#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Confidence	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_NTotCov	i_NVarCov	i_NVarRat	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_TVarRat	i_Transcript_Id	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNPPopFreq	i_dbSNP_AF	i_dbSNP_PopFreq	i_dbSNP_Strength	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
RBP7	116362	hgsc.bcm.edu	37	1	10068242	10068242	+	Missense_Mutation	SNP	C	C	G			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:10068242C>G	ENST00000294435.7	+	3	307	c.264C>G	c.(262-264)atC>atG	p.I88M		NM_052960.2	NP_443192.1	Q96R05	RET7_HUMAN	retinol binding protein 7, cellular	88						cytoplasm (GO:0005737)	retinal binding (GO:0016918)|retinol binding (GO:0019841)|transporter activity (GO:0005215)			endometrium(1)|large_intestine(1)	2		all_lung(284;0.000407)|Renal(390;0.000469)|Lung NSC(185;0.000577)|Colorectal(325;0.0062)|Breast(348;0.00686)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.5e-08)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;0.000249)|BRCA - Breast invasive adenocarcinoma(304;0.000302)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.00856)|READ - Rectum adenocarcinoma(331;0.0419)	Vitamin A(DB00162)	GTTTGGTTATCTGGGACAATG	0.468																																					p.I88M		Atlas-SNP	.											.	RBP7	11	.	0			c.C264G						PASS	.						112.0	104.0	107.0					1																	10068242		2203	4300	6503	SO:0001583	missense	116362	exon3			GGTTATCTGGGAC	AF399927	CCDS109.1	1p36.22	2013-03-01			ENSG00000162444	ENSG00000162444		"""Fatty acid binding protein family"""	30316	protein-coding gene	gene with protein product		608604				12177003	Standard	NM_052960		Approved	CRBPIV	uc001aqq.3	Q96R05	OTTHUMG00000001798	ENST00000294435.7:c.264C>G	chr1.hg19:g.10068242C>G	ENSP00000294435:p.Ile88Met	194.0	0.0	.		148.0	15.0	.	NM_052960	B2R517|Q5SWJ4	Missense_Mutation	SNP	ENST00000294435.7	hg19	CCDS109.1	.	.	.	.	.	.	.	.	.	.	C	6.871	0.529995	0.13127	.	.	ENSG00000162444	ENST00000315901;ENST00000294435	T	0.07688	3.17	4.07	0.988	0.19796	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.599344	0.15592	N	0.254321	T	0.07143	0.0181	N	0.19112	0.55	0.09310	N	0.99999	B	0.23650	0.089	B	0.37601	0.254	T	0.37526	-0.9702	10	0.87932	D	0	.	6.2468	0.20823	0.1332:0.6539:0.1302:0.0827	.	88	Q96R05	RET7_HUMAN	M	135;88	ENSP00000294435:I88M	ENSP00000294435:I88M	I	+	3	3	RBP7	9990829	0.000000	0.05858	0.746000	0.31095	0.291000	0.27294	-1.010000	0.03656	0.945000	0.37605	0.644000	0.83932	ATC	.	.	.	none		0.468	RBP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005027.2	NM_052960	
PRDM2	7799	hgsc.bcm.edu	37	1	14108836	14108836	+	Missense_Mutation	SNP	C	C	T			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:14108836C>T	ENST00000235372.7	+	8	5402	c.4546C>T	c.(4546-4548)Cgg>Tgg	p.R1516W	PRDM2_ENST00000376048.5_Intron|PRDM2_ENST00000503842.1_Intron|PRDM2_ENST00000343137.4_Missense_Mutation_p.R1315W|PRDM2_ENST00000413440.1_Missense_Mutation_p.R1315W|PRDM2_ENST00000505823.1_Intron|PRDM2_ENST00000311066.5_Missense_Mutation_p.R1516W	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	1516					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(16)|lung(20)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	55	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)		CCACCGCAGACGGACAGCGGA	0.512																																					p.R1516W		Atlas-SNP	.											.	PRDM2	147	.	0			c.C4546T						PASS	.						72.0	82.0	79.0					1																	14108836		2203	4300	6503	SO:0001583	missense	7799	exon8			CGCAGACGGACAG	U17838	CCDS150.1, CCDS151.1, CCDS30603.1, CCDS44061.1	1p36	2011-07-01			ENSG00000116731	ENSG00000116731		"""Chromatin-modifying enzymes / K-methyltransferases"""	9347	protein-coding gene	gene with protein product	"""retinoblastoma protein-binding zinc finger protein"", ""retinoblastoma protein-interacting zinc finger protein"", ""MTE-binding protein"", ""zinc-finger DNA-binding protein"", ""GATA-3 binding protein G3B"""	601196				7538672	Standard	NM_012231		Approved	RIZ, RIZ1, RIZ2, KMT8, MTB-ZF, HUMHOXY1	uc001avi.3	Q13029	OTTHUMG00000007917	ENST00000235372.7:c.4546C>T	chr1.hg19:g.14108836C>T	ENSP00000235372:p.Arg1516Trp	121.0	0.0	.		107.0	39.0	.	NM_015866	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	Missense_Mutation	SNP	ENST00000235372.7	hg19	CCDS150.1	.	.	.	.	.	.	.	.	.	.	C	16.45	3.127315	0.56721	.	.	ENSG00000116731	ENST00000235372;ENST00000311066;ENST00000400800;ENST00000413440;ENST00000343137	T;T;T;T	0.02032	4.6;4.49;4.49;4.49	5.98	4.06	0.47325	.	0.060868	0.64402	D	0.000003	T	0.09598	0.0236	M	0.69823	2.125	0.49051	D	0.999741	D;B;B	0.89917	1.0;0.14;0.445	D;B;B	0.73708	0.981;0.015;0.034	T	0.00638	-1.1632	10	0.87932	D	0	.	8.67	0.34145	0.1498:0.7733:0.0:0.0769	.	1374;1516;1516	Q5THJ0;Q13029;Q13029-2	.;PRDM2_HUMAN;.	W	1516;1516;1516;1315;1315	ENSP00000235372:R1516W;ENSP00000312352:R1516W;ENSP00000411103:R1315W;ENSP00000341621:R1315W	ENSP00000235372:R1516W	R	+	1	2	PRDM2	13981423	0.364000	0.24997	0.793000	0.32043	0.983000	0.72400	0.980000	0.29513	0.815000	0.34398	0.591000	0.81541	CGG	.	.	.	none		0.512	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231	
MST1L	11223	hgsc.bcm.edu	37	1	17087368	17087368	+	RNA	SNP	C	C	A			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:17087368C>A	ENST00000455405.2	-	0	0							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										AGTGGAACGCCCTGGAGAGAA	0.607																																					p.W72C		Atlas-SNP	.											.	.	.	.	0			c.G216T						PASS	.																																					11223	exon3			GAACGCCCTGGAG	U28055, AF083416		1p36.33	2013-03-27	2012-11-09	2012-11-09	ENSG00000186715	ENSG00000186715			7390	other	unknown			"""macrophage stimulating, pseudogene 7"", ""macrophage stimulating, pseudogene 9"", ""macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9"""	MSTP7, MSTP9, MST1P9		10728827	Standard	NM_001271733		Approved	D1F15S1A, MSPL7, MSPL-7	uc010ock.3	Q2TV78	OTTHUMG00000002578		chr1.hg19:g.17087368C>A		303.0	0.0	.		276.0	28.0	.	NM_001271733	B7WPB1|Q13209	Missense_Mutation	SNP	ENST00000455405.2	hg19		.	.	.	.	.	.	.	.	.	.	.	11.16	1.556309	0.27827	.	.	ENSG00000186715	ENST00000389184;ENST00000334998;ENST00000442552;ENST00000545160	.	.	.	.	.	.	.	0.179285	0.26642	N	0.023257	T	0.40347	0.1113	.	.	.	.	.	.	P	0.50819	0.939	P	0.50136	0.632	T	0.49273	-0.8957	6	0.87932	D	0	.	2.6652	0.05046	0.0:0.5:0.0:0.5	.	72	Q2TV78-2	.	C	42;72;72;4	.	ENSP00000439273:W72C	W	-	3	0	MST1P9	16959955	0.999000	0.42202	0.000000	0.03702	0.000000	0.00434	0.116000	0.15561	-0.000000	0.14550	0.000000	0.15137	TGG	.	.	.	none		0.607	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
E2F2	1870	hgsc.bcm.edu	37	1	23848337	23848337	+	Missense_Mutation	SNP	G	G	C			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:23848337G>C	ENST00000361729.2	-	3	996	c.570C>G	c.(568-570)atC>atG	p.I190M	E2F2_ENST00000487237.1_5'Flank	NM_004091.3	NP_004082.1	Q14209	E2F2_HUMAN	E2F transcription factor 2	190					intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|lens fiber cell apoptotic process (GO:1990086)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(4)|large_intestine(2)|lung(1)|ovary(3)|skin(2)|urinary_tract(1)	13		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.52e-24)|Colorectal(126;6.25e-08)|COAD - Colon adenocarcinoma(152;3.42e-06)|GBM - Glioblastoma multiforme(114;8.98e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00102)|KIRC - Kidney renal clear cell carcinoma(1967;0.00366)|STAD - Stomach adenocarcinoma(196;0.0132)|READ - Rectum adenocarcinoma(331;0.0652)|Lung(427;0.0888)|LUSC - Lung squamous cell carcinoma(448;0.19)		ACACCCACTGGATGTTGTTCT	0.612																																					p.I190M		Atlas-SNP	.											.	E2F2	31	.	0			c.C570G						PASS	.						123.0	104.0	110.0					1																	23848337		2203	4300	6503	SO:0001583	missense	1870	exon3			CCACTGGATGTTG	L22846	CCDS236.1	1p36	2008-02-05			ENSG00000007968	ENSG00000007968			3114	protein-coding gene	gene with protein product		600426				8246995, 8246996	Standard	NM_004091		Approved	E2F-2	uc001bhe.2	Q14209	OTTHUMG00000003223	ENST00000361729.2:c.570C>G	chr1.hg19:g.23848337G>C	ENSP00000355249:p.Ile190Met	156.0	0.0	.		118.0	45.0	.	NM_004091	B2R9W1|Q7Z6H1	Missense_Mutation	SNP	ENST00000361729.2	hg19	CCDS236.1	.	.	.	.	.	.	.	.	.	.	G	17.41	3.382364	0.61845	.	.	ENSG00000007968	ENST00000361729	T	0.15256	2.44	5.35	4.42	0.53409	Transcription factor E2F/dimerisation partner (TDP) (1);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.058637	0.64402	D	0.000003	T	0.48840	0.1522	M	0.93241	3.395	0.58432	D	0.999998	D	0.56968	0.978	D	0.65323	0.934	T	0.60865	-0.7178	10	0.87932	D	0	-24.1713	11.9214	0.52793	0.0:0.0:0.6839:0.3161	.	190	Q14209	E2F2_HUMAN	M	190	ENSP00000355249:I190M	ENSP00000355249:I190M	I	-	3	3	E2F2	23720924	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.406000	0.44557	1.212000	0.43366	0.591000	0.81541	ATC	.	.	.	none		0.612	E2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008885.1	NM_004091	
