786			BC022485	CCDS1607.1	1q42.3	2008-02-05			ENSG00000168243	ENSG00000168243			4407	protein-coding gene	gene with protein product		604388				7665596	Standard	NM_001098721		Approved		uc001hxh.4	P50150	OTTHUMG00000040740	ENST00000366598.4:c.198C>T	1.37:g.235715439G>A		Somatic		Capture	Illumina HiSeq	Phase_I	233782062		Silent	SNP	ENST00000366598.4	37	CCDS1607.1																																																																																				GNG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097906.1	NM_004485	
OR2AG2	338755	hgsc.bcm.edu	37	11	6789380	6789380	+	Missense_Mutation	SNP	T	T	C			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr11:6789380T>C	ENST00000338569.2	-	1	906	c.809A>G	c.(808-810)cAa>cGa	p.Q270R		NM_001004490.1	NP_001004490.1	A6NM03	O2AG2_HUMAN	olfactory receptor, family 2, subfamily AG, member 2	270						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(13)|ovary(1)|skin(5)|stomach(1)|urinary_tract(1)	28		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)		Epithelial(150;2.15e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		GATGTTGTCTTGTTTGGGGCT	0.512																																																	0			11											152.0	138.0	143.0					11																	6789380		2201	4296	6497	6745956	SO:0001583	missense	338755			AB065539	CCDS31413.1	11p15.4	2012-08-09		2004-03-10	ENSG00000188124	ENSG00000188124		"""GPCR / Class A : Olfactory receptors"""	15143	protein-coding gene	gene with protein product				OR2AG2P			Standard	NM_001004490		Approved		uc001meq.1	A6NM03	OTTHUMG00000165868	ENST00000338569.2:c.809A>G	11.37:g.6789380T>C	ENSP00000342697:p.Gln270Arg	Somatic		Capture	Illumina HiSeq	Phase_I	6745956		Missense_Mutation	SNP	ENST00000338569.2	37	CCDS31413.1	.	.	.	.	.	.	.	.	.	.	T	15.87	2.961065	0.53400	.	.	ENSG00000188124	ENST00000338569	T	0.00152	8.66	4.47	4.47	0.54385	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48286	D	0.000198	T	0.00300	0.0009	L	0.50919	1.6	0.26717	N	0.970863	D	0.89917	1.0	D	0.77557	0.99	T	0.54098	-0.8344	10	0.54805	T	0.06	.	7.6239	0.28202	0.1888:0.0:0.0:0.8112	.	270	A6NM03	O2AG2_HUMAN	R	270	ENSP00000342697:Q270R	ENSP00000342697:Q270R	Q	-	2	0	OR2AG2	6745956	0.000000	0.05858	0.580000	0.28601	0.992000	0.81027	-0.259000	0.08721	2.241000	0.73720	0.533000	0.62120	CAA		OR2AG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386775.1	NM_001004490	
MRGPRX1	259249	hgsc.bcm.edu	37	11	18955439	18955439	+	Missense_Mutation	SNP	G	G	A	rs183845903		TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr11:18955439G>A	ENST00000302797.3	-	1	1117	c.893C>T	c.(892-894)gCg>gTg	p.A298V	MRGPRX1_ENST00000526914.1_5'Flank|RP11-583F24.8_ENST00000528646.1_RNA	NM_147199.3	NP_671732.3	Q96LB2	MRGX1_HUMAN	MAS-related GPR, member X1	298				AS -> TP (in Ref. 2; AAL86880). {ECO:0000305}.	acute-phase response (GO:0006953)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(12)|pancreas(2)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						CACCTCAGACGCGTCCTGCAG	0.562													G|||	1	0.000199681	0.0008	0.0	5008	,	,		24102	0.0		0.0	False		,,,				2504	0.0																0			11											71.0	67.0	69.0					11																	18955439		2194	4286	6480	18912015	SO:0001583	missense	259249				CCDS7846.1	11p15.1	2013-10-10			ENSG00000170255	ENSG00000170255		"""GPCR / Class A : Orphans"""	17962	protein-coding gene	gene with protein product		607227				11551509	Standard	NM_147199		Approved	MRGX1	uc001mpg.3	Q96LB2	OTTHUMG00000162655	ENST00000302797.3:c.893C>T	11.37:g.18955439G>A	ENSP00000305766:p.Ala298Val	Somatic		Capture	Illumina HiSeq	Phase_I	18912015	Q4V9L2|Q8TDD8|Q8TDD9	Missense_Mutation	SNP	ENST00000302797.3	37	CCDS7846.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	.	10.27	1.304888	0.23736	.	.	ENSG00000170255	ENST00000302797	T	0.20332	2.08	2.28	1.35	0.21983	.	0.891913	0.09559	N	0.785768	T	0.06188	0.0160	N	0.00926	-1.1	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.35748	-0.9776	10	0.30078	T	0.28	.	4.4439	0.11588	0.331:0.0:0.669:0.0	.	298	Q96LB2	MRGX1_HUMAN	V	298	ENSP00000305766:A298V	ENSP00000305766:A298V	A	-	2	0	MRGPRX1	18912015	0.000000	0.05858	0.036000	0.18154	0.088000	0.18126	-0.652000	0.05366	0.512000	0.28257	0.491000	0.48974	GCG		MRGPRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369913.1	NM_147199	
OR5W2	390148	hgsc.bcm.edu	37	11	55681572	55681572	+	Missense_Mutation	SNP	C	C	A	rs17148883	byFrequency	TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr11:55681572C>A	ENST00000344514.1	-	1	486	c.487G>T	c.(487-489)Gcc>Tcc	p.A163S		NM_001001960.1	NP_001001960.1	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W, member 2	163			A -> P (in dbSNP:rs17148883).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(28)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						AGGCGGAAGGCCAGTGTCATA	0.438																																					Melanoma(48;171 1190 15239 43886 49348)												0			11											87.0	77.0	80.0					11																	55681572		2201	4296	6497	55438148	SO:0001583	missense	390148			BK004398	CCDS31513.1	11q11	2012-08-09		2004-03-10	ENSG00000187612	ENSG00000187612		"""GPCR / Class A : Olfactory receptors"""	15299	protein-coding gene	gene with protein product				OR5W2P, OR5W3P			Standard	NM_001001960		Approved		uc010rir.2	Q8NH69	OTTHUMG00000166818	ENST00000344514.1:c.487G>T	11.37:g.55681572C>A	ENSP00000342448:p.Ala163Ser	Somatic		Capture	Illumina HiSeq	Phase_I	55438148		Missense_Mutation	SNP	ENST00000344514.1	37	CCDS31513.1	.	.	.	.	.	.	.	.	.	.	C	10.28	1.306775	0.23821	.	.	ENSG00000187612	ENST00000344514	T	0.00099	8.73	5.01	-10.0	0.00425	GPCR, rhodopsin-like superfamily (1);	0.563390	0.14710	N	0.302993	T	0.00144	0.0004	L	0.46741	1.465	0.09310	N	1	B	0.31290	0.318	B	0.43155	0.41	T	0.31668	-0.9935	10	0.87932	D	0	.	8.2433	0.31673	0.1908:0.1019:0.0:0.7073	.	163	Q8NH69	OR5W2_HUMAN	S	163	ENSP00000342448:A163S	ENSP00000342448:A163S	A	-	1	0	OR5W2	55438148	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.231000	0.01206	-1.772000	0.01292	-1.179000	0.01719	GCC		OR5W2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391523.1	NM_001001960	
OR10G8	219869	hgsc.bcm.edu	37	11	123901210	123901210	+	Missense_Mutation	SNP	T	T	C			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr11:123901210T>C	ENST00000431524.1	+	1	914	c.881T>C	c.(880-882)gTg>gCg	p.V294A		NM_001004464.1	NP_001004464.1	Q8NGN5	O10G8_HUMAN	olfactory receptor, family 10, subfamily G, member 8	294						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(7)|large_intestine(2)|lung(21)|ovary(1)|prostate(5)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	44		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		AACAAGGAGGTGAAGAAAGCT	0.473																																																	0			11											104.0	98.0	100.0					11																	123901210		2201	4299	6500	123406420	SO:0001583	missense	219869			AB065755	CCDS31704.1	11q24.1	2012-08-09			ENSG00000234560	ENSG00000234560		"""GPCR / Class A : Olfactory receptors"""	14845	protein-coding gene	gene with protein product							Standard	NM_001004464		Approved		uc001pzp.1	Q8NGN5	OTTHUMG00000165968	ENST00000431524.1:c.881T>C	11.37:g.123901210T>C	ENSP00000389072:p.Val294Ala	Somatic		Capture	Illumina HiSeq	Phase_I	123406420	B2RNJ3|Q6IEV2	Missense_Mutation	SNP	ENST00000431524.1	37	CCDS31704.1	.	.	.	.	.	.	.	.	.	.	T	13.87	2.365784	0.41902	.	.	ENSG00000234560	ENST00000431524	T	0.39592	1.07	2.91	2.91	0.33838	.	0.000000	0.37761	N	0.001959	T	0.59404	0.2191	M	0.71206	2.165	0.28092	N	0.931774	D	0.64830	0.994	D	0.70716	0.97	T	0.54583	-0.8272	10	0.87932	D	0	.	11.0743	0.48021	0.0:0.0:0.0:1.0	.	294	Q8NGN5	O10G8_HUMAN	A	294	ENSP00000389072:V294A	ENSP00000389072:V294A	V	+	2	0	OR10G8	123406420	0.995000	0.38212	0.997000	0.53966	0.389000	0.30415	4.406000	0.59748	1.319000	0.45190	0.455000	0.32223	GTG		OR10G8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387270.1	NM_001004464	
ADAMTS8	11095	hgsc.bcm.edu	37	11	130275579	130275579	+	Silent	SNP	G	G	A			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr11:130275579G>A	ENST00000257359.6	-	9	3250	c.2544C>T	c.(2542-2544)tgC>tgT	p.C848C		NM_007037.4	NP_008968.4	Q9UP79	ATS8_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 8	848	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.				negative regulation of cell proliferation (GO:0008285)|phosphate ion transmembrane transport (GO:0035435)	proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)|low-affinity phosphate transmembrane transporter activity (GO:0009673)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	10	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.039)|Lung(977;0.213)		AGCCGGCCCCGCAGGTGCTAG	0.637																																																	0			11											65.0	77.0	73.0					11																	130275579		2037	4201	6238	129780789	SO:0001819	synonymous_variant	11095			AF060153	CCDS41732.1	11q25	2008-07-18	2005-08-19		ENSG00000134917	ENSG00000134917		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	224	protein-coding gene	gene with protein product		605175	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 8"""			10438512	Standard	NM_007037		Approved	METH2, FLJ41712, ADAM-TS8	uc001qgg.4	Q9UP79	OTTHUMG00000165656	ENST00000257359.6:c.2544C>T	11.37:g.130275579G>A		Somatic		Capture	Illumina HiSeq	Phase_I	129780789	Q9NZS0	Silent	SNP	ENST00000257359.6	37	CCDS41732.1																																																																																				ADAMTS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385636.1	NM_007037	
FAM65B	9750	hgsc.bcm.edu	37	6	24832525	24832525	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr6:24832525A>G	ENST00000259698.4	-	17	2541	c.2366T>C	c.(2365-2367)gTc>gCc	p.V789A	FAM65B_ENST00000538035.1_Missense_Mutation_p.V768A	NM_014722.2	NP_055537.2	Q9Y4F9	FA65B_HUMAN	family with sequence similarity 65, member B	789					cell differentiation (GO:0030154)|muscle organ development (GO:0007517)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	25						CTCATCACTGACAGCTGCGAG	0.438																																																	0			6											198.0	147.0	162.0					6																	24832525		692	1591	2283	24940504	SO:0001583	missense	9750			U49187	CCDS47383.1, CCDS47384.1, CCDS69057.1, CCDS69058.1, CCDS75410.1	6p22.3-p21.32	2012-11-30	2008-06-13	2008-06-13	ENSG00000111913	ENSG00000111913			13872	protein-coding gene	gene with protein product	"""myogenesis-related and NCAM-associated protein homolog (chicken)"""	611410	"""chromosome 6 open reading frame 32"""	C6orf32		9205841, 17150207, 17825087	Standard	NM_001286447		Approved	KIAA0386, DIFF48, MYONAP	uc003neo.1	Q9Y4F9	OTTHUMG00000014375	ENST00000259698.4:c.2366T>C	6.37:g.24832525A>G	ENSP00000259698:p.Val789Ala	Somatic		Capture	Illumina HiSeq	Phase_I	24940504	A6NHP2|Q13529|Q5VV37|Q5VV38|Q9BQ28	Missense_Mutation	SNP	ENST00000259698.4	37	CCDS47383.1	.	.	.	.	.	.	.	.	.	.	A	15.86	2.957291	0.53400	.	.	ENSG00000111913	ENST00000259698;ENST00000538035	T;T	0.38240	1.15;1.15	5.04	5.04	0.67666	.	0.644640	0.16377	N	0.217090	T	0.09512	0.0234	N	0.03608	-0.345	0.80722	D	1	B;B	0.10296	0.002;0.003	B;B	0.11329	0.004;0.006	T	0.07888	-1.0749	10	0.42905	T	0.14	-17.4841	14.4485	0.67370	1.0:0.0:0.0:0.0	.	768;789	F5GX51;Q9Y4F9	.;FA65B_HUMAN	A	789;768	ENSP00000259698:V789A;ENSP00000441138:V768A	ENSP00000259698:V789A	V	-	2	0	FAM65B	24940504	1.000000	0.71417	0.869000	0.34112	0.929000	0.56500	6.848000	0.75409	1.878000	0.54408	0.477000	0.44152	GTC		FAM65B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040024.2		
MDC1	9656	hgsc.bcm.edu	37	6	30671047	30671047	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr6:30671047A>G	ENST00000376406.3	-	12	6346	c.5699T>C	c.(5698-5700)gTg>gCg	p.V1900A	MDC1-AS1_ENST00000442150.1_RNA|MDC1_ENST00000376405.2_Missense_Mutation_p.V1636A	NM_014641.2	NP_055456.2	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	1900	BRCT 1. {ECO:0000255|PROSITE- ProRule:PRU00033}.|Required for nuclear localization (NLS2).				DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intra-S DNA damage checkpoint (GO:0031573)	chromosome (GO:0005694)|focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	FHA domain binding (GO:0070975)|protein C-terminus binding (GO:0008022)			breast(2)|kidney(1)|ovary(1)	4						AGCATCCACCACTCCTGTGAA	0.612								Other conserved DNA damage response genes																																									0			6											60.0	66.0	64.0					6																	30671047		1509	2709	4218	30779026	SO:0001583	missense	9656			D79992	CCDS34384.1	6p21.3	2010-02-17	2009-06-12		ENSG00000137337	ENSG00000137337			21163	protein-coding gene	gene with protein product		607593				10975465, 12607005	Standard	NM_014641		Approved	NFBD1, KIAA0170, Em:AB023051.5	uc003nrg.4	Q14676	OTTHUMG00000031075	ENST00000376406.3:c.5699T>C	6.37:g.30671047A>G	ENSP00000365588:p.Val1900Ala	Somatic		Capture	Illumina HiSeq	Phase_I	30779026	A2AB04|A2BF04|A2RRA8|A7YY86|B0S8A2|Q0EFC2|Q2L6H7|Q2TAZ4|Q5JP55|Q5JP56|Q5ST83|Q68CQ3|Q86Z06|Q96QC2	Missense_Mutation	SNP	ENST00000376406.3	37	CCDS34384.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.357129	0.82243	.	.	ENSG00000137337	ENST00000376406;ENST00000376405;ENST00000429610;ENST00000422104	D;D	0.86432	-2.12;-2.12	5.19	5.19	0.71726	BRCT (3);	0.000000	0.33610	N	0.004740	D	0.91185	0.7223	M	0.76574	2.34	0.39624	D	0.970079	D;D	0.89917	0.993;1.0	D;D	0.81914	0.965;0.995	D	0.92315	0.5861	10	0.62326	D	0.03	-13.2275	13.3393	0.60535	1.0:0.0:0.0:0.0	.	1900;877	Q14676;Q14676-4	MDC1_HUMAN;.	A	1900;1636;1613;1466	ENSP00000365588:V1900A;ENSP00000365587:V1636A	ENSP00000365587:V1636A	V	-	2	0	MDC1	30779026	0.998000	0.40836	0.970000	0.41538	0.859000	0.49053	7.451000	0.80668	2.100000	0.63781	0.254000	0.18369	GTG		MDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076103.1	NM_014641	
TCP11	6954	hgsc.bcm.edu	37	6	35088056	35088056	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr6:35088056A>G	ENST00000512012.1	-	7	1151	c.995T>C	c.(994-996)gTc>gCc	p.V332A	TCP11_ENST00000412155.2_Missense_Mutation_p.V294A|TCP11_ENST00000311875.5_Missense_Mutation_p.V345A|TCP11_ENST00000418521.2_Missense_Mutation_p.V269A|TCP11_ENST00000373974.4_Missense_Mutation_p.V299A|TCP11_ENST00000444780.2_Missense_Mutation_p.V340A|TCP11_ENST00000244645.3_Missense_Mutation_p.V270A|TCP11_ENST00000373979.2_Missense_Mutation_p.V270A			Q8WWU5	TCP11_HUMAN	t-complex 11, testis-specific	332					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)				breast(1)|kidney(5)|large_intestine(3)|lung(10)|ovary(3)|prostate(1)|skin(4)	27						TGAGGCCATGACGGTTAACTG	0.532																																																	0			6											70.0	71.0	71.0					6																	35088056		2203	4300	6503	35196034	SO:0001583	missense	6954				CCDS4799.1, CCDS47413.1, CCDS59015.1, CCDS59016.1, CCDS59017.1, CCDS59018.1	6p21.31	2012-09-20	2012-09-20		ENSG00000124678	ENSG00000124678			11658	protein-coding gene	gene with protein product	"""fertilization-promoting peptide receptor"""	186982	"""t-complex 11 (a murine tcp homolog)"", ""t-complex 11 homolog (mouse)"""	D6S230E		1427894, 11756566, 21597245	Standard	NM_001093728		Approved	KIAA0229, FPPR	uc003okd.2	Q8WWU5	OTTHUMG00000014560	ENST00000512012.1:c.995T>C	6.37:g.35088056A>G	ENSP00000425995:p.Val332Ala	Somatic		Capture	Illumina HiSeq	Phase_I	35196034	B2RCE9|B3KQ27|B7Z7B5|B7Z7G1|B7Z7H4|B7Z7S8|E7EP29|J3KNG1|Q8NF85|Q9NQZ9|Q9NR39	Missense_Mutation	SNP	ENST00000512012.1	37		.	.	.	.	.	.	.	.	.	.	A	12.30	1.895322	0.33442	.	.	ENSG00000124678	ENST00000373979;ENST00000412155;ENST00000244645;ENST00000311875;ENST00000444780;ENST00000373974;ENST00000418521;ENST00000512012;ENST00000486638	T;T;T;T;T;T;T;T;T	0.12465	2.68;2.68;2.68;2.68;2.68;2.68;2.68;2.68;2.68	5.03	5.03	0.67393	.	0.711091	0.13681	N	0.370211	T	0.07279	0.0184	L	0.60455	1.87	0.09310	N	1	B;B;B;B;B;B	0.29188	0.236;0.236;0.236;0.236;0.236;0.083	B;B;B;B;B;B	0.34038	0.174;0.174;0.174;0.174;0.111;0.087	T	0.28870	-1.0030	10	0.19147	T	0.46	.	13.2819	0.60219	1.0:0.0:0.0:0.0	.	299;294;340;405;332;270	B7Z7G1;E7EP29;B7Z7B5;Q5TB88;Q8WWU5;Q8WWU5-2	.;.;.;.;TCP11_HUMAN;.	A	270;294;270;345;340;299;269;332;191	ENSP00000363091:V270A;ENSP00000402816:V294A;ENSP00000244645:V270A;ENSP00000308708:V345A;ENSP00000404479:V340A;ENSP00000363085:V299A;ENSP00000415320:V269A;ENSP00000425995:V332A;ENSP00000421103:V191A	ENSP00000244645:V270A	V	-	2	0	TCP11	35196034	0.997000	0.39634	0.967000	0.41034	0.130000	0.20726	5.258000	0.65479	2.022000	0.59522	0.455000	0.32223	GTC		TCP11-014	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000370354.1	NM_001093728	
TULP1	7287	hgsc.bcm.edu	37	6	35477518	35477518	+	Missense_Mutation	SNP	T	T	C			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr6:35477518T>C	ENST00000229771.6	-	7	690	c.611A>G	c.(610-612)gAg>gGg	p.E204G	TULP1_ENST00000322263.4_Missense_Mutation_p.E151G	NM_003322.3	NP_003313.3	O00294	TULP1_HUMAN	tubby like protein 1	204					dendrite development (GO:0016358)|detection of light stimulus involved in visual perception (GO:0050908)|eye photoreceptor cell development (GO:0042462)|phagocytosis (GO:0006909)|photoreceptor cell maintenance (GO:0045494)|phototransduction (GO:0007602)|positive regulation of phagocytosis (GO:0050766)|retina development in camera-type eye (GO:0060041)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|synapse (GO:0045202)	actin filament binding (GO:0051015)|G-protein coupled photoreceptor activity (GO:0008020)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	19						CTTGTCGGCCTCCCCAGACCC	0.602																																					GBM(55;1027 1091 11115 23439)												0			6											117.0	116.0	116.0					6																	35477518		2203	4300	6503	35585496	SO:0001583	missense	7287			U82468	CCDS4807.1, CCDS75436.1	6p21.3	2014-01-28			ENSG00000112041	ENSG00000112041			12423	protein-coding gene	gene with protein product		602280		RP14		9096357, 9521870	Standard	NM_003322		Approved	TUBL1, LCA15	uc003okv.4	O00294	OTTHUMG00000014575	ENST00000229771.6:c.611A>G	6.37:g.35477518T>C	ENSP00000229771:p.Glu204Gly	Somatic		Capture	Illumina HiSeq	Phase_I	35585496	O43536|Q5TGM5|Q8N571	Missense_Mutation	SNP	ENST00000229771.6	37	CCDS4807.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.095286	0.76870	.	.	ENSG00000112041	ENST00000229771;ENST00000322263;ENST00000545327;ENST00000428978	D;D;T	0.83335	-1.71;-1.62;-0.18	4.16	4.16	0.48862	.	0.389460	0.23760	N	0.044821	D	0.83376	0.5241	L	0.59436	1.845	0.44330	D	0.997215	D;D	0.63880	0.993;0.988	D;P	0.63033	0.91;0.815	D	0.85118	0.0967	10	0.66056	D	0.02	-29.3315	9.5049	0.39040	0.0:0.0:0.0:1.0	.	151;204	O00294-2;O00294	.;TULP1_HUMAN	G	204;151;151;156	ENSP00000229771:E204G;ENSP00000319414:E151G;ENSP00000406765:E156G	ENSP00000229771:E204G	E	-	2	0	TULP1	35585496	0.746000	0.28272	0.877000	0.34402	0.042000	0.13812	2.839000	0.48207	1.747000	0.51819	0.379000	0.24179	GAG		TULP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040307.2		
MCM3	4172	hgsc.bcm.edu	37	6	52138562	52138562	+	Silent	SNP	T	T	C			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr6:52138562T>C	ENST00000229854.7	-	10	1603	c.1527A>G	c.(1525-1527)gcA>gcG	p.A509A	MCM3_ENST00000419835.2_Silent_p.A463A|MCM3_ENST00000476448.1_5'Flank|MCM3_ENST00000596288.1_Silent_p.A554A			P25205	MCM3_HUMAN	minichromosome maintenance complex component 3	509					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	alpha DNA polymerase:primase complex (GO:0005658)|centrosome (GO:0005813)|intracellular membrane-bounded organelle (GO:0043231)|MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			endometrium(4)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	20	Lung NSC(77;0.0931)					GCTCCCCAGGTGCTCTGTAAC	0.507																																																	0			6											124.0	97.0	106.0					6																	52138562		2203	4300	6503	52246521	SO:0001819	synonymous_variant	4172			X62153	CCDS4940.1, CCDS4940.2, CCDS75468.1	6p12	2008-02-05	2007-04-04		ENSG00000112118	ENSG00000112118			6945	protein-coding gene	gene with protein product		602693	"""minichromosome maintenance deficient (S. cerevisiae) 3"", ""MCM3 minichromosome maintenance deficient 3 (S. cerevisiae)"""			1549468	Standard	NM_002388		Approved		uc011dwu.2	P25205	OTTHUMG00000014844	ENST00000229854.7:c.1527A>G	6.37:g.52138562T>C		Somatic		Capture	Illumina HiSeq	Phase_I	52246521	B4DWW4|Q92660|Q9BTR3|Q9NUE7	Silent	SNP	ENST00000229854.7	37																																																																																					MCM3-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470784.1		
PDE10A	10846	hgsc.bcm.edu	37	6	165756927	165756927	+	Missense_Mutation	SNP	C	C	T	rs117826255	byFrequency	TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr6:165756927C>T	ENST00000366882.1	-	20	2174	c.2020G>A	c.(2020-2022)Gtt>Att	p.V674I	PDE10A_ENST00000539869.2_Missense_Mutation_p.V684I|PDE10A_ENST00000354448.4_Missense_Mutation_p.V674I			Q9Y233	PDE10_HUMAN	phosphodiesterase 10A	674					blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of protein kinase A signaling (GO:0010738)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|metal ion binding (GO:0046872)			breast(4)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(39)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	71		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Caffeine(DB00201)|Dipyridamole(DB00975)|Papaverine(DB01113)|Tofisopam(DB08811)|Triflusal(DB08814)	AATTTTGTAACGGGCCACAGT	0.388													C|||	2	0.000399361	0.0	0.0	5008	,	,		17547	0.002		0.0	False		,,,				2504	0.0				Esophageal Squamous(22;308 615 5753 12038 40624)												0			6						C	ILE/VAL,ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	124.0	119.0	120.0		2050,2020	5.7	1.0	6	dbSNP_132	120	0,8600		0,0,4300	yes	missense,missense	PDE10A	NM_001130690.1,NM_006661.2	29,29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign,benign	684/790,674/780	165756927	1,13005	2203	4300	6503	165676917	SO:0001583	missense	10846			AB020593	CCDS47513.1	6q26	2008-03-18			ENSG00000112541	ENSG00000112541	3.1.4.17	"""Phosphodiesterases"""	8772	protein-coding gene	gene with protein product		610652				10373451	Standard	NM_001130690		Approved		uc003quo.3	Q9Y233	OTTHUMG00000015986	ENST00000366882.1:c.2020G>A	6.37:g.165756927C>T	ENSP00000355847:p.Val674Ile	Somatic		Capture	Illumina HiSeq	Phase_I	165676917	Q6FHX1|Q9HCP9|Q9NTV4|Q9ULW9|Q9Y5T1	Missense_Mutation	SNP	ENST00000366882.1	37		2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	C	10.09	1.254205	0.22965	2.27E-4	0.0	ENSG00000112541	ENST00000366882;ENST00000539869;ENST00000343842;ENST00000354448;ENST00000392126	T;T	0.76709	-1.04;-1.04	5.67	5.67	0.87782	Metal-dependent phosphohydrolase, HD domain (1);5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	0.054660	0.85682	D	0.000000	T	0.53802	0.1819	L	0.31207	0.915	0.58432	D	0.999991	B;B	0.22003	0.063;0.005	B;B	0.15870	0.014;0.007	T	0.56481	-0.7972	10	0.10636	T	0.68	.	19.3597	0.94432	0.0:1.0:0.0:0.0	.	684;674	Q9ULW9;Q9Y233	.;PDE10_HUMAN	I	674;702;684;674;673	ENSP00000355847:V674I;ENSP00000346435:V674I	ENSP00000341187:V684I	V	-	1	0	PDE10A	165676917	1.000000	0.71417	0.951000	0.38953	0.977000	0.68977	4.175000	0.58263	2.671000	0.90904	0.585000	0.79938	GTT		PDE10A-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000043031.1		
ERMARD	55780	hgsc.bcm.edu	37	6	170168265	170168265	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr6:170168265A>G	ENST00000366773.3	+	11	1090	c.1057A>G	c.(1057-1059)Atg>Gtg	p.M353V	RP1-266L20.9_ENST00000586101.1_RNA|ERMARD_ENST00000392095.4_Missense_Mutation_p.M227V|ERMARD_ENST00000588451.1_Missense_Mutation_p.M217V|ERMARD_ENST00000418781.3_Missense_Mutation_p.M353V|ERMARD_ENST00000366772.2_Missense_Mutation_p.M353V	NM_001278532.1|NM_018341.1	NP_001265461.1|NP_060811.1	Q5T6L9	EMARD_HUMAN	ER membrane-associated RNA degradation	353					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)											AGAGCCTGCTATGGTAAGTAT	0.328																																																	0			6											111.0	109.0	109.0					6																	170168265		2203	4300	6503	169910190	SO:0001583	missense	55780			AK002014	CCDS34576.1, CCDS64572.1, CCDS64573.1, CCDS64574.1	6q27	2013-08-28	2013-08-28	2013-08-28	ENSG00000130023	ENSG00000130023			21056	protein-coding gene	gene with protein product		615532	"""chromosome 6 open reading frame 70"""	C6orf70		23768067	Standard	NM_018341		Approved	FLJ11152, dJ266L20.3	uc003qxg.1	Q5T6L9	OTTHUMG00000016067	ENST00000366773.3:c.1057A>G	6.37:g.170168265A>G	ENSP00000355735:p.Met353Val	Somatic		Capture	Illumina HiSeq	Phase_I	169910190	B4DFH0|F8WAF1|Q3ZCS8|Q5T6L8|Q9NUT5|Q9NVU2	Missense_Mutation	SNP	ENST00000366773.3	37	CCDS34576.1	.	.	.	.	.	.	.	.	.	.	A	14.92	2.678369	0.47886	.	.	ENSG00000130023	ENST00000366773;ENST00000366772;ENST00000418781;ENST00000392095;ENST00000366771	T;T	0.47177	0.86;0.85	5.1	5.1	0.69264	.	0.150630	0.46758	D	0.000263	T	0.60209	0.2251	M	0.71581	2.175	0.37030	D	0.896614	D;D;P	0.71674	0.998;0.996;0.61	D;D;B	0.76071	0.987;0.98;0.15	T	0.67452	-0.5667	10	0.72032	D	0.01	.	14.8493	0.70284	1.0:0.0:0.0:0.0	.	353;353;353	Q5T6L9-3;Q5T6L9-2;Q5T6L9	.;.;CF070_HUMAN	V	353;353;353;227;1	ENSP00000355735:M353V;ENSP00000375945:M227V	ENSP00000355733:M1V	M	+	1	0	C6orf70	169910190	0.986000	0.35501	0.932000	0.37286	0.873000	0.50193	2.842000	0.48230	2.059000	0.61396	0.533000	0.62120	ATG		ERMARD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043238.2	NM_018341	