CD52	1043	hgsc.bcm.edu	37	1	26646661	26646661	+	Splice_Site	SNP	G	G	T			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:26646661G>T	ENST00000374213.2	+	2	115		c.e2-1		UBXN11_ENST00000374217.2_5'Flank|UBXN11_ENST00000374222.1_5'Flank	NM_001803.2	NP_001794.2	P31358	CD52_HUMAN	CD52 molecule						positive regulation of cytosolic calcium ion concentration (GO:0007204)|respiratory burst (GO:0045730)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				large_intestine(1)	1		all_cancers(24;5.02e-24)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;7.56e-28)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000946)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0137)|READ - Rectum adenocarcinoma(331;0.0649)	Alemtuzumab(DB00087)	TCCTCCTACAGATACAAACTG	0.488																																					.		Atlas-SNP	.											.	CD52	7	.	0			c.55-1G>T						PASS	.						108.0	108.0	108.0					1																	26646661		2203	4300	6503	SO:0001630	splice_region_variant	1043	exon2			CCTACAGATACAA		CCDS30647.1	1p36	2008-02-05	2006-03-28	2005-02-07	ENSG00000169442	ENSG00000169442		"""CD molecules"""	1804	protein-coding gene	gene with protein product		114280	"""CD52 antigen (CAMPATH-1 antigen)"""	CDW52		1711975	Standard	NM_001803		Approved		uc001bmc.3	P31358	OTTHUMG00000003491	ENST00000374213.2:c.55-1G>T	chr1.hg19:g.26646661G>T		52.0	0.0	.		42.0	6.0	.	NM_001803	Q5T138|Q9BW46	Splice_Site	SNP	ENST00000374213.2	hg19	CCDS30647.1	.	.	.	.	.	.	.	.	.	.	G	13.65	2.299548	0.40694	.	.	ENSG00000169442	ENST00000374213	.	.	.	3.6	3.6	0.41247	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.042	0.47835	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CD52	26519248	0.969000	0.33509	0.935000	0.37517	0.213000	0.24496	3.220000	0.51207	2.312000	0.78011	0.655000	0.94253	.	.	.	.	none		0.488	CD52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009704.1	NM_001803	Intron
COL8A2	1296	hgsc.bcm.edu	37	1	36564106	36564106	+	Silent	SNP	A	A	G			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:36564106A>G	ENST00000397799.1	-	4	1400	c.1176T>C	c.(1174-1176)atT>atC	p.I392I	COL8A2_ENST00000303143.4_Silent_p.I392I|COL8A2_ENST00000481785.1_Silent_p.I327I			P25067	CO8A2_HUMAN	collagen, type VIII, alpha 2	392	Triple-helical region.				angiogenesis (GO:0001525)|camera-type eye morphogenesis (GO:0048593)|collagen catabolic process (GO:0030574)|epithelial cell proliferation (GO:0050673)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)			NS(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				GGTCACCTCGAATGCCAGGCA	0.692																																					p.I392I		Atlas-SNP	.											.	COL8A2	41	.	0			c.T1176C						PASS	.						9.0	10.0	10.0					1																	36564106		2188	4274	6462	SO:0001819	synonymous_variant	1296	exon2			ACCTCGAATGCCA	M60832	CCDS403.1, CCDS72756.1	1p34.2-p32.3	2014-02-14			ENSG00000171812	ENSG00000171812		"""Collagens"""	2216	protein-coding gene	gene with protein product		120252		FECD		11689488	Standard	XM_005270477		Approved	PPCD, FECD1, PPCD2	uc001bzv.2	P25067	OTTHUMG00000007665	ENST00000397799.1:c.1176T>C	chr1.hg19:g.36564106A>G		187.0	0.0	.		108.0	32.0	.	NM_005202	Q5JV31|Q8TEJ5	Silent	SNP	ENST00000397799.1	hg19	CCDS403.1																																																																																			.	.	.	none		0.692	COL8A2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313674.1	NM_005202	
CDC20	991	hgsc.bcm.edu	37	1	43826814	43826814	+	Missense_Mutation	SNP	G	G	C			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:43826814G>C	ENST00000372462.1	+	8	1304	c.1101G>C	c.(1099-1101)caG>caC	p.Q367H	ELOVL1_ENST00000470769.1_5'Flank|CDC20_ENST00000310955.6_Missense_Mutation_p.Q367H|RP1-92O14.3_ENST00000424948.1_RNA			Q12834	CDC20_HUMAN	cell division cycle 20	367					activation of anaphase-promoting complex activity (GO:0051488)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell cycle (GO:0007049)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of cell proliferation (GO:0008284)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic plasticity (GO:0031915)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein ubiquitination (GO:0016567)|regulation of dendrite development (GO:0050773)|regulation of meiosis (GO:0040020)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|spindle (GO:0005819)	enzyme binding (GO:0019899)|protein C-terminus binding (GO:0008022)			endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	15	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				GTCCCTGGCAGTCCAATGTCC	0.572																																					p.Q367H	Esophageal Squamous(137;1154 1759 10362 10401 46925)	Atlas-SNP	.											.	CDC20	34	.	0			c.G1101C						PASS	.						85.0	76.0	79.0					1																	43826814		2203	4300	6503	SO:0001583	missense	991	exon9			CTGGCAGTCCAAT	U05340	CCDS484.1	1p34.1	2013-01-17	2013-01-17		ENSG00000117399	ENSG00000117399		"""WD repeat domain containing"""	1723	protein-coding gene	gene with protein product		603618	"""CDC20 (cell division cycle 20, S. cerevisiae, homolog)"", ""CDC20 cell division cycle 20 homolog (S. cerevisiae)"", ""cell division cycle 20 homolog (S. cerevisiae)"""			7513050, 9353311	Standard	NM_001255		Approved	p55CDC, CDC20A	uc001cix.3	Q12834	OTTHUMG00000007420	ENST00000372462.1:c.1101G>C	chr1.hg19:g.43826814G>C	ENSP00000361540:p.Gln367His	118.0	0.0	.		82.0	32.0	.	NM_001255	B2R6Z6|D3DPJ1|Q5JUY4|Q9BW56|Q9UQI9	Missense_Mutation	SNP	ENST00000372462.1	hg19	CCDS484.1	.	.	.	.	.	.	.	.	.	.	G	15.62	2.886198	0.51908	.	.	ENSG00000117399	ENST00000437896;ENST00000310955;ENST00000372462	T;T	0.29397	1.57;1.57	5.73	0.649	0.17806	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.27098	0.0664	L	0.33668	1.02	0.58432	D	0.999997	P	0.38992	0.653	P	0.45099	0.469	T	0.04481	-1.0948	10	0.62326	D	0.03	-17.7133	9.4478	0.38708	0.4049:0.0:0.5951:0.0	.	367	Q12834	CDC20_HUMAN	H	343;367;367	ENSP00000308450:Q367H;ENSP00000361540:Q367H	ENSP00000308450:Q367H	Q	+	3	2	CDC20	43599401	1.000000	0.71417	0.997000	0.53966	0.993000	0.82548	3.104000	0.50306	0.090000	0.17273	-0.291000	0.09656	CAG	.	.	.	none		0.572	CDC20-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019488.1	NM_001255	
KLF17	128209	hgsc.bcm.edu	37	1	44595144	44595144	+	Missense_Mutation	SNP	G	G	T			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:44595144G>T	ENST00000372299.3	+	2	259	c.201G>T	c.(199-201)atG>atT	p.M67I	KLF17_ENST00000476802.1_3'UTR	NM_173484.3	NP_775755.3	Q5JT82	KLF17_HUMAN	Kruppel-like factor 17	67					gamete generation (GO:0007276)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|central_nervous_system(1)|large_intestine(1)|lung(6)|ovary(3)|prostate(1)|skin(2)|stomach(1)	18	Acute lymphoblastic leukemia(166;0.155)					GCGCAGAGATGCTGGGGTCCC	0.547																																					p.M67I		Atlas-SNP	.											.	KLF17	92	.	0			c.G201T						PASS	.						77.0	68.0	71.0					1																	44595144		2203	4300	6503	SO:0001583	missense	128209	exon2			AGAGATGCTGGGG	BC049844	CCDS508.1	1p34.1	2011-11-15	2006-02-17	2006-02-17	ENSG00000171872	ENSG00000171872		"""Zinc fingers, C2H2-type"", ""Kruppel-like transcription factors"""	18830	protein-coding gene	gene with protein product		609602	"""zinc finger protein 393"""	ZNF393		16460907	Standard	NM_173484		Approved	Zfp393, FLJ40160	uc001clp.3	Q5JT82	OTTHUMG00000009664	ENST00000372299.3:c.201G>T	chr1.hg19:g.44595144G>T	ENSP00000361373:p.Met67Ile	136.0	0.0	.		112.0	5.0	.	NM_173484	Q86VQ7|Q8N805	Missense_Mutation	SNP	ENST00000372299.3	hg19	CCDS508.1	.	.	.	.	.	.	.	.	.	.	G	12.28	1.890870	0.33348	.	.	ENSG00000171872	ENST00000372299	T	0.07327	3.2	4.58	3.66	0.41972	.	0.565978	0.16022	N	0.233274	T	0.05960	0.0155	N	0.19112	0.55	0.09310	N	1	B	0.26809	0.16	B	0.19946	0.027	T	0.30179	-0.9987	10	0.49607	T	0.09	.	10.2955	0.43620	0.0:0.0:0.804:0.196	.	67	Q5JT82	KLF17_HUMAN	I	67	ENSP00000361373:M67I	ENSP00000361373:M67I	M	+	3	0	KLF17	44367731	0.376000	0.25098	0.006000	0.13384	0.003000	0.03518	1.800000	0.38833	1.520000	0.48965	0.650000	0.86243	ATG	.	.	.	none		0.547	KLF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026646.1	NM_173484	
GPBP1L1	60313	hgsc.bcm.edu	37	1	46124748	46124748	+	Silent	SNP	A	A	G			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:46124748A>G	ENST00000290795.3	-	3	1233	c.12T>C	c.(10-12)caT>caC	p.H4H	GPBP1L1_ENST00000355105.3_Silent_p.H4H			Q9HC44	GPBL1_HUMAN	GC-rich promoter binding protein 1-like 1	4					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)		GPBP1L1/MAST2_ENST00000361297(2)	breast(1)|endometrium(2)|large_intestine(4)|lung(10)|ovary(1)|skin(2)|stomach(1)	21	Acute lymphoblastic leukemia(166;0.155)					GAACAAAATCATGCTGCGCCA	0.428																																					p.H4H		Atlas-SNP	.											.	GPBP1L1	43	.	0			c.T12C						PASS	.						146.0	137.0	140.0					1																	46124748		2203	4300	6503	SO:0001819	synonymous_variant	60313	exon4			AAAATCATGCTGC		CCDS528.1	1p34.1	2008-02-05			ENSG00000159592	ENSG00000159592			28843	protein-coding gene	gene with protein product						12477932	Standard	NM_021639		Approved	SP192	uc001coq.3	Q9HC44	OTTHUMG00000040990	ENST00000290795.3:c.12T>C	chr1.hg19:g.46124748A>G		97.0	0.0	.		89.0	13.0	.	NM_021639	D3DQ10|Q9H751	Silent	SNP	ENST00000290795.3	hg19	CCDS528.1																																																																																			.	.	.	none		0.428	GPBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098375.1	NM_021639	