ABCA5	23461	hgsc.bcm.edu	37	17	67270117	67270117	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr17:67270117A>G	ENST00000392676.3	-	20	2811	c.2747T>C	c.(2746-2748)cTt>cCt	p.L916P	ABCA5_ENST00000392677.2_Missense_Mutation_p.L916P|ABCA5_ENST00000588877.1_Missense_Mutation_p.L916P			Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 5	916					cholesterol efflux (GO:0033344)|high-density lipoprotein particle remodeling (GO:0034375)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|reverse cholesterol transport (GO:0043691)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(18)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	54	Breast(10;3.72e-11)				Tacrolimus(DB00864)	ATTTTGAAGAAGCAGACTTGT	0.403																																																	0			17											111.0	111.0	111.0					17																	67270117		2203	4300	6503	64781712	SO:0001583	missense	23461			U66672	CCDS11685.1	17q24.3	2012-03-14			ENSG00000154265	ENSG00000154265		"""ATP binding cassette transporters / subfamily A"""	35	protein-coding gene	gene with protein product		612503				8894702	Standard	NM_172232		Approved	EST90625	uc002jig.2	Q8WWZ7		ENST00000392676.3:c.2747T>C	17.37:g.67270117A>G	ENSP00000376443:p.Leu916Pro	Somatic		Capture	Illumina HiSeq	Phase_I	64781712	Q8IVJ2|Q96LJ1|Q96MS4|Q96PZ9|Q9NY14	Missense_Mutation	SNP	ENST00000392676.3	37	CCDS11685.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.106958	0.77096	.	.	ENSG00000154265	ENST00000392677;ENST00000392676	D;D	0.90261	-2.64;-2.25	5.53	5.53	0.82687	.	0.113240	0.39759	N	0.001264	D	0.95408	0.8509	M	0.82823	2.61	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.95504	0.8580	9	.	.	.	.	15.6048	0.76658	1.0:0.0:0.0:0.0	.	916;916	Q8WWZ7-2;Q8WWZ7	.;ABCA5_HUMAN	P	916	ENSP00000376444:L916P;ENSP00000376443:L916P	.	L	-	2	0	ABCA5	64781712	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.583000	0.74053	2.222000	0.72286	0.477000	0.44152	CTT		ABCA5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450654.1	NM_018672	
PGS1	9489	hgsc.bcm.edu	37	17	76420232	76420232	+	3'UTR	SNP	C	C	T			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr17:76420232C>T	ENST00000262764.6	+	0	1798				DNAH17_ENST00000389840.5_Missense_Mutation_p.A4405T|DNAH17_ENST00000585328.1_Missense_Mutation_p.A4377T|DNAH17_ENST00000586052.1_5'UTR|AC061992.1_ENST00000600087.1_5'Flank|PGS1_ENST00000588281.1_3'UTR	NM_024419.3	NP_077733.3	Q32NB8	PGPS1_HUMAN	phosphatidylglycerophosphate synthase 1						cardiolipin biosynthetic process (GO:0032049)|diacylglycerol metabolic process (GO:0046339)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity (GO:0008444)			cervix(2)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)|urinary_tract(1)	10			BRCA - Breast invasive adenocarcinoma(99;0.00144)|OV - Ovarian serous cystadenocarcinoma(97;0.031)			TCCCAGCGAGCCCCTGCAGGG	0.637																																					Esophageal Squamous(45;182 1126 10685 43198)												0			17											26.0	28.0	27.0					17																	76420232		2203	4299	6502	73931827	SO:0001624	3_prime_UTR_variant	8632				CCDS42391.1	17q25.3	2006-02-09							30029	protein-coding gene	gene with protein product		614942				9880566	Standard	XR_243691		Approved	DKFZP762M186	uc002jvm.3	Q32NB8		ENST00000262764.6:c.*101C>T	17.37:g.76420232C>T		Somatic		Capture	Illumina HiSeq	Phase_I	73931827	B7ZA32|Q8IYK9|Q8TA85|Q96A75|Q9H7G9|Q9NPW7	Missense_Mutation	SNP	ENST00000262764.6	37	CCDS42391.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.624165	0.87560	.	.	ENSG00000187775	ENST00000300671;ENST00000389840	T	0.16073	2.37	5.23	5.23	0.72850	.	0.215793	0.32343	N	0.006225	T	0.62060	0.2397	H	0.98559	4.265	0.51012	D	0.9999	D	0.89917	1.0	D	0.91635	0.999	T	0.78309	-0.2254	10	0.87932	D	0	.	19.0108	0.92872	0.0:1.0:0.0:0.0	.	4377	E7EUM8	.	T	4377;4405	ENSP00000374490:A4405T	ENSP00000300671:A4377T	A	-	1	0	DNAH17	73931827	0.999000	0.42202	0.996000	0.52242	0.671000	0.39405	4.153000	0.58118	2.713000	0.92767	0.655000	0.94253	GCT		PGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437301.1	NM_024419	
DUS1L	64118	hgsc.bcm.edu	37	17	80019497	80019497	+	Missense_Mutation	SNP	C	C	T	rs114350519		TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr17:80019497C>T	ENST00000354321.7	-	6	1179	c.694G>A	c.(694-696)Gca>Aca	p.A232T	DUS1L_ENST00000306796.5_Missense_Mutation_p.A232T			Q6P1R4	DUS1L_HUMAN	dihydrouridine synthase 1-like (S. cerevisiae)	232							flavin adenine dinucleotide binding (GO:0050660)|tRNA dihydrouridine synthase activity (GO:0017150)			breast(1)|endometrium(1)|lung(2)|ovary(1)|skin(1)	6	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0211)			TGCCCACCTGCGCTCATGACG	0.677													.|||	1	0.000199681	0.0	0.0	5008	,	,		7250	0.001		0.0	False		,,,				2504	0.0																0			17											66.0	61.0	62.0					17																	80019497		2203	4300	6503	77612786	SO:0001583	missense	64118				CCDS32775.1	17q25.3	2005-08-09				ENSG00000169718			30086	protein-coding gene	gene with protein product						12477932	Standard	NM_022156		Approved	PP3111, DUS1	uc002kdr.4	Q6P1R4		ENST00000354321.7:c.694G>A	17.37:g.80019497C>T	ENSP00000346280:p.Ala232Thr	Somatic		Capture	Illumina HiSeq	Phase_I	77612786	A6NHV4|Q96AI3	Missense_Mutation	SNP	ENST00000354321.7	37	CCDS32775.1	.	.	.	.	.	.	.	.	.	.	C	16.37	3.103184	0.56183	.	.	ENSG00000169718	ENST00000354321;ENST00000306796;ENST00000542088;ENST00000538833	T;T;T	0.29655	1.56;1.56;1.56	4.26	4.26	0.50523	Aldolase-type TIM barrel (1);	0.108387	0.64402	D	0.000007	T	0.71937	0.3399	H	0.98333	4.205	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.996;0.997	D	0.85254	0.1046	10	0.87932	D	0	.	16.9981	0.86373	0.0:1.0:0.0:0.0	.	105;232;101	B4DPG7;Q6P1R4;Q9BTJ3	.;DUS1L_HUMAN;.	T	232;232;105;100	ENSP00000346280:A232T;ENSP00000303515:A232T;ENSP00000445110:A100T	ENSP00000303515:A232T	A	-	1	0	DUS1L	77612786	1.000000	0.71417	1.000000	0.80357	0.629000	0.37895	7.290000	0.78711	2.069000	0.61940	0.563000	0.77884	GCA		DUS1L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442347.1	NM_022156	
GABPA	2551	hgsc.bcm.edu	37	21	27124543	27124543	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr21:27124543A>G	ENST00000354828.3	+	5	1078	c.551A>G	c.(550-552)tAt>tGt	p.Y184C	GABPA_ENST00000487266.1_3'UTR|GABPA_ENST00000400075.3_Missense_Mutation_p.Y184C	NM_001197297.1	NP_001184226.1	Q06546	GABPA_HUMAN	GA binding protein transcription factor, alpha subunit 60kDa	184	PNT. {ECO:0000255|PROSITE- ProRule:PRU00762}.				cell differentiation (GO:0030154)|in utero embryonic development (GO:0001701)|negative regulation of megakaryocyte differentiation (GO:0045653)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|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 positive regulation of transcription (GO:0001077)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(5)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	24						GGGATACCCTATGGTAATAAA	0.368																																																	0			21											44.0	44.0	44.0					21																	27124543		2203	4299	6502	26046414	SO:0001583	missense	2551				CCDS13575.1	21q21-q22.1	2008-07-31	2002-08-29		ENSG00000154727	ENSG00000154727			4071	protein-coding gene	gene with protein product	"""human nuclear respiratory factor-2 subunit alpha"", ""nuclear respiratory factor 2 alpha subunit"""	600609	"""GA-binding protein transcription factor, alpha subunit (60kD)"""			8441384	Standard	NM_002040		Approved	E4TF1A, NFT2, NRF2, E4TF1-60, NRF2A	uc002yly.4	Q06546	OTTHUMG00000078443	ENST00000354828.3:c.551A>G	21.37:g.27124543A>G	ENSP00000346886:p.Tyr184Cys	Somatic		Capture	Illumina HiSeq	Phase_I	26046414	Q12939	Missense_Mutation	SNP	ENST00000354828.3	37	CCDS13575.1	.	.	.	.	.	.	.	.	.	.	A	16.67	3.187081	0.57909	.	.	ENSG00000154727	ENST00000354828;ENST00000400075	T;T	0.29917	1.55;1.55	4.84	3.66	0.41972	Sterile alpha motif/pointed domain (2);Pointed domain (3);	0.187799	0.47852	D	0.000208	T	0.42131	0.1189	L	0.44542	1.39	0.80722	D	1	D	0.64830	0.994	D	0.63033	0.91	T	0.23619	-1.0183	10	0.56958	D	0.05	.	10.8759	0.46911	0.8587:0.0:0.0:0.1413	.	184	Q06546	GABPA_HUMAN	C	184	ENSP00000346886:Y184C;ENSP00000382948:Y184C	ENSP00000346886:Y184C	Y	+	2	0	GABPA	26046414	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	8.585000	0.90802	0.946000	0.37632	-0.333000	0.08304	TAT		GABPA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171365.1	NM_002040	
PRSS27	83886	hgsc.bcm.edu	37	16	2763552	2763552	+	Missense_Mutation	SNP	T	T	C			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr16:2763552T>C	ENST00000302641.3	-	5	710	c.656A>G	c.(655-657)gAg>gGg	p.E219G	AC092117.1_ENST00000410123.1_RNA	NM_031948.3	NP_114154.1	Q9BQR3	PRS27_HUMAN	protease, serine 27	219	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)	8						CTTCTTGCCCTCCTCGAAGCC	0.592																																																	0			16											228.0	164.0	186.0					16																	2763552		2198	4300	6498	2703553	SO:0001583	missense	83886			AB056161	CCDS10476.1	16p13.3	2010-05-07			ENSG00000172382	ENSG00000172382		"""Serine peptidases / Serine peptidases"""	15475	protein-coding gene	gene with protein product		608018					Standard	NM_031948		Approved	MPN, pancreasin, CAPH2, marapsin	uc002crf.3	Q9BQR3	OTTHUMG00000128929	ENST00000302641.3:c.656A>G	16.37:g.2763552T>C	ENSP00000306390:p.Glu219Gly	Somatic		Capture	Illumina HiSeq	Phase_I	2703553		Missense_Mutation	SNP	ENST00000302641.3	37	CCDS10476.1	.	.	.	.	.	.	.	.	.	.	.	10.47	1.358492	0.24598	.	.	ENSG00000172382	ENST00000302641;ENST00000543965	T	0.81163	-1.46	5.26	5.26	0.73747	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.53938	D	0.000046	T	0.73713	0.3622	L	0.35723	1.085	0.38950	D	0.958337	B;B	0.25809	0.071;0.135	B;B	0.27887	0.047;0.084	T	0.74520	-0.3638	10	0.62326	D	0.03	.	13.1214	0.59329	0.0:0.0:0.0:1.0	.	219;183	Q9BQR3;B3KP25	PRS27_HUMAN;.	G	219;183	ENSP00000306390:E219G	ENSP00000306390:E219G	E	-	2	0	PRSS27	2703553	1.000000	0.71417	0.995000	0.50966	0.139000	0.21198	3.749000	0.55150	1.991000	0.58162	0.363000	0.22086	GAG		PRSS27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250908.1	NM_031948	
SETD1A	9739	hgsc.bcm.edu	37	16	30991490	30991490	+	Silent	SNP	C	C	T	rs368388561		TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr16:30991490C>T	ENST00000262519.8	+	14	5069	c.4383C>T	c.(4381-4383)aaC>aaT	p.N1461N		NM_014712.1	NP_055527.1	O15047	SET1A_HUMAN	SET domain containing 1A	1461	Interaction with ASH2L, RBBP5 and WDR5.				histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(21)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	59						ACTGGCTCAACGACACTCACT	0.617																																																	0			16						C		1,4393	2.1+/-5.4	0,1,2196	39.0	43.0	42.0		4383	-6.5	0.1	16		42	0,8600		0,0,4300	no	coding-synonymous	SETD1A	NM_014712.1		0,1,6496	TT,TC,CC		0.0,0.0228,0.0077		1461/1708	30991490	1,12993	2197	4300	6497	30898991	SO:0001819	synonymous_variant	9739			AB002337	CCDS32435.1	16p11.2	2013-02-12			ENSG00000099381	ENSG00000099381		"""Chromatin-modifying enzymes / K-methyltransferases"", ""RNA binding motif (RRM) containing"""	29010	protein-coding gene	gene with protein product		611052				9205841, 12670868	Standard	XM_005255723		Approved	KIAA0339, Set1, KMT2F	uc002ead.1	O15047	OTTHUMG00000150474	ENST00000262519.8:c.4383C>T	16.37:g.30991490C>T		Somatic		Capture	Illumina HiSeq	Phase_I	30898991	A6NP62|Q6PIF3|Q8TAJ6	Silent	SNP	ENST00000262519.8	37	CCDS32435.1																																																																																				SETD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318244.2	NM_014712	
GPT2	84706	hgsc.bcm.edu	37	16	46958408	46958408	+	Silent	SNP	C	C	T			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr16:46958408C>T	ENST00000340124.4	+	10	1432	c.1320C>T	c.(1318-1320)taC>taT	p.Y440Y	GPT2_ENST00000440783.2_Silent_p.Y340Y	NM_133443.2	NP_597700.1	Q8TD30	ALAT2_HUMAN	glutamic pyruvate transaminase (alanine aminotransferase) 2	440					2-oxoglutarate metabolic process (GO:0006103)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-alanine catabolic process (GO:0042853)|L-alanine metabolic process (GO:0042851)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	L-alanine:2-oxoglutarate aminotransferase activity (GO:0004021)|pyridoxal phosphate binding (GO:0030170)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(2)	23		all_cancers(37;0.0276)|all_epithelial(9;0.0498)|all_lung(18;0.0522)			L-Alanine(DB00160)|Phenelzine(DB00780)	GGGCCATGTACGCCTTCCCTC	0.562																																																	0			16											103.0	98.0	100.0					16																	46958408		2203	4300	6503	45515909	SO:0001819	synonymous_variant	84706				CCDS10725.1, CCDS45478.1	16q12.1	2008-02-05			ENSG00000166123	ENSG00000166123	2.6.1.2		18062	protein-coding gene	gene with protein product		138210					Standard	NM_133443		Approved	ALT2	uc002eel.3	Q8TD30	OTTHUMG00000132541	ENST00000340124.4:c.1320C>T	16.37:g.46958408C>T		Somatic		Capture	Illumina HiSeq	Phase_I	45515909	Q8N9E2	Silent	SNP	ENST00000340124.4	37	CCDS10725.1																																																																																				GPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255741.2		
CDH5	1003	hgsc.bcm.edu	37	16	66434779	66434779	+	Missense_Mutation	SNP	C	C	T			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr16:66434779C>T	ENST00000341529.3	+	11	1845	c.1697C>T	c.(1696-1698)aCg>aTg	p.T566M	CDH5_ENST00000539168.1_Missense_Mutation_p.T5M	NM_001795.3	NP_001786.2	P33151	CADH5_HUMAN	cadherin 5, type 2 (vascular endothelium)	566	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|blood vessel maturation (GO:0001955)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|negative regulation of cell proliferation (GO:0008285)|regulation of establishment of cell polarity (GO:2000114)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(3)|kidney(18)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	54		Ovarian(137;0.0955)		OV - Ovarian serous cystadenocarcinoma(108;0.107)	Lenalidomide(DB00480)	CCAAGTCGCACGGGCACCAGC	0.602																																																	0			16											108.0	88.0	95.0					16																	66434779		2201	4300	6501	64992280	SO:0001583	missense	1003			X79981	CCDS10804.1	16q22.1	2010-01-26	2008-07-25		ENSG00000179776	ENSG00000179776		"""CD molecules"", ""Cadherins / Major cadherins"""	1764	protein-coding gene	gene with protein product	"""VE-cadherin"""	601120	"""cadherin 5, type 2, VE-cadherin (vascular epithelium)"""			2059658	Standard	NM_001795		Approved	7B4, CD144	uc002eom.4	P33151	OTTHUMG00000137495	ENST00000341529.3:c.1697C>T	16.37:g.66434779C>T	ENSP00000344115:p.Thr566Met	Somatic		Capture	Illumina HiSeq	Phase_I	64992280	Q4VAI5|Q4VAI6	Missense_Mutation	SNP	ENST00000341529.3	37	CCDS10804.1	.	.	.	.	.	.	.	.	.	.	C	12.70	2.017710	0.35606	.	.	ENSG00000179776	ENST00000341529;ENST00000379531;ENST00000539262;ENST00000539168	T;T	0.75477	0.56;-0.94	5.06	5.06	0.68205	Cadherin (4);Cadherin-like (1);	.	.	.	.	D	0.87124	0.6099	M	0.87097	2.86	0.34762	D	0.732888	D	0.89917	1.0	D	0.81914	0.995	D	0.92262	0.5818	9	0.87932	D	0	.	13.5108	0.61511	0.0:0.7205:0.2795:0.0	.	566	P33151	CADH5_HUMAN	M	566;451;307;5	ENSP00000344115:T566M;ENSP00000461880:T5M	ENSP00000344115:T566M	T	+	2	0	CDH5	64992280	0.870000	0.30015	0.872000	0.34217	0.002000	0.02628	1.387000	0.34430	2.348000	0.79779	0.555000	0.69702	ACG		CDH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268767.1	NM_001795	
TWSG1	57045	hgsc.bcm.edu	37	18	9396379	9396379	+	Missense_Mutation	SNP	G	G	C			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr18:9396379G>C	ENST00000262120.5	+	4	516	c.325G>C	c.(325-327)Gaa>Caa	p.E109Q	TWSG1_ENST00000581641.1_Missense_Mutation_p.E109Q	NM_020648.5	NP_065699.1	Q9GZX9	TWSG1_HUMAN	twisted gastrulation BMP signaling modulator 1	109					BMP signaling pathway (GO:0030509)|camera-type eye development (GO:0043010)|cell differentiation (GO:0030154)|forebrain development (GO:0030900)|hemopoiesis (GO:0030097)|mesoderm formation (GO:0001707)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of osteoblast differentiation (GO:0045668)|ossification (GO:0001503)|positive regulation of BMP signaling pathway (GO:0030513)|salivary gland morphogenesis (GO:0007435)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|pancreas(2)	10						GGCACTCACAGAAGGAGATAC	0.428																																																	0			18											116.0	110.0	112.0					18																	9396379		2203	4300	6503	9386379	SO:0001583	missense	57045			AA486291	CCDS11844.1	18p11.3	2013-10-03	2013-10-03		ENSG00000128791	ENSG00000128791			12429	protein-coding gene	gene with protein product		605049	"""twisted gastrulation homolog 1 (Drosophila)"""			11260715	Standard	NM_020648		Approved	TSG	uc002knz.3	Q9GZX9	OTTHUMG00000131597	ENST00000262120.5:c.325G>C	18.37:g.9396379G>C	ENSP00000262120:p.Glu109Gln	Somatic		Capture	Illumina HiSeq	Phase_I	9386379	B2RE08|D3DUH9|Q8NBI7|Q96K46	Missense_Mutation	SNP	ENST00000262120.5	37	CCDS11844.1	.	.	.	.	.	.	.	.	.	.	G	18.14	3.557750	0.65425	.	.	ENSG00000128791	ENST00000262120	.	.	.	5.33	4.44	0.53790	.	0.000000	0.85682	D	0.000000	T	0.60779	0.2295	M	0.68952	2.095	0.58432	D	0.999999	B	0.26002	0.139	B	0.24541	0.054	T	0.62412	-0.6860	9	0.72032	D	0.01	-19.7869	13.3428	0.60555	0.0771:0.0:0.9229:0.0	.	109	Q9GZX9	TWSG1_HUMAN	Q	109	.	ENSP00000262120:E109Q	E	+	1	0	TWSG1	9386379	1.000000	0.71417	0.980000	0.43619	0.998000	0.95712	7.821000	0.86641	1.232000	0.43678	0.561000	0.74099	GAA		TWSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254480.2		
ANKRD28	23243	hgsc.bcm.edu	37	3	15727739	15727739	+	Missense_Mutation	SNP	C	C	T			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr3:15727739C>T	ENST00000399451.2	-	19	2318	c.1951G>A	c.(1951-1953)Gga>Aga	p.G651R	ANKRD28_ENST00000383777.1_Missense_Mutation_p.G684R|ANKRD28_ENST00000497037.1_5'UTR	NM_001195098.1|NM_001195099.1|NM_015199.3	NP_001182027.1|NP_001182028.1|NP_056014.2	O15084	ANR28_HUMAN	ankyrin repeat domain 28	651						nucleus (GO:0005634)				breast(2)|endometrium(1)|large_intestine(2)|prostate(1)	6						TGTCCATTTCCATCTTGAATA	0.368																																																	0			3											131.0	111.0	118.0					3																	15727739		1900	4117	6017	15702743	SO:0001583	missense	23243			AY367056	CCDS46769.1, CCDS74908.1	3p25.1	2013-01-10			ENSG00000206560	ENSG00000206560		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"", ""Ankyrin repeat domain containing"""	29024	protein-coding gene	gene with protein product	"""phosphatase interactor targeting K protein"", ""protein phosphatase 6 ankyrin repeat subunit A"", ""protein phosphatase 1, regulatory subunit 65"""	611122				9205841	Standard	NM_015199		Approved	KIAA0379, PITK, PP6-ARS-A, PPP1R65	uc003caj.1	O15084	OTTHUMG00000155379	ENST00000399451.2:c.1951G>A	3.37:g.15727739C>T	ENSP00000382379:p.Gly651Arg	Somatic		Capture	Illumina HiSeq	Phase_I	15702743	B4DES5|Q1WWL4|Q29RW6|Q3B857|Q6ULS0|Q6ZT57	Missense_Mutation	SNP	ENST00000399451.2	37	CCDS46769.1	.	.	.	.	.	.	.	.	.	.	C	17.02	3.281168	0.59758	.	.	ENSG00000206560	ENST00000399451;ENST00000383777;ENST00000412318	T;T;T	0.15487	2.42;2.42;2.42	5.79	5.79	0.91817	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.12347	0.0300	N	0.12611	0.24	0.80722	D	1	B;B;B	0.25390	0.08;0.125;0.105	B;B;B	0.19391	0.022;0.022;0.025	T	0.16541	-1.0399	10	0.27785	T	0.31	.	20.024	0.97514	0.0:1.0:0.0:0.0	.	684;681;651	O15084-1;O15084-4;O15084	.;.;ANR28_HUMAN	R	651;684;651	ENSP00000382379:G651R;ENSP00000373287:G684R;ENSP00000397341:G651R	ENSP00000373287:G684R	G	-	1	0	ANKRD28	15702743	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.718000	0.92993	0.655000	0.94253	GGA		ANKRD28-003	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339758.1	NM_015199	
DLEC1	9940	hgsc.bcm.edu	37	3	38104250	38104250	+	Missense_Mutation	SNP	C	C	T			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr3:38104250C>T	ENST00000308059.6	+	5	1073	c.1052C>T	c.(1051-1053)cCa>cTa	p.P351L	DLEC1_ENST00000452631.2_Missense_Mutation_p.P351L|DLEC1_ENST00000346219.3_Missense_Mutation_p.P351L					deleted in lung and esophageal cancer 1									p.P351R(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		CCAAAGAAGCCAGCACCGATA	0.463																																																	1	Substitution - Missense(1)	breast(1)	3											77.0	74.0	75.0					3																	38104250		1846	4093	5939	38079254	SO:0001583	missense	9940			AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 81"""	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.1052C>T	3.37:g.38104250C>T	ENSP00000308597:p.Pro351Leu	Somatic		Capture	Illumina HiSeq	Phase_I	38079254		Missense_Mutation	SNP	ENST00000308059.6	37	CCDS2672.2	.	.	.	.	.	.	.	.	.	.	C	6.499	0.460334	0.12342	.	.	ENSG00000008226	ENST00000308059;ENST00000346219;ENST00000452631	T;T;T	0.05649	3.42;3.41;3.65	4.67	3.8	0.43715	.	0.850025	0.10774	N	0.635668	T	0.07863	0.0197	L	0.56769	1.78	0.27107	N	0.962483	B;P;B;P	0.34864	0.344;0.473;0.335;0.473	B;B;B;B	0.31751	0.054;0.088;0.135;0.088	T	0.23190	-1.0195	10	0.26408	T	0.33	-3.0099	8.914	0.35570	0.0:0.8974:0.0:0.1026	.	351;351;351;351	A1L305;F8W6T4;Q9Y238-3;Q9Y238	.;.;.;DLEC1_HUMAN	L	351	ENSP00000308597:P351L;ENSP00000315914:P351L;ENSP00000410427:P351L	ENSP00000308597:P351L	P	+	2	0	DLEC1	38079254	0.071000	0.21146	0.175000	0.22980	0.200000	0.23975	0.735000	0.26115	1.324000	0.45282	-0.140000	0.14226	CCA		DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337	
DNAH12	201625	hgsc.bcm.edu	37	3	57454539	57454539	+	Missense_Mutation	SNP	T	T	C			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr3:57454539T>C	ENST00000351747.2	-	17	2453	c.2273A>G	c.(2272-2274)aAa>aGa	p.K758R	DNAH12_ENST00000389536.4_Missense_Mutation_p.K758R|snoU13_ENST00000459308.1_RNA	NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	758	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|prostate(1)|skin(1)	25						TTCTTCAATTTTCTCTTCTTC	0.294																																																	0			3											130.0	105.0	113.0					3																	57454539		692	1591	2283	57429579	SO:0001583	missense	201625			U53532, AK126276	CCDS33771.1	3p21.1	2009-02-04	2006-09-04		ENSG00000174844	ENSG00000174844		"""Axonemal dyneins"""	2943	protein-coding gene	gene with protein product		603340	"""dynein, axonemal, heavy polypeptide 12"", ""dynein heavy chain domain 2"", ""dynein heavy domain 2"", ""dynein, axonemal, heavy chain 12-like"", ""dynein, axonemal, heavy chain 7-like"""	DNHD2, DNAH12L, DNAH7L		8812413, 8666668	Standard	NM_198564		Approved	DLP12, Dnahc3, HL-19, hdhc3, DHC3, FLJ40427, FLJ44290	uc003dit.2	Q6ZR08	OTTHUMG00000158598	ENST00000351747.2:c.2273A>G	3.37:g.57454539T>C	ENSP00000295937:p.Lys758Arg	Somatic		Capture	Illumina HiSeq	Phase_I	57429579	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Missense_Mutation	SNP	ENST00000351747.2	37		.	.	.	.	.	.	.	.	.	.	T	7.149	0.583418	0.13749	.	.	ENSG00000174844	ENST00000351747;ENST00000495027;ENST00000389536	T;T;T	0.62105	0.05;1.92;3.59	4.39	0.673	0.17941	Dynein heavy chain, domain-2 (1);	.	.	.	.	T	0.49304	0.1549	L	0.41415	1.275	0.51482	D	0.999925	B	0.06786	0.001	B	0.11329	0.006	T	0.38156	-0.9674	9	0.54805	T	0.06	.	8.5034	0.33173	0.0:0.3238:0.0:0.6762	.	758	Q6ZR08	DYH12_HUMAN	R	758	ENSP00000295937:K758R;ENSP00000418137:K758R;ENSP00000374187:K758R	ENSP00000295937:K758R	K	-	2	0	DNAH12	57429579	0.860000	0.29831	0.553000	0.28255	0.287000	0.27160	1.061000	0.30542	0.027000	0.15297	-0.911000	0.02809	AAA		DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504	
GPR128	84873	hgsc.bcm.edu	37	3	100362136	100362136	+	Missense_Mutation	SNP	C	C	T			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr3:100362136C>T	ENST00000273352.3	+	7	993	c.725C>T	c.(724-726)tCc>tTc	p.S242F	SNORA31_ENST00000517180.1_RNA|GPR128_ENST00000475887.1_Intron	NM_032787.2	NP_116176.2	Q96K78	GP128_HUMAN	G protein-coupled receptor 128	242					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	56						GAGACTTATTCCTTGTCTTTG	0.363																																					Pancreas(87;185 1975 7223 18722)												0			3											145.0	155.0	152.0					3																	100362136		2203	4300	6503	101844826	SO:0001583	missense	84873			AK027360	CCDS2938.1	3q12.3	2014-08-08			ENSG00000144820	ENSG00000144820		"""-"", ""GPCR / Class B : Orphans"""	19241	protein-coding gene	gene with protein product		612307					Standard	NM_032787		Approved	FLJ14454	uc003duc.3	Q96K78	OTTHUMG00000159083	ENST00000273352.3:c.725C>T	3.37:g.100362136C>T	ENSP00000273352:p.Ser242Phe	Somatic		Capture	Illumina HiSeq	Phase_I	101844826	Q14D94|Q86SQ2	Missense_Mutation	SNP	ENST00000273352.3	37	CCDS2938.1	.	.	.	.	.	.	.	.	.	.	C	17.78	3.473135	0.63737	.	.	ENSG00000144820	ENST00000273352	T	0.40476	1.03	4.91	4.91	0.64330	.	0.000000	0.52532	D	0.000070	T	0.51041	0.1651	M	0.73598	2.24	0.80722	D	1	P	0.47350	0.894	P	0.47044	0.535	T	0.57997	-0.7714	10	0.72032	D	0.01	.	13.4682	0.61268	0.0:1.0:0.0:0.0	.	242	Q96K78	GP128_HUMAN	F	242	ENSP00000273352:S242F	ENSP00000273352:S242F	S	+	2	0	GPR128	101844826	0.981000	0.34729	0.870000	0.34147	0.824000	0.46624	3.202000	0.51067	2.553000	0.86117	0.650000	0.86243	TCC		GPR128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353236.1		
ALCAM	214	hgsc.bcm.edu	37	3	105268975	105268975	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr3:105268975A>G	ENST00000306107.5	+	12	1879	c.1379A>G	c.(1378-1380)gAg>gGg	p.E460G	ALCAM_ENST00000389927.4_Missense_Mutation_p.E182G|ALCAM_ENST00000472644.2_Missense_Mutation_p.E460G|ALCAM_ENST00000486979.2_Missense_Mutation_p.E409G	NM_001627.3	NP_001618.2	Q13740	CD166_HUMAN	activated leukocyte cell adhesion molecule	460	Ig-like C2-type 3.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|motor neuron axon guidance (GO:0008045)|signal transduction (GO:0007165)	axon (GO:0030424)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	receptor binding (GO:0005102)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	28						TTCCAGACAGAGGAATCTCCT	0.353																																																	0			3											95.0	118.0	110.0					3																	105268975		2196	4294	6490	106751665	SO:0001583	missense	214			AK054632	CCDS33810.1, CCDS58841.1	3q13.1	2013-01-29	2002-08-08		ENSG00000170017	ENSG00000170017		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	400	protein-coding gene	gene with protein product		601662	"""activated leucocyte cell adhesion molecule"""			7760007	Standard	NM_001627		Approved	CD166, MEMD	uc003dvx.3	Q13740	OTTHUMG00000159192	ENST00000306107.5:c.1379A>G	3.37:g.105268975A>G	ENSP00000305988:p.Glu460Gly	Somatic		Capture	Illumina HiSeq	Phase_I	106751665	B2RNS3|B4DTU0|O60892|Q1HGM8|Q1HGM9|Q6PEY4|Q6ZS95	Missense_Mutation	SNP	ENST00000306107.5	37	CCDS33810.1	.	.	.	.	.	.	.	.	.	.	A	18.13	3.554794	0.65425	.	.	ENSG00000170017	ENST00000306107;ENST00000472644;ENST00000486979;ENST00000389927	T;T;T;T	0.74209	4.05;4.05;4.05;-0.82	5.92	5.92	0.95590	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.619093	0.18841	N	0.129698	T	0.71392	0.3334	L	0.29908	0.895	0.38384	D	0.945206	P;P;P	0.47484	0.896;0.505;0.722	P;B;P	0.47941	0.519;0.355;0.562	T	0.73534	-0.3952	10	0.40728	T	0.16	-1.0867	16.3782	0.83418	1.0:0.0:0.0:0.0	.	182;460;460	Q6ZS95;B4DTU0;Q13740	.;.;CD166_HUMAN	G	460;460;409;182	ENSP00000305988:E460G;ENSP00000419236:E460G;ENSP00000418213:E409G;ENSP00000374577:E182G	ENSP00000305988:E460G	E	+	2	0	ALCAM	106751665	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.055000	0.71103	2.277000	0.76020	0.528000	0.53228	GAG		ALCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353764.1	NM_001627	
MYH15	22989	hgsc.bcm.edu	37	3	108124275	108124275	+	Missense_Mutation	SNP	T	T	C			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr3:108124275T>C	ENST00000273353.3	-	34	4762	c.4706A>G	c.(4705-4707)aAg>aGg	p.K1569R		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	1569						cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.K1569M(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						ATGAAGAATCTTGCTTTCATT	0.318																																																	1	Substitution - Missense(1)	ovary(1)	3											62.0	59.0	60.0					3																	108124275		1813	4069	5882	109606965	SO:0001583	missense	22989			AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"""Myosins / Myosin superfamily : Class II"""	31073	protein-coding gene	gene with protein product		609929	"""myosin, heavy polypeptide 15"""			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.4706A>G	3.37:g.108124275T>C	ENSP00000273353:p.Lys1569Arg	Somatic		Capture	Illumina HiSeq	Phase_I	109606965		Missense_Mutation	SNP	ENST00000273353.3	37	CCDS43127.1	.	.	.	.	.	.	.	.	.	.	T	17.51	3.406675	0.62399	.	.	ENSG00000144821	ENST00000273353	T	0.80824	-1.42	5.13	5.13	0.70059	Myosin tail (1);	.	.	.	.	D	0.87958	0.6309	M	0.63169	1.94	0.58432	D	0.999997	D	0.89917	1.0	D	0.97110	1.0	D	0.89008	0.3426	9	0.66056	D	0.02	.	15.1071	0.72329	0.0:0.0:0.0:1.0	.	1569	Q9Y2K3	MYH15_HUMAN	R	1569	ENSP00000273353:K1569R	ENSP00000273353:K1569R	K	-	2	0	MYH15	109606965	1.000000	0.71417	1.000000	0.80357	0.133000	0.20885	4.058000	0.57463	2.150000	0.67090	0.533000	0.62120	AAG		MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988	
FAM162A	26355	hgsc.bcm.edu	37	3	122123189	122123189	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr3:122123189A>G	ENST00000477892.1	+	3	326	c.242A>G	c.(241-243)gAt>gGt	p.D81G	FAM162A_ENST00000469967.1_Missense_Mutation_p.D81G|FAM162A_ENST00000232125.5_Missense_Mutation_p.D71G	NM_014367.3	NP_055182.3	Q96A26	F162A_HUMAN	family with sequence similarity 162, member A	81	Required for proapoptotic activity.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to hypoxia (GO:0071456)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|transformed cell apoptotic process (GO:0006927)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)	6						AAAAAGGAAGATGAAATCCCA	0.423																																																	0			3											86.0	84.0	84.0					3																	122123189		1902	4120	6022	123605879	SO:0001583	missense	26355			AF191020	CCDS43139.1	3q21.1	2008-06-05	2008-06-05	2008-06-05	ENSG00000114023	ENSG00000114023			17865	protein-coding gene	gene with protein product		608017	"""chromosome 3 open reading frame 28"""	C3orf28		11085516	Standard	NM_014367		Approved	E2IG5	uc003eez.3	Q96A26	OTTHUMG00000159494	ENST00000477892.1:c.242A>G	3.37:g.122123189A>G	ENSP00000419088:p.Asp81Gly	Somatic		Capture	Illumina HiSeq	Phase_I	123605879	Q9NRN6|Q9UJX8	Missense_Mutation	SNP	ENST00000477892.1	37	CCDS43139.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.208224	0.79240	.	.	ENSG00000114023	ENST00000232125;ENST00000477892;ENST00000469967;ENST00000440333	T;T;T	0.35421	1.31;1.31;1.31	5.65	5.65	0.86999	.	0.296854	0.39544	N	0.001323	T	0.48537	0.1505	M	0.76328	2.33	0.30516	N	0.76889	P;P	0.48834	0.916;0.722	P;B	0.49799	0.622;0.423	T	0.60265	-0.7297	10	0.72032	D	0.01	.	12.1892	0.54261	1.0:0.0:0.0:0.0	.	81;81	E9PH05;Q96A26	.;F162A_HUMAN	G	71;81;81;80	ENSP00000232125:D71G;ENSP00000419088:D81G;ENSP00000419491:D81G	ENSP00000232125:D71G	D	+	2	0	FAM162A	123605879	1.000000	0.71417	0.980000	0.43619	0.998000	0.95712	5.653000	0.67967	2.371000	0.80710	0.533000	0.62120	GAT		FAM162A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355766.1	NM_014367	
CHST2	9435	hgsc.bcm.edu	37	3	142840199	142840199	+	Missense_Mutation	SNP	G	G	A			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr3:142840199G>A	ENST00000309575.3	+	2	1925	c.541G>A	c.(541-543)Ggc>Agc	p.G181S		NM_004267.4	NP_004258.2	Q9Y4C5	CHST2_HUMAN	carbohydrate (N-acetylglucosamine-6-O) sulfotransferase 2	181					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|inflammatory response (GO:0006954)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|multicellular organismal development (GO:0007275)|N-acetylglucosamine metabolic process (GO:0006044)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intrinsic component of Golgi membrane (GO:0031228)|trans-Golgi network (GO:0005802)	N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)|sulfotransferase activity (GO:0008146)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(2)	22						GTCGTTCTTCGGCGAGCTATT	0.622																																																	0			3											39.0	48.0	45.0					3																	142840199		2203	4300	6503	144322889	SO:0001583	missense	9435			BC042160	CCDS3129.1	3q24	2007-03-14			ENSG00000175040	ENSG00000175040		"""Sulfotransferases, membrane-bound"""	1970	protein-coding gene	gene with protein product		603798				10049591	Standard	NM_004267		Approved	C6ST	uc003evm.3	Q9Y4C5	OTTHUMG00000159351	ENST00000309575.3:c.541G>A	3.37:g.142840199G>A	ENSP00000307911:p.Gly181Ser	Somatic		Capture	Illumina HiSeq	Phase_I	144322889	D3DNG5|Q2M370|Q9GZN5|Q9UED5|Q9Y6F2	Missense_Mutation	SNP	ENST00000309575.3	37	CCDS3129.1	.	.	.	.	.	.	.	.	.	.	G	32	5.183040	0.94885	.	.	ENSG00000175040	ENST00000309575	D	0.82526	-1.62	4.45	4.45	0.53987	Sulfotransferase domain (1);	0.000000	0.64402	U	0.000001	D	0.92211	0.7530	M	0.88031	2.925	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.92983	0.6408	10	0.48119	T	0.1	-6.4267	17.2545	0.87051	0.0:0.0:1.0:0.0	.	181	Q9Y4C5	CHST2_HUMAN	S	181	ENSP00000307911:G181S	ENSP00000307911:G181S	G	+	1	0	CHST2	144322889	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	9.651000	0.98493	2.295000	0.77249	0.407000	0.27541	GGC		CHST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354850.1	NM_004267	
SI	6476	hgsc.bcm.edu	37	3	164785145	164785145	+	Silent	SNP	T	T	C			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr3:164785145T>C	ENST00000264382.3	-	6	680	c.618A>G	c.(616-618)aaA>aaG	p.K206K		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	206	Isomaltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	brush border (GO:0005903)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|oligo-1,6-glucosidase activity (GO:0004574)|sucrose alpha-glucosidase activity (GO:0004575)	p.K206N(1)		NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)|Scopolamine(DB00747)	TACCGTTGCTTTTCCTAATAA	0.308										HNSCC(35;0.089)																																							1	Substitution - Missense(1)	ovary(1)	3											86.0	85.0	85.0					3																	164785145		2203	4298	6501	166267839	SO:0001819	synonymous_variant	6490			X63597	CCDS3196.1	3q25.2-q26.2	2004-04-06	2004-04-06		ENSG00000090402	ENSG00000090402	3.2.1.10		10856	protein-coding gene	gene with protein product	"""Oligosaccharide alpha-1,6-glucosidase"""	609845	"""sucrase-isomaltase"""			2962903, 1353958	Standard	NM_001041		Approved		uc003fei.3	P14410	OTTHUMG00000158065	ENST00000264382.3:c.618A>G	3.37:g.164785145T>C		Somatic		Capture	Illumina HiSeq	Phase_I	166267839	A2RUC3|Q1JQ80|Q1RMC2	Silent	SNP	ENST00000264382.3	37	CCDS3196.1																																																																																				SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041	
PIK3CA	5290	hgsc.bcm.edu	37	3	178952140	178952140	+	Silent	SNP	T	T	C			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr3:178952140T>C	ENST00000263967.3	+	21	3352	c.3195T>C	c.(3193-3195)caT>caC	p.H1065H	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1065	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		H -> L (found in an endometrial carcinoma sample; unknown pathological significance). {ECO:0000269|PubMed:16322209}.|H -> Y (found in brain tumors; unknown pathological significance). {ECO:0000269|PubMed:15289301}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|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)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TTAAACAGCATGCATTGAACT	0.398		57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)			Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	0			3											89.0	79.0	82.0					3																	178952140		1907	4141	6048	180434834	SO:0001819	synonymous_variant	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3195T>C	3.37:g.178952140T>C		Somatic		Capture	Illumina HiSeq	Phase_I	180434834	Q14CW1|Q99762	Silent	SNP	ENST00000263967.3	37	CCDS43171.1																																																																																				PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2		
KRAS	3845	hgsc.bcm.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	rs121913529		TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr12:25398284C>T	ENST00000256078.4	-	2	98	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000311936.3_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000556131.1_Missense_Mutation_p.G12D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"""pancreatic, colorectal, lung, thyroid, AML, others"""				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)			Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"""L, E, M, O"""	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	12											91.0	81.0	85.0					12																	25398284		2203	4300	6503	25289551	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"""v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog"", ""v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"""	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>A	12.37:g.25398284C>T	ENSP00000256078:p.Gly12Asp	Somatic		Capture	Illumina HiSeq	Phase_I	25289551	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360	
FAM186A	121006	hgsc.bcm.edu	37	12	50745821	50745821	+	Missense_Mutation	SNP	T	T	A			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr12:50745821T>A	ENST00000327337.5	-	4	4793	c.4794A>T	c.(4792-4794)gaA>gaT	p.E1598D	FAM186A_ENST00000543096.1_5'Flank|FAM186A_ENST00000543111.1_Missense_Mutation_p.E1598D	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	1598								p.E1598D(1)									GGATCCCCAGTTCCTGCGCCT	0.682																																					NSCLC(138;1796 1887 12511 19463 37884)												1	Substitution - Missense(1)	skin(1)	12											6.0	6.0	6.0					12																	50745821		685	1557	2242	49032088	SO:0001583	missense	121006				CCDS44878.1	12q13.13	2009-04-22			ENSG00000185958	ENSG00000185958			26980	protein-coding gene	gene with protein product							Standard	NM_001145475		Approved	LOC121006	uc001rwl.2	A6NE01	OTTHUMG00000167889	ENST00000327337.5:c.4794A>T	12.37:g.50745821T>A	ENSP00000329995:p.Glu1598Asp	Somatic		Capture	Illumina HiSeq	Phase_I	49032088		Missense_Mutation	SNP	ENST00000327337.5	37	CCDS44878.1	.	.	.	.	.	.	.	.	.	.	t	0.464	-0.887781	0.02511	.	.	ENSG00000185958	ENST00000543111;ENST00000327337	T;T	0.04317	3.65;3.65	4.05	-8.09	0.01090	.	.	.	.	.	T	0.02012	0.0063	N	0.08118	0	0.09310	N	1	B;B	0.19706	0.038;0.0	B;B	0.14578	0.011;0.0	T	0.33497	-0.9866	9	0.11794	T	0.64	.	8.6931	0.34278	0.5013:0.0:0.3403:0.1584	.	1598;1598	F5GYN0;A6NE01	.;F186A_HUMAN	D	1598	ENSP00000441337:E1598D;ENSP00000329995:E1598D	ENSP00000329995:E1598D	E	-	3	2	FAM186A	49032088	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.664000	0.00399	-5.832000	0.00009	-5.863000	0.00000	GAA		FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1	XM_001718353	
XPOT	11260	hgsc.bcm.edu	37	12	64812700	64812700	+	Silent	SNP	C	C	T	rs372746587		TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr12:64812700C>T	ENST00000332707.5	+	6	844	c.315C>T	c.(313-315)gcC>gcT	p.A105A		NM_007235.4	NP_009166.2	O43592	XPOT_HUMAN	exportin, tRNA	105	Necessary for interaction with Ran, nuclear localization and nuclear import.				intracellular protein transport (GO:0006886)|tRNA export from nucleus (GO:0006409)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	tRNA binding (GO:0000049)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(7)|lung(12)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				GBM - Glioblastoma multiforme(28;0.0404)		GAAATAAAGCCGCCCAAGTCT	0.398																																																	0			12						C		2,4404	2.1+/-5.4	0,2,2201	83.0	81.0	82.0		315	-2.6	1.0	12		82	0,8600		0,0,4300	no	coding-synonymous	XPOT	NM_007235.4		0,2,6501	TT,TC,CC		0.0,0.0454,0.0154		105/963	64812700	2,13004	2203	4300	6503	63098967	SO:0001819	synonymous_variant	11260			AF039022	CCDS31852.1	12q14.1	2012-10-17	2012-10-17		ENSG00000184575	ENSG00000184575		"""Exportins"""	12826	protein-coding gene	gene with protein product		603180	"""exportin, tRNA (nuclear export receptor for tRNAs)"""			9660920, 9512417	Standard	NM_007235		Approved	XPO3	uc001ssb.3	O43592	OTTHUMG00000168794	ENST00000332707.5:c.315C>T	12.37:g.64812700C>T		Somatic		Capture	Illumina HiSeq	Phase_I	63098967	A6NLH1|O43784|Q8WUG2|Q9BVS7	Silent	SNP	ENST00000332707.5	37	CCDS31852.1																																																																																				XPOT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401122.1	NM_007235	
KSR2	283455	hgsc.bcm.edu	37	12	118293321	118293321	+	Silent	SNP	G	G	A	rs371982174		TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr12:118293321G>A	ENST00000339824.5	-	3	1111	c.384C>T	c.(382-384)tgC>tgT	p.C128C	KSR2_ENST00000425217.1_Silent_p.C99C			Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2	128					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.C160C(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(25)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CCACAGTCTCGCACACCTGTT	0.612																																																	1	Substitution - coding silent(1)	central_nervous_system(1)	12						G		1,4163		0,1,2081	91.0	99.0	96.0		297	-2.0	1.0	12		96	0,8436		0,0,4218	no	coding-synonymous	KSR2	NM_173598.4		0,1,6299	AA,AG,GG		0.0,0.024,0.0079		99/922	118293321	1,12599	2082	4218	6300	116777704	SO:0001819	synonymous_variant	283455			AY345972	CCDS61250.1	12q24.22-q24.23	2014-08-12			ENSG00000171435	ENSG00000171435			18610	protein-coding gene	gene with protein product		610737				12471243	Standard	NM_173598		Approved	FLJ25965	uc001two.2	Q6VAB6	OTTHUMG00000169020	ENST00000339824.5:c.384C>T	12.37:g.118293321G>A		Somatic		Capture	Illumina HiSeq	Phase_I	116777704	A0PJT2|Q3B828|Q8N775	Silent	SNP	ENST00000339824.5	37																																																																																					KSR2-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401987.2	NM_173598	
ATP10A	57194	hgsc.bcm.edu	37	15	25925284	25925284	+	Missense_Mutation	SNP	C	C	T	rs116641809	byFrequency	TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr15:25925284C>T	ENST00000356865.6	-	20	3961	c.3850G>A	c.(3850-3852)Gct>Act	p.A1284T		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	1284					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		AGCAGTGCAGCGACAGGCGTC	0.572													C|||	13	0.00259585	0.0	0.0101	5008	,	,		16818	0.0		0.006	False		,,,				2504	0.0																0			15						C	THR/ALA	5,4401	9.9+/-24.2	0,5,2198	131.0	120.0	124.0		3850	-2.6	0.0	15	dbSNP_132	124	77,8523	45.4+/-104.0	0,77,4223	yes	missense	ATP10A	NM_024490.3	58	0,82,6421	TT,TC,CC		0.8953,0.1135,0.6305	benign	1284/1500	25925284	82,12924	2203	4300	6503	23476377	SO:0001583	missense	57194			AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"""ATPases / P-type"""	13542	protein-coding gene	gene with protein product		605855	"""ATPase, Class V, type 10C"", ""ATPase, Class V, type 10A"""	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.3850G>A	15.37:g.25925284C>T	ENSP00000349325:p.Ala1284Thr	Somatic		Capture	Illumina HiSeq	Phase_I	23476377	Q4G0S9|Q969I4	Missense_Mutation	SNP	ENST00000356865.6	37	CCDS32178.1	8	0.003663003663003663	0	0.0	3	0.008287292817679558	0	0.0	5	0.006596306068601583	C	6.597	0.478427	0.12521	0.001135	0.008953	ENSG00000206190	ENST00000356865	T	0.41758	0.99	5.07	-2.59	0.06209	.	0.568870	0.19381	N	0.115668	T	0.19927	0.0479	L	0.28400	0.85	0.09310	N	1	B	0.15141	0.012	B	0.10450	0.005	T	0.10177	-1.0641	10	0.45353	T	0.12	-1.3667	10.8772	0.46917	0.0:0.4562:0.0:0.5438	.	1284	O60312	AT10A_HUMAN	T	1284	ENSP00000349325:A1284T	ENSP00000349325:A1284T	A	-	1	0	ATP10A	23476377	0.008000	0.16893	0.000000	0.03702	0.002000	0.02628	0.216000	0.17585	-0.776000	0.04578	-0.345000	0.07892	GCT		ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490	
ATP10A	57194	hgsc.bcm.edu	37	15	25947099	25947099	+	Silent	SNP	G	G	A	rs114930132	byFrequency	TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr15:25947099G>A	ENST00000356865.6	-	13	2835	c.2724C>T	c.(2722-2724)caC>caT	p.H908H		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	908					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		CCTCCTCGTCGTGGTCCAGCA	0.542													G|||	10	0.00199681	0.0045	0.0014	5008	,	,		20704	0.0		0.0	False		,,,				2504	0.0031																0			15						G		16,4390	24.3+/-50.5	0,16,2187	179.0	155.0	163.0		2724	-11.0	0.0	15	dbSNP_132	163	0,8600		0,0,4300	no	coding-synonymous	ATP10A	NM_024490.3		0,16,6487	AA,AG,GG		0.0,0.3631,0.123		908/1500	25947099	16,12990	2203	4300	6503	23498192	SO:0001819	synonymous_variant	57194			AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"""ATPases / P-type"""	13542	protein-coding gene	gene with protein product		605855	"""ATPase, Class V, type 10C"", ""ATPase, Class V, type 10A"""	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.2724C>T	15.37:g.25947099G>A		Somatic		Capture	Illumina HiSeq	Phase_I	23498192	Q4G0S9|Q969I4	Silent	SNP	ENST00000356865.6	37	CCDS32178.1																																																																																				ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490	
RYR3	6263	hgsc.bcm.edu	37	15	33936562	33936562	+	Missense_Mutation	SNP	C	C	T			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr15:33936562C>T	ENST00000389232.4	+	28	3677	c.3607C>T	c.(3607-3609)Ctc>Ttc	p.L1203F	RYR3_ENST00000415757.3_Missense_Mutation_p.L1203F	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	1203	4 X approximate repeats.|B30.2/SPRY 2. {ECO:0000255|PROSITE- ProRule:PRU00548}.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)	p.L1203I(2)		NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		CCGCATGAATCTCGGGACAGA	0.517																																																	2	Substitution - Missense(2)	lung(2)	15											69.0	69.0	69.0					15																	33936562		1963	4153	6116	31723854	SO:0001583	missense	6263				CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.3607C>T	15.37:g.33936562C>T	ENSP00000373884:p.Leu1203Phe	Somatic		Capture	Illumina HiSeq	Phase_I	31723854	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	37	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	C	14.27	2.486127	0.44147	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	T;T	0.70045	-0.45;-0.45	5.13	5.13	0.70059	SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.64402	D	0.000001	T	0.63640	0.2528	N	0.11064	0.09	0.58432	D	0.999999	B;D	0.76494	0.011;0.999	B;D	0.68483	0.016;0.958	T	0.60974	-0.7156	10	0.24483	T	0.36	.	13.4439	0.61129	0.0:0.9247:0.0:0.0753	.	1203;1203	Q15413-2;Q15413	.;RYR3_HUMAN	F	1203	ENSP00000373884:L1203F;ENSP00000399610:L1203F	ENSP00000354735:L1203F	L	+	1	0	RYR3	31723854	1.000000	0.71417	0.987000	0.45799	0.940000	0.58332	3.923000	0.56469	2.826000	0.97356	0.655000	0.94253	CTC		RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
SPG21	51324	hgsc.bcm.edu	37	15	65262514	65262514	+	Missense_Mutation	SNP	T	T	G			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr15:65262514T>G	ENST00000204566.2	-	6	794	c.499A>C	c.(499-501)Aat>Cat	p.N167H	SPG21_ENST00000416889.2_Missense_Mutation_p.N140H|SPG21_ENST00000559199.1_Missense_Mutation_p.N13H|SPG21_ENST00000433215.2_Missense_Mutation_p.N167H	NM_016630.3	NP_057714.1	Q9NZD8	SPG21_HUMAN	spastic paraplegia 21 (autosomal recessive, Mast syndrome)	167					antigen receptor-mediated signaling pathway (GO:0050851)|cell death (GO:0008219)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network transport vesicle (GO:0030140)	CD4 receptor binding (GO:0042609)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|urinary_tract(1)	10						GATGAAAAATTTCCAAGAACT	0.398																																																	0			15											175.0	193.0	187.0					15																	65262514		2202	4299	6501	63049567	SO:0001583	missense	51324			AF208861	CCDS10198.1, CCDS45279.1	15q21-q22	2008-02-05	2007-04-23		ENSG00000090487	ENSG00000090487			20373	protein-coding gene	gene with protein product	"""maspardin"""	608181				11113139, 14564668	Standard	XM_006720564		Approved	ACP33, GL010, BM-019, MAST	uc002aoe.3	Q9NZD8	OTTHUMG00000133098	ENST00000204566.2:c.499A>C	15.37:g.65262514T>G	ENSP00000204566:p.Asn167His	Somatic		Capture	Illumina HiSeq	Phase_I	63049567	B4DW44|Q6ZMB6	Missense_Mutation	SNP	ENST00000204566.2	37	CCDS10198.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.264905	0.80358	.	.	ENSG00000090487	ENST00000204566;ENST00000416889;ENST00000433215	T;T;T	0.67171	-0.25;-0.25;-0.25	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	T	0.79387	0.4437	M	0.71206	2.165	0.80722	D	1	D;P	0.89917	1.0;0.951	D;P	0.74348	0.983;0.63	T	0.76069	-0.3094	10	0.21014	T	0.42	-15.5812	15.3687	0.74545	0.0:0.0:0.0:1.0	.	140;167	Q9NZD8-2;Q9NZD8	.;SPG21_HUMAN	H	167;140;167	ENSP00000204566:N167H;ENSP00000394846:N140H;ENSP00000404111:N167H	ENSP00000204566:N167H	N	-	1	0	SPG21	63049567	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	8.015000	0.88690	2.311000	0.77944	0.533000	0.62120	AAT		SPG21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256758.3	NM_016630	