AGBL4	84871	hgsc.bcm.edu	37	1	48999847	48999847	+	Nonstop_Mutation	SNP	A	A	G			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:48999847A>G	ENST00000371839.1	-	14	1626	c.1510T>C	c.(1510-1512)Taa>Caa	p.*504Q	AGBL4_ENST00000334103.7_Nonstop_Mutation_p.*228Q	NM_032785.3	NP_116174.3	Q5VU57	CBPC6_HUMAN	ATP/GTP binding protein-like 4	0					C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytosol (GO:0005829)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)	15				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)		CCGTGTCTTTAAAAAGGGGTT	0.507																																					p.X504Q		Atlas-SNP	.											.	AGBL4	54	.	0			c.T1510C						PASS	.						168.0	152.0	157.0					1																	48999847		692	1591	2283	SO:0001578	stop_lost	84871	exon14			GTCTTTAAAAAGG	AK027348	CCDS44137.1	1p33	2014-06-23			ENSG00000186094	ENSG00000186094			25892	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase 6"""					21074048	Standard	NM_032785		Approved	FLJ14442, CCP6	uc001cru.2	Q5VU57	OTTHUMG00000007793	ENST00000371839.1:c.1510T>C	chr1.hg19:g.48999847A>G	ENSP00000360905:p.*504Gluext*27	179.0	0.0	.		156.0	20.0	.	NM_032785	B3KT26|B4DG37	Missense_Mutation	SNP	ENST00000371839.1	hg19	CCDS44137.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.7|21.7	4.181371|4.181371	0.78677|0.78677	.|.	.|.	ENSG00000186094|ENSG00000186094	ENST00000411952|ENST00000371839;ENST00000334103	.|.	.|.	.|.	5.35|5.35	5.35|5.35	0.76521|0.76521	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.18873|0.18873	N|N	0.999988|0.999988	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	11.9|11.9	0.52678|0.52678	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|.	.|.	.|.	.|Q	-1|504;228	.|.	.|.	.|X	-|-	.|1	.|0	AGBL4|AGBL4	48772434|48772434	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.851000|0.851000	0.48451|0.48451	3.026000|3.026000	0.49689|0.49689	2.371000|2.371000	0.80710|0.80710	0.533000|0.533000	0.62120|0.62120	.|TAA	.	.	.	none		0.507	AGBL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021346.4	NM_032785	
FNBP1L	54874	hgsc.bcm.edu	37	1	93965136	93965136	+	Missense_Mutation	SNP	T	T	A			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:93965136T>A	ENST00000271234.7	+	2	287	c.136T>A	c.(136-138)Ttg>Atg	p.L46M	FNBP1L_ENST00000604705.1_Missense_Mutation_p.L46M|FNBP1L_ENST00000260506.8_Missense_Mutation_p.L46M|FNBP1L_ENST00000370253.2_Missense_Mutation_p.L46M|FNBP1L_ENST00000370256.4_Missense_Mutation_p.L46M	NM_001164473.2	NP_001157945.1	Q5T0N5	FBP1L_HUMAN	formin binding protein 1-like	46	F-BAR domain. {ECO:0000250}.|FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.				autophagy (GO:0006914)|clathrin-mediated endocytosis (GO:0072583)|membrane budding (GO:0006900)|membrane invagination (GO:0010324)|membrane tubulation (GO:0097320)|positive regulation of filopodium assembly (GO:0051491)|vesicle organization (GO:0016050)|vesicle transport along actin filament (GO:0030050)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			breast(2)|kidney(2)|large_intestine(4)|lung(2)|urinary_tract(1)	11		all_lung(203;0.00206)|Lung NSC(277;0.00902)|Melanoma(281;0.155)		all cancers(265;0.00666)|GBM - Glioblastoma multiforme(16;0.0378)|Epithelial(280;0.111)		TGCGAAACAATTGAGGTAAGT	0.308																																					p.L46M		Atlas-SNP	.											.	FNBP1L	56	.	0			c.T136A						PASS	.						46.0	44.0	45.0					1																	93965136		1815	4062	5877	SO:0001583	missense	54874	exon2			AAACAATTGAGGT		CCDS53343.1, CCDS53344.1, CCDS60192.1	1p22.1	2008-02-05	2004-11-16	2004-11-17	ENSG00000137942	ENSG00000137942			20851	protein-coding gene	gene with protein product		608848	"""chromosome 1 open reading frame 39"""	C1orf39		14654988	Standard	NM_017737		Approved	TOCA1, FLJ20275	uc010otk.2	Q5T0N5	OTTHUMG00000010863	ENST00000271234.7:c.136T>A	chr1.hg19:g.93965136T>A	ENSP00000271234:p.Leu46Met	91.0	0.0	.		97.0	44.0	.	NM_001164473	J3QSS4|Q5T0N6|Q6B097|Q6P653|Q6R4Q4|Q9NXG1	Missense_Mutation	SNP	ENST00000271234.7	hg19	CCDS53343.1	.	.	.	.	.	.	.	.	.	.	T	18.19	3.568848	0.65765	.	.	ENSG00000137942	ENST00000370256;ENST00000271234;ENST00000260506;ENST00000370253	T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21	5.55	2.05	0.26809	.	0.000000	0.85682	D	0.000000	T	0.69223	0.3087	M	0.84326	2.69	0.80722	D	1	D;P	0.54207	0.965;0.938	P;P	0.61328	0.887;0.855	T	0.69847	-0.5034	10	0.54805	T	0.06	-7.6767	6.8376	0.23945	0.0:0.465:0.0:0.535	.	46;46	Q5T0N5-4;Q5T0N5-3	.;.	M	46	ENSP00000359278:L46M;ENSP00000271234:L46M;ENSP00000260506:L46M;ENSP00000359275:L46M	ENSP00000260506:L46M	L	+	1	2	FNBP1L	93737724	0.711000	0.27906	0.997000	0.53966	0.913000	0.54294	0.165000	0.16564	0.401000	0.25424	-0.605000	0.04089	TTG	.	.	.	none		0.308	FNBP1L-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_017737	
AQP10	89872	hgsc.bcm.edu	37	1	154296801	154296801	+	Missense_Mutation	SNP	G	G	T			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:154296801G>T	ENST00000324978.3	+	6	791	c.751G>T	c.(751-753)Gtg>Ttg	p.V251L	ATP8B2_ENST00000368487.3_5'Flank|AQP10_ENST00000484864.1_3'UTR	NM_080429.2	NP_536354.2	Q96PS8	AQP10_HUMAN	aquaporin 10	251					response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(14)|stomach(2)|upper_aerodigestive_tract(1)	23	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			GGCCCCTCTGGTGGGGGCCAC	0.602											OREG0013832	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V251L		Atlas-SNP	.											.	AQP10	44	.	0			c.G751T						PASS	.						32.0	35.0	34.0					1																	154296801		2201	4290	6491	SO:0001583	missense	89872	exon6			CCTCTGGTGGGGG	AF159174	CCDS1065.1	1q21.3	2008-02-05			ENSG00000143595	ENSG00000143595		"""Ion channels / Aquaporins"""	16029	protein-coding gene	gene with protein product		606578				11573934	Standard	NM_080429		Approved		uc001feu.3	Q96PS8	OTTHUMG00000035980	ENST00000324978.3:c.751G>T	chr1.hg19:g.154296801G>T	ENSP00000318355:p.Val251Leu	41.0	0.0	.	1762	33.0	16.0	.	NM_080429	Q5VYD3|Q5VYD4|Q8NG70	Missense_Mutation	SNP	ENST00000324978.3	hg19	CCDS1065.1	.	.	.	.	.	.	.	.	.	.	G	5.726	0.318459	0.10845	.	.	ENSG00000143595	ENST00000324978	D	0.88124	-2.34	4.46	4.46	0.54185	Aquaporin-like (2);	0.142496	0.45126	D	0.000385	T	0.65688	0.2715	L	0.28608	0.87	0.80722	D	1	B	0.32939	0.391	B	0.34722	0.188	T	0.67345	-0.5694	10	0.02654	T	1	.	12.9205	0.58230	0.0:0.1648:0.8352:0.0	.	251	Q96PS8	AQP10_HUMAN	L	251	ENSP00000318355:V251L	ENSP00000318355:V251L	V	+	1	0	AQP10	152563425	1.000000	0.71417	1.000000	0.80357	0.871000	0.50021	1.571000	0.36450	2.510000	0.84645	0.555000	0.69702	GTG	.	.	.	none		0.602	AQP10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087661.1	NM_080429	
CENPL	91687	hgsc.bcm.edu	37	1	173772300	173772300	+	Missense_Mutation	SNP	G	G	T			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:173772300G>T	ENST00000345664.6	-	4	977	c.764C>A	c.(763-765)gCa>gAa	p.A255E	CENPL_ENST00000356198.2_Missense_Mutation_p.A301E|CENPL_ENST00000367710.3_Missense_Mutation_p.A255E	NM_001171182.1	NP_001164653.1	Q8N0S6	CENPL_HUMAN	centromere protein L	255					mitotic cell cycle (GO:0000278)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(3)	11						TGGATGTATTGCGAAAGAAAT	0.458																																					p.A301E		Atlas-SNP	.											.	CENPL	26	.	0			c.C902A						PASS	.						95.0	97.0	96.0					1																	173772300		2203	4300	6503	SO:0001583	missense	91687	exon6			TGTATTGCGAAAG	BC033154, BC019022, AK055606	CCDS30938.1, CCDS44277.1	1q25.1	2013-11-05	2006-06-15	2006-06-15	ENSG00000120334	ENSG00000120334			17879	protein-coding gene	gene with protein product		611503	"""chromosome 1 open reading frame 155"""	C1orf155		16622420, 16622419	Standard	NM_033319		Approved	dJ383J4.3, FLJ31044	uc001gje.4	Q8N0S6	OTTHUMG00000034802	ENST00000345664.6:c.764C>A	chr1.hg19:g.173772300G>T	ENSP00000323543:p.Ala255Glu	122.0	0.0	.		75.0	19.0	.	NM_001127181	Q5TEL5|Q96ND4	Missense_Mutation	SNP	ENST00000345664.6	hg19	CCDS30938.1	.	.	.	.	.	.	.	.	.	.	G	18.51	3.640619	0.67244	.	.	ENSG00000120334	ENST00000356198;ENST00000345664;ENST00000367710	T;T;T	0.41758	1.58;0.99;0.99	5.24	5.24	0.73138	.	0.172946	0.50627	D	0.000109	T	0.47691	0.1459	L	0.43152	1.355	0.39487	D	0.967975	D;P	0.69078	0.997;0.896	D;P	0.63283	0.913;0.602	T	0.50882	-0.8775	10	0.72032	D	0.01	-5.8243	17.633	0.88114	0.0:0.0:1.0:0.0	.	301;255	Q8N0S6-2;Q8N0S6	.;CENPL_HUMAN	E	301;255;255	ENSP00000348527:A301E;ENSP00000323543:A255E;ENSP00000356683:A255E	ENSP00000323543:A255E	A	-	2	0	CENPL	172038923	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	5.635000	0.67841	2.456000	0.83038	0.655000	0.94253	GCA	.	.	.	none		0.458	CENPL-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084213.1	NM_033319	
RFWD2	64326	hgsc.bcm.edu	37	1	175996826	175996826	+	Splice_Site	SNP	T	T	C			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:175996826T>C	ENST00000367669.3	-	15	2127		c.e15-2		RFWD2_ENST00000308769.8_Splice_Site	NM_022457.5	NP_071902.2	Q8NHY2	RFWD2_HUMAN	ring finger and WD repeat domain 2, E3 ubiquitin protein ligase						DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|response to ionizing radiation (GO:0010212)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin protein ligase activity (GO:0061630)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(5)|lung(17)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						ACAGCTTCACTAAGGGCAAAG	0.388																																					.	Ovarian(134;1413 1765 5706 35534 51541)	Atlas-SNP	.											.	RFWD2	67	.	0			c.1613-2A>G						PASS	.						63.0	54.0	57.0					1																	175996826		2203	4300	6503	SO:0001630	splice_region_variant	64326	exon16			CTTCACTAAGGGC	AK001278	CCDS30944.1, CCDS44279.1	1q25.1-q25.2	2013-01-09	2012-02-23		ENSG00000143207	ENSG00000143207		"""WD repeat domain containing"", ""RING-type (C3HC4) zinc fingers"""	17440	protein-coding gene	gene with protein product		608067	"""ring finger and WD repeat domain 2"""			10395541	Standard	XM_005245447		Approved	FLJ10416, COP1, RNF200	uc001gku.1	Q8NHY2	OTTHUMG00000034986	ENST00000367669.3:c.1613-2A>G	chr1.hg19:g.175996826T>C		72.0	0.0	.		78.0	31.0	.	NM_022457	E9PKI0|Q504W6|Q6H103|Q9H6L7|X5D9B4	Splice_Site	SNP	ENST00000367669.3	hg19	CCDS30944.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.586435	0.86851	.	.	ENSG00000143207	ENST00000367665;ENST00000367669;ENST00000367666;ENST00000308769	.	.	.	5.73	5.73	0.89815	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.6701	0.77267	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	RFWD2	174263449	1.000000	0.71417	0.986000	0.45419	0.994000	0.84299	7.563000	0.82314	2.174000	0.68829	0.528000	0.53228	.	.	.	.	none		0.388	RFWD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084672.2	NM_022457	Intron