CLCN4	1183	hgsc.bcm.edu	37	X	10182007	10182007	+	Silent	SNP	C	C	T	rs36049237		TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chrX:10182007C>T	ENST00000380833.4	+	11	2254	c.1863C>T	c.(1861-1863)gaC>gaT	p.D621D	CLCN4_ENST00000380829.1_Silent_p.D590D|AC003666.1_ENST00000410201.1_RNA|CLCN4_ENST00000421085.2_Silent_p.D527D	NM_001256944.1|NM_001830.3	NP_001243873.1|NP_001821.2	P51793	CLCN4_HUMAN	chloride channel, voltage-sensitive 4	621	CBS 1. {ECO:0000255|PROSITE- ProRule:PRU00703}.				chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(11)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						CTGTCGAGGACGTGGAGACGC	0.627													C|||	1	0.000264901	0.0008	0.0	3775	,	,		12410	0.0		0.0	False		,,,				2504	0.0				Melanoma(74;1050 1296 1576 30544 38374)												0			X						C		1,3834		0,0,1,1632,570	37.0	30.0	32.0		1863	-5.5	0.7	X	dbSNP_126	32	2,6726		0,2,0,2426,1872	no	coding-synonymous	CLCN4	NM_001830.3		0,2,1,4058,2442	TT,TC,T,CC,C		0.0297,0.0261,0.0284		621/761	10182007	3,10560	2203	4300	6503	10142007	SO:0001819	synonymous_variant	1183			X77197	CCDS14137.1, CCDS59159.1	Xp22.3	2012-09-26	2012-02-23		ENSG00000073464	ENSG00000073464		"""Ion channels / Chloride channels : Voltage-sensitive"""	2022	protein-coding gene	gene with protein product		302910	"""chloride channel 4"""			8069296	Standard	NM_001830		Approved	CLC4, ClC-4	uc004csy.4	P51793	OTTHUMG00000021125	ENST00000380833.4:c.1863C>T	X.37:g.10182007C>T		Somatic		Capture	Illumina HiSeq	Phase_I	10142007	A1L3U1|B7Z5Z4|Q9UBU1	Silent	SNP	ENST00000380833.4	37	CCDS14137.1																																																																																				CLCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055730.1		
SAT1	6303	hgsc.bcm.edu	37	X	23803819	23803819	+	Missense_Mutation	SNP	G	G	A			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chrX:23803819G>A	ENST00000379270.4	+	6	541	c.362G>A	c.(361-363)cGc>cAc	p.R121H	RP13-314C10.5_ENST00000366134.2_RNA|SAT1_ENST00000489394.1_3'UTR|SAT1_ENST00000379254.1_Missense_Mutation_p.R93H	NM_002970.2	NP_002961.1	Q9H2B4	S26A1_HUMAN	spermidine/spermine N1-acetyltransferase 1	0					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|chloride transport (GO:0006821)|glycosaminoglycan metabolic process (GO:0030203)|ion transport (GO:0006811)|oxalate transport (GO:0019532)|small molecule metabolic process (GO:0044281)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	anion:anion antiporter activity (GO:0015301)|chloride transmembrane transporter activity (GO:0015108)|oxalate transmembrane transporter activity (GO:0019531)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)			breast(1)|endometrium(3)|kidney(3)|lung(3)	10						ATGAGGTGTCGCTGCAGCAGC	0.418																																																	0			X											117.0	110.0	113.0					X																	23803819		2203	4300	6503	23713740	SO:0001583	missense	81539			M55580	CCDS14207.1	Xp22.1	2011-11-16	2006-08-24	2006-08-24	ENSG00000130066	ENSG00000130066	2.3.1.57		10540	protein-coding gene	gene with protein product	"""diamine N-acetyltransferase 1"""	313020	"""spermidine/spermine N1-acetyltransferase"""	SAT		1985966, 1417826	Standard	NM_002970		Approved	SSAT	uc004dau.3	P21673	OTTHUMG00000021256	ENST00000379270.4:c.362G>A	X.37:g.23803819G>A	ENSP00000368572:p.Arg121His	Somatic		Capture	Illumina HiSeq	Phase_I	23713740	A8K9N2|Q7Z5R3|Q96BK0	Missense_Mutation	SNP	ENST00000379270.4	37	CCDS14207.1	.	.	.	.	.	.	.	.	.	.	G	12.75	2.031733	0.35797	.	.	ENSG00000130066	ENST00000379270;ENST00000379254	T;T	0.42131	0.98;0.98	5.62	5.62	0.85841	GCN5-related N-acetyltransferase (GNAT) domain (2);Acyl-CoA N-acyltransferase (2);	.	.	.	.	T	0.35098	0.0920	N	0.25332	0.735	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.06570	-1.0819	9	0.46703	T	0.11	.	18.6745	0.91524	0.0:0.0:1.0:0.0	.	121	P21673	SAT1_HUMAN	H	121;93	ENSP00000368572:R121H;ENSP00000368556:R93H	ENSP00000368556:R93H	R	+	2	0	SAT1	23713740	1.000000	0.71417	1.000000	0.80357	0.807000	0.45602	9.476000	0.97823	2.354000	0.79902	0.594000	0.82650	CGC		SAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056056.1	NM_002970	
RPGR	6103	hgsc.bcm.edu	37	X	38147244	38147244	+	Silent	SNP	G	G	A			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chrX:38147244G>A	ENST00000339363.3	-	14	1790	c.1623C>T	c.(1621-1623)aaC>aaT	p.N541N	RPGR_ENST00000338898.3_3'UTR|RPGR_ENST00000318842.7_Silent_p.N541N|RPGR_ENST00000309513.3_Silent_p.N479N|RPGR_ENST00000378505.2_Silent_p.N541N|RPGR_ENST00000342811.3_Silent_p.N541N|TM4SF2_ENST00000465127.1_Intron			Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator	541	Glu-rich.				cilium assembly (GO:0042384)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|intraciliary transport (GO:0042073)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|Golgi apparatus (GO:0005794)|photoreceptor outer segment (GO:0001750)|sperm flagellum (GO:0036126)	guanyl-nucleotide exchange factor activity (GO:0005085)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						CACTATCATCGTTTTCAGTAA	0.358																																																	0			X											226.0	180.0	196.0					X																	38147244		2202	4300	6502	38032188	SO:0001819	synonymous_variant	6103			U57629	CCDS14246.1, CCDS35229.1	Xp11.4	2013-06-06	2004-02-13		ENSG00000156313	ENSG00000156313			10295	protein-coding gene	gene with protein product		312610	"""retinitis pigmentosa 15"", ""cone dystrophy 1 (X-linked)"""	CRD, RP3, RP15, COD1		8673101, 8817343	Standard	XM_005272633		Approved	CORDX1	uc004ded.1	Q92834	OTTHUMG00000021361	ENST00000339363.3:c.1623C>T	X.37:g.38147244G>A		Somatic		Capture	Illumina HiSeq	Phase_I	38032188	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	Silent	SNP	ENST00000339363.3	37																																																																																					RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328	
ZNF41	7592	hgsc.bcm.edu	37	X	47308221	47308221	+	Silent	SNP	T	T	C			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chrX:47308221T>C	ENST00000377065.4	-	5	1587	c.948A>G	c.(946-948)gtA>gtG	p.V316V	ZNF41_ENST00000313116.7_Silent_p.V316V|ZNF41_ENST00000465311.1_5'Flank|ZNF41_ENST00000397050.2_Silent_p.V326V	NM_153380.2	NP_700359.1	P51814	ZNF41_HUMAN	zinc finger protein 41	358					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|upper_aerodigestive_tract(2)	24		all_lung(315;0.000129)				CACTTGGATGTACATCAACCT	0.398																																																	0			X											71.0	69.0	69.0					X																	47308221		2203	4298	6501	47193165	SO:0001819	synonymous_variant	7592			X60155	CCDS14279.1	Xp11.23	2013-01-08			ENSG00000147124	ENSG00000147124		"""Zinc fingers, C2H2-type"", ""-"""	13107	protein-coding gene	gene with protein product		314995				2037297	Standard	NM_007130		Approved	MGC8941, MRX89	uc004dhy.4	P51814	OTTHUMG00000021448	ENST00000377065.4:c.948A>G	X.37:g.47308221T>C		Somatic		Capture	Illumina HiSeq	Phase_I	47193165	A8K1V6|B4DH01|Q96LE8|Q9UMC4|Q9UMV5|Q9UMV6|Q9UMV7|Q9UMV8|Q9UMV9|Q9UMW0|Q9UMW1	Silent	SNP	ENST00000377065.4	37	CCDS14279.1																																																																																				ZNF41-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056429.1	NM_153380	
HEPH	9843	hgsc.bcm.edu	37	X	65418745	65418745	+	Missense_Mutation	SNP	T	T	C			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chrX:65418745T>C	ENST00000343002.2	+	10	2403	c.1739T>C	c.(1738-1740)cTt>cCt	p.L580P	HEPH_ENST00000519389.1_Missense_Mutation_p.L634P|HEPH_ENST00000374727.3_Missense_Mutation_p.L583P|HEPH_ENST00000419594.1_Intron|HEPH_ENST00000441993.2_Missense_Mutation_p.L583P|HEPH_ENST00000336279.5_Missense_Mutation_p.L313P			Q9BQS7	HEPH_HUMAN	hephaestin	580	Plastocyanin-like 4.				cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|iron ion transport (GO:0006826)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	copper ion binding (GO:0005507)|ferrous iron binding (GO:0008198)|ferroxidase activity (GO:0004322)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(56)|ovary(5)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	89						GAATTCTTTCTTCTCTTCACT	0.433																																																	0			X											147.0	126.0	133.0					X																	65418745		2203	4300	6503	65335470	SO:0001583	missense	9843			AB014598	CCDS14384.2, CCDS14385.1, CCDS48133.1, CCDS14384.3, CCDS65277.1	Xq11-q12	2008-02-05			ENSG00000089472	ENSG00000089472			4866	protein-coding gene	gene with protein product		300167				9988272, 9734811	Standard	NM_014799		Approved	KIAA0698, CPL	uc011moz.2	Q9BQS7	OTTHUMG00000021732	ENST00000343002.2:c.1739T>C	X.37:g.65418745T>C	ENSP00000343939:p.Leu580Pro	Somatic		Capture	Illumina HiSeq	Phase_I	65335470	B1AJX8|D3DVT7|E9PHN8|O75180|Q6UW45|Q9C058	Missense_Mutation	SNP	ENST00000343002.2	37		.	.	.	.	.	.	.	.	.	.	t	17.49	3.401585	0.62288	.	.	ENSG00000089472	ENST00000519389;ENST00000374727;ENST00000336279;ENST00000441993;ENST00000343002;ENST00000425114	D;D;D;D;D;D	0.99129	-5.46;-5.46;-5.46;-5.46;-5.46;-5.46	4.43	4.43	0.53597	Cupredoxin (2);	0.000000	0.64402	D	0.000001	D	0.99302	0.9756	M	0.90082	3.085	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.99194	1.0871	10	0.87932	D	0	.	11.7993	0.52118	0.0:0.0:0.0:1.0	.	634;580	E9PHN8;Q9BQS7	.;HEPH_HUMAN	P	634;583;313;583;580;537	ENSP00000430620:L634P;ENSP00000363859:L583P;ENSP00000337418:L313P;ENSP00000411687:L583P;ENSP00000343939:L580P;ENSP00000398078:L537P	ENSP00000337418:L313P	L	+	2	0	HEPH	65335470	1.000000	0.71417	0.998000	0.56505	0.924000	0.55760	6.695000	0.74593	1.455000	0.47813	0.225000	0.17782	CTT		HEPH-002	KNOWN	alternative_5_UTR|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000056995.1	NM_138737	
NOX1	27035	hgsc.bcm.edu	37	X	100117757	100117757	+	Silent	SNP	T	T	C			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chrX:100117757T>C	ENST00000372966.3	-	5	595	c.390A>G	c.(388-390)cgA>cgG	p.R130R	NOX1_ENST00000217885.5_Silent_p.R130R|NOX1_ENST00000372960.4_Silent_p.R93R|NOX1_ENST00000372964.1_Silent_p.R130R	NM_007052.4|NM_013955.2	NP_008983.2|NP_039249.1	Q9Y5S8	NOX1_HUMAN	NADPH oxidase 1	130	Ferric oxidoreductase.				angiogenesis (GO:0001525)|cell migration (GO:0016477)|cellular response to hyperoxia (GO:0071455)|cellular stress response to acidic pH (GO:1990451)|extracellular matrix organization (GO:0030198)|hydrogen peroxide metabolic process (GO:0042743)|inflammatory response (GO:0006954)|intracellular pH elevation (GO:0051454)|NADP metabolic process (GO:0006739)|oxidation-reduction process (GO:0055114)|oxygen metabolic process (GO:0072592)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of JNK cascade (GO:0046330)|positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902177)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation vascular endothelial growth factor production (GO:0010575)|proton transport (GO:0015992)|regulation of blood pressure (GO:0008217)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|respiratory burst (GO:0045730)|signal transduction (GO:0007165)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	cell junction (GO:0030054)|early endosome (GO:0005769)|integral component of membrane (GO:0016021)|invadopodium membrane (GO:0071438)|NADPH oxidase complex (GO:0043020)	metal ion binding (GO:0046872)|NADP binding (GO:0050661)|Rac GTPase binding (GO:0048365)|superoxide-generating NADPH oxidase activity (GO:0016175)|voltage-gated proton channel activity (GO:0030171)			cervix(1)|lung(3)|ovary(1)|skin(2)	7						CTGTGGCCTGTCGGCTTCTGC	0.463																																																	0			X											143.0	143.0	143.0					X																	100117757		2203	4299	6502	100004413	SO:0001819	synonymous_variant	27035			AF127763	CCDS14474.1, CCDS14475.1, CCDS65298.1	Xq22	2008-08-01			ENSG00000007952	ENSG00000007952			7889	protein-coding gene	gene with protein product	"""mitogenic oxidase (pyridine nucleotide-dependent superoxide-generating)"", ""NADPH oxidase homolog-1"", ""NADPH oxidase 1 variant NOH-1L"""	300225				10485709, 10615049	Standard	NM_007052		Approved	NOH1, NOH-1, MOX1, GP91-2	uc004egj.3	Q9Y5S8	OTTHUMG00000022007	ENST00000372966.3:c.390A>G	X.37:g.100117757T>C		Somatic		Capture	Illumina HiSeq	Phase_I	100004413	A8K836|O95691|Q2PP02	Silent	SNP	ENST00000372966.3	37	CCDS14474.1																																																																																				NOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057495.1	NM_007052	
THOC2	57187	hgsc.bcm.edu	37	X	122772837	122772837	+	Silent	SNP	A	A	T			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chrX:122772837A>T	ENST00000245838.8	-	17	1819	c.1788T>A	c.(1786-1788)ccT>ccA	p.P596P	THOC2_ENST00000355725.4_Silent_p.P596P|THOC2_ENST00000491737.1_Silent_p.P481P	NM_001081550.1	NP_001075019.1	Q8NI27	THOC2_HUMAN	THO complex 2	596					mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|poly(A)+ mRNA export from nucleus (GO:0016973)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)			breast(2)|endometrium(13)|kidney(4)|large_intestine(11)|lung(26)|ovary(3)|skin(1)|upper_aerodigestive_tract(3)	63						AATCTACTACAGGTGTTATTA	0.328																																																	0			X											203.0	192.0	195.0					X																	122772837		1851	4087	5938	122600518	SO:0001819	synonymous_variant	57187			AF441770	CCDS43988.1	Xq25-q26.3	2013-02-11	2004-08-09		ENSG00000125676	ENSG00000125676		"""THO complex subunits"""	19073	protein-coding gene	gene with protein product		300395	"""chromosome X open reading frame 3"""	CXorf3		11979277	Standard	NM_001081550		Approved	THO2, dJ506G2.1	uc004etu.3	Q8NI27	OTTHUMG00000022334	ENST00000245838.8:c.1788T>A	X.37:g.122772837A>T		Somatic		Capture	Illumina HiSeq	Phase_I	122600518	A6NM50|Q5JZ12|Q6IN92|Q9H8I6	Silent	SNP	ENST00000245838.8	37	CCDS43988.1																																																																																				THOC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058153.3		
RBMX	27316	hgsc.bcm.edu	37	X	135956396	135956396	+	Missense_Mutation	SNP	G	G	A			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chrX:135956396G>A	ENST00000320676.7	-	9	1235	c.1081C>T	c.(1081-1083)Cgt>Tgt	p.R361C	RBMX_ENST00000562646.1_3'UTR|RBMX_ENST00000570135.1_Missense_Mutation_p.R226C|RBMX_ENST00000565438.1_Missense_Mutation_p.R233C|RBMX_ENST00000431446.3_Intron|RBMX_ENST00000496459.2_5'Flank	NM_002139.3	NP_002130.2	P38159	RBMX_HUMAN	RNA binding motif protein, X-linked	361	Necessary for RNA-binding.				cellular response to interleukin-1 (GO:0071347)|gene expression (GO:0010467)|membrane protein ectodomain proteolysis (GO:0006509)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|osteoblast differentiation (GO:0001649)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homooligomerization (GO:0051260)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|supraspliceosomal complex (GO:0044530)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|urinary_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					TAGGAATCACGTGGAGGAGGG	0.557																																																	0			X											69.0	67.0	67.0					X																	135956396		2203	4300	6503	135784062	SO:0001583	missense	27316				CCDS14661.1, CCDS55510.1	Xq26	2013-05-23	2003-09-12		ENSG00000147274	ENSG00000147274		"""RNA binding motif (RRM) containing"""	9910	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein G"""	300199	"""RNA binding motif protein, X chromosome"""			10391206, 10391207	Standard	NM_002139		Approved	RNMX, hnRNP-G, HNRNPG	uc004fae.2	P38159	OTTHUMG00000022517	ENST00000320676.7:c.1081C>T	X.37:g.135956396G>A	ENSP00000359645:p.Arg361Cys	Somatic		Capture	Illumina HiSeq	Phase_I	135784062	B4E3U4|D3DWH0|E9PG86|Q5JQ67|Q8N8Y7|Q969R3	Missense_Mutation	SNP	ENST00000320676.7	37	CCDS14661.1	.	.	.	.	.	.	.	.	.	.	.	13.29	2.193159	0.38707	.	.	ENSG00000147274	ENST00000320676;ENST00000449161	T	0.80566	-1.39	5.66	5.66	0.87406	.	0.000000	0.64402	U	0.000001	D	0.86678	0.5990	L	0.42245	1.32	0.80722	D	1	D	0.89917	1.0	D	0.71414	0.973	D	0.87823	0.2639	10	0.87932	D	0	.	18.7648	0.91868	0.0:0.0:1.0:0.0	.	361	P38159	HNRPG_HUMAN	C	361;348	ENSP00000359645:R361C	ENSP00000359645:R361C	R	-	1	0	RBMX	135784062	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.953000	0.63624	2.377000	0.81083	0.596000	0.82720	CGT		RBMX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058507.1	NM_002139	
KIT	3815	hgsc.bcm.edu	37	4	55592211	55592211	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr4:55592211A>G	ENST00000288135.5	+	9	1632	c.1535A>G	c.(1534-1536)aAc>aGc	p.N512S		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	512					actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	AAAGGTAACAACAAAGGTATA	0.363		1	"""Mis, O"""		"""GIST, AML, TGCT, mastocytosis, mucosal melanoma"""	"""GIST, epithelioma"""	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																														yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"""L, M, O, E"""	0			4											79.0	72.0	74.0					4																	55592211		2203	4300	6503	55286968	SO:0001583	missense	3815	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6342	protein-coding gene	gene with protein product		164920	"""piebald trait"""	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.1535A>G	4.37:g.55592211A>G	ENSP00000288135:p.Asn512Ser	Somatic		Capture	Illumina HiSeq	Phase_I	55286968	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	37	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	A	8.065	0.768914	0.15983	.	.	ENSG00000157404	ENST00000288135	T	0.75704	-0.96	6.02	-4.81	0.03180	.	0.525534	0.18335	N	0.144364	T	0.34395	0.0896	N	0.00926	-1.1	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.18999	-1.0319	10	0.10377	T	0.69	.	9.1068	0.36703	0.3889:0.0:0.5056:0.1055	.	512	P10721	KIT_HUMAN	S	512	ENSP00000288135:N512S	ENSP00000288135:N512S	N	+	2	0	KIT	55286968	0.166000	0.22962	0.968000	0.41197	0.997000	0.91878	-0.582000	0.05814	-0.328000	0.08539	0.533000	0.62120	AAC		KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1		
MAB21L2	10586	hgsc.bcm.edu	37	4	151504985	151504985	+	Silent	SNP	G	G	A	rs374360655		TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr4:151504985G>A	ENST00000317605.4	+	1	1909	c.804G>A	c.(802-804)ccG>ccA	p.P268P	LRBA_ENST00000507224.1_Intron|RP11-1336O20.2_ENST00000507934.1_RNA|LRBA_ENST00000510413.1_Intron|LRBA_ENST00000503716.1_5'Flank|LRBA_ENST00000357115.3_Intron|LRBA_ENST00000535741.1_Intron	NM_006439.4	NP_006430.1	Q9Y586	MB212_HUMAN	mab-21-like 2 (C. elegans)	268					camera-type eye development (GO:0043010)|embryonic body morphogenesis (GO:0010172)|eye development (GO:0001654)|nervous system development (GO:0007399)|positive regulation of cell proliferation (GO:0008284)	nucleus (GO:0005634)				breast(2)|endometrium(6)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|skin(2)	21	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.159)		CCGGCCAGCCGCTCAACAACT	0.637																																																	0			4											60.0	58.0	59.0					4																	151504985		2203	4300	6503	151724435	SO:0001819	synonymous_variant	10586			AF155219	CCDS3774.1	4q31.3	2013-10-22	2001-11-28		ENSG00000181541	ENSG00000181541			6758	protein-coding gene	gene with protein product		604357	"""mab-21 (C. elegans)-like 2"""				Standard	NM_006439		Approved		uc003ilw.3	Q9Y586	OTTHUMG00000161442	ENST00000317605.4:c.804G>A	4.37:g.151504985G>A		Somatic		Capture	Illumina HiSeq	Phase_I	151724435	B3KP37|Q9HBA7	Silent	SNP	ENST00000317605.4	37	CCDS3774.1																																																																																				MAB21L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364937.1	NM_006439	
SPOCK3	50859	hgsc.bcm.edu	37	4	167656168	167656168	+	Silent	SNP	T	T	C			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr4:167656168T>C	ENST00000357154.3	-	12	1352	c.1215A>G	c.(1213-1215)gaA>gaG	p.E405E	SPOCK3_ENST00000511269.1_Silent_p.E402E|SPOCK3_ENST00000541637.1_Silent_p.E307E|SPOCK3_ENST00000506886.1_Silent_p.E405E|SPOCK3_ENST00000504953.1_Silent_p.E402E|SPOCK3_ENST00000510741.1_Silent_p.E362E|SPOCK3_ENST00000507137.1_5'UTR|SPOCK3_ENST00000357545.4_Silent_p.E402E|SPOCK3_ENST00000534949.1_Silent_p.E309E|SPOCK3_ENST00000541354.1_Silent_p.E285E|SPOCK3_ENST00000421836.2_Silent_p.E354E|SPOCK3_ENST00000511531.1_Silent_p.E405E|SPOCK3_ENST00000535728.1_Silent_p.E273E|SPOCK3_ENST00000512681.1_Silent_p.E307E|SPOCK3_ENST00000502330.1_Silent_p.E405E	NM_016950.2	NP_058646.2	Q9BQ16	TICN3_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 3	405	Asp-rich.			E -> G (in Ref. 4; BAG58265). {ECO:0000305}.	negative regulation of endopeptidase activity (GO:0010951)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|signal transduction (GO:0007165)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|glycosaminoglycan binding (GO:0005539)|metalloendopeptidase inhibitor activity (GO:0008191)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	38	all_hematologic(180;0.221)	Prostate(90;0.0181)|Renal(120;0.0184)|Melanoma(52;0.0198)		GBM - Glioblastoma multiforme(119;0.02)		taatatcgtcttcatcatcct	0.353																																																	0			4											193.0	179.0	184.0					4																	167656168		2203	4299	6502	167892743	SO:0001819	synonymous_variant	50859			AJ001454	CCDS34095.1, CCDS54817.1, CCDS56343.1, CCDS56344.1, CCDS56346.1, CCDS56347.1, CCDS58931.1, CCDS75207.1	4q32.3	2011-10-10			ENSG00000196104	ENSG00000196104			13565	protein-coding gene	gene with protein product		607989				11751414	Standard	NM_001204352		Approved	testican-3	uc003iri.1	Q9BQ16	OTTHUMG00000161190	ENST00000357154.3:c.1215A>G	4.37:g.167656168T>C		Somatic		Capture	Illumina HiSeq	Phase_I	167892743	B2R7M7|B3KR67|B4DGK5|B4DHB4|B4DHV3|B4DI46|B4DJY3|E7EP61|F5H099|O75705|Q6UW53|Q96Q26	Silent	SNP	ENST00000357154.3	37	CCDS54817.1																																																																																				SPOCK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364091.1		
AADAT	51166	hgsc.bcm.edu	37	4	170988506	170988506	+	Missense_Mutation	SNP	C	C	T			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr4:170988506C>T	ENST00000337664.4	-	9	1210	c.934G>A	c.(934-936)Gaa>Aaa	p.E312K	AADAT_ENST00000515480.1_Missense_Mutation_p.E312K|AADAT_ENST00000509167.1_Missense_Mutation_p.E316K|AADAT_ENST00000353187.2_Missense_Mutation_p.E312K	NM_016228.3	NP_057312.1	Q8N5Z0	AADAT_HUMAN	aminoadipate aminotransferase	312					2-oxoglutarate metabolic process (GO:0006103)|biosynthetic process (GO:0009058)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate metabolic process (GO:0006536)|kynurenine metabolic process (GO:0070189)|L-kynurenine metabolic process (GO:0097052)|L-lysine catabolic process to acetyl-CoA via saccharopine (GO:0033512)|lysine catabolic process (GO:0006554)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)|tryptophan catabolic process to kynurenine (GO:0019441)	mitochondrial matrix (GO:0005759)	2-aminoadipate transaminase activity (GO:0047536)|kynurenine-oxoglutarate transaminase activity (GO:0016212)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|pancreas(1)|stomach(1)	11		Prostate(90;0.00601)|Renal(120;0.0183)|all_neural(102;0.122)|Melanoma(52;0.17)		GBM - Glioblastoma multiforme(119;0.0355)|LUSC - Lung squamous cell carcinoma(193;0.118)		AAACCTTCTTCTCCCCATTCG	0.348																																																	0			4											90.0	88.0	89.0					4																	170988506		2203	4300	6503	171225081	SO:0001583	missense	51166			AF097994	CCDS3814.1, CCDS75209.1	4q33	2010-12-09			ENSG00000109576	ENSG00000109576	2.6.1.39		17929	protein-coding gene	gene with protein product	"""kynurenine aminotransferase II"", ""L kynurenine/alpha aminoadipate aminotransferase"""	611754				12126930, 10441733	Standard	NM_182662		Approved	KATII, KAT2	uc003isr.3	Q8N5Z0	OTTHUMG00000160912	ENST00000337664.4:c.934G>A	4.37:g.170988506C>T	ENSP00000336808:p.Glu312Lys	Somatic		Capture	Illumina HiSeq	Phase_I	171225081	B3KP84|Q9UL02	Missense_Mutation	SNP	ENST00000337664.4	37	CCDS3814.1	.	.	.	.	.	.	.	.	.	.	C	8.801	0.933006	0.18131	.	.	ENSG00000109576	ENST00000337664;ENST00000515480;ENST00000509167;ENST00000353187	D;D;D;D	0.90069	-2.61;-2.61;-2.61;-2.61	5.93	2.02	0.26589	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.325067	0.37053	N	0.002276	D	0.85570	0.5727	L	0.39085	1.19	0.40851	D	0.983756	B;B	0.24258	0.1;0.057	B;B	0.28465	0.079;0.09	T	0.75861	-0.3168	10	0.29301	T	0.29	-17.084	21.2527	0.99949	0.0:0.3899:0.6101:0.0	.	316;312	Q8N5Z0-2;Q8N5Z0	.;AADAT_HUMAN	K	312;312;316;312	ENSP00000336808:E312K;ENSP00000423341:E312K;ENSP00000423190:E316K;ENSP00000226840:E312K	ENSP00000336808:E312K	E	-	1	0	AADAT	171225081	0.978000	0.34361	0.998000	0.56505	0.161000	0.22273	0.063000	0.14410	0.048000	0.15891	-0.176000	0.13171	GAA		AADAT-004	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000362952.1	NM_016228	
PQLC3	130814	hgsc.bcm.edu	37	2	11300652	11300652	+	Silent	SNP	G	G	A			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr2:11300652G>A	ENST00000295083.3	+	2	379	c.204G>A	c.(202-204)gaG>gaA	p.E68E	PQLC3_ENST00000402361.1_Silent_p.E68E|PQLC3_ENST00000441908.2_Silent_p.E68E|PQLC3_ENST00000476787.1_3'UTR	NM_152391.3	NP_689604.1	Q8N755	PQLC3_HUMAN	PQ loop repeat containing 3	68						integral component of membrane (GO:0016021)				kidney(2)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	6	all_hematologic(175;0.0797)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.0978)|OV - Ovarian serous cystadenocarcinoma(76;0.132)		CCTACCTGGAGTACCCCATCC	0.592																																																	0			2											163.0	139.0	147.0					2																	11300652		2203	4300	6503	11218103	SO:0001819	synonymous_variant	130814			BC027625	CCDS1679.1, CCDS62856.1, CCDS62857.1	2p25.1	2004-02-05	2005-07-19	2005-07-19	ENSG00000162976	ENSG00000162976			28503	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 22"""	C2orf22		12477932	Standard	NM_001282711		Approved	MGC33602	uc002rbc.3	Q8N755	OTTHUMG00000119055	ENST00000295083.3:c.204G>A	2.37:g.11300652G>A		Somatic		Capture	Illumina HiSeq	Phase_I	11218103	B2R8K1|B4DWA4	Silent	SNP	ENST00000295083.3	37	CCDS1679.1	.	.	.	.	.	.	.	.	.	.	G	10.36	1.329526	0.24167	.	.	ENSG00000162976	ENST00000428481	.	.	.	5.01	3.17	0.36434	.	.	.	.	.	T	0.56262	0.1973	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51624	-0.8682	4	.	.	.	-23.0111	7.5261	0.27656	0.2049:0.0:0.7951:0.0	.	.	.	.	I	48	.	.	V	+	1	0	PQLC3	11218103	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.295000	0.33377	1.066000	0.40716	0.561000	0.74099	GTA		PQLC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239266.4	NM_152391	
ITSN2	50618	hgsc.bcm.edu	37	2	24438975	24438975	+	Silent	SNP	T	T	C			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr2:24438975T>C	ENST00000355123.4	-	32	4376	c.3933A>G	c.(3931-3933)ggA>ggG	p.G1311G	AC009228.1_ENST00000413254.1_RNA|AC009228.1_ENST00000430105.1_RNA|AC009228.1_ENST00000413989.1_RNA|ITSN2_ENST00000361999.3_Silent_p.G1284G	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	1311	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				endocytosis (GO:0006897)|positive regulation of signal transduction (GO:0009967)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(8)|large_intestine(11)|liver(3)|lung(28)|ovary(2)|stomach(1)	61	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ACAGAGCTGCTCCATTAAGCT	0.522																																																	0			2											79.0	79.0	79.0					2																	24438975		2203	4300	6503	24292479	SO:0001819	synonymous_variant	50618			AB033082	CCDS1710.2, CCDS1711.2, CCDS46230.1	2p23.3	2013-09-19	2002-10-30		ENSG00000198399	ENSG00000198399		"""Rho guanine nucleotide exchange factors"", ""EF-hand domain containing"""	6184	protein-coding gene	gene with protein product	"""SH3 domain protein 1B"", ""SH3P18-like WASP associated protein"""	604464	"""SH3 domain protein 1B"""	SH3D1B		10922467, 11748279	Standard	NM_006277		Approved	KIAA1256, SWAP, SH3P18, SWA, PRO2015	uc002rfe.2	Q9NZM3	OTTHUMG00000090818	ENST00000355123.4:c.3933A>G	2.37:g.24438975T>C		Somatic		Capture	Illumina HiSeq	Phase_I	24292479	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	Silent	SNP	ENST00000355123.4	37	CCDS1710.2																																																																																				ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	NM_006277	
MCFD2	90411	hgsc.bcm.edu	37	2	47136283	47136283	+	Missense_Mutation	SNP	G	G	C			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr2:47136283G>C	ENST00000409105.1	-	3	207	c.28C>G	c.(28-30)Ccc>Gcc	p.P10A	AC016722.4_ENST00000429761.1_RNA|MCFD2_ENST00000409147.1_Intron|MCFD2_ENST00000409218.1_Missense_Mutation_p.P10A|MCFD2_ENST00000409207.1_Missense_Mutation_p.P10A|MCFD2_ENST00000409973.1_Missense_Mutation_p.P10A|MCFD2_ENST00000409913.1_Intron|MCFD2_ENST00000493804.1_Intron|MCFD2_ENST00000319466.4_Missense_Mutation_p.P10A|MCFD2_ENST00000444761.2_Intron|MCFD2_ENST00000409800.1_Intron	NM_001171506.2	NP_001164977.1	Q8NI22	MCFD2_HUMAN	multiple coagulation factor deficiency 2	10					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)			central_nervous_system(1)|large_intestine(1)|lung(2)	4		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)		Antihemophilic Factor(DB00025)	CACAGGAAGGGGGTTCTGAGC	0.577																																																	0			2											35.0	38.0	37.0					2																	47136283		2203	4300	6503	46989787	SO:0001583	missense	90411			AF475284	CCDS33192.1, CCDS54354.1, CCDS54355.1	2p21	2014-09-17			ENSG00000180398	ENSG00000180398		"""EF-hand domain containing"""	18451	protein-coding gene	gene with protein product		607788				12717434, 2463956	Standard	NM_139279		Approved	F5F8D, LMAN1IP, SDNSF	uc021vha.1	Q8NI22	OTTHUMG00000153100	ENST00000409105.1:c.28C>G	2.37:g.47136283G>C	ENSP00000386651:p.Pro10Ala	Somatic		Capture	Illumina HiSeq	Phase_I	46989787	A8K7W2|D6W5A9|E9PD95|Q53SS3|Q68D61|Q8N3M5	Missense_Mutation	SNP	ENST00000409105.1	37	CCDS33192.1	.	.	.	.	.	.	.	.	.	.	G	11.65	1.702211	0.30232	.	.	ENSG00000180398	ENST00000409105;ENST00000319466;ENST00000409207;ENST00000409973;ENST00000409218;ENST00000412438;ENST00000417180	D;D;D;D;D;D	0.83914	-1.78;-1.78;-1.78;-1.78;-1.78;-1.78	5.36	2.4	0.29515	.	0.490245	0.24488	N	0.038084	T	0.66733	0.2819	L	0.27053	0.805	0.36606	D	0.874934	B	0.20368	0.044	B	0.15870	0.014	T	0.57585	-0.7786	10	0.16896	T	0.51	-9.5311	5.5064	0.16856	0.2455:0.0:0.6031:0.1514	.	10	Q8NI22	MCFD2_HUMAN	A	10	ENSP00000386651:P10A;ENSP00000317271:P10A;ENSP00000386386:P10A;ENSP00000386279:P10A;ENSP00000386261:P10A;ENSP00000402717:P10A	ENSP00000317271:P10A	P	-	1	0	MCFD2	46989787	0.011000	0.17503	0.180000	0.23079	0.897000	0.52465	0.511000	0.22739	0.848000	0.35191	0.561000	0.74099	CCC		MCFD2-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329518.1	NM_139279	
AMER3	205147	hgsc.bcm.edu	37	2	131520567	131520567	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr2:131520567A>G	ENST00000423981.1	+	2	1032	c.922A>G	c.(922-924)Agg>Ggg	p.R308G	AMER3_ENST00000321420.4_Missense_Mutation_p.R308G	NM_001105193.1|NM_001105194.1|NM_001105195.1|NM_152698.2	NP_001098663.1|NP_001098664.1|NP_001098665.1|NP_689911.2	Q8N944	AMER3_HUMAN	APC membrane recruitment protein 3	308					Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	lipid binding (GO:0008289)	p.R308W(1)									TGACTTCACCAGGTTCTGGGA	0.657																																																	1	Substitution - Missense(1)	ovary(1)	2											32.0	38.0	36.0					2																	131520567		2202	4299	6501	131237037	SO:0001583	missense	205147			AK095696	CCDS2164.1	2q21.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000178171	ENSG00000178171		"""-"""	26771	protein-coding gene	gene with protein product			"""family with sequence similarity 123C"""	FAM123C		20843316	Standard	NM_001105195		Approved	FLJ38377	uc002trw.2	Q8N944	OTTHUMG00000131637	ENST00000423981.1:c.922A>G	2.37:g.131520567A>G	ENSP00000392700:p.Arg308Gly	Somatic		Capture	Illumina HiSeq	Phase_I	131237037	B7ZLH6	Missense_Mutation	SNP	ENST00000423981.1	37	CCDS2164.1	.	.	.	.	.	.	.	.	.	.	A	7.947	0.744053	0.15710	.	.	ENSG00000178171	ENST00000321420;ENST00000423981	T;T	0.16196	2.36;2.36	5.21	4.04	0.47022	.	0.525997	0.20253	N	0.096032	T	0.10895	0.0266	N	0.14661	0.345	0.19575	N	0.999962	B	0.14805	0.011	B	0.19391	0.025	T	0.23547	-1.0185	10	0.40728	T	0.16	.	10.7781	0.46361	0.8406:0.1594:0.0:0.0	.	308	Q8N944	F123C_HUMAN	G	308	ENSP00000314914:R308G;ENSP00000392700:R308G	ENSP00000314914:R308G	R	+	1	2	FAM123C	131237037	0.988000	0.35896	0.338000	0.25549	0.133000	0.20885	6.134000	0.71689	0.913000	0.36797	-0.488000	0.04728	AGG		AMER3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254531.3	NM_152698	
SCN3A	6328	hgsc.bcm.edu	37	2	165952157	165952157	+	Splice_Site	SNP	A	A	G			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr2:165952157A>G	ENST00000360093.3	-	25	4786	c.4295T>C	c.(4294-4296)gTt>gCt	p.V1432A	SCN3A_ENST00000283254.7_Splice_Site_p.V1432A|SCN3A_ENST00000540861.1_5'Flank|SCN3A_ENST00000409101.3_Splice_Site_p.V1383A|SCN3A_ENST00000465043.1_5'Flank	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	1432					membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(19)|liver(2)|lung(47)|ovary(6)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(3)	120					Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CTGAAGTTTAACCTAAATGAT	0.264																																																	0			2											37.0	36.0	37.0					2																	165952157		2197	4294	6491	165660403	SO:0001630	splice_region_variant	6328			AF035685	CCDS33312.1, CCDS46440.1	2q24	2012-02-26	2007-01-23		ENSG00000153253	ENSG00000153253		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10590	protein-coding gene	gene with protein product		182391	"""sodium channel, voltage-gated, type III, alpha polypeptide"""			9589372, 16382098	Standard	NM_001081676		Approved	Nav1.3	uc002ucx.3	Q9NY46	OTTHUMG00000044171	ENST00000360093.3:c.4294-1T>C	2.37:g.165952157A>G		Somatic		Capture	Illumina HiSeq	Phase_I	165660403	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	Missense_Mutation	SNP	ENST00000360093.3	37		.	.	.	.	.	.	.	.	.	.	A	10.23	1.293585	0.23564	.	.	ENSG00000153253	ENST00000360093;ENST00000283254;ENST00000409101	D;D;D	0.96522	-4.04;-4.04;-3.99	5.25	5.25	0.73442	.	0.000000	0.64402	D	0.000003	D	0.95739	0.8614	M	0.85542	2.76	0.80722	D	1	B;B;B	0.25272	0.122;0.122;0.01	B;B;B	0.25291	0.059;0.059;0.042	D	0.94256	0.7498	10	0.66056	D	0.02	.	10.8051	0.46514	0.8589:0.0:0.0:0.1411	.	1383;1383;1432	Q9NY46-2;Q9NY46-4;Q9NY46-3	.;.;.	A	1432;1432;1383	ENSP00000353206:V1432A;ENSP00000283254:V1432A;ENSP00000386726:V1383A	ENSP00000283254:V1432A	V	-	2	0	SCN3A	165660403	1.000000	0.71417	1.000000	0.80357	0.074000	0.17049	3.968000	0.56809	2.333000	0.79357	0.482000	0.46254	GTT		SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_006922	Missense_Mutation
TTN	7273	hgsc.bcm.edu	37	2	179641543	179641543	+	Missense_Mutation	SNP	C	C	A	rs368122582		TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr2:179641543C>A	ENST00000591111.1	-	28	5272	c.5048G>T	c.(5047-5049)cGa>cTa	p.R1683L	TTN-AS1_ENST00000584485.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R1683L|TTN-AS1_ENST00000610005.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R1683L|TTN_ENST00000342175.6_Missense_Mutation_p.R1637L|RP11-88L24.4_ENST00000582038.2_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R1637L|TTN_ENST00000360870.5_Missense_Mutation_p.R1683L|TTN_ENST00000359218.5_Missense_Mutation_p.R1637L			Q8WZ42	TITIN_HUMAN	titin	12526					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTGGCCATATCGCAAATGGAG	0.458																																																	0			2											78.0	74.0	75.0					2																	179641543		2203	4300	6503	179349788	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.5048G>T	2.37:g.179641543C>A	ENSP00000465570:p.Arg1683Leu	Somatic		Capture	Illumina HiSeq	Phase_I	179349788	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	13.46	2.245101	0.39697	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.69561	-0.41;-0.23;-0.24;-0.2;-0.07	5.33	5.33	0.75918	Ribonuclease H-like (1);	.	.	.	.	T	0.73598	0.3607	N	0.24115	0.695	0.40384	D	0.979479	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.995;0.995;0.995;0.995;0.999	T	0.78196	-0.2298	9	0.87932	D	0	.	19.0298	0.92952	0.0:1.0:0.0:0.0	.	1637;1637;1637;1683;1683	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	L	1683;1637;1637;1637;1637;1683	ENSP00000343764:R1683L;ENSP00000434586:R1637L;ENSP00000340554:R1637L;ENSP00000352154:R1637L;ENSP00000354117:R1683L	ENSP00000340554:R1637L	R	-	2	0	TTN	179349788	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.757000	0.85209	2.518000	0.84900	0.650000	0.86243	CGA		TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
DNAH7	56171	hgsc.bcm.edu	37	2	196737143	196737143	+	Missense_Mutation	SNP	C	C	T			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr2:196737143C>T	ENST00000312428.6	-	40	6564	c.6464G>A	c.(6463-6465)gGc>gAc	p.G2155D		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	2155	AAA 3. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						AGTCATTGTGCCATTTACGAT	0.318																																																	0			2											168.0	150.0	155.0					2																	196737143		1827	4085	5912	196445388	SO:0001583	missense	56171			AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"""Axonemal dyneins"", ""EF-hand domain containing"""	18661	protein-coding gene	gene with protein product		610061	"""dynein, axonemal, heavy polypeptide 7"""			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.6464G>A	2.37:g.196737143C>T	ENSP00000311273:p.Gly2155Asp	Somatic		Capture	Illumina HiSeq	Phase_I	196445388	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	37	CCDS42794.1	.	.	.	.	.	.	.	.	.	.	C	16.89	3.248389	0.59103	.	.	ENSG00000118997	ENST00000312428	T	0.35421	1.31	4.53	3.62	0.41486	.	0.310442	0.34245	N	0.004121	T	0.53658	0.1810	M	0.76727	2.345	0.80722	D	1	P	0.46912	0.886	P	0.55260	0.772	T	0.61441	-0.7062	10	0.87932	D	0	.	14.3448	0.66654	0.0:0.8503:0.1497:0.0	.	2155	Q8WXX0	DYH7_HUMAN	D	2155	ENSP00000311273:G2155D	ENSP00000311273:G2155D	G	-	2	0	DNAH7	196445388	0.092000	0.21681	0.974000	0.42286	0.972000	0.66771	1.582000	0.36568	1.215000	0.43411	0.650000	0.86243	GGC		DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897	
ABCA12	26154	hgsc.bcm.edu	37	2	215866332	215866332	+	Missense_Mutation	SNP	T	T	C			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr2:215866332T>C	ENST00000272895.7	-	21	3032	c.2813A>G	c.(2812-2814)gAa>gGa	p.E938G	ABCA12_ENST00000389661.4_Missense_Mutation_p.E620G	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	938					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		TCTCTCCATTTCATCTATGGT	0.388																																					Ovarian(66;664 1488 5121 34295)												0			2											188.0	179.0	182.0					2																	215866332		2203	4300	6503	215574577	SO:0001583	missense	26154			AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"""ATP binding cassette transporters / subfamily A"""	14637	protein-coding gene	gene with protein product		607800	"""ichthyosis congenita II, lamellar ichthyosis B"""	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.2813A>G	2.37:g.215866332T>C	ENSP00000272895:p.Glu938Gly	Somatic		Capture	Illumina HiSeq	Phase_I	215574577	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	37	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	T	16.03	3.005699	0.54254	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	D;D	0.87334	-2.24;-2.24	5.77	5.77	0.91146	.	0.083518	0.51477	D	0.000092	D	0.89801	0.6820	M	0.73962	2.25	0.80722	D	1	P;B	0.51653	0.947;0.246	P;B	0.50378	0.639;0.197	D	0.88456	0.3052	10	0.27785	T	0.31	.	16.0948	0.81112	0.0:0.0:0.0:1.0	.	938;620	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	G	938;620	ENSP00000272895:E938G;ENSP00000374312:E620G	ENSP00000272895:E938G	E	-	2	0	ABCA12	215574577	1.000000	0.71417	0.993000	0.49108	0.984000	0.73092	6.513000	0.73742	2.206000	0.71126	0.459000	0.35465	GAA		ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076	
COL6A3	1293	hgsc.bcm.edu	37	2	238259820	238259820	+	Missense_Mutation	SNP	C	C	T	rs372154635		TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr2:238259820C>T	ENST00000295550.4	-	27	7221	c.6769G>A	c.(6769-6771)Gct>Act	p.A2257T	COL6A3_ENST00000346358.4_Missense_Mutation_p.A2057T|COL6A3_ENST00000353578.4_Missense_Mutation_p.A2051T|COL6A3_ENST00000472056.1_Missense_Mutation_p.A1650T|COL6A3_ENST00000409809.1_Missense_Mutation_p.A2051T|COL6A3_ENST00000347401.3_Missense_Mutation_p.A2056T	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2257	Collagen-like 4.|Triple-helical region.			A -> R (in Ref. 1; CAA36267 and 7; M20778). {ECO:0000305}.	axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		GGAGCACCAGCGGCACCTCCG	0.572																																																	0			2						C	THR/ALA,THR/ALA,THR/ALA	0,4406		0,0,2203	95.0	79.0	85.0		6151,4948,6769	2.5	0.0	2		85	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense,missense	COL6A3	NM_057167.3,NM_057166.4,NM_004369.3	58,58,58	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign,benign,benign	2051/2972,1650/2571,2257/3178	238259820	2,13004	2203	4300	6503	237924559	SO:0001583	missense	1293			X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"""Collagens"""	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.6769G>A	2.37:g.238259820C>T	ENSP00000295550:p.Ala2257Thr	Somatic		Capture	Illumina HiSeq	Phase_I	237924559	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	C	6.249	0.414096	0.11870	0.0	2.33E-4	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	D;D;D;D;D;D	0.93659	-3.21;-3.21;-3.26;-3.21;-3.26;-3.21	5.42	2.55	0.30701	.	0.360730	0.23440	N	0.048145	D	0.85004	0.5598	L	0.31294	0.92	0.09310	N	1	B;B;B;B	0.16396	0.01;0.01;0.017;0.004	B;B;B;B	0.08055	0.001;0.001;0.003;0.001	T	0.70417	-0.4877	10	0.26408	T	0.33	.	3.8456	0.08933	0.123:0.4958:0.2847:0.0964	.	1650;1650;2051;2257	E9PFQ6;B7ZMJ7;P12111-2;P12111	.;.;.;CO6A3_HUMAN	T	2257;2056;2051;1650;2051;2057	ENSP00000295550:A2257T;ENSP00000315609:A2056T;ENSP00000315873:A2051T;ENSP00000418285:A1650T;ENSP00000386844:A2051T;ENSP00000295546:A2057T	ENSP00000295550:A2257T	A	-	1	0	COL6A3	237924559	0.007000	0.16637	0.001000	0.08648	0.042000	0.13812	0.351000	0.20096	0.658000	0.30925	0.650000	0.86243	GCT		COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
KIF1A	547	hgsc.bcm.edu	37	2	241657477	241657477	+	Missense_Mutation	SNP	C	C	T			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr2:241657477C>T	ENST00000320389.7	-	46	5178	c.5020G>A	c.(5020-5022)Ggg>Agg	p.G1674R	KIF1A_ENST00000498729.2_Missense_Mutation_p.G1775R	NM_004321.6	NP_004312.2	Q12756	KIF1A_HUMAN	kinesin family member 1A	1674					anterograde axon cargo transport (GO:0008089)|ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			NS(1)|central_nervous_system(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(25)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	66		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)		CGTATGGTCCCGGCCAGGAGG	0.662																																																	0			2											23.0	29.0	27.0					2																	241657477		2086	4213	6299	241306150	SO:0001583	missense	547			AF004425	CCDS46561.1, CCDS58757.1	2q37.2	2014-09-17	2004-01-09	2004-01-14	ENSG00000130294	ENSG00000130294		"""Kinesins"", ""Pleckstrin homology (PH) domain containing"""	888	protein-coding gene	gene with protein product		601255	"""axonal transport of synaptic vesicles"", ""chromosome 2 open reading frame 20"", ""spastic paraplegia 30 (autosomal recessive)"""	ATSV, C2orf20, SPG30		7539720, 10323250, 22258533	Standard	NM_001244008		Approved	UNC104	uc010fzk.3	Q12756	OTTHUMG00000151940	ENST00000320389.7:c.5020G>A	2.37:g.241657477C>T	ENSP00000322791:p.Gly1674Arg	Somatic		Capture	Illumina HiSeq	Phase_I	241306150	B0I1S5|F5H045|O95068|Q13355|Q14752|Q2NKJ6|Q4LE42|Q53T78|Q59GH1|Q63Z40|Q6P1R9|Q7KZ57	Missense_Mutation	SNP	ENST00000320389.7	37	CCDS46561.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.324389	0.81580	.	.	ENSG00000130294	ENST00000320389;ENST00000498729;ENST00000373308	T;T	0.81247	-1.36;-1.47	4.3	4.3	0.51218	Pleckstrin homology domain (1);	0.000000	0.85682	U	0.000000	D	0.89361	0.6693	M	0.77313	2.365	0.80722	D	1	D;D	0.89917	1.0;0.993	D;P	0.76575	0.988;0.866	D	0.91248	0.5027	10	0.87932	D	0	.	16.3405	0.83080	0.0:1.0:0.0:0.0	.	1775;1674	F5H045;Q12756	.;KIF1A_HUMAN	R	1674;1775;1783	ENSP00000322791:G1674R;ENSP00000438388:G1775R	ENSP00000322791:G1674R	G	-	1	0	KIF1A	241306150	1.000000	0.71417	0.879000	0.34478	0.585000	0.36419	7.560000	0.82277	1.949000	0.56562	0.563000	0.77884	GGG		KIF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324536.3	NM_138483	
TAF1L	138474	hgsc.bcm.edu	37	9	32631117	32631117	+	Missense_Mutation	SNP	C	C	A			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr9:32631117C>A	ENST00000242310.4	-	1	4550	c.4461G>T	c.(4459-4461)caG>caT	p.Q1487H	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	1487					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)			breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		ATTGAGAGATCTGAGTCAATG	0.428																																																	0			9											191.0	175.0	181.0					9																	32631117		2203	4300	6503	32621117	SO:0001583	missense	138474			AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"""TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"""			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.4461G>T	9.37:g.32631117C>A	ENSP00000418379:p.Gln1487His	Somatic		Capture	Illumina HiSeq	Phase_I	32621117	Q0VG57	Missense_Mutation	SNP	ENST00000242310.4	37	CCDS35003.1	.	.	.	.	.	.	.	.	.	.	C	11.41	1.629394	0.28978	.	.	ENSG00000122728	ENST00000242310	T	0.31769	1.48	0.489	0.489	0.16854	Bromodomain (4);	0.124572	0.56097	D	0.000028	T	0.23806	0.0576	L	0.59436	1.845	0.32448	N	0.5458	B	0.28419	0.211	B	0.29524	0.103	T	0.17592	-1.0364	10	0.62326	D	0.03	.	2.8749	0.05628	0.0:0.6151:0.0:0.3849	.	1487	Q8IZX4	TAF1L_HUMAN	H	1487	ENSP00000418379:Q1487H	ENSP00000418379:Q1487H	Q	-	3	2	TAF1L	32621117	0.284000	0.24287	0.984000	0.44739	0.380000	0.30137	0.203000	0.17315	0.514000	0.28300	0.205000	0.17691	CAG		TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2		
SLC25A51	92014	hgsc.bcm.edu	37	9	37887989	37887989	+	Missense_Mutation	SNP	T	T	C			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr9:37887989T>C	ENST00000377716.2	-	3	1302	c.559A>G	c.(559-561)Aat>Gat	p.N187D	SLC25A51_ENST00000380590.3_Missense_Mutation_p.N187D|RP11-613M10.9_ENST00000540557.1_Intron|SLC25A51_ENST00000242275.6_Missense_Mutation_p.N187D|SLC25A51_ENST00000496760.1_Intron			Q9H1U9	S2551_HUMAN	solute carrier family 25, member 51	187					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)											AACAAGACATTGCTGAGTCCA	0.463																																																	0			9											76.0	73.0	74.0					9																	37887989		2203	4296	6499	37877989	SO:0001583	missense	92014			BC008500	CCDS6614.1	9p13.3-p12	2013-05-22	2012-03-29	2012-03-29	ENSG00000122696	ENSG00000122696		"""Solute carriers"""	23323	protein-coding gene	gene with protein product			"""mitochondrial carrier triple repeat 1"""	MCART1		12477932	Standard	NM_033412		Approved	MGC14836, CG7943	uc004aav.2	Q9H1U9	OTTHUMG00000019935	ENST00000377716.2:c.559A>G	9.37:g.37887989T>C	ENSP00000366945:p.Asn187Asp	Somatic		Capture	Illumina HiSeq	Phase_I	37877989		Missense_Mutation	SNP	ENST00000377716.2	37	CCDS6614.1	.	.	.	.	.	.	.	.	.	.	.	23.1	4.380790	0.82792	.	.	ENSG00000122696	ENST00000380590;ENST00000377716;ENST00000242275	T;T;T	0.78816	-1.21;-1.21;-1.21	4.64	4.64	0.57946	Mitochondrial carrier domain (2);	0.058414	0.64402	N	0.000004	D	0.87406	0.6169	M	0.81802	2.56	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.88858	0.3324	10	0.72032	D	0.01	.	12.3163	0.54958	0.0:0.0:0.0:1.0	.	187	Q9H1U9	MCAR1_HUMAN	D	187	ENSP00000369964:N187D;ENSP00000366945:N187D;ENSP00000242275:N187D	ENSP00000242275:N187D	N	-	1	0	MCART1	37877989	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.568000	0.82369	1.868000	0.54150	0.477000	0.44152	AAT		SLC25A51-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313746.1	NM_033412	