ETNK2	55224	hgsc.bcm.edu	37	1	204101322	204101322	+	Missense_Mutation	SNP	A	A	T			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:204101322A>T	ENST00000367202.4	-	8	1301	c.1151T>A	c.(1150-1152)aTg>aAg	p.M384K	RP11-74C13.4_ENST00000565388.1_RNA|ETNK2_ENST00000367199.2_Missense_Mutation_p.M315K|ETNK2_ENST00000367198.2_Missense_Mutation_p.M206K|ETNK2_ENST00000367201.3_3'UTR|ETNK2_ENST00000367197.1_Missense_Mutation_p.M66K	NM_018208.2	NP_060678.2	Q9NVF9	EKI2_HUMAN	ethanolamine kinase 2	384					glycerophospholipid biosynthetic process (GO:0046474)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|placenta development (GO:0001890)|post-embryonic development (GO:0009791)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ethanolamine kinase activity (GO:0004305)			breast(1)|central_nervous_system(1)|large_intestine(4)|ovary(1)	7	all_cancers(21;0.032)|Breast(84;0.116)|all_epithelial(62;0.196)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.109)			TCACTTTGGCATCTCCAAGGC	0.557																																					p.M384K		Atlas-SNP	.											.	ETNK2	48	.	0			c.T1151A						PASS	.						80.0	77.0	78.0					1																	204101322		1564	3580	5144	SO:0001583	missense	55224	exon8			TTTGGCATCTCCA	AK001623	CCDS1442.2, CCDS73006.1	1q32.1	2008-02-05			ENSG00000143845	ENSG00000143845			25575	protein-coding gene	gene with protein product		609859				12477932	Standard	XM_005245302		Approved	FLJ10761, EKI2	uc001hao.4	Q9NVF9	OTTHUMG00000036061	ENST00000367202.4:c.1151T>A	chr1.hg19:g.204101322A>T	ENSP00000356170:p.Met384Lys	165.0	0.0	.		101.0	34.0	.	NM_018208	B7Z7K1|Q5SXX5|Q68CK3|Q96G05	Missense_Mutation	SNP	ENST00000367202.4	hg19	CCDS1442.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.99|18.99	3.740600|3.740600	0.69304|0.69304	.|.	.|.	ENSG00000143845|ENSG00000143845	ENST00000422072|ENST00000367202;ENST00000367199;ENST00000455266;ENST00000367198;ENST00000367197	.|T;T;T;T	.|0.64260	.|0.34;-0.02;-0.02;-0.09	5.0|5.0	3.82|3.82	0.43975|0.43975	.|.	.|.	.|.	.|.	.|.	T|T	0.62780|0.62780	0.2456|0.2456	L|L	0.58669|0.58669	1.825|1.825	0.38499|0.38499	D|D	0.948185|0.948185	.|P;P	.|0.46859	.|0.877;0.885	.|P;B	.|0.50754	.|0.649;0.446	T|T	0.62305|0.62305	-0.6882|-0.6882	5|9	.|0.28530	.|T	.|0.3	.|.	8.0791|8.0791	0.30733|0.30733	0.7042:0.0:0.0:0.2958|0.7042:0.0:0.0:0.2958	.|.	.|343;384	.|Q9NVF9-3;Q9NVF9	.|.;EKI2_HUMAN	S|K	147|384;315;250;206;66	.|ENSP00000356170:M384K;ENSP00000356167:M315K;ENSP00000356166:M206K;ENSP00000356165:M66K	.|ENSP00000356165:M66K	C|M	-|-	1|2	0|0	ETNK2|ETNK2	202367945|202367945	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.878000|0.878000	0.50629|0.50629	6.504000|6.504000	0.73704|0.73704	1.880000|1.880000	0.54463|0.54463	0.533000|0.533000	0.62120|0.62120	TGC|ATG	.	.	.	none		0.557	ETNK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087893.1	NM_018208	
DIEXF	27042	hgsc.bcm.edu	37	1	210006562	210006562	+	Nonsense_Mutation	SNP	G	G	T			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:210006562G>T	ENST00000491415.2	+	4	478	c.421G>T	c.(421-423)Gaa>Taa	p.E141*		NM_014388.6	NP_055203.4	Q68CQ4	DIEXF_HUMAN	digestive organ expansion factor homolog (zebrafish)	141	Glu-rich.				multicellular organismal development (GO:0007275)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(15)|large_intestine(7)|lung(12)|ovary(1)|skin(3)|stomach(1)|urinary_tract(2)	53						TGAGGGAAAAGAAGATGGGGA	0.398																																					p.E141X		Atlas-SNP	.											.	DIEXF	97	.	0			c.G421T						PASS	.						59.0	56.0	57.0					1																	210006562		2203	4300	6503	SO:0001587	stop_gained	27042	exon4			GGAAAAGAAGATG	BC022964	CCDS1493.1	1q32.2	2011-08-12	2011-02-16	2011-02-16	ENSG00000117597	ENSG00000117597			28440	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 107"""	C1orf107		16322560	Standard	NM_014388		Approved	MGC29875, DEF, UTP25	uc001hhr.2	Q68CQ4	OTTHUMG00000036654	ENST00000491415.2:c.421G>T	chr1.hg19:g.210006562G>T	ENSP00000419005:p.Glu141*	59.0	0.0	.		51.0	17.0	.	NM_014388	O75992|Q4VY00|Q63HL9	Nonsense_Mutation	SNP	ENST00000491415.2	hg19	CCDS1493.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.380543	0.82792	.	.	ENSG00000117597	ENST00000491415	.	.	.	0.225	0.225	0.15325	.	1.807870	0.04544	U	0.388703	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.14252	T	0.57	.	.	.	.	.	.	.	.	X	141	.	ENSP00000419005:E141X	E	+	1	0	DIEXF	208073185	0.949000	0.32298	0.212000	0.23672	0.934000	0.57294	0.364000	0.20325	0.300000	0.22699	0.305000	0.20034	GAA	.	.	.	none		0.398	DIEXF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089127.2	NM_014388	
CENPF	1063	hgsc.bcm.edu	37	1	214820696	214820696	+	Missense_Mutation	SNP	A	A	T			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:214820696A>T	ENST00000366955.3	+	13	7951	c.7783A>T	c.(7783-7785)Aat>Tat	p.N2595Y		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	2691	Sufficient for centromere localization.|Sufficient for self-association.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		GAATCTAGAGAATGAGCTTGA	0.378																																					p.N2595Y	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											.	CENPF	321	.	0			c.A7783T						PASS	.						37.0	37.0	37.0					1																	214820696		2203	4300	6503	SO:0001583	missense	1063	exon13			CTAGAGAATGAGC	U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"""mitosin"""	600236	"""centromere protein F, 350/400kDa (mitosin)"""			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.7783A>T	chr1.hg19:g.214820696A>T	ENSP00000355922:p.Asn2595Tyr	66.0	0.0	.		55.0	24.0	.	NM_016343	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	hg19	CCDS31023.1	.	.	.	.	.	.	.	.	.	.	A	12.11	1.839067	0.32513	.	.	ENSG00000117724	ENST00000366955	T	0.03301	3.98	5.61	3.16	0.36331	.	0.728326	0.11309	N	0.577293	T	0.03608	0.0103	N	0.19112	0.55	0.25270	N	0.989526	P	0.51653	0.947	P	0.44732	0.459	T	0.45963	-0.9225	10	0.59425	D	0.04	.	7.1052	0.25360	0.777:0.1469:0.0761:0.0	.	2691	P49454	CENPF_HUMAN	Y	2595	ENSP00000355922:N2595Y	ENSP00000355922:N2595Y	N	+	1	0	CENPF	212887319	1.000000	0.71417	0.126000	0.21872	0.167000	0.22549	1.705000	0.37867	0.427000	0.26145	0.496000	0.49642	AAT	.	.	.	none		0.378	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343	
FBXO11	80204	hgsc.bcm.edu	37	2	48040950	48040950	+	Missense_Mutation	SNP	C	C	T			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr2:48040950C>T	ENST00000403359.3	-	17	2135	c.2063G>A	c.(2062-2064)gGa>gAa	p.G688E	FBXO11_ENST00000316377.4_Missense_Mutation_p.G604E|FBXO11_ENST00000434523.2_Missense_Mutation_p.G112E|FBXO11_ENST00000402508.1_Missense_Mutation_p.G604E	NM_001190274.1	NP_001177203.1	Q86XK2	FBX11_HUMAN	F-box protein 11	688					cellular protein modification process (GO:0006464)|peptidyl-arginine N-methylation (GO:0035246)|protein ubiquitination (GO:0016567)|sensory perception of sound (GO:0007605)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	protein-arginine N-methyltransferase activity (GO:0016274)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.0?(2)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	26		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			AACTAGAATTCCACCATTCTG	0.388			"""Mis, F, D"""		DLBCL																																p.G688E		Atlas-SNP	.		Rec	yes		2	2p16.3	80204	F-box protein 11		L	.	FBXO11	127	.	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	c.G2063A						PASS	.						118.0	116.0	117.0					2																	48040950		2202	4300	6502	SO:0001583	missense	80204	exon17			AGAATTCCACCAT	AF174599	CCDS1837.1, CCDS54357.1	2p16.3	2014-01-29	2008-06-23	2008-06-23	ENSG00000138081	ENSG00000138081		"""Ubiquitin protein ligase E3 component n-recognins"", ""F-boxes /  ""other"""""	13590	protein-coding gene	gene with protein product	"""ubiquitin protein ligase E3 component n-recognin 6"""	607871	"""F-box only protein 11"""			10531035, 16487488, 18162545	Standard	NM_025133		Approved	FBX11, UBR6	uc002rwe.3	Q86XK2	OTTHUMG00000129130	ENST00000403359.3:c.2063G>A	chr2.hg19:g.48040950C>T	ENSP00000384823:p.Gly688Glu	61.0	0.0	.		44.0	5.0	.	NM_001190274	A1L491|Q52ZP1|Q53EP7|Q53RT5|Q8IXG3|Q96E90|Q9H6V8|Q9H9L1|Q9NR14|Q9UFK1|Q9UHI1|Q9UKC2	Missense_Mutation	SNP	ENST00000403359.3	hg19	CCDS54357.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	32|32	5.136371|5.136371	0.94517|0.94517	.|.	.|.	ENSG00000138081|ENSG00000138081	ENST00000402508;ENST00000403359;ENST00000316377;ENST00000434523|ENST00000493962	D;D;D;D|.	0.90133|.	-2.62;-2.62;-2.62;-2.62|.	5.43|5.43	5.43|5.43	0.79202|0.79202	Pectin lyase fold/virulence factor (2);Carbohydrate-binding/sugar hydrolysis domain (1);F-box domain, Skp2-like (1);Pectin lyase fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|.	0.86789|.	0.6017|.	M|M	0.92880|0.92880	3.355|3.355	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	0.998;1.0|.	D|.	0.89459|.	0.3735|.	10|.	0.66056|.	D|.	0.02|.	-12.1201|-12.1201	19.5994|19.5994	0.95554|0.95554	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	112;688|.	B3KUR1;Q86XK2|.	.;FBX11_HUMAN|.	E|X	604;688;604;112|479	ENSP00000385398:G604E;ENSP00000384823:G688E;ENSP00000323822:G604E;ENSP00000397359:G112E|.	ENSP00000323822:G604E|.	G|W	-|-	2|3	0|0	FBXO11|FBXO11	47894454|47894454	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.776000|7.776000	0.85560|0.85560	2.699000|2.699000	0.92147|0.92147	0.655000|0.655000	0.94253|0.94253	GGA|TGG	.	.	.	none		0.388	FBXO11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251181.3	NM_012167, NM_018693, NM_025133	
AAK1	22848	hgsc.bcm.edu	37	2	69757189	69757189	+	Silent	SNP	G	G	A			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr2:69757189G>A	ENST00000409085.4	-	8	1198	c.822C>T	c.(820-822)ttC>ttT	p.F274F	AAK1_ENST00000406297.3_Silent_p.F274F|AAK1_ENST00000470281.1_5'Flank|AAK1_ENST00000409068.1_Silent_p.F274F	NM_014911.3	NP_055726	Q2M2I8	AAK1_HUMAN	AP2 associated kinase 1	274	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				endocytosis (GO:0006897)|positive regulation of Notch signaling pathway (GO:0045747)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of clathrin-mediated endocytosis (GO:2000369)|regulation of protein localization (GO:0032880)	cell leading edge (GO:0031252)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extrinsic component of plasma membrane (GO:0019897)|terminal bouton (GO:0043195)	AP-2 adaptor complex binding (GO:0035612)|ATP binding (GO:0005524)|Notch binding (GO:0005112)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)	17						CAGGAATTGTGAAGTTTCCAT	0.313																																					p.F274F		Atlas-SNP	.											.	AAK1	121	.	0			c.C822T						PASS	.						58.0	54.0	55.0					2																	69757189		1830	4085	5915	SO:0001819	synonymous_variant	22848	exon8			AATTGTGAAGTTT	AB028971	CCDS1893.2	2p13.3	2012-07-10			ENSG00000115977	ENSG00000115977			19679	protein-coding gene	gene with protein product						11877461, 12471243	Standard	NM_014911		Approved	KIAA1048, DKFZp686K16132	uc002sfp.2	Q2M2I8	OTTHUMG00000129648	ENST00000409085.4:c.822C>T	chr2.hg19:g.69757189G>A		170.0	0.0	.		125.0	44.0	.	NM_014911	Q4ZFZ3|Q53RX6|Q9UPV4	Silent	SNP	ENST00000409085.4	hg19	CCDS1893.2																																																																																			.	.	.	none		0.313	AAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251847.4	NM_014911	
RTKN	6242	hgsc.bcm.edu	37	2	74668862	74668862	+	Silent	SNP	G	G	T			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr2:74668862G>T	ENST00000272430.5	-	1	164	c.82C>A	c.(82-84)Cga>Aga	p.R28R	RTKN_ENST00000484453.1_5'UTR|RTKN_ENST00000305557.5_5'Flank|RTKN_ENST00000233330.6_5'Flank	NM_001015055.1	NP_001015055.1			rhotekin											endometrium(3)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	16						AGGCTGAGTCGGAAGCGGCCG	0.697																																					p.R28R		Atlas-SNP	.											.	RTKN	80	.	0			c.C82A						PASS	.						28.0	33.0	31.0					2																	74668862		2202	4300	6502	SO:0001819	synonymous_variant	6242	exon1			TGAGTCGGAAGCG	AF049227	CCDS1941.1, CCDS33226.1, CCDS42699.1	2p13.1	2013-01-10			ENSG00000114993	ENSG00000114993		"""Pleckstrin homology (PH) domain containing"""	10466	protein-coding gene	gene with protein product		602288				9073523, 10940294	Standard	XM_005264478		Approved	B5	uc002sle.3	Q9BST9	OTTHUMG00000129955	ENST00000272430.5:c.82C>A	chr2.hg19:g.74668862G>T		65.0	0.0	.		38.0	12.0	.	NM_001015055		Silent	SNP	ENST00000272430.5	hg19	CCDS33226.1																																																																																			.	.	.	none		0.697	RTKN-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000328234.1	NM_001015055	
DQX1	165545	hgsc.bcm.edu	37	2	74755401	74755401	+	5'Flank	SNP	G	G	T			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr2:74755401G>T	ENST00000404568.3	-	0	0				DQX1_ENST00000393951.2_5'Flank|AUP1_ENST00000377526.3_Missense_Mutation_p.F215L|HTRA2_ENST00000258080.3_5'Flank|HTRA2_ENST00000352222.3_5'Flank	NM_133637.2	NP_598376.2	Q8TE96	DQX1_HUMAN	DEAQ box RNA-dependent ATPase 1							nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	18						TGAAAGGGACGAAAAGTGACC	0.537																																					p.F215L		Atlas-SNP	.											.	AUP1	29	.	0			c.C645A						PASS	.						74.0	80.0	78.0					2																	74755401		2044	4193	6237	SO:0001631	upstream_gene_variant	550	exon6			AGGGACGAAAAGT	AK074337	CCDS1949.2	2p12	2010-04-20	2009-01-15		ENSG00000144045	ENSG00000144045			20410	protein-coding gene	gene with protein product			"""DEAQ box polypeptide 1 (RNA-dependent ATPase)"""				Standard	NM_133637		Approved	FLJ23757	uc010yrw.2	Q8TE96	OTTHUMG00000129965		chr2.hg19:g.74755401G>T	Exception_encountered	70.0	0.0	.		60.0	24.0	.	NM_181575	Q6B017|Q8NAM8	Missense_Mutation	SNP	ENST00000404568.3	hg19	CCDS1949.2	.	.	.	.	.	.	.	.	.	.	G	18.80	3.701042	0.68501	.	.	ENSG00000115307	ENST00000377526;ENST00000258081;ENST00000412627	D	0.92495	-3.05	5.1	3.01	0.34805	.	0.000000	0.85682	D	0.000000	D	0.94000	0.8078	M	0.66506	2.035	0.54753	D	0.999982	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.85130	0.984;0.992;0.997	D	0.91236	0.5018	10	0.33940	T	0.23	-15.5435	8.4169	0.32676	0.226:0.0:0.774:0.0	.	272;281;215	E7EU18;Q9Y679;Q9Y679-2	.;AUP1_HUMAN;.	L	215;279;217	ENSP00000366748:F215L	ENSP00000258081:F279L	F	-	3	2	AUP1	74608909	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.450000	0.35134	0.528000	0.28580	0.462000	0.41574	TTC	.	.	.	none		0.537	DQX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252230.3	NM_133637	
LRP2	4036	hgsc.bcm.edu	37	2	170136009	170136009	+	Nonsense_Mutation	SNP	T	T	A			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr2:170136009T>A	ENST00000263816.3	-	12	1723	c.1438A>T	c.(1438-1440)Aaa>Taa	p.K480*	LRP2_ENST00000443831.1_Nonsense_Mutation_p.K480*	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	480					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""""""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"""	AGATAGATTTTATTATTAACC	0.393																																					p.K480X		Atlas-SNP	.											.	LRP2	751	.	0			c.A1438T						PASS	.						98.0	105.0	103.0					2																	170136009		2203	4300	6503	SO:0001587	stop_gained	4036	exon12			AGATTTTATTATT		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"""Low density lipoprotein receptors"""	6694	protein-coding gene	gene with protein product	"""megalin"""	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.1438A>T	chr2.hg19:g.170136009T>A	ENSP00000263816:p.Lys480*	72.0	0.0	.		81.0	26.0	.	NM_004525	O00711|Q16215	Nonsense_Mutation	SNP	ENST00000263816.3	hg19	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	T	39	7.557577	0.98358	.	.	ENSG00000081479	ENST00000263816;ENST00000443831	.	.	.	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7574	0.78046	0.0:0.0:0.0:1.0	.	.	.	.	X	480	.	.	K	-	1	0	LRP2	169844255	1.000000	0.71417	0.998000	0.56505	0.410000	0.31052	7.971000	0.88012	2.136000	0.66102	0.528000	0.53228	AAA	.	.	.	none		0.393	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
GAD1	2571	hgsc.bcm.edu	37	2	171700591	171700591	+	Missense_Mutation	SNP	G	G	T			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr2:171700591G>T	ENST00000358196.3	+	7	1225	c.675G>T	c.(673-675)atG>atT	p.M225I	GAD1_ENST00000429023.1_3'UTR	NM_000817.2	NP_000808.2	Q99259	DCE1_HUMAN	glutamate decarboxylase 1 (brain, 67kDa)	225					gamma-aminobutyric acid biosynthetic process (GO:0009449)|glutamate catabolic process (GO:0006538)|glutamate decarboxylation to succinate (GO:0006540)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|protein-pyridoxal-5-phosphate linkage (GO:0018352)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|pyridoxal phosphate binding (GO:0030170)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(15)|ovary(1)|urinary_tract(2)	35						TTGTCCTCATGGAACAAATAA	0.368																																					p.M225I		Atlas-SNP	.											.	GAD1	79	.	0			c.G675T						PASS	.						210.0	215.0	213.0					2																	171700591		2203	4300	6503	SO:0001583	missense	2571	exon7			CCTCATGGAACAA		CCDS2239.1, CCDS2240.1	2q31	2008-02-05	2002-08-29		ENSG00000128683	ENSG00000128683	4.1.1.15		4092	protein-coding gene	gene with protein product		605363	"""glutamate decarboxylase 1 (brain, 67kD)"""	GAD		1549570	Standard	XM_005246443		Approved		uc002ugi.3	Q99259	OTTHUMG00000044175	ENST00000358196.3:c.675G>T	chr2.hg19:g.171700591G>T	ENSP00000350928:p.Met225Ile	122.0	0.0	.		119.0	40.0	.	NM_000817	Q49AK1|Q53TQ7|Q9BU91|Q9UHH4	Missense_Mutation	SNP	ENST00000358196.3	hg19	CCDS2239.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.500461	0.85176	.	.	ENSG00000128683	ENST00000358196	T	0.36520	1.25	6.17	6.17	0.99709	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	T	0.37865	0.1019	L	0.33624	1.015	0.80722	D	1	B	0.30021	0.265	B	0.35312	0.2	T	0.15350	-1.0440	10	0.72032	D	0.01	-26.7667	20.8794	0.99867	0.0:0.0:1.0:0.0	.	225	Q99259	DCE1_HUMAN	I	225	ENSP00000350928:M225I	ENSP00000350928:M225I	M	+	3	0	GAD1	171408837	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.394000	0.97261	2.941000	0.99782	0.655000	0.94253	ATG	.	.	.	none		0.368	GAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102664.2		