APBA1	320	hgsc.bcm.edu	37	9	72071249	72071249	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr9:72071249A>G	ENST00000265381.4	-	8	1924	c.1702T>C	c.(1702-1704)Tcc>Ccc	p.S568P	APBA1_ENST00000470082.1_5'UTR	NM_001163.3	NP_001154.2	Q02410	APBA1_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 1	568	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				axon cargo transport (GO:0008088)|cell adhesion (GO:0007155)|gamma-aminobutyric acid secretion (GO:0014051)|glutamate secretion (GO:0014047)|in utero embryonic development (GO:0001701)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein complex assembly (GO:0006461)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synaptic vesicle (GO:0008021)	beta-amyloid binding (GO:0001540)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(4)|kidney(2)|large_intestine(12)|lung(13)|prostate(3)|skin(3)	37						TTCTCCTGGGAGTTGGAGCGA	0.562																																																	0			9											241.0	231.0	234.0					9																	72071249		2203	4300	6503	71261069	SO:0001583	missense	320			AF029106	CCDS6630.1	9q13-q21	2008-07-18	2008-07-18		ENSG00000107282	ENSG00000107282			578	protein-coding gene	gene with protein product		602414		MINT1		7678331, 7719031	Standard	NM_001163		Approved	D9S411E, X11	uc004ahh.2	Q02410	OTTHUMG00000019984	ENST00000265381.4:c.1702T>C	9.37:g.72071249A>G	ENSP00000265381:p.Ser568Pro	Somatic		Capture	Illumina HiSeq	Phase_I	71261069	O14914|O60570|Q5VYR8	Missense_Mutation	SNP	ENST00000265381.4	37	CCDS6630.1	.	.	.	.	.	.	.	.	.	.	A	16.97	3.268499	0.59540	.	.	ENSG00000107282	ENST00000265381	T	0.54675	0.56	6.06	6.06	0.98353	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	0.110411	0.64402	D	0.000008	T	0.59542	0.2201	L	0.41906	1.305	0.58432	D	0.999999	D	0.54397	0.966	P	0.55303	0.773	T	0.59490	-0.7445	10	0.49607	T	0.09	-18.3886	16.6003	0.84812	1.0:0.0:0.0:0.0	.	568	Q02410	APBA1_HUMAN	P	568	ENSP00000265381:S568P	ENSP00000265381:S568P	S	-	1	0	APBA1	71261069	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.224000	0.51238	2.319000	0.78375	0.533000	0.62120	TCC		APBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052589.2	NM_001163	
C9orf41	138199	hgsc.bcm.edu	37	9	77631258	77631258	+	Silent	SNP	A	A	T			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr9:77631258A>T	ENST00000376834.3	-	3	668	c.516T>A	c.(514-516)acT>acA	p.T172T	RP11-197P3.5_ENST00000455336.2_RNA|C9orf41_ENST00000376837.3_Silent_p.T172T	NM_152420.1	NP_689633.1	Q8N4J0	CI041_HUMAN	chromosome 9 open reading frame 41	172										endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|skin(1)|urinary_tract(2)	17						CTGCTTTCCCAGTTTCACTCC	0.353																																																	0			9											176.0	178.0	177.0					9																	77631258		2203	4300	6503	76821078	SO:0001819	synonymous_variant	138199			AK098661	CCDS6649.1	9q21.31	2012-03-15			ENSG00000156017	ENSG00000156017			23435	protein-coding gene	gene with protein product						12477932	Standard	NM_152420		Approved	FLJ25795	uc004ajq.3	Q8N4J0	OTTHUMG00000020032	ENST00000376834.3:c.516T>A	9.37:g.77631258A>T		Somatic		Capture	Illumina HiSeq	Phase_I	76821078	Q7Z383|Q8N7C5	Silent	SNP	ENST00000376834.3	37	CCDS6649.1																																																																																				C9orf41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052703.1	NM_152420	
PTPN3	5774	hgsc.bcm.edu	37	9	112168802	112168802	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr9:112168802A>G	ENST00000374541.2	-	18	1836	c.1732T>C	c.(1732-1734)Ttc>Ctc	p.F578L	PTPN3_ENST00000412145.1_Missense_Mutation_p.F447L|PTPN3_ENST00000262539.3_Missense_Mutation_p.F424L|PTPN3_ENST00000394827.3_Missense_Mutation_p.F46L|PTPN3_ENST00000446349.1_Missense_Mutation_p.F402L	NM_001145368.1|NM_002829.3	NP_001138840.1|NP_002820.3	P26045	PTN3_HUMAN	protein tyrosine phosphatase, non-receptor type 3	578	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				negative regulation of membrane protein ectodomain proteolysis (GO:0051045)|negative regulation of mitotic cell cycle (GO:0045930)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of membrane depolarization during action potential (GO:0098902)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)	ATPase binding (GO:0051117)|phosphotyrosine binding (GO:0001784)|protein tyrosine phosphatase activity (GO:0004725)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	41						GCTTTGATGAACATCACCACT	0.572																																																	0			9											176.0	159.0	165.0					9																	112168802		2203	4300	6503	111208623	SO:0001583	missense	5774				CCDS6776.1, CCDS48000.1, CCDS48001.1	9q31	2011-06-09			ENSG00000070159	ENSG00000070159		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9655	protein-coding gene	gene with protein product		176877				1648725	Standard	NM_002829		Approved	PTPH1	uc004bed.2	P26045	OTTHUMG00000020475	ENST00000374541.2:c.1732T>C	9.37:g.112168802A>G	ENSP00000363667:p.Phe578Leu	Somatic		Capture	Illumina HiSeq	Phase_I	111208623	A0AUW9|E7EN99|E9PGU7	Missense_Mutation	SNP	ENST00000374541.2	37	CCDS6776.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.205511	0.79127	.	.	ENSG00000070159	ENST00000394831;ENST00000412145;ENST00000446349;ENST00000374541;ENST00000394827;ENST00000262539	T;T;T;T;T	0.26223	1.75;1.75;1.75;1.75;1.75	5.74	5.74	0.90152	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.24736	0.0600	N	0.02266	-0.62	0.80722	D	1	D;B;B	0.89917	1.0;0.333;0.047	D;B;B	0.87578	0.998;0.326;0.267	T	0.41466	-0.9507	10	0.13470	T	0.59	.	16.0229	0.80512	1.0:0.0:0.0:0.0	.	424;533;578	B7Z3H5;B7Z9V1;P26045	.;.;PTN3_HUMAN	L	578;447;402;578;46;424	ENSP00000416654:F447L;ENSP00000395384:F402L;ENSP00000363667:F578L;ENSP00000378304:F46L;ENSP00000262539:F424L	ENSP00000262539:F424L	F	-	1	0	PTPN3	111208623	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.189000	0.69895	0.459000	0.35465	TTC		PTPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053598.4		
ASTN2	23245	hgsc.bcm.edu	37	9	119976742	119976742	+	Missense_Mutation	SNP	G	G	A	rs554132287		TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr9:119976742G>A	ENST00000313400.4	-	3	1010	c.910C>T	c.(910-912)Cgg>Tgg	p.R304W	ASTN2_ENST00000361477.3_5'UTR|ASTN2_ENST00000373996.3_Missense_Mutation_p.R304W|ASTN2_ENST00000361209.2_Missense_Mutation_p.R304W			O75129	ASTN2_HUMAN	astrotactin 2	304					negative regulation of protein localization to cell surface (GO:2000009)	cell pole (GO:0060187)|endosome (GO:0005768)|integral component of membrane (GO:0016021)				breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(21)|lung(45)|ovary(4)|pancreas(2)|prostate(2)|skin(9)|stomach(1)|urinary_tract(1)	102						TGGTTGGCCCGCCTAGGTGGC	0.587													G|||	1	0.000199681	0.0008	0.0	5008	,	,		16810	0.0		0.0	False		,,,				2504	0.0																0			9											77.0	76.0	76.0					9																	119976742		2203	4300	6503	119016563	SO:0001583	missense	23245			AF116574	CCDS6814.1, CCDS6815.1, CCDS48009.1, CCDS48009.2, CCDS55334.1	9q33	2008-02-05			ENSG00000148219	ENSG00000148219			17021	protein-coding gene	gene with protein product		612856				9734811	Standard	NM_014010		Approved	KIAA0634	uc004bjt.2	O75129	OTTHUMG00000021013	ENST00000313400.4:c.910C>T	9.37:g.119976742G>A	ENSP00000314038:p.Arg304Trp	Somatic		Capture	Illumina HiSeq	Phase_I	119016563	A2A2T7|A2A2T9|Q52LQ2|Q5JVX8|Q5JVX9|Q5JVY1|Q5VXG8|Q5VZX6|Q8N6P8|Q8WV47|Q96FL4|Q9UHW6	Missense_Mutation	SNP	ENST00000313400.4	37		.	.	.	.	.	.	.	.	.	.	G	16.93	3.256896	0.59321	.	.	ENSG00000148219	ENST00000313400;ENST00000373996;ENST00000373986;ENST00000361209	T;T;T;T	0.12569	2.85;2.85;2.67;2.78	5.16	3.08	0.35506	.	0.297842	0.26967	N	0.021589	T	0.15739	0.0379	N	0.14661	0.345	0.39201	D	0.963149	P;D;D	0.89917	0.932;0.993;1.0	B;P;D	0.67382	0.079;0.727;0.951	T	0.11348	-1.0591	9	.	.	.	-22.0226	8.2197	0.31534	0.0822:0.0:0.5902:0.3276	.	304;304;304	O75129-2;O75129;O75129-3	.;ASTN2_HUMAN;.	W	304;304;31;304	ENSP00000314038:R304W;ENSP00000363108:R304W;ENSP00000363098:R31W;ENSP00000354504:R304W	.	R	-	1	2	ASTN2	119016563	0.251000	0.23961	0.996000	0.52242	0.769000	0.43574	0.547000	0.23299	1.115000	0.41800	0.655000	0.94253	CGG		ASTN2-201	KNOWN	basic	protein_coding	protein_coding		NM_014010	
RB1	5925	hgsc.bcm.edu	37	13	49037913	49037913	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr13:49037913A>G	ENST00000267163.4	+	21	2291	c.2153A>G	c.(2152-2154)gAc>gGc	p.D718G		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	718	Domain B.|Pocket; binds T and E1A.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|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 during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(10)|p.I703_E737del(2)|p.C712_A727del(1)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	AAGAATATAGACCTTAAATTC	0.299		6	"""D, Mis, N, F, S"""		"""retinoblastoma, sarcoma, breast, small cell lung"""	"""retinoblastoma, sarcoma, breast, small cell lung"""			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																													yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"""L, E, M, O"""	28	Whole gene deletion(15)|Unknown(10)|Deletion - In frame(3)	bone(10)|haematopoietic_and_lymphoid_tissue(4)|breast(4)|lung(2)|adrenal_gland(1)|eye(1)|soft_tissue(1)|endometrium(1)|urinary_tract(1)|ovary(1)|prostate(1)|liver(1)	13											113.0	118.0	116.0					13																	49037913		2203	4292	6495	47935914	SO:0001583	missense	5925	Familial Cancer Database		M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"""Endogenous ligands"""	9884	protein-coding gene	gene with protein product	"""prepro-retinoblastoma-associated protein"", ""protein phosphatase 1, regulatory subunit 130"""	614041	"""osteosarcoma"""	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.2153A>G	13.37:g.49037913A>G	ENSP00000267163:p.Asp718Gly	Somatic		Capture	Illumina HiSeq	Phase_I	47935914	A8K5E3|P78499|Q5VW46|Q8IZL4	Missense_Mutation	SNP	ENST00000267163.4	37	CCDS31973.1	.	.	.	.	.	.	.	.	.	.	A	27.1	4.796854	0.90453	.	.	ENSG00000139687	ENST00000542917;ENST00000267163	D	0.92348	-3.02	6.07	6.07	0.98685	Retinoblastoma-associated protein, B-box (1);Cyclin-like (3);	0.000000	0.85682	D	0.000000	D	0.95723	0.8609	M	0.71296	2.17	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.96024	0.9011	10	0.87932	D	0	-15.7516	16.6406	0.85098	1.0:0.0:0.0:0.0	.	718	P06400	RB_HUMAN	G	697;718	ENSP00000267163:D718G	ENSP00000267163:D718G	D	+	2	0	RB1	47935914	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.962000	0.93254	2.326000	0.78906	0.533000	0.62120	GAC		RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1		
AKR1C4	1109	hgsc.bcm.edu	37	10	5247796	5247796	+	Splice_Site	SNP	A	A	G			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr10:5247796A>G	ENST00000380448.1	+	6	699	c.446A>G	c.(445-447)gAg>gGg	p.E149G	AKR1C4_ENST00000263126.1_Splice_Site_p.E149G			P17516	AK1C4_HUMAN	aldo-keto reductase family 1, member C4	149					androgen metabolic process (GO:0008209)|bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular response to jasmonic acid stimulus (GO:0071395)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aldo-keto reductase (NADP) activity (GO:0004033)|androsterone dehydrogenase activity (GO:0047023)|bile acid transmembrane transporter activity (GO:0015125)|chlordecone reductase activity (GO:0047743)|electron carrier activity (GO:0009055)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|retinal dehydrogenase activity (GO:0001758)	p.E149A(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|skin(2)|stomach(2)|urinary_tract(1)	18						GCCACATGGGAGGTGAGTGCT	0.448																																																	1	Substitution - Missense(1)	ovary(1)	10											119.0	105.0	109.0					10																	5247796		2203	4300	6503	5237796	SO:0001630	splice_region_variant	1109			M33375	CCDS7064.1	10p15.1	2012-12-04	2012-12-04		ENSG00000198610	ENSG00000198610	1.1.1.225	"""Aldo-keto reductases"""	387	protein-coding gene	gene with protein product	"""chlordecone reductase; 3-alpha hydroxysteroid dehydrogenase, type I; dihydrodiol dehydrogenase 4"""	600451	"""aldo-keto reductase family 1, member C4 (chlordecone reductase; 3-alpha hydroxysteroid dehydrogenase, type I; dihydrodiol dehydrogenase 4)"""	CHDR		7789999	Standard	NM_001818		Approved	DD4, HAKRA, C11, 3-alpha-HSD, CDR, MGC22581	uc001ihw.2	P17516	OTTHUMG00000017591	ENST00000380448.1:c.447+1A>G	10.37:g.5247796A>G		Somatic		Capture	Illumina HiSeq	Phase_I	5237796	Q5T6A3|Q8WW84|Q9NS54	Missense_Mutation	SNP	ENST00000380448.1	37	CCDS7064.1	.	.	.	.	.	.	.	.	.	.	A	11.31	1.600639	0.28534	.	.	ENSG00000198610	ENST00000380448;ENST00000263126	T;T	0.52526	0.66;0.66	3.16	3.16	0.36331	NADP-dependent oxidoreductase domain (3);	0.270365	0.31031	N	0.008395	T	0.42017	0.1184	L	0.37561	1.115	0.45390	D	0.998371	B	0.31459	0.324	B	0.39904	0.313	T	0.44605	-0.9317	10	0.72032	D	0.01	.	9.6032	0.39617	1.0:0.0:0.0:0.0	.	149	P17516	AK1C4_HUMAN	G	149	ENSP00000369814:E149G;ENSP00000263126:E149G	ENSP00000263126:E149G	E	+	2	0	AKR1C4	5237796	1.000000	0.71417	0.995000	0.50966	0.028000	0.11728	7.251000	0.78297	1.195000	0.43115	0.260000	0.18958	GAG		AKR1C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046543.2	NM_001818	Missense_Mutation
NSUN6	221078	hgsc.bcm.edu	37	10	18937509	18937509	+	Silent	SNP	T	T	C			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr10:18937509T>C	ENST00000377304.4	-	2	559	c.141A>G	c.(139-141)tcA>tcG	p.S47S	RP11-139J15.7_ENST00000606425.1_Silent_p.S35S	NM_182543.2	NP_872349.1	Q8TEA1	NSUN6_HUMAN	NOP2/Sun domain family, member 6	47							methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			endometrium(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	15						ATGGAGGATGTGACAGGTGCT	0.348																																																	0			10											214.0	202.0	206.0					10																	18937509		2203	4300	6503	18977515	SO:0001819	synonymous_variant	221078			BC035778	CCDS7130.1	10p13	2014-06-23	2009-11-23	2004-08-26	ENSG00000241058	ENSG00000241058		"""NOP2/Sun domain containing"""	23529	protein-coding gene	gene with protein product			"""NOL1/NOP2/Sun domain family 6"", ""NOL1/NOP2/Sun domain family, member 6"", ""ARL5B antisense RNA 1"""	NOPD1, ARL5B-AS1			Standard	XM_005252394		Approved	FLJ23743	uc010qcp.1	Q8TEA1	OTTHUMG00000017767	ENST00000377304.4:c.141A>G	10.37:g.18937509T>C		Somatic		Capture	Illumina HiSeq	Phase_I	18977515	B0YJ54	Silent	SNP	ENST00000377304.4	37	CCDS7130.1																																																																																				NSUN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047083.1	NM_182543	
CDH23	64072	hgsc.bcm.edu	37	10	73326628	73326628	+	Missense_Mutation	SNP	G	G	A	rs369624952		TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr10:73326628G>A	ENST00000224721.6	+	6	579	c.574G>A	c.(574-576)Gtc>Atc	p.V192I	CDH23_ENST00000461841.3_Missense_Mutation_p.V232I|CDH23_ENST00000398842.3_Missense_Mutation_p.V187I|CDH23_ENST00000299366.7_Missense_Mutation_p.V232I|CDH23_ENST00000398809.4_Missense_Mutation_p.V187I	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	187	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						CCGCGGTATCGTCACAGTGAT	0.652																																																	0			10						G	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	0,4104		0,0,2052	43.0	47.0	46.0		559,559,559,559,559	4.8	0.9	10		46	1,8375		0,1,4187	no	missense,missense,missense,missense,missense	CDH23	NM_001171930.1,NM_001171931.1,NM_001171932.1,NM_022124.5,NM_052836.3	29,29,29,29,29	0,1,6239	AA,AG,GG		0.0119,0.0,0.0080	benign,benign,benign,benign,benign	187/1382,187/1062,187/407,187/3355,187/531	73326628	1,12479	2052	4188	6240	72996634	SO:0001583	missense	64072			AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"""Cadherins / Cadherin-related"""	13733	protein-coding gene	gene with protein product	"""cadherin-related family member 23"""	605516	"""cadherin related 23"", ""cadherin-like 23"""	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.574G>A	10.37:g.73326628G>A	ENSP00000224721:p.Val192Ile	Somatic		Capture	Illumina HiSeq	Phase_I	72996634	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	37		.	.	.	.	.	.	.	.	.	.	G	9.582	1.123744	0.20959	0.0	1.19E-4	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000398828;ENST00000398809;ENST00000398842;ENST00000299366;ENST00000224721;ENST00000416060	T;T	0.57107	0.42;0.42	5.7	4.8	0.61643	Cadherin (4);Cadherin-like (1);	0.093767	0.41097	N	0.000956	T	0.28566	0.0707	N	0.03029	-0.43	0.80722	D	1	B;B;B;B	0.20052	0.014;0.018;0.041;0.019	B;B;B;B	0.17722	0.004;0.019;0.006;0.015	T	0.08597	-1.0714	10	0.17832	T	0.49	.	14.9766	0.71277	0.0683:0.0:0.9317:0.0	.	187;187;187;187	A5D6V9;Q9H251;Q9H251-5;E7ESV7	.;CAD23_HUMAN;.;.	I	192;187;187;187;187;192;192;128	ENSP00000381789:V187I;ENSP00000381822:V187I	ENSP00000224721:V192I	V	+	1	0	CDH23	72996634	1.000000	0.71417	0.915000	0.36163	0.291000	0.27294	7.514000	0.81750	1.445000	0.47624	-0.219000	0.12488	GTC		CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
PTEN	5728	hgsc.bcm.edu	37	10	89717616	89717616	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr10:89717616A>G	ENST00000371953.3	+	7	1998	c.641A>G	c.(640-642)cAg>cGg	p.Q214R	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	214	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.Q214fs*1(1)|p.?(1)|p.Q214fs*22(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		GCAGATCCTCAGTTTGTGGTC	0.388		31	"""D, Mis, N, F, S"""		"""glioma,  prostate, endometrial"""	"""harmartoma, glioma,  prostate, endometrial"""			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																													yes	Rec	yes	"""Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"""	10	10q23.3	5728	phosphatase and tensin homolog gene		"""L, E, M, O"""	50	Whole gene deletion(37)|Deletion - Frameshift(10)|Complex - frameshift(1)|Deletion - In frame(1)|Unknown(1)	prostate(16)|central_nervous_system(10)|skin(6)|lung(4)|haematopoietic_and_lymphoid_tissue(3)|breast(3)|ovary(3)|endometrium(2)|urinary_tract(2)|soft_tissue(1)	10											113.0	100.0	104.0					10																	89717616		2203	4300	6503	89707596	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	9588	protein-coding gene	gene with protein product	"""mutated in multiple advanced cancers 1"""	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.641A>G	10.37:g.89717616A>G	ENSP00000361021:p.Gln214Arg	Somatic		Capture	Illumina HiSeq	Phase_I	89707596	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	A	15.87	2.960540	0.53400	.	.	ENSG00000171862	ENST00000371953	D	0.85339	-1.97	5.67	5.67	0.87782	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.164422	0.56097	D	0.000025	D	0.82692	0.5092	L	0.45228	1.405	0.80722	D	1	P	0.42584	0.784	B	0.43225	0.412	T	0.81786	-0.0773	9	.	.	.	-2.2072	15.9118	0.79477	1.0:0.0:0.0:0.0	.	214	P60484	PTEN_HUMAN	R	214	ENSP00000361021:Q214R	.	Q	+	2	0	PTEN	89707596	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.973000	0.76116	2.162000	0.67917	0.477000	0.44152	CAG		PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314	
IRX1	79192	hgsc.bcm.edu	37	5	3599404	3599404	+	Silent	SNP	G	G	A	rs200766970		TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr5:3599404G>A	ENST00000302006.3	+	2	394	c.342G>A	c.(340-342)gcG>gcA	p.A114A	CTD-2012M11.3_ENST00000559410.1_RNA	NM_024337.3	NP_077313.3	P78414	IRX1_HUMAN	iroquois homeobox 1	114					proximal/distal pattern formation involved in metanephric nephron development (GO:0072272)|regulation of transcription, DNA-templated (GO:0006355)|specification of loop of Henle identity (GO:0072086)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			biliary_tract(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(18)|ovary(2)|pancreas(1)|prostate(5)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						CCCACACGGCGCCGGCTTATT	0.652																																																	0			5											39.0	44.0	43.0					5																	3599404		2203	4300	6503	3652404	SO:0001819	synonymous_variant	79192			U90307	CCDS34132.1	5p15.33	2011-12-16	2007-07-13		ENSG00000170549	ENSG00000170549		"""Homeoboxes / TALE class"""	14358	protein-coding gene	gene with protein product		606197					Standard	NM_024337		Approved	IRX-5	uc003jde.3	P78414	OTTHUMG00000161632	ENST00000302006.3:c.342G>A	5.37:g.3599404G>A		Somatic		Capture	Illumina HiSeq	Phase_I	3652404	Q7Z2F8|Q8N312	Silent	SNP	ENST00000302006.3	37	CCDS34132.1																																																																																				IRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365546.1	NM_024337	
C5orf42	65250	hgsc.bcm.edu	37	5	37120431	37120431	+	Missense_Mutation	SNP	T	T	C			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr5:37120431T>C	ENST00000508244.1	-	48	9128	c.9035A>G	c.(9034-9036)cAt>cGt	p.H3012R	C5orf42_ENST00000512288.1_5'UTR|C5orf42_ENST00000425232.2_Missense_Mutation_p.H3012R|C5orf42_ENST00000274258.7_Missense_Mutation_p.H1910R			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	3012						integral component of membrane (GO:0016021)		p.H1910R(1)		breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			ACTGTGACCATGTTGATTCTC	0.353																																																	1	Substitution - Missense(1)	ovary(1)	5											81.0	79.0	80.0					5																	37120431		2203	4300	6503	37156188	SO:0001583	missense	65250				CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.9035A>G	5.37:g.37120431T>C	ENSP00000421690:p.His3012Arg	Somatic		Capture	Illumina HiSeq	Phase_I	37156188	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	37	CCDS34146.2	.	.	.	.	.	.	.	.	.	.	T	11.83	1.755291	0.31046	.	.	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429	T;T;T;T	0.47869	0.83;0.83;0.83;0.83	5.21	4.05	0.47172	.	0.623087	0.16618	N	0.206614	T	0.33323	0.0859	L	0.48362	1.52	0.09310	N	1	B;P	0.41848	0.007;0.763	B;B	0.33960	0.007;0.173	T	0.10847	-1.0612	10	0.20519	T	0.43	.	7.7843	0.29083	0.0:0.0948:0.0:0.9052	.	3012;1910	E9PH94;Q9H799	.;CE042_HUMAN	R	3012;3012;1910;2078	ENSP00000421690:H3012R;ENSP00000389014:H3012R;ENSP00000274258:H1910R;ENSP00000424223:H2078R	ENSP00000274258:H1910R	H	-	2	0	C5orf42	37156188	0.005000	0.15991	0.002000	0.10522	0.049000	0.14656	1.052000	0.30429	0.838000	0.34948	0.529000	0.55759	CAT		C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073	
SPZ1	84654	hgsc.bcm.edu	37	5	79617086	79617086	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr5:79617086A>G	ENST00000296739.4	+	1	1297	c.1052A>G	c.(1051-1053)gAg>gGg	p.E351G		NM_032567.3	NP_115956.3	Q9BXG8	SPZ1_HUMAN	spermatogenic leucine zipper 1	351					transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(5)|large_intestine(4)|lung(12)|ovary(1)|skin(2)	26		Lung NSC(167;0.0393)|all_lung(232;0.0428)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;3.43e-47)|Epithelial(54;2.25e-41)|all cancers(79;4.19e-36)		ACTCTGCAAGAGAAGCCAATT	0.393																																																	0			5											84.0	80.0	81.0					5																	79617086		1842	4092	5934	79652842	SO:0001583	missense	84654				CCDS43336.1	5q14.1	2014-06-13				ENSG00000164299			30721	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 148"""					11165476, 12778315, 15226296, 15829580, 15899793	Standard	NM_032567		Approved	NYD-TSP1, FLJ25709, PPP1R148	uc003kgn.3	Q9BXG8		ENST00000296739.4:c.1052A>G	5.37:g.79617086A>G	ENSP00000369611:p.Glu351Gly	Somatic		Capture	Illumina HiSeq	Phase_I	79652842	B2RA21|Q8N4P1|Q8N7E9	Missense_Mutation	SNP	ENST00000296739.4	37	CCDS43336.1	.	.	.	.	.	.	.	.	.	.	A	10.30	1.313297	0.23908	.	.	ENSG00000164299	ENST00000296739	T	0.34275	1.37	4.04	0.123	0.14709	.	1.013970	0.07924	N	0.976388	T	0.26919	0.0659	L	0.34521	1.04	0.09310	N	1	B	0.17667	0.023	B	0.16289	0.015	T	0.30880	-0.9963	10	0.54805	T	0.06	-13.0592	7.4159	0.27044	0.5626:0.0:0.4374:0.0	.	351	Q9BXG8	SPZ1_HUMAN	G	351	ENSP00000369611:E351G	ENSP00000369611:E351G	E	+	2	0	SPZ1	79652842	0.024000	0.19004	0.000000	0.03702	0.211000	0.24417	0.824000	0.27379	0.025000	0.15241	-0.385000	0.06624	GAG		SPZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369322.1	NM_032567	
ANKRD32	84250	hgsc.bcm.edu	37	5	94022411	94022411	+	Silent	SNP	T	T	C			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr5:94022411T>C	ENST00000265140.5	+	16	2528	c.2109T>C	c.(2107-2109)tcT>tcC	p.S703S		NM_032290.3	NP_115666.2	Q9BQI6	ANR32_HUMAN	ankyrin repeat domain 32	703						centrosome (GO:0005813)|nucleus (GO:0005634)				NS(1)|breast(2)|endometrium(2)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|skin(1)	13		all_cancers(142;1.51e-09)|all_epithelial(76;4.68e-12)|all_lung(232;5.94e-05)|Ovarian(174;0.000953)|Lung NSC(167;0.00105)|Colorectal(57;0.122)|Lung SC(612;0.152)		all cancers(79;3.88e-18)		AGCCACTCTCTCTTCAGAAAA	0.363																																																	0			5											99.0	100.0	99.0					5																	94022411		2203	4300	6503	94048167	SO:0001819	synonymous_variant	84250			AL136560	CCDS4071.2	5q15	2013-01-10			ENSG00000133302	ENSG00000133302		"""Ankyrin repeat domain containing"""	25408	protein-coding gene	gene with protein product			"""BRCT domain containing 1"""	BRCTD1			Standard	NM_032290		Approved	DKFZp761C121, DKFZp564C0469	uc003kkr.4	Q9BQI6	OTTHUMG00000121133	ENST00000265140.5:c.2109T>C	5.37:g.94022411T>C		Somatic		Capture	Illumina HiSeq	Phase_I	94048167	B4DMG4|Q3B7K4|Q6NSA5|Q6PHW9|Q9Y402	Silent	SNP	ENST00000265140.5	37	CCDS4071.2																																																																																				ANKRD32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241610.1	NM_032290	