MSTN	2660	hgsc.bcm.edu	37	2	190927181	190927181	+	Missense_Mutation	SNP	T	T	C			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr2:190927181T>C	ENST00000260950.4	-	1	274	c.142A>G	c.(142-144)Act>Gct	p.T48A	C2orf88_ENST00000478197.1_Intron	NM_005259.2	NP_005250.1	O14793	GDF8_HUMAN	myostatin	48					cellular response to dexamethasone stimulus (GO:0071549)|muscle organ development (GO:0007517)|negative regulation of muscle hypertrophy (GO:0014741)|negative regulation of skeletal muscle tissue growth (GO:0048632)|ovulation cycle process (GO:0022602)|positive regulation of transcription, DNA-templated (GO:0045893)|response to electrical stimulus (GO:0051602)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to gravity (GO:0009629)|response to heat (GO:0009408)|response to muscle activity (GO:0014850)|response to testosterone (GO:0033574)|skeletal muscle atrophy (GO:0014732)|skeletal muscle tissue regeneration (GO:0043403)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|receptor binding (GO:0005102)			endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|skin(1)	12			OV - Ovarian serous cystadenocarcinoma(117;0.000742)|Epithelial(96;0.0121)|all cancers(119;0.0395)			GAAGATTTAGTGTTTTGTCTC	0.378																																					p.T48A		Atlas-SNP	.											.	MSTN	46	.	0			c.A142G						PASS	.						198.0	194.0	195.0					2																	190927181		2203	4300	6503	SO:0001583	missense	2660	exon1			ATTTAGTGTTTTG	AF019627	CCDS2303.1	2q32.1	2014-09-17	2007-06-21	2007-06-21	ENSG00000138379	ENSG00000138379			4223	protein-coding gene	gene with protein product		601788	"""growth differentiation factor 8"""	GDF8		9288100, 10610713, 17003236	Standard	NM_005259		Approved		uc002urp.3	O14793	OTTHUMG00000132663	ENST00000260950.4:c.142A>G	chr2.hg19:g.190927181T>C	ENSP00000260950:p.Thr48Ala	52.0	0.0	.		49.0	22.0	.	NM_005259	A1C2J7|A1C2K0|Q6B0H2	Missense_Mutation	SNP	ENST00000260950.4	hg19	CCDS2303.1	.	.	.	.	.	.	.	.	.	.	T	13.67	2.307916	0.40895	.	.	ENSG00000138379	ENST00000260950	T	0.64085	-0.08	5.64	5.64	0.86602	Transforming growth factor-beta, N-terminal (1);	0.217803	0.48286	D	0.000186	T	0.51753	0.1693	L	0.29908	0.895	0.43195	D	0.995031	B	0.09022	0.002	B	0.15870	0.014	T	0.43877	-0.9364	10	0.30854	T	0.27	-11.9215	16.0238	0.80522	0.0:0.0:0.0:1.0	.	48	O14793	GDF8_HUMAN	A	48	ENSP00000260950:T48A	ENSP00000260950:T48A	T	-	1	0	MSTN	190635426	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	5.928000	0.70088	2.367000	0.80283	0.528000	0.53228	ACT	.	.	.	none		0.378	MSTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255917.2	NM_005259	
C2orf69	205327	hgsc.bcm.edu	37	2	200789854	200789854	+	Missense_Mutation	SNP	G	G	T			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr2:200789854G>T	ENST00000319974.5	+	2	586	c.403G>T	c.(403-405)Gct>Tct	p.A135S	C2orf69_ENST00000491721.1_Intron	NM_153689.5	NP_710156.3	Q8N8R5	CB069_HUMAN	chromosome 2 open reading frame 69	135						extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(2)|stomach(1)|urinary_tract(1)	11						AGAAAATGTTGCTACCATTTT	0.353																																					p.A135S		Atlas-SNP	.											.	C2orf69	17	.	0			c.G403T						PASS	.						51.0	48.0	48.0					2																	200789854		1819	4077	5896	SO:0001583	missense	205327	exon2			AATGTTGCTACCA		CCDS46482.1	2q33.1	2008-08-08			ENSG00000178074	ENSG00000178074			26799	protein-coding gene	gene with protein product	"""hypothetical protein FLJ38973"""					12477932	Standard	NM_153689		Approved	FLJ38973	uc010zhb.2	Q8N8R5	OTTHUMG00000154480	ENST00000319974.5:c.403G>T	chr2.hg19:g.200789854G>T	ENSP00000312770:p.Ala135Ser	56.0	0.0	.		92.0	31.0	.	NM_153689	Q8NE30	Missense_Mutation	SNP	ENST00000319974.5	hg19	CCDS46482.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.667963	0.88348	.	.	ENSG00000178074	ENST00000319974	.	.	.	6.03	6.03	0.97812	.	0.049006	0.85682	D	0.000000	D	0.82600	0.5072	M	0.76328	2.33	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.82600	-0.0377	9	0.62326	D	0.03	-10.3396	19.5548	0.95338	0.0:0.0:1.0:0.0	.	135	Q8N8R5	CB069_HUMAN	S	135	.	ENSP00000312770:A135S	A	+	1	0	C2orf69	200498099	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.827000	0.99397	2.854000	0.98071	0.655000	0.94253	GCT	.	.	.	none		0.353	C2orf69-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335446.1	NM_153689	
DGKD	8527	hgsc.bcm.edu	37	2	234368926	234368926	+	Missense_Mutation	SNP	G	G	T			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr2:234368926G>T	ENST00000264057.2	+	24	2928	c.2916G>T	c.(2914-2916)atG>atT	p.M972I	DGKD_ENST00000409813.3_Missense_Mutation_p.M928I	NM_152879.2	NP_690618.2	Q16760	DGKD_HUMAN	diacylglycerol kinase, delta 130kDa	972					blood coagulation (GO:0007596)|cell growth (GO:0016049)|diacylglycerol metabolic process (GO:0046339)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|multicellular organismal development (GO:0007275)|platelet activation (GO:0030168)|protein homooligomerization (GO:0051260)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein transport (GO:0015031)|response to organic substance (GO:0010033)|second-messenger-mediated signaling (GO:0019932)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol binding (GO:0019992)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(13)|lung(15)|ovary(1)|pancreas(1)|skin(1)	38		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0538)		Epithelial(121;1.31e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000416)|Lung(119;0.00285)|LUSC - Lung squamous cell carcinoma(224;0.00655)	Phosphatidylserine(DB00144)	ACCCGGAGATGCTGTCCGAGG	0.617																																					p.M972I		Atlas-SNP	.											.	DGKD	106	.	0			c.G2916T						PASS	.						87.0	79.0	81.0					2																	234368926		2203	4300	6503	SO:0001583	missense	8527	exon24			GGAGATGCTGTCC	D63479	CCDS2504.1, CCDS46546.1	2q37	2013-01-10	2002-08-29		ENSG00000077044	ENSG00000077044		"""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"""	2851	protein-coding gene	gene with protein product	"""diglyceride kinase"""	601826	"""diacylglycerol kinase, delta (130kD)"""			8626538, 12810723	Standard	NM_003648		Approved	KIAA0145, DGKdelta	uc002vui.1	Q16760	OTTHUMG00000133290	ENST00000264057.2:c.2916G>T	chr2.hg19:g.234368926G>T	ENSP00000264057:p.Met972Ile	544.0	1.0	.		376.0	143.0	.	NM_152879	Q14158|Q6PK55|Q8NG53	Missense_Mutation	SNP	ENST00000264057.2	hg19	CCDS2504.1	.	.	.	.	.	.	.	.	.	.	G	7.872	0.728341	0.15507	.	.	ENSG00000077044	ENST00000264057;ENST00000409813	T;T	0.78364	-0.99;-1.17	4.93	3.12	0.35913	.	0.425083	0.24007	N	0.042416	T	0.41419	0.1158	N	0.00652	-1.29	0.20403	N	0.999909	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.33214	-0.9877	10	0.21014	T	0.42	.	4.9917	0.14218	0.132:0.4809:0.3087:0.0784	.	928;972	Q16760-2;Q16760	.;DGKD_HUMAN	I	972;928	ENSP00000264057:M972I;ENSP00000386455:M928I	ENSP00000264057:M972I	M	+	3	0	DGKD	234033665	1.000000	0.71417	0.994000	0.49952	0.551000	0.35334	1.017000	0.29989	0.790000	0.33803	0.563000	0.77884	ATG	.	.	.	none		0.617	DGKD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257072.2	NM_003648	
SATB1	6304	hgsc.bcm.edu	37	3	18390936	18390936	+	Missense_Mutation	SNP	T	T	C			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr3:18390936T>C	ENST00000338745.6	-	11	3752	c.2018A>G	c.(2017-2019)gAg>gGg	p.E673G	SATB1_ENST00000417717.2_Missense_Mutation_p.E705G|TBC1D5_ENST00000414318.2_Intron|SATB1_ENST00000454909.2_Missense_Mutation_p.E673G	NM_002971.4	NP_002962.1	Q01826	SATB1_HUMAN	SATB homeobox 1	673					activated T cell proliferation (GO:0050798)|apoptotic process (GO:0006915)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|epidermis development (GO:0008544)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|reflex (GO:0060004)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(2)|endometrium(6)|large_intestine(4)|lung(10)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	32						CTGGATGGCCTCTTCGTCAGG	0.517																																					p.E705G		Atlas-SNP	.											.	SATB1	96	.	0			c.A2114G						PASS	.						141.0	140.0	140.0					3																	18390936		2203	4300	6503	SO:0001583	missense	6304	exon12			ATGGCCTCTTCGT		CCDS2631.1, CCDS56242.1	3p24.3	2011-07-19	2007-02-15		ENSG00000182568	ENSG00000182568		"""Homeoboxes / CUT class"""	10541	protein-coding gene	gene with protein product		602075	"""special AT-rich sequence binding protein 1 (binds to nuclear matrix/scaffold-associating DNA)"""			1505028	Standard	NM_002971		Approved		uc003cbj.3	Q01826	OTTHUMG00000129890	ENST00000338745.6:c.2018A>G	chr3.hg19:g.18390936T>C	ENSP00000341024:p.Glu673Gly	202.0	0.0	.		175.0	73.0	.	NM_001195470	B3KXF1|C9JTR6|Q59EQ0	Missense_Mutation	SNP	ENST00000338745.6	hg19	CCDS2631.1	.	.	.	.	.	.	.	.	.	.	T	17.36	3.370587	0.61624	.	.	ENSG00000182568	ENST00000338745;ENST00000454909;ENST00000417717	D;D;D	0.96745	-4.11;-4.11;-4.11	5.27	5.27	0.74061	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.049242	0.85682	N	0.000000	D	0.96642	0.8904	L	0.32530	0.975	0.80722	D	1	B;D	0.89917	0.013;1.0	B;D	0.97110	0.004;1.0	D	0.97662	1.0161	10	0.87932	D	0	-15.8047	15.186	0.73002	0.0:0.0:0.0:1.0	.	705;673	Q01826-2;Q01826	.;SATB1_HUMAN	G	673;673;705	ENSP00000341024:E673G;ENSP00000399708:E673G;ENSP00000399518:E705G	ENSP00000341024:E673G	E	-	2	0	SATB1	18365940	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.911000	0.87458	1.993000	0.58246	0.460000	0.39030	GAG	.	.	.	none		0.517	SATB1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252138.4	NM_001131010	