APC	324	hgsc.bcm.edu	37	5	112154869	112154869	+	Silent	SNP	G	G	A			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr5:112154869G>A	ENST00000457016.1	+	10	1520	c.1140G>A	c.(1138-1140)cgG>cgA	p.R380R	APC_ENST00000508376.2_Silent_p.R380R|APC_ENST00000257430.4_Silent_p.R380R			P25054	APC_HUMAN	adenomatous polyposis coli	380	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)			NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AAGAGGCTCGGGCCAGGGCCA	0.507		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)		yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	0			5											57.0	54.0	55.0					5																	112154869		2202	4300	6502	112182768	SO:0001819	synonymous_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.1140G>A	5.37:g.112154869G>A		Somatic		Capture	Illumina HiSeq	Phase_I	112182768	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																				APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
APC	324	hgsc.bcm.edu	37	5	112173917	112173917	+	Nonsense_Mutation	SNP	C	C	T	rs121913333		TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr5:112173917C>T	ENST00000457016.1	+	16	3006	c.2626C>T	c.(2626-2628)Cga>Tga	p.R876*	APC_ENST00000508376.2_Nonsense_Mutation_p.R876*|APC_ENST00000257430.4_Nonsense_Mutation_p.R876*|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	876	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R876*(38)|p.S874_R876>*(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TTCTTCAAAGCGAGGTTTGCA	0.463		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)		yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	40	Substitution - Nonsense(38)|Unknown(1)|Complex - deletion inframe(1)	large_intestine(37)|lung(1)|breast(1)|skin(1)	5	GRCh37	CM942020	APC	M	rs121913333						70.0	72.0	71.0					5																	112173917		2202	4300	6502	112201816	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.2626C>T	5.37:g.112173917C>T	ENSP00000413133:p.Arg876*	Somatic		Capture	Illumina HiSeq	Phase_I	112201816	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	37	6.588996	0.97688	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.92	4.09	0.47781	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.2738	14.8639	0.70401	0.3912:0.6088:0.0:0.0	.	.	.	.	X	876;858;876;876;876	.	ENSP00000257430:R876X	R	+	1	2	APC	112201816	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	1.385000	0.34408	0.785000	0.33685	0.557000	0.71058	CGA		APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
PCDHGA3	56112	hgsc.bcm.edu	37	5	140724410	140724410	+	Silent	SNP	C	C	T	rs547334260		TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr5:140724410C>T	ENST00000253812.6	+	1	810	c.810C>T	c.(808-810)gaC>gaT	p.D270D	PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018916.3|NM_032011.1	NP_061739.2|NP_114400.1	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3	270	Cadherin 3. {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)	p.D270D(1)		breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGACCCTGACGAGGGATTCA	0.468													N|||	1	0.000199681	0.0	0.0014	5008	,	,		20544	0.0		0.0	False		,,,				2504	0.0																1	Substitution - coding silent(1)	endometrium(1)	5											52.0	54.0	54.0					5																	140724410		2051	4214	6265	140704594	SO:0001819	synonymous_variant	56112			AF152510	CCDS47290.1, CCDS75329.1	5q31	2010-01-26			ENSG00000254245	ENSG00000254245		"""Cadherins / Protocadherins : Clustered"""	8701	other	protocadherin		606290				10380929	Standard	NM_032011		Approved	PCDH-GAMMA-A3		Q9Y5H0	OTTHUMG00000163680	ENST00000253812.6:c.810C>T	5.37:g.140724410C>T		Somatic		Capture	Illumina HiSeq	Phase_I	140704594	Q9Y5D4	Silent	SNP	ENST00000253812.6	37	CCDS47290.1																																																																																				PCDHGA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377017.1	NM_018916	
CAMK2A	815	hgsc.bcm.edu	37	5	149602710	149602710	+	Silent	SNP	C	C	T			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr5:149602710C>T	ENST00000348628.6	-	17	1940	c.1275G>A	c.(1273-1275)gaG>gaA	p.E425E	CAMK2A_ENST00000351010.6_5'UTR|CAMK2A_ENST00000398376.3_Silent_p.E436E	NM_015981.3|NM_171825.2	NP_057065.2|NP_741960.1	Q9UQM7	KCC2A_HUMAN	calcium/calmodulin-dependent protein kinase II alpha	425					calcium ion transport (GO:0006816)|cytokine-mediated signaling pathway (GO:0019221)|G1/S transition of mitotic cell cycle (GO:0000082)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of neurotransmitter secretion (GO:0046928)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|kinase activity (GO:0016301)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|skin(1)|stomach(1)	15		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGCAGGCTGACTCGTCGCCCA	0.667																																																	0			5											75.0	85.0	82.0					5																	149602710		2202	4300	6502	149582903	SO:0001819	synonymous_variant	815			AB023185	CCDS43386.1, CCDS43387.1	5q32	2013-09-20	2008-10-30		ENSG00000070808	ENSG00000070808	2.7.11.17		1460	protein-coding gene	gene with protein product	"""CaM-kinase II alpha chain"", ""calcium/calmodulin-dependent protein kinase II alpha-B subunit"", ""CaM kinase II alpha subunit"", ""CaMK-II alpha subunit"", ""calcium/calmodulin-dependent protein kinase type II alpha chain"""	114078	"""calcium/calmodulin-dependent protein kinase (CaM kinase) II alpha"""	CAMKA		10231032, 3475713	Standard	NM_015981		Approved	KIAA0968, CaMKIINalpha	uc003lrt.2	Q9UQM7	OTTHUMG00000134281	ENST00000348628.6:c.1275G>A	5.37:g.149602710C>T		Somatic		Capture	Illumina HiSeq	Phase_I	149582903	Q9UL21|Q9Y2H4|Q9Y352	Silent	SNP	ENST00000348628.6	37	CCDS43386.1																																																																																				CAMK2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258869.2	NM_015981	
CCDC69	26112	hgsc.bcm.edu	37	5	150585025	150585025	+	Silent	SNP	T	T	C			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr5:150585025T>C	ENST00000355417.2	-	2	234	c.60A>G	c.(58-60)gaA>gaG	p.E20E	CCDC69_ENST00000521308.1_Intron	NM_015621.2	NP_056436.2	A6NI79	CCD69_HUMAN	coiled-coil domain containing 69	20								p.E20D(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(2)|stomach(1)	9		Medulloblastoma(196;0.091)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CTGGTTCTGGTTCTTGGCGCT	0.572																																																	1	Substitution - Missense(1)	ovary(1)	5											171.0	154.0	160.0					5																	150585025		2203	4300	6503	150565218	SO:0001819	synonymous_variant	26112				CCDS4312.1	5q33.1	2008-02-05			ENSG00000198624	ENSG00000198624			24487	protein-coding gene	gene with protein product						12477932	Standard	NM_015621		Approved	FLJ13705, DKFZP434C171	uc011dcq.3	A6NI79	OTTHUMG00000130127	ENST00000355417.2:c.60A>G	5.37:g.150585025T>C		Somatic		Capture	Illumina HiSeq	Phase_I	150565218	A8K9X6	Silent	SNP	ENST00000355417.2	37	CCDS4312.1																																																																																				CCDC69-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252435.1	NM_015621	
KCNQ2	3785	hgsc.bcm.edu	37	20	62076010	62076010	+	Splice_Site	SNP	A	A	G			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr20:62076010A>G	ENST00000359125.2	-	4	865		c.e4+1		KCNQ2_ENST00000360480.3_Splice_Site|KCNQ2_ENST00000357249.2_Splice_Site|KCNQ2_ENST00000370224.1_Splice_Site|KCNQ2_ENST00000354587.3_Splice_Site|KCNQ2_ENST00000344425.5_Splice_Site|KCNQ2_ENST00000344462.4_Splice_Site|KCNQ2_ENST00000359689.1_Splice_Site	NM_172107.2	NP_742105.1	O43526	KCNQ2_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 2						axon guidance (GO:0007411)|nervous system development (GO:0007399)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ankyrin binding (GO:0030506)|delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|liver(1)|lung(30)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	GCCGTGACTCACCTTGCTGTG	0.687																																																	0			20											14.0	15.0	15.0					20																	62076010		2194	4283	6477	61546454	SO:0001630	splice_region_variant	3785			AF033348	CCDS13518.1, CCDS13519.1, CCDS13520.1, CCDS13521.1, CCDS46629.1	20q13.33	2012-07-05			ENSG00000075043	ENSG00000075043		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6296	protein-coding gene	gene with protein product		602235		EBN, EBN1		9425895, 16382104	Standard	NM_172107		Approved	Kv7.2, ENB1, BFNC, KCNA11, HNSPC	uc002yex.3	O43526	OTTHUMG00000033049	ENST00000359125.2:c.690+1T>C	20.37:g.62076010A>G		Somatic		Capture	Illumina HiSeq	Phase_I	61546454	O43796|O75580|O95845|Q4VXP4|Q4VXR6|Q5VYT8|Q96J59|Q99454	Splice_Site	SNP	ENST00000359125.2	37	CCDS13520.1	.	.	.	.	.	.	.	.	.	.	A	17.03	3.284296	0.59867	.	.	ENSG00000075043	ENST00000357249;ENST00000359125;ENST00000370226;ENST00000354587;ENST00000359689;ENST00000430658;ENST00000360480;ENST00000344462;ENST00000370224;ENST00000370222;ENST00000370221;ENST00000344425	.	.	.	3.89	3.89	0.44902	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.0255	0.58812	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	KCNQ2	61546454	1.000000	0.71417	0.998000	0.56505	0.797000	0.45037	6.093000	0.71422	1.544000	0.49359	0.477000	0.44152	.		KCNQ2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080353.1	NM_172109	Intron
CREBBP	1387	hgsc.bcm.edu	37	16	3789726	3789726	+	Splice_Site	SNP	C	C	T			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr16:3789726C>T	ENST00000262367.5	-	25	4943		c.e25-1		CREBBP_ENST00000382070.3_Splice_Site	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein						cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|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 transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		ATCCACAAACCTGAAACAAAA	0.483			"""T, N, F, Mis, O"""	"""MLL, MORF, RUNXBP2"""	"""ALL, AML, DLBCL, B-NHL """		Rubinstein-Taybi syndrome																																	Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	0			16											57.0	56.0	56.0					16																	3789726		2197	4300	6497	3729727	SO:0001630	splice_region_variant	1387			U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"""Chromatin-modifying enzymes / K-acetyltransferases"""	2348	protein-coding gene	gene with protein product		600140	"""Rubinstein-Taybi syndrome"""	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.4134-1G>A	16.37:g.3789726C>T		Somatic		Capture	Illumina HiSeq	Phase_I	3729727	D3DUC9|O00147|Q16376|Q4LE28	Splice_Site	SNP	ENST00000262367.5	37	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.564514	0.86439	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070	.	.	.	5.54	5.54	0.83059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.8419	0.96692	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CREBBP	3729727	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	7.713000	0.84693	2.767000	0.95098	0.561000	0.74099	.		CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380	Intron
MIB2	142678	hgsc.bcm.edu	37	1	1558755	1558796	+	Splice_Site	DEL	CCCTCTGCCCACAGGTCCCGAGCAGCCCGGCCCACCATGGAC	CCCTCTGCCCACAGGTCCCGAGCAGCCCGGCCCACCATGGAC	-	rs368037861|rs374321114|rs12755088|rs201820622	byFrequency	TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	CCCTCTGCCCACAGGTCCCGAGCAGCCCGGCCCACCATGGAC	CCCTCTGCCCACAGGTCCCGAGCAGCCCGGCCCACCATGGAC					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr1:1558755_1558796delCCCTCTGCCCACAGGTCCCGAGCAGCCCGGCCCACCATGGAC	ENST00000357210.4	+	3	326_354	c.110_138delCCCTCTGCCCACAGGTCCCGAGCAGCCCGGCCCACCATGGAC	c.(109-138)accctctgcccacaggtcccgagcagcccg>a	p.TLCPQVPSSP37del	MIB2_ENST00000378712.1_Intron|MIB2_ENST00000355826.5_Intron|MIB2_ENST00000505820.2_Splice_Site_p.TLCPQVPSSP94del|MIB2_ENST00000520777.1_Splice_Site_p.TLCPQVPSSP94del|MIB2_ENST00000512004.1_3'UTR|MIB2_ENST00000360522.4_Splice_Site_p.TLCPQVPSSP37del|MIB2_ENST00000378708.1_Intron|MIB2_ENST00000518681.1_Splice_Site_p.TLCPQVPSSP94del|MIB2_ENST00000504599.1_Start_Codon_Del|MIB2_ENST00000378710.3_Splice_Site_p.TLCPQVPSSP37del	NM_080875.2	NP_543151.2	Q96AX9	MIB2_HUMAN	mindbomb E3 ubiquitin protein ligase 2	37					Notch signaling pathway (GO:0007219)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)	early endosome (GO:0005769)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|lung(7)|prostate(4)|upper_aerodigestive_tract(1)	18	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;6.04e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;5.26e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.54e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|STAD - Stomach adenocarcinoma(132;0.00644)|BRCA - Breast invasive adenocarcinoma(365;0.00786)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		CCTGAGAATACCCTCTGCCCACAGGTCCCGAGCAGCCCGGCCCACCATGGACCCCTCTGCCC	0.711																																																	0			1																																								1548659	SO:0001630	splice_region_variant	142678			AK097106	CCDS41224.1, CCDS41224.2, CCDS53261.1, CCDS53262.1, CCDS53263.1, CCDS53264.1	1p36.33	2013-01-10	2012-02-23	2005-04-01	ENSG00000197530	ENSG00000197530		"""Zinc fingers, ZZ-type"", ""Ankyrin repeat domain containing"""	30577	protein-coding gene	gene with protein product		611141	"""zinc finger, ZZ type with ankyrin repeat domain 1"", ""mindbomb homolog 2 (Drosophila)"""	ZZANK1		12761501	Standard	NM_080875		Approved	skeletrophin, ZZZ5, FLJ39787	uc001agg.3	Q96AX9	OTTHUMG00000074647	ENST00000357210.4:c.111-1CCCTCTGCCCACAGGTCCCGAGCAGCCCGGCCCACCATGGAC>-	1.37:g.1558755_1558796delCCCTCTGCCCACAGGTCCCGAGCAGCCCGGCCCACCATGGAC		Somatic		Capture	Illumina HiSeq	Phase_I	1548618	A2AGM5|A2AGM6|B3KV93|B3KVF4|B3KXY1|B4DZ57|E9PGU1|E9PHQ1|F8WA73|J3KNZ7|Q7Z437|Q8IY62|Q8N786|Q8N897|Q8N8R2|Q8N911|Q8NB36|Q8NCY1|Q8NG59|Q8NG60|Q8NG61|Q8NI59|Q8WYN1	In_Frame_Del	DEL	ENST00000357210.4	37																																																																																					MIB2-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_080875	In_Frame_Del
SCTR	6344	hgsc.bcm.edu	37	2	120194651	120194652	+	IGR	INS	-	-	GTGTGC	rs3217464|rs201433053|rs201077606	byFrequency	TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr2:120194651_120194652insGTGTGC	ENST00000019103.5	-	0	1865				TMEM37_ENST00000465296.1_3'UTR|TMEM37_ENST00000306406.4_In_Frame_Ins_p.70_70T>SVP|TMEM37_ENST00000409826.1_In_Frame_Ins_p.82_82T>SVP	NM_002980.2	NP_002971.2	P47872	SCTR_HUMAN	secretin receptor						digestion (GO:0007586)|excretion (GO:0007588)|G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasmic microtubule (GO:0005881)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	secretin receptor activity (GO:0015055)	p.T70>SVP(1)		central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)	19					Secretin(DB00021)	CACCAACCAGACGATCTGCTTC	0.668														4489	0.896366	0.9705	0.8386	5008	,	,		15646	0.8919		0.8748	False		,,,				2504	0.864																1	Complex - insertion inframe(1)	ovary(1)	2								4023,213		1924,175,19						3.4	0.6		dbSNP_126	56	6958,1218		3018,922,148	no	coding	TMEM37	NM_183240.2		4942,1097,167	A1A1,A1R,RR		14.8973,5.0283,11.5292				10981,1431				119911122	SO:0001628	intergenic_variant	140738				CCDS2127.1	2q14.1	2012-08-10			ENSG00000080293	ENSG00000080293		"""GPCR / Class B : Glucagon receptors"""	10608	protein-coding gene	gene with protein product		182098				1646711	Standard	NM_002980		Approved		uc002tma.3	P47872	OTTHUMG00000131407		2.37:g.120194651_120194652insGTGTGC		Somatic		Capture	Illumina HiSeq	Phase_I	119911121	Q12961|Q13213|Q53T00	In_Frame_Ins	INS	ENST00000019103.5	37	CCDS2127.1																																																																																				SCTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254198.2		
DLX2	1746	hgsc.bcm.edu	37	2	172967128	172967129	+	In_Frame_Ins	INS	-	-	GCT	rs201510837|rs376692475	byFrequency	TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr2:172967128_172967129insGCT	ENST00000234198.4	-	1	499_500	c.138_139insAGC	c.(136-141)agcctc>agcAGCctc	p.46_47insS	DLX2_ENST00000466293.2_In_Frame_Ins_p.46_47insS|AC104801.1_ENST00000448117.1_lincRNA	NM_004405.3	NP_004396.1	Q07687	DLX2_HUMAN	distal-less homeobox 2	46	Poly-Ser.				brain development (GO:0007420)|branching morphogenesis of a nerve (GO:0048755)|cartilage development (GO:0051216)|cerebral cortex GABAergic interneuron fate commitment (GO:0021893)|embryonic cranial skeleton morphogenesis (GO:0048701)|hippocampus development (GO:0021766)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis of dentin-containing tooth (GO:0042475)|olfactory bulb development (GO:0021772)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment (GO:0021882)|subpallium development (GO:0021544)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded RNA binding (GO:0003727)			endometrium(1)|large_intestine(1)|lung(6)|ovary(2)|urinary_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(117;0.216)			GGCTTGTGGAGgctgctgctgc	0.738														113	0.0225639	0.0008	0.0865	5008	,	,		12199	0.0387		0.0109	False		,,,				2504	0.002				GBM(188;775 2993 11256 23072)												0			2																																								172675375	SO:0001652	inframe_insertion	9856			U51003	CCDS2248.1	2q31.1	2011-06-20	2005-12-22		ENSG00000115844	ENSG00000115844		"""Homeoboxes / ANTP class : NKL subclass"""	2915	protein-coding gene	gene with protein product		126255	"""distal-less homeo box 2"""			1354641	Standard	NM_004405		Approved	TES-1	uc002uhn.3	Q07687	OTTHUMG00000132276	ENST00000234198.4:c.136_138dupAGC	2.37:g.172967135_172967137dupGCT	ENSP00000234198:p.Ser46_Ser46dup	Somatic		Capture	Illumina HiSeq	Phase_I	172675374	B4DMK4|B7ZA14	In_Frame_Ins	INS	ENST00000234198.4	37	CCDS2248.1																																																																																				DLX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255368.3		
ZNF717	100131827	hgsc.bcm.edu	37	3	75786315	75786323	+	In_Frame_Del	DEL	CTACATTCT	CTACATTCT	-	rs146447046|rs202196860		TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	CTACATTCT	CTACATTCT					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr3:75786315_75786323delCTACATTCT	ENST00000478296.1	-	4	2577_2585	c.2301_2309delAGAATGTAG	c.(2299-2310)aaagaatgtagg>aag	p.ECR768del	ZNF717_ENST00000477374.1_Intron|ZNF717_ENST00000491507.1_Intron|MIR4273_ENST00000582824.1_RNA|ZNF717_ENST00000422325.1_In_Frame_Del_p.ECR818del|ZNF717_ENST00000400845.3_In_Frame_Del_p.ECR811del			Q9BY31	ZN717_HUMAN	zinc finger protein 717	808					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)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						GAAGGTTTTCCTACATTCTTTACATTCAA	0.383																																																	0			3																																								75869013	SO:0001651	inframe_deletion	100131827			AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124		"""Zinc fingers, C2H2-type"", ""-"""	29448	protein-coding gene	gene with protein product			"""zinc finger protein 838"""	ZNF838			Standard	NM_001128223		Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.2301_2309delAGAATGTAG	3.37:g.75786315_75786323delCTACATTCT	ENSP00000419377:p.Glu768_Arg770del	Somatic		Capture	Illumina HiSeq	Phase_I	75869005		In_Frame_Del	DEL	ENST00000478296.1	37																																																																																					ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000352764.2	NM_001128223	
Unknown	0	hgsc.bcm.edu	37	Unknown	0	0	+	IGR	DEL	CTGAGGAAGGGCTAGTGACAGGAAGAGGCGTGGTGTCACCTGTGGATA	CTGAGGAAGGGCTAGTGACAGGAAGAGGCGTGGTGTCACCTGTGGATA	-			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	CTGAGGAAGGGCTAGTGACAGGAAGAGGCGTGGTGTCACCTGTGGATA	CTGAGGAAGGGCTAGTGACAGGAAGAGGCGTGGTGTCACCTGTGGATA					Unknown	Invalid:failed_liftOver	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chrUnknown:0delCTGAGGAAGGGCTAGTGACAGGAAGAGGCGTGGTGTCACCTGTGGATA								None (None upstream) : None (None downstream)																								0																																																	0			3																																								196996676	SO:0001628	intergenic_variant	4585																															Unknown.37:g.0delCTGAGGAAGGGCTAGTGACAGGAAGAGGCGTGGTGTCACCTGTGGATA		Somatic		Capture	Illumina HiSeq	Phase_I	196996629		In_Frame_Del	DEL		37																																																																																				0								
MUC4	4585	hgsc.bcm.edu	37	3	195512556	195512603	+	In_Frame_Del	DEL	GTGACCTGTGGGTACTGAGGAAGCGTCGGTGACAGGAAGAGGGGTGGT	GTGACCTGTGGGTACTGAGGAAGCGTCGGTGACAGGAAGAGGGGTGGT	-	rs6799339|rs79969373|rs71254296|rs150659095|rs555584675|rs558165743|rs576374543|rs537525175|rs539429280|rs199625793	byFrequency	TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	GTGACCTGTGGGTACTGAGGAAGCGTCGGTGACAGGAAGAGGGGTGGT	GTGACCTGTGGGTACTGAGGAAGCGTCGGTGACAGGAAGAGGGGTGGT					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr3:195512556_195512603delGTGACCTGTGGGTACTGAGGAAGCGTCGGTGACAGGAAGAGGGGTGGT	ENST00000463781.3	-	2	6307_6354	c.5848_5895delACCACCCCTCTTCCTGTCACCGACGCTTCCTCAGTACCCACAGGTCAC	c.(5848-5895)accacccctcttcctgtcaccgacgcttcctcagtacccacaggtcacdel	p.TTPLPVTDASSVPTGH1950del	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_In_Frame_Del_p.TTPLPVTDASSVPTGH1950del	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.P1952_T1967delPLPVTDASSVPTGHAT(4)|p.P1952S(1)|p.V1961V(1)|p.P1962S(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGAGGTGGCGTGACCTGTGGGTACTGAGGAAGCGTCGGTGACAGGAAGAGGGGTGGTGTGACCTGAG	0.597																																																	7	Deletion - In frame(4)|Substitution - Missense(2)|Substitution - coding silent(1)	stomach(4)|endometrium(3)	3																																								196996998	SO:0001651	inframe_deletion	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.5848_5895delACCACCCCTCTTCCTGTCACCGACGCTTCCTCAGTACCCACAGGTCAC	3.37:g.195512556_195512603delGTGACCTGTGGGTACTGAGGAAGCGTCGGTGACAGGAAGAGGGGTGGT	ENSP00000417498:p.Thr1950_His1965del	Somatic		Capture	Illumina HiSeq	Phase_I	196996951	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	In_Frame_Del	DEL	ENST00000463781.3	37	CCDS54700.1																																																																																				MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CRIPAK	285464	hgsc.bcm.edu	37	4	1389220	1389248	+	Frame_Shift_Del	DEL	TGGAGTGCCCGCCTGCTCACGTGCCCATA	TGGAGTGCCCGCCTGCTCACGTGCCCATA	-	rs1140009|rs200438890|rs141376932|rs550271289|rs150174653|rs145563943|rs547759244	byFrequency	TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	TGGAGTGCCCGCCTGCTCACGTGCCCATA	TGGAGTGCCCGCCTGCTCACGTGCCCATA					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr4:1389220_1389248delTGGAGTGCCCGCCTGCTCACGTGCCCATA	ENST00000324803.4	+	1	3881_3909	c.921_949delTGGAGTGCCCGCCTGCTCACGTGCCCATA	c.(919-951)cgtggagtgcccgcctgctcacgtgcccatatgfs	p.GVPACSRAHM308fs		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	308					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.P310fs*95(1)		NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CGTGCCGACGTGGAGTGCCCGCCTGCTCACGTGCCCATATGGAGTGCCC	0.668																																																	1	Deletion - Frameshift(1)	prostate(1)	4								1378,2876		542,294,1291						0.8	0.0			153	3662,4580		1557,548,2016	no	frameshift	CRIPAK	NM_175918.3		2099,842,3307	A1A1,A1R,RR		44.431,32.393,40.3329				5040,7456				1379248	SO:0001589	frameshift_variant	285464			AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.921_949delTGGAGTGCCCGCCTGCTCACGTGCCCATA	4.37:g.1389220_1389248delTGGAGTGCCCGCCTGCTCACGTGCCCATA	ENSP00000323978:p.Gly308fs	Somatic		Capture	Illumina HiSeq	Phase_I	1379220	Q8NB03	Frame_Shift_Del	DEL	ENST00000324803.4	37	CCDS3349.1																																																																																				CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