EPM2AIP1	9852	hgsc.bcm.edu	37	3	37033483	37033483	+	Missense_Mutation	SNP	C	C	A			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr3:37033483C>A	ENST00000322716.5	-	1	1312	c.1086G>T	c.(1084-1086)ttG>ttT	p.L362F	MLH1_ENST00000536378.1_5'Flank|MLH1_ENST00000458205.2_5'Flank|MLH1_ENST00000435176.1_5'Flank|MLH1_ENST00000539477.1_5'Flank|MLH1_ENST00000455445.2_5'Flank|MLH1_ENST00000231790.2_5'Flank	NM_014805.3	NP_055620.1	Q7L775	EPMIP_HUMAN	EPM2A (laforin) interacting protein 1	362					positive regulation of glycogen (starch) synthase activity (GO:2000467)|positive regulation of glycogen biosynthetic process (GO:0045725)|response to insulin (GO:0032868)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)				breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|liver(1)|lung(12)|ovary(2)	27						CTACTGAAACCAAGAACGCTT	0.413																																					p.L362F		Atlas-SNP	.											.	EPM2AIP1	47	.	0			c.G1086T						PASS	.						190.0	192.0	191.0					3																	37033483		1871	4110	5981	SO:0001583	missense	9852	exon1			TGAAACCAAGAAC	AB018309	CCDS46790.1	3p22.1	2003-03-26							19735	protein-coding gene	gene with protein product		607911					Standard	NM_014805		Approved	KIAA0766, FLJ11207	uc003cgk.3	Q7L775		ENST00000322716.5:c.1086G>T	chr3.hg19:g.37033483C>A	ENSP00000406027:p.Leu362Phe	62.0	0.0	.		62.0	10.0	.	NM_014805	O94866|Q9H3L3	Missense_Mutation	SNP	ENST00000322716.5	hg19	CCDS46790.1	.	.	.	.	.	.	.	.	.	.	C	17.00	3.275856	0.59649	.	.	ENSG00000178567	ENST00000322716	T	0.31247	1.5	4.71	4.71	0.59529	.	.	.	.	.	T	0.41834	0.1176	L	0.27053	0.805	0.47698	D	0.999499	D	0.76494	0.999	D	0.74674	0.984	T	0.29549	-1.0008	9	0.49607	T	0.09	-10.3057	15.1824	0.72968	0.0:1.0:0.0:0.0	.	362	Q7L775	EPMIP_HUMAN	F	362	ENSP00000406027:L362F	ENSP00000406027:L362F	L	-	3	2	EPM2AIP1	37008487	1.000000	0.71417	1.000000	0.80357	0.797000	0.45037	2.648000	0.46647	2.424000	0.82194	0.591000	0.81541	TTG	.	.	.	none		0.413	EPM2AIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000470593.1	NM_014805	
LIMD1	8994	hgsc.bcm.edu	37	3	45637412	45637412	+	Missense_Mutation	SNP	T	T	G			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr3:45637412T>G	ENST00000273317.4	+	1	1062	c.1041T>G	c.(1039-1041)agT>agG	p.S347R	LIMD1_ENST00000465039.1_Intron|LIMD1_ENST00000440097.1_Missense_Mutation_p.S347R	NM_014240.2	NP_055055.1	Q9UGP4	LIMD1_HUMAN	LIM domains containing 1	347					cell migration (GO:0016477)|cytoplasmic mRNA processing body assembly (GO:0033962)|cytoskeleton organization (GO:0007010)|gene silencing by miRNA (GO:0035195)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of hippo signaling (GO:0035331)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|phosphorylation (GO:0016310)|positive regulation of gene silencing by miRNA (GO:2000637)|regulation of cell shape (GO:0008360)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|RISC complex (GO:0016442)	transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(193;0.011)|KIRC - Kidney renal clear cell carcinoma(197;0.0264)|Kidney(197;0.0315)		ACCTTTCCAGTTCTGCCCCGT	0.622																																					p.S347R		Atlas-SNP	.											.	LIMD1	34	.	0			c.T1041G						PASS	.						78.0	78.0	78.0					3																	45637412		2203	4300	6503	SO:0001583	missense	8994	exon1			TTCCAGTTCTGCC	AJ132408	CCDS2729.1	3p21.31	2008-02-01			ENSG00000144791	ENSG00000144791			6612	protein-coding gene	gene with protein product		604543				10647888	Standard	NM_014240		Approved		uc003coq.3	Q9UGP4	OTTHUMG00000133453	ENST00000273317.4:c.1041T>G	chr3.hg19:g.45637412T>G	ENSP00000273317:p.Ser347Arg	251.0	0.0	.		231.0	79.0	.	NM_014240	Q17RQ1|Q9BQQ9|Q9NQ47	Missense_Mutation	SNP	ENST00000273317.4	hg19	CCDS2729.1	.	.	.	.	.	.	.	.	.	.	T	9.543	1.113931	0.20795	.	.	ENSG00000144791	ENST00000440097;ENST00000273317	T;T	0.58506	0.33;0.53	4.73	1.1	0.20463	.	1.824180	0.02460	N	0.086523	T	0.44953	0.1318	L	0.29908	0.895	0.09310	N	1	B	0.15141	0.012	B	0.09377	0.004	T	0.14420	-1.0473	10	0.22706	T	0.39	.	6.3277	0.21253	0.0:0.4757:0.0:0.5243	.	347	Q9UGP4	LIMD1_HUMAN	R	347	ENSP00000394537:S347R;ENSP00000273317:S347R	ENSP00000273317:S347R	S	+	3	2	LIMD1	45612416	0.001000	0.12720	0.006000	0.13384	0.180000	0.23129	-0.032000	0.12266	0.203000	0.20529	0.533000	0.62120	AGT	.	.	.	none		0.622	LIMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257327.1	NM_014240	
DNAH1	25981	hgsc.bcm.edu	37	3	52416419	52416419	+	Missense_Mutation	SNP	T	T	C			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr3:52416419T>C	ENST00000420323.2	+	50	8150	c.7889T>C	c.(7888-7890)cTc>cCc	p.L2630P		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	2630	AAA 4. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		AAGGTCCTGCTCAAGGCGGGC	0.582																																					p.L2630P		Atlas-SNP	.											.	DNAH1	534	.	0			c.T7889C						PASS	.						169.0	177.0	175.0					3																	52416419		2125	4239	6364	SO:0001583	missense	25981	exon50			TCCTGCTCAAGGC	U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"""Axonemal dyneins"""	2940	protein-coding gene	gene with protein product		603332	"""dynein, axonemal, heavy polypeptide 1"""			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.7889T>C	chr3.hg19:g.52416419T>C	ENSP00000401514:p.Leu2630Pro	197.0	0.0	.		143.0	57.0	.	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	hg19	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	T	18.02	3.529987	0.64860	.	.	ENSG00000114841	ENST00000420323	T	0.54279	0.58	4.49	4.49	0.54785	.	0.155058	0.30126	N	0.010343	T	0.76898	0.4052	M	0.93507	3.425	0.80722	D	1	D	0.61697	0.99	D	0.67725	0.953	T	0.80817	-0.1213	10	0.35671	T	0.21	.	13.9669	0.64213	0.0:0.0:0.0:1.0	.	2630	C9JXH6	.	P	2630	ENSP00000401514:L2630P	ENSP00000401514:L2630P	L	+	2	0	DNAH1	52391459	1.000000	0.71417	1.000000	0.80357	0.723000	0.41478	5.444000	0.66587	1.883000	0.54544	0.379000	0.24179	CTC	.	.	.	none		0.582	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512	
IGSF10	285313	hgsc.bcm.edu	37	3	151166796	151166796	+	Missense_Mutation	SNP	C	C	T			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr3:151166796C>T	ENST00000282466.3	-	4	972	c.973G>A	c.(973-975)Gga>Aga	p.G325R		NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	325					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			GCTTCATTTCCAGACTGATCT	0.433																																					p.G325R		Atlas-SNP	.											IGSF10,NS,malignant_melanoma,0,1	IGSF10	279	.	0			c.G973A						PASS	.						108.0	109.0	109.0					3																	151166796		2203	4300	6503	SO:0001583	missense	285313	exon4			CATTTCCAGACTG	AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"""Immunoglobulin superfamily / I-set domain containing"""	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.973G>A	chr3.hg19:g.151166796C>T	ENSP00000282466:p.Gly325Arg	126.0	0.0	.		117.0	46.0	.	NM_178822	Q86YJ9|Q8N772|Q8NA84	Missense_Mutation	SNP	ENST00000282466.3	hg19	CCDS3160.1	.	.	.	.	.	.	.	.	.	.	C	13.46	2.243180	0.39697	.	.	ENSG00000152580	ENST00000282466	T	0.75260	-0.92	5.37	4.5	0.54988	.	0.000000	0.47093	D	0.000256	T	0.67915	0.2944	M	0.64997	1.995	0.38362	D	0.944634	B	0.34200	0.441	B	0.26094	0.066	T	0.72513	-0.4270	10	0.87932	D	0	.	10.7221	0.46046	0.0:0.7971:0.1309:0.072	.	325	Q6WRI0	IGS10_HUMAN	R	325	ENSP00000282466:G325R	ENSP00000282466:G325R	G	-	1	0	IGSF10	152649486	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.805000	0.38883	1.270000	0.44297	0.650000	0.86243	GGA	.	.	.	none		0.433	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822	
BOD1L1	259282	hgsc.bcm.edu	37	4	13601745	13601745	+	Missense_Mutation	SNP	G	G	A			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr4:13601745G>A	ENST00000040738.5	-	10	6914	c.6779C>T	c.(6778-6780)tCg>tTg	p.S2260L		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	2260						nucleus (GO:0005634)	DNA binding (GO:0003677)										GTCTTCCACCGAGCTCGTAGA	0.542																																					p.S2260L		Atlas-SNP	.											BOD1L,colon,carcinoma,0,1	.	.	.	0			c.C6779T						PASS	.						79.0	69.0	72.0					4																	13601745		2203	4300	6503	SO:0001583	missense	259282	exon10			TCCACCGAGCTCG	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"""family with sequence similarity 44, member A"", ""biorientation of chromosomes in cell division 1-like"""	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.6779C>T	chr4.hg19:g.13601745G>A	ENSP00000040738:p.Ser2260Leu	171.0	0.0	.		149.0	16.0	.	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	hg19	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	G	21.7	4.194306	0.78902	.	.	ENSG00000038219	ENST00000040738	T	0.12255	2.7	5.46	5.46	0.80206	.	0.000000	0.45126	D	0.000387	T	0.23727	0.0574	M	0.64997	1.995	0.30881	N	0.731467	D	0.63046	0.992	P	0.51055	0.657	T	0.15350	-1.0440	10	0.72032	D	0.01	-3.6924	11.8817	0.52579	0.0832:0.0:0.9168:0.0	.	2260	Q8NFC6	BOD1L_HUMAN	L	2260	ENSP00000040738:S2260L	ENSP00000040738:S2260L	S	-	2	0	BOD1L	13210843	0.993000	0.37304	0.944000	0.38274	0.889000	0.51656	2.414000	0.44627	2.573000	0.86826	0.650000	0.86243	TCG	.	.	.	none		0.542	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894	
RUFY3	22902	hgsc.bcm.edu	37	4	71588406	71588406	+	Missense_Mutation	SNP	G	G	T			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr4:71588406G>T	ENST00000226328.4	+	1	679	c.116G>T	c.(115-117)tGg>tTg	p.W39L	RUFY3_ENST00000417478.2_Intron|RUFY3_ENST00000381006.3_Missense_Mutation_p.W39L|RUFY3_ENST00000536664.1_Missense_Mutation_p.W5L	NM_014961.3	NP_055776.1	Q7L099	RUFY3_HUMAN	RUN and FYVE domain containing 3	39					negative regulation of axonogenesis (GO:0050771)	filopodium (GO:0030175)|growth cone (GO:0030426)				endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)	16		all_hematologic(202;0.248)	Lung(101;0.235)			GATGGAGAATGGCTCTGCCTG	0.532																																					p.W39L		Atlas-SNP	.											.	RUFY3	61	.	0			c.G116T						PASS	.						204.0	166.0	179.0					4																	71588406		2203	4300	6503	SO:0001583	missense	22902	exon1			GAGAATGGCTCTG	AF112221	CCDS3547.1, CCDS34001.1, CCDS47068.1, CCDS75138.1	4q13.3	2009-05-29			ENSG00000018189	ENSG00000018189		"""Zinc fingers, FYVE domain containing"""	30285	protein-coding gene	gene with protein product	"""single axon-related 1"""	611194				17439943	Standard	NM_001130709		Approved	RIPx, KIAA0871, Singar1	uc003hfr.3	Q7L099	OTTHUMG00000129910	ENST00000226328.4:c.116G>T	chr4.hg19:g.71588406G>T	ENSP00000226328:p.Trp39Leu	284.0	1.0	.		247.0	93.0	.	NM_001037442	B3KM25|B4DYW7|D9N163|O94948|Q9UI00	Missense_Mutation	SNP	ENST00000226328.4	hg19	CCDS3547.1	.	.	.	.	.	.	.	.	.	.	G	19.28	3.797286	0.70567	.	.	ENSG00000018189	ENST00000381006;ENST00000226328;ENST00000536664	T;T;T	0.35973	1.81;1.28;2.13	5.51	5.51	0.81932	.	0.200815	0.47852	D	0.000210	T	0.57227	0.2039	L	0.52011	1.625	0.58432	D	0.999999	B;D;D	0.67145	0.001;0.996;0.967	B;D;P	0.78314	0.002;0.991;0.901	T	0.58301	-0.7660	10	0.87932	D	0	0.0099	19.4131	0.94683	0.0:0.0:1.0:0.0	.	5;39;39	B4DKC2;Q7L099-3;Q7L099	.;.;RUFY3_HUMAN	L	39;39;5	ENSP00000370394:W39L;ENSP00000226328:W39L;ENSP00000443652:W5L	ENSP00000226328:W39L	W	+	2	0	RUFY3	71807270	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	9.476000	0.97823	2.590000	0.87494	0.555000	0.69702	TGG	.	.	.	none		0.532	RUFY3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252161.2	NM_014961	
TAF7	6879	hgsc.bcm.edu	37	5	140699374	140699374	+	Missense_Mutation	SNP	T	T	C			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr5:140699374T>C	ENST00000313368.5	-	1	956	c.238A>G	c.(238-240)Att>Gtt	p.I80V		NM_005642.2	NP_005633.2	Q15545	TAF7_HUMAN	TAF7 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 55kDa	80					DNA-templated transcription, initiation (GO:0006352)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of histone acetylation (GO:0035067)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermine transport (GO:0000296)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	histone acetyltransferase binding (GO:0035035)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|vitamin D receptor binding (GO:0042809)			central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	12			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTTTTATCAATGGTTTTCAAG	0.443																																					p.I80V		Atlas-SNP	.											.	TAF7	28	.	0			c.A238G						PASS	.						120.0	113.0	116.0					5																	140699374		2203	4300	6503	SO:0001583	missense	6879	exon1			TATCAATGGTTTT	AF349038	CCDS4259.1	5q31	2008-02-05	2002-08-29	2001-12-07	ENSG00000178913	ENSG00000178913			11541	protein-coding gene	gene with protein product		600573	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, F, 55kD"""	TAF2F		7824954	Standard	NM_005642		Approved	TAFII55	uc003ljg.3	Q15545	OTTHUMG00000129628	ENST00000313368.5:c.238A>G	chr5.hg19:g.140699374T>C	ENSP00000312709:p.Ile80Val	111.0	0.0	.		90.0	29.0	.	NM_005642	B2RBV9|Q13036	Missense_Mutation	SNP	ENST00000313368.5	hg19	CCDS4259.1	.	.	.	.	.	.	.	.	.	.	T	10.28	1.307342	0.23821	.	.	ENSG00000178913	ENST00000313368	T	0.23348	1.91	5.08	3.93	0.45458	TAFII55 protein, conserved region (1);	0.259807	0.37809	N	0.001931	T	0.13586	0.0329	N	0.17312	0.475	0.41194	D	0.986322	B	0.09022	0.002	B	0.12837	0.008	T	0.10567	-1.0624	10	0.19590	T	0.45	-6.4089	7.5444	0.27757	0.0:0.0947:0.0:0.9053	.	80	Q15545	TAF7_HUMAN	V	80	ENSP00000312709:I80V	ENSP00000312709:I80V	I	-	1	0	TAF7	140679558	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.373000	0.59537	1.092000	0.41356	0.533000	0.62120	ATT	.	.	.	none		0.443	TAF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251823.2	NM_005642	
TFAP2A	7020	hgsc.bcm.edu	37	6	10398689	10398689	+	Missense_Mutation	SNP	G	G	C			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr6:10398689G>C	ENST00000482890.1	-	8	1627	c.1275C>G	c.(1273-1275)aaC>aaG	p.N425K	TFAP2A_ENST00000497266.1_5'Flank|TFAP2A_ENST00000379608.3_Missense_Mutation_p.N419K|TFAP2A_ENST00000319516.4_Missense_Mutation_p.N421K|TFAP2A_ENST00000379613.3_Missense_Mutation_p.N427K|TFAP2A_ENST00000379604.2_Missense_Mutation_p.N425K			P05549	AP2A_HUMAN	transcription factor AP-2 alpha (activating enhancer binding protein 2 alpha)	425					anterior neuropore closure (GO:0021506)|basement membrane organization (GO:0071711)|bone morphogenesis (GO:0060349)|cellular response to iron ion (GO:0071281)|cornea development in camera-type eye (GO:0061303)|embryonic body morphogenesis (GO:0010172)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic forelimb morphogenesis (GO:0035115)|embryonic pattern specification (GO:0009880)|epidermis morphogenesis (GO:0048730)|eyelid development in camera-type eye (GO:0061029)|face morphogenesis (GO:0060325)|forebrain neuron development (GO:0021884)|inner ear morphogenesis (GO:0042472)|keratinocyte development (GO:0003334)|kidney development (GO:0001822)|lens induction in camera-type eye (GO:0060235)|metanephric nephron development (GO:0072210)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell development (GO:0014032)|oculomotor nerve formation (GO:0021623)|optic cup structural organization (GO:0003409)|optic vesicle morphogenesis (GO:0003404)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cell migration (GO:0030335)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of tooth mineralization (GO:0070172)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell differentiation (GO:0045595)|regulation of neuron differentiation (GO:0045664)|retina layer formation (GO:0010842)|sensory perception of sound (GO:0007605)|sympathetic nervous system development (GO:0048485)|transcription from RNA polymerase II promoter (GO:0006366)|trigeminal nerve development (GO:0021559)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|protein dimerization activity (GO:0046983)|protein homodimerization activity (GO:0042803)|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 (GO:0000982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|endometrium(1)|large_intestine(5)|lung(5)|ovary(1)	13	Breast(50;0.0427)|Ovarian(93;0.0991)	all_hematologic(90;0.107)				TGCTTTTGGCGTTGTTGTCCG	0.637																																					p.N425K		Atlas-SNP	.											.	TFAP2A	129	.	0			c.C1275G						PASS	.						303.0	314.0	310.0					6																	10398689		2203	4300	6503	SO:0001583	missense	7020	exon7			TTTGGCGTTGTTG	X52611	CCDS4510.1, CCDS34337.1, CCDS43422.1	6p24.3	2013-09-19	2001-11-28		ENSG00000137203	ENSG00000137203			11742	protein-coding gene	gene with protein product		107580	"""transcription factor AP-2 alpha (activating enhancer-binding protein 2 alpha)"""	TFAP2, AP2TF		1916817, 3063603	Standard	NM_001032280		Approved	AP-2	uc003myr.3	P05549	OTTHUMG00000014235	ENST00000482890.1:c.1275C>G	chr6.hg19:g.10398689G>C	ENSP00000418541:p.Asn425Lys	193.0	0.0	.		146.0	46.0	.	NM_003220	Q13777|Q5TAV5|Q8N1C6	Missense_Mutation	SNP	ENST00000482890.1	hg19	CCDS4510.1	.	.	.	.	.	.	.	.	.	.	G	5.052	0.195211	0.09599	.	.	ENSG00000137203	ENST00000379613;ENST00000379604;ENST00000319516;ENST00000379608;ENST00000482890	D;D;D;D;D	0.96913	-4.17;-4.17;-4.17;-4.17;-4.17	5.41	5.41	0.78517	.	0.166295	0.64402	D	0.000003	T	0.82139	0.4972	N	0.02539	-0.55	0.34515	D	0.707504	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.04013	0.0;0.0;0.001	T	0.74665	-0.3589	10	0.08381	T	0.77	-4.3896	19.197	0.93693	0.0:0.0:1.0:0.0	.	421;425;419	Q5TAV5;P05549;Q8N1C6	.;AP2A_HUMAN;.	K	427;425;421;419;425	ENSP00000368933:N427K;ENSP00000368924:N425K;ENSP00000316516:N421K;ENSP00000368928:N419K;ENSP00000418541:N425K	ENSP00000316516:N421K	N	-	3	2	TFAP2A	10506675	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.556000	0.53734	2.532000	0.85374	0.655000	0.94253	AAC	.	.	.	none		0.637	TFAP2A-007	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353619.2	NM_003220	
KIF13A	63971	hgsc.bcm.edu	37	6	17817447	17817447	+	Missense_Mutation	SNP	C	C	T			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr6:17817447C>T	ENST00000259711.6	-	17	1909	c.1804G>A	c.(1804-1806)Gtt>Att	p.V602I	KIF13A_ENST00000378826.2_Missense_Mutation_p.V602I|KIF13A_ENST00000378816.5_Missense_Mutation_p.V602I|KIF13A_ENST00000378843.2_Missense_Mutation_p.V602I|KIF13A_ENST00000378814.5_Missense_Mutation_p.V602I|KIF13A_ENST00000503342.1_5'Flank	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	602					ATP catabolic process (GO:0006200)|cargo loading into vesicle (GO:0035459)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|Golgi to plasma membrane protein transport (GO:0043001)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)	centrosome (GO:0005813)|endosome membrane (GO:0010008)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|trans-Golgi network membrane (GO:0032588)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	64	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			AGGACCTGAACCACATTTTGA	0.532																																					p.V602I		Atlas-SNP	.											.	KIF13A	276	.	0			c.G1804A						PASS	.						74.0	79.0	78.0					6																	17817447		2040	4210	6250	SO:0001583	missense	63971	exon17			CCTGAACCACATT	AJ291578	CCDS47380.1, CCDS47381.1, CCDS54967.1, CCDS54968.1, CCDS58998.1	6p23	2008-10-21			ENSG00000137177	ENSG00000137177		"""Kinesins"""	14566	protein-coding gene	gene with protein product		605433				11106728	