KIAA1211	57482	hgsc.bcm.edu	37	4	57180576	57180577	+	In_Frame_Ins	INS	-	-	GGAGCGGAGGGAGCGGAG	rs71921617|rs138358443|rs11276076	byFrequency	TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr4:57180576_57180577insGGAGCGGAGGGAGCGGAG	ENST00000504228.1	+	6	1013_1014	c.908_909insGGAGCGGAGGGAGCGGAG	c.(907-912)gcggag>gcGGAGCGGAGGGAGCGGAGggag	p.304_305insRRERRE	KIAA1211_ENST00000264229.6_In_Frame_Ins_p.304_305insRRERRE|KIAA1211_ENST00000541073.1_In_Frame_Ins_p.297_298insRRERRE			Q6ZU35	K1211_HUMAN	KIAA1211	304	Glu-rich.									endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					TGGGAGGACGCGGAGCGGAGGG	0.733														1350	0.269569	0.2716	0.2781	5008	,	,		14300	0.0694		0.4076	False		,,,				2504	0.3252																0			4								903,2311		258,387,962						-10.2	0.0		dbSNP_130	6	2065,4451		612,841,1805	no	coding	KIAA1211	NM_020722.1		870,1228,2767	A1A1,A1R,RR		31.6912,28.0958,30.5036				2968,6762				56875334	SO:0001652	inframe_insertion	57482			AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	Exception_encountered	4.37:g.57180576_57180577insGGAGCGGAGGGAGCGGAG	ENSP00000423366:p.Glu304_Arg305insArgArgGluArgArgGlu	Somatic		Capture	Illumina HiSeq	Phase_I	56875333	Q9NTE2|Q9NTP8|Q9ULK9	In_Frame_Ins	INS	ENST00000504228.1	37	CCDS43230.1																																																																																				KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722	
CNOT6L	246175	hgsc.bcm.edu	37	4	78641724	78641725	+	Frame_Shift_Del	DEL	TG	TG	-			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	TG	TG					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr4:78641724_78641725delTG	ENST00000504123.1	-	12	1658_1659	c.1528_1529delCA	c.(1528-1530)caafs	p.Q510fs	CNOT6L_ENST00000264903.4_Frame_Shift_Del_p.Q510fs			Q96LI5	CNO6L_HUMAN	CCR4-NOT transcription complex, subunit 6-like	510	Nuclease domain.				gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA destabilization (GO:0061157)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A)-specific ribonuclease activity (GO:0004535)			kidney(1)|large_intestine(1)|lung(6)|urinary_tract(1)	9						AACCAGCCATTGAGGATCTAAA	0.470																																																	0			4																																								78860749	SO:0001589	frameshift_variant	246175			AL133112	CCDS68731.1	4q13.3	2014-06-17				ENSG00000138767			18042	protein-coding gene	gene with protein product							Standard	NM_144571		Approved	DKFZp434K098, Ccr4b	uc003hks.3	Q96LI5		ENST00000504123.1:c.1528_1529delCA	4.37:g.78641724_78641725delTG	ENSP00000424896:p.Gln510fs	Somatic		Capture	Illumina HiSeq	Phase_I	78860748	Q9UF92	Frame_Shift_Del	DEL	ENST00000504123.1	37																																																																																					CNOT6L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000362515.1		
FBXW7	55294	hgsc.bcm.edu	37	4	153247327	153247327	+	Frame_Shift_Del	DEL	T	T	-			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr4:153247327delT	ENST00000281708.4	-	10	2704	c.1475delA	c.(1474-1476)cagfs	p.Q492fs	FBXW7_ENST00000393956.3_Frame_Shift_Del_p.Q316fs|FBXW7_ENST00000603841.1_Frame_Shift_Del_p.Q492fs|FBXW7_ENST00000263981.5_Frame_Shift_Del_p.Q412fs|FBXW7_ENST00000603548.1_Frame_Shift_Del_p.Q492fs|FBXW7_ENST00000296555.5_Frame_Shift_Del_p.Q374fs	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	492					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				ATGTAAACACTGGCCTGTCTC	0.433			"""Mis, N, D, F"""		"""colorectal, endometrial, T-ALL"""																																			Rec	yes		4	4q31.3	55294	"""F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"""		"""E, L"""	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	4											135.0	126.0	129.0					4																	153247327		2203	4300	6503	153466777	SO:0001589	frameshift_variant	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	16712	protein-coding gene	gene with protein product	"""archipelago homolog (Drosophila)"""	606278	"""F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"", ""F-box and WD repeat domain containing 7"""			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1475delA	4.37:g.153247327delT	ENSP00000281708:p.Gln492fs	Somatic		Capture	Illumina HiSeq	Phase_I	153466777	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Frame_Shift_Del	DEL	ENST00000281708.4	37	CCDS3777.1																																																																																				FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1		
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32609239	32609241	+	In_Frame_Del	DEL	GGT	GGT	-	rs12722072|rs41556812|rs12722074|rs534654325	byFrequency	TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	GGT	GGT					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr6:32609239_32609241delGGT	ENST00000343139.5	+	2	337_339	c.235_237delGGT	c.(235-237)ggtdel	p.G79del	HLA-DQA1_ENST00000395363.1_In_Frame_Del_p.G79del|HLA-DQA1_ENST00000374949.2_In_Frame_Del_p.G79del	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	78	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						CAAATTTGGAGGTTTTGACCCGC	0.502														1751	0.349641	0.3646	0.4236	5008	,	,		12241	0.2669		0.4046	False		,,,				2504	0.3057																0			6																																								32717219	SO:0001651	inframe_deletion	3117				CCDS4752.1	6p21.3	2013-01-11			ENSG00000196735	ENSG00000196735		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4942	protein-coding gene	gene with protein product		146880		HLA-DQA			Standard	NM_002122		Approved	CELIAC1	uc003obr.3	P01909	OTTHUMG00000031106	ENST00000343139.5:c.235_237delGGT	6.37:g.32609239_32609241delGGT	ENSP00000339398:p.Gly79del	Somatic		Capture	Illumina HiSeq	Phase_I	32717217	O19630|O19706|P01907|P01908|P04225|P04226|P05536|P79553|Q06751|Q29876|Q29994|Q2Q6Y6|Q2Q6Y7|Q2Q6Y8|Q2WCM3|Q30064|Q30067|Q30068|Q30070|Q30071|Q30072|Q30073|Q30086|Q30101|Q5Y7D5|Q5Y7F5|Q6ICU6|Q6PR46|Q6QDB1|Q860W2|Q860W4|Q9BD37|Q9TPM3|Q9UM31	In_Frame_Del	DEL	ENST00000343139.5	37	CCDS4752.1																																																																																				HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
ABO	28	hgsc.bcm.edu	37	9	136131057	136131057	+	RNA	DEL	G	G	-	rs8176750|rs56392308	byFrequency	TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr9:136131057delG	ENST00000453660.2	-	0	1071				RP11-430N14.4_ENST00000606717.1_RNA			P16442	BGAT_HUMAN	ABO blood group (transferase A, alpha 1-3-N-acetylgalactosaminyltransferase; transferase B, alpha 1-3-galactosyltransferase)						protein glycosylation (GO:0006486)	extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	fucosylgalactoside 3-alpha-galactosyltransferase activity (GO:0004381)|glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity (GO:0004380)|metal ion binding (GO:0046872)	p.P353fs?(1)		central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(2)|prostate(1)|stomach(2)	11				OV - Ovarian serous cystadenocarcinoma(145;5.82e-06)|Epithelial(140;3.45e-05)		AGCCGCTCACGGGTTCCGGAC	0.662													GGG|GGG|GG|deletion	242	0.0483227	0.0658	0.0432	5008	,	,		13669	0.0		0.0954	False		,,,				2504	0.0297																1	Deletion - Frameshift(1)	central_nervous_system(1)	9								234,3304		17,200,1552	9.0	10.0	10.0			-7.1	0.0	9	dbSNP_129	10	533,7273		35,463,3405	no	frameshift	ABO	NM_020469.2		52,663,4957	A1A1,A1R,RR		6.8281,6.6139,6.7613			136131057	767,10577	1853	4054	5907	135120878			28			AF134415		9q34.2	2014-07-19			ENSG00000175164	ENSG00000175164	2.4.1.40, 2.4.1.37	"""Blood group antigens"", ""Glycosyltransferase family 6 domain containing"""	79	protein-coding gene	gene with protein product		110300				184030	Standard	NM_020469		Approved	A3GALNT, A3GALT1	uc004cda.1	P16442	OTTHUMG00000020872		9.37:g.136131057delG		Somatic		Capture	Illumina HiSeq	Phase_I	135120878	B0JDB9|O14758|Q14490|Q53I57|Q6ISD4|Q6KFZ2|Q70V27|Q99484|Q99485|Q9NY01|Q9UQ68|Q9UQ69	Frame_Shift_Del	DEL	ENST00000453660.2	37																																																																																					ABO-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000054907.4	NM_020469	
GPRIN2	9721	hgsc.bcm.edu	37	10	46999591	46999592	+	In_Frame_Ins	INS	-	-	ATGAGGGAG	rs112620425	byFrequency	TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr10:46999591_46999592insATGAGGGAG	ENST00000374317.1	+	3	984_985	c.711_712insATGAGGGAG	c.(712-714)atg>ATGAGGGAGatg	p.238_238M>MREM	GPRIN2_ENST00000374314.4_In_Frame_Ins_p.238_238M>MREM	NM_014696.3	NP_055511.2	O60269	GRIN2_HUMAN	G protein regulated inducer of neurite outgrowth 2	238								p.G237_M238insMRE(1)		breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	18						TACTCTGTGGCATGAGGGAGGT	0.629														2399	0.479034	0.4697	0.4856	5008	,	,		38874	0.4782		0.4761	False		,,,				2504	0.4908																1	Insertion - In frame(1)	breast(1)	10								2080,27,2157		11,3,2055,0,24,39						0.9	0.0		dbSNP_130	49	3974,98,4180		16,7,3935,0,91,77	no	codingComplex	GPRIN2	NM_014696.3		27,10,5990,0,115,116	A1A1,A1A2,A1R,A2A2,A2R,RR		49.3456,49.4137,49.3688				6054,125,6337				46419598	SO:0001652	inframe_insertion	9721			BC011672	CCDS73101.1	10q11.22	2006-08-24	2006-08-24	2006-08-24	ENSG00000204175	ENSG00000204175			23730	protein-coding gene	gene with protein product		611240	"""KIAA0514"""	KIAA0514		9628581	Standard	NM_014696		Approved	MGC15171	uc001jec.3	O60269	OTTHUMG00000018107	ENST00000374317.1:c.712_720dupATGAGGGAG	10.37:g.46999592_46999600dupATGAGGGAG	Exception_encountered	Somatic		Capture	Illumina HiSeq	Phase_I	46419597	Q5SVF0	In_Frame_Ins	INS	ENST00000374317.1	37	CCDS31192.1																																																																																				GPRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047836.1	NM_014696	
KRTAP5-2	440021	hgsc.bcm.edu	37	11	1619173	1619202	+	In_Frame_Del	DEL	CCCCCACAGGAGCCACAGCCCCCCTTGGAG	CCCCCACAGGAGCCACAGCCCCCCTTGGAG	-	rs61869706|rs199811378|rs36134435|rs61869704|rs59506446	byFrequency	TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	CCCCCACAGGAGCCACAGCCCCCCTTGGAG	CCCCCACAGGAGCCACAGCCCCCCTTGGAG					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr11:1619173_1619202delCCCCCACAGGAGCCACAGCCCCCCTTGGAG	ENST00000412090.1	-	1	322_351	c.279_308delCTCCAAGGGGGGCTGTGGCTCCTGTGGGGG	c.(277-309)ggctccaaggggggctgtggctcctgtgggggt>ggt	p.93_103GSKGGCGSCGG>G	KRTAP5-AS1_ENST00000524947.1_RNA|KRTAP5-AS1_ENST00000424148.1_RNA|KRTAP5-AS1_ENST00000532922.1_RNA|KRTAP5-AS1_ENST00000534077.1_RNA	NM_001004325.1	NP_001004325.1	Q701N4	KRA52_HUMAN	keratin associated protein 5-2	93	6 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				large_intestine(1)|lung(2)|skin(1)	4		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		CCCCTTGGAACCCCCACAGGAGCCACAGCCCCCCTTGGAGCCCCCACAGG	0.657																																																	0			11																																								1575778	SO:0001651	inframe_deletion	440021			AB126071	CCDS31331.1	11p15.5	2008-02-05				ENSG00000205867		"""Keratin associated proteins"""	23597	protein-coding gene	gene with protein product						15144888	Standard	NM_001004325		Approved	KRTAP5.2, KRTAP5-8	uc001ltv.3	Q701N4		ENST00000412090.1:c.279_308delCTCCAAGGGGGGCTGTGGCTCCTGTGGGGG	11.37:g.1619173_1619202delCCCCCACAGGAGCCACAGCCCCCCTTGGAG	ENSP00000400041:p.Gly103_Gly112del	Somatic		Capture	Illumina HiSeq	Phase_I	1575749	A9JTZ1	In_Frame_Del	DEL	ENST00000412090.1	37	CCDS31331.1																																																																																				KRTAP5-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384775.1	NM_001004325	
DDHD1	80821	hgsc.bcm.edu	37	14	53619480	53619481	+	In_Frame_Ins	INS	-	-	GCCGCC	rs140904345|rs55671452|rs200797826	byFrequency	TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr14:53619480_53619481insGCCGCC	ENST00000323669.5	-	1	335_336	c.336_337insGGCGGC	c.(334-339)ggcagc>ggcGGCGGCagc	p.111_112insGG	RP11-547D23.1_ENST00000554235.1_RNA|AL356020.1_ENST00000584587.1_RNA|DDHD1_ENST00000357758.3_In_Frame_Ins_p.111_112insGG|DDHD1_ENST00000395606.1_In_Frame_Ins_p.111_112insGG	NM_001160148.1	NP_001153620.1	Q8NEL9	DDHD1_HUMAN	DDHD domain containing 1	111					cell death (GO:0008219)|lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)	25	Breast(41;0.037)					GACAAGGAGCTGCCGCCGCCGC	0.703														3933	0.785343	0.4962	0.8718	5008	,	,		9770	0.9673		0.833	False		,,,				2504	0.8783																0			14																																								52689231	SO:0001652	inframe_insertion	80821			AB051492	CCDS9714.1, CCDS53895.1, CCDS53896.1	14q21	2012-11-23			ENSG00000100523	ENSG00000100523			19714	protein-coding gene	gene with protein product	"""phosphatidic acid-preferring phospholipase A1"""	614603	"""spastic paraplegia 28 (autosomal recessive)"""	SPG28		11214970, 20359546	Standard	NM_030637		Approved	KIAA1705, PA-PLA1	uc001xai.3	Q8NEL9	OTTHUMG00000140305	ENST00000323669.5:c.331_336dupGGCGGC	14.37:g.53619481_53619486dupGCCGCC	ENSP00000327104:p.Gly110_Gly111dup	Somatic		Capture	Illumina HiSeq	Phase_I	52689230	G5E9D1|Q8WVH3|Q96LL2|Q9C0F8	In_Frame_Ins	INS	ENST00000323669.5	37	CCDS53895.1																																																																																				DDHD1-003	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276901.1		
ATP2A1	487	hgsc.bcm.edu	37	16	28909713	28909714	+	Frame_Shift_Ins	INS	-	-	C			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr16:28909713_28909714insC	ENST00000357084.3	+	14	1972_1973	c.1705_1706insC	c.(1705-1707)accfs	p.T569fs	ATP2A1_ENST00000395503.4_Frame_Shift_Ins_p.T569fs|ATP2A1_ENST00000536376.1_Frame_Shift_Ins_p.T444fs	NM_173201.3	NP_775293.1	O14983	AT2A1_HUMAN	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	569					apoptotic mitochondrial changes (GO:0008637)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|ion transmembrane transport (GO:0034220)|maintenance of mitochondrion location (GO:0051659)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|negative regulation of striated muscle contraction (GO:0045988)|positive regulation of endoplasmic reticulum calcium ion concentration (GO:0032470)|positive regulation of fast-twitch skeletal muscle fiber contraction (GO:0031448)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|regulation of striated muscle contraction (GO:0006942)|relaxation of skeletal muscle (GO:0090076)|response to endoplasmic reticulum stress (GO:0034976)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|H zone (GO:0031673)|I band (GO:0031674)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-transporting ATPase activity (GO:0005388)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(2)	38						CACCCGGGACACCCCCCCGAAG	0.639																																																	0			16																																								28817215	SO:0001589	frameshift_variant	487				CCDS10643.1, CCDS42139.1, CCDS66997.1	16p12.1	2012-10-22			ENSG00000196296	ENSG00000196296	3.6.3.8	"""ATPases / P-type"""	811	protein-coding gene	gene with protein product	"""sarcoplasmic/endoplasmic reticulum calcium ATPase 1"", ""calcium pump 1"""	108730		ATP2A			Standard	NM_004320		Approved	SERCA1	uc002dro.1	O14983	OTTHUMG00000131760	ENST00000357084.3:c.1712dupC	16.37:g.28909720_28909720dupC	ENSP00000349595:p.Thr569fs	Somatic		Capture	Illumina HiSeq	Phase_I	28817214	A8K5J9|B3KY17|O14984	Frame_Shift_Ins	INS	ENST00000357084.3	37	CCDS10643.1																																																																																				ATP2A1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254686.2	NM_004320	
CRISPLD2	83716	hgsc.bcm.edu	37	16	84883102	84883103	+	Frame_Shift_Ins	INS	-	-	T	rs8061351	byFrequency	TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr16:84883102_84883103insT	ENST00000262424.5	+	4	695_696	c.471_472insT	c.(472-474)atgfs	p.M158fs	CRISPLD2_ENST00000567845.1_Frame_Shift_Ins_p.M158fs|CRISPLD2_ENST00000566431.1_3'UTR|CRISPLD2_ENST00000564567.1_Frame_Shift_Ins_p.M158fs	NM_031476.3	NP_113664.1	Q9H0B8	CRLD2_HUMAN	cysteine-rich secretory protein LCCL domain containing 2	158	SCP.				extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|lung development (GO:0030324)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|transport vesicle (GO:0030133)	heparin binding (GO:0008201)			endometrium(3)|large_intestine(5)|lung(8)|prostate(1)|stomach(1)	18						GCTCGGGGCCCATGTGCACGCA	0.619																																																	0			16																																								83440604	SO:0001589	frameshift_variant	83716			AL136861	CCDS10949.1	16q24.1	2008-02-05	2005-02-16	2005-02-16	ENSG00000103196	ENSG00000103196			25248	protein-coding gene	gene with protein product		612434	"""LCCL domain containing cysteine-rich secretory protein 2"""	LCRISP2		11230166	Standard	NM_031476		Approved	DKFZP434B044	uc010voh.1	Q9H0B8	OTTHUMG00000137644	Exception_encountered	16.37:g.84883102_84883103insT	ENSP00000262424:p.Met158fs	Somatic		Capture	Illumina HiSeq	Phase_I	83440603	D3DUM0|Q6P590|Q6UWH0|Q6UXC6|Q96IB1|Q96K61	Frame_Shift_Ins	INS	ENST00000262424.5	37	CCDS10949.1																																																																																				CRISPLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269086.2	NM_031476	
TP53	7157	hgsc.bcm.edu	37	17	7577582	7577583	+	Frame_Shift_Ins	INS	-	-	TGGA			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr17:7577582_7577583insTGGA	ENST00000269305.4	-	7	887_888	c.698_699insTCCA	c.(697-699)cacfs	p.-233fs	TP53_ENST00000574684.1_5'UTR|TP53_ENST00000455263.2_Frame_Shift_Ins_p.-233fs|TP53_ENST00000359597.4_Frame_Shift_Ins_p.-233fs|TP53_ENST00000445888.2_Frame_Shift_Ins_p.-233fs|TP53_ENST00000420246.2_Frame_Shift_Ins_p.-233fs|TP53_ENST00000413465.2_Frame_Shift_Ins_p.-233fs	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53						apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|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 core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.?(5)|p.H233fs*6(3)|p.H233L(2)|p.H233Q(2)|p.T230fs*6(2)|p.C229_H233delCTTIH(2)|p.H233R(1)|p.I232_Y236delIHYNY(1)|p.Y234fs*2(1)|p.H233del(1)|p.T230_Y234delTTIHY(1)|p.V225fs*23(1)|p.D228fs*12(1)|p.I232fs*5(1)|p.H233_C242del10(1)|p.H233P(1)|p.Y234fs*6(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TGTAGTTGTAGTGGATGGTGGT	0.564		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)		yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	35	Deletion - Frameshift(9)|Whole gene deletion(8)|Deletion - In frame(6)|Substitution - Missense(6)|Unknown(5)|Insertion - Frameshift(1)	upper_aerodigestive_tract(5)|biliary_tract(5)|breast(4)|bone(4)|haematopoietic_and_lymphoid_tissue(3)|stomach(2)|central_nervous_system(2)|lung(2)|oesophagus(2)|ovary(2)|pleura(1)|salivary_gland(1)|urinary_tract(1)|liver(1)	17																																								7518308	SO:0001589	frameshift_variant	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.695_698dupTCCA	17.37:g.7577583_7577586dupTGGA	ENSP00000269305:p.His233fs	Somatic		Capture	Illumina HiSeq	Phase_I	7518307	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Ins	INS	ENST00000269305.4	37	CCDS11118.1																																																																																				TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
TGIF1	7050	hgsc.bcm.edu	37	18	3452223	3452223	+	Frame_Shift_Del	DEL	T	T	-	rs11571510|rs557543525|rs202189171	byFrequency	TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr18:3452223delT	ENST00000330513.5	+	1	549	c.246delT	c.(244-246)cctfs	p.P85fs	TGIF1_ENST00000551541.1_Intron|TGIF1_ENST00000577543.1_Intron|TGIF1_ENST00000400167.2_5'Flank|TGIF1_ENST00000551402.1_Intron|TGIF1_ENST00000401449.1_Intron|TGIF1_ENST00000405385.3_Intron|TGIF1_ENST00000407501.2_Intron|TGIF1_ENST00000345133.5_Intron|TGIF1_ENST00000343820.5_Intron|TGIF1_ENST00000548489.2_Intron	NM_170695.2	NP_733796.2	Q15583	TGIF1_HUMAN	TGFB-induced factor homeobox 1	85					determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|gene expression (GO:0010467)|multicellular organismal development (GO:0007275)|negative regulation of cell proliferation (GO:0008285)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nodal signaling pathway (GO:0038092)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of neuron differentiation (GO:0045666)|regulation of gastrulation (GO:0010470)|response to drug (GO:0042493)|retina development in camera-type eye (GO:0060041)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|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)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.P83fs*51(1)		cervix(1)|endometrium(3)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	13	Esophageal squamous(4;0.0859)	Colorectal(8;0.0104)				GCGCCCCCCCTCCTCCACCGG	0.766													T|T|-|deletion	1280	0.255591	0.3419	0.2349	5008	,	,		10884	0.0109		0.4304	False		,,,				2504	0.226																1	Deletion - Frameshift(1)	large_intestine(1)	18											10.0	11.0	10.0					18																	3452223		2031	3818	5849	3442223	SO:0001589	frameshift_variant	7050			X89750	CCDS11832.1, CCDS11833.1, CCDS11834.1, CCDS11835.1	18p11.31	2011-06-20	2007-01-30	2007-01-30	ENSG00000177426	ENSG00000177426		"""Homeoboxes / TALE class"""	11776	protein-coding gene	gene with protein product		602630	"""TGFB-induced factor (TALE family homeobox)"""	HPE4, TGIF		8537382, 10835638	Standard	NM_173211		Approved		uc002klz.3	Q15583	OTTHUMG00000131511	ENST00000330513.5:c.246delT	18.37:g.3452223delT	ENSP00000327959:p.Pro85fs	Somatic		Capture	Illumina HiSeq	Phase_I	3442223	A6NE42|A6NLU7|F8VZB6|Q6ICR0|Q8N5X9|Q9NRS0	Frame_Shift_Del	DEL	ENST00000330513.5	37	CCDS11834.1																																																																																				TGIF1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254368.4	NM_170695	
Unknown	0	hgsc.bcm.edu	37	Unknown	0	0	+	IGR	INS	-	-	C			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	-	-					Unknown	Invalid:failed_liftOver	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chrUnknown:0_0insC								None (None upstream) : None (None downstream)																								0																																																	0			20																																								55400100	SO:0001628	intergenic_variant	55544																															Unknown.37:g.0_0insC		Somatic		Capture	Illumina HiSeq	Phase_I	55400099		Frame_Shift_Ins	INS		37																																																																																				0								
KRTAP10-7	386675	hgsc.bcm.edu	37	21	46020656	46020670	+	In_Frame_Del	DEL	CTGCTGCGCCCCCAG	CTGCTGCGCCCCCAG	-	rs36208679|rs60739860|rs373191083		TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	CTGCTGCGCCCCCAG	CTGCTGCGCCCCCAG					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr21:46020656_46020670delCTGCTGCGCCCCCAG	ENST00000380102.2	+	1	160_174	c.135_149delCTGCTGCGCCCCCAG	c.(133-150)ccctgctgcgcccccagc>ccc	p.CCAPS46del	TSPEAR_ENST00000323084.4_Intron	NM_198689.2	NP_941962.1	P60409	KR107_HUMAN	keratin associated protein 10-7	46	30 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)		p.S50_P54delSCCAP(1)		breast(1)|large_intestine(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	8						GCGAGCCCCCCTGCTGCGCCCCCAGCTGCTGCGCC	0.698																																																	1	Deletion - In frame(1)	upper_aerodigestive_tract(1)	21							,	2258,1042		849,560,241					,	-0.7	1.0		dbSNP_126	22	6001,1123		2605,791,166	no	coding,intron	TSPEAR,KRTAP10-7	NM_198689.2,NM_144991.2	,	3454,1351,407	A1A1,A1R,RR		15.7636,31.5758,20.7694	,	,		8259,2165				44845098	SO:0001651	inframe_deletion	386675			AJ566385	CCDS74803.1	21q22.3	2014-04-10			ENSG00000205441	ENSG00000272804		"""Keratin associated proteins"""	22970	protein-coding gene	gene with protein product				KRTAP18-7			Standard	NM_198689		Approved	KAP10.7, KAP18.7	uc002zfn.4	P60409	OTTHUMG00000188307	ENST00000380102.2:c.135_149delCTGCTGCGCCCCCAG	21.37:g.46020656_46020670delCTGCTGCGCCCCCAG	ENSP00000369445:p.Cys46_Ser50del	Somatic		Capture	Illumina HiSeq	Phase_I	44845084	Q0VDJ8|Q70LJ2	Frame_Shift_Del	DEL	ENST00000380102.2	37																																																																																					KRTAP10-7-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000128038.1	NM_198689	
NEFH	4744	hgsc.bcm.edu	37	22	29885589	29885590	+	In_Frame_Ins	INS	-	-	CCCCTGAGAAGGCCAAGT	rs200984527|rs267607533		TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr22:29885589_29885590insCCCCTGAGAAGGCCAAGT	ENST00000310624.6	+	4	1993_1994	c.1960_1961insCCCCTGAGAAGGCCAAGT	c.(1960-1962)tcc>tCCCCTGAGAAGGCCAAGTcc	p.654_654S>SPEKAKS		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	660	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						GAAGGCCAAGTCCCCAGAGAAG	0.559																																																	0			22																																								28215590	SO:0001652	inframe_insertion	4744				CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1943_1960dupCCCCTGAGAAGGCCAAGT	22.37:g.29885589_29885590insCCCCTGAGAAGGCCAAGT	ENSP00000311997:p.ProGluLysAlaLysSer654dup	Somatic		Capture	Illumina HiSeq	Phase_I	28215589	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	In_Frame_Ins	INS	ENST00000310624.6	37	CCDS13858.1																																																																																				NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
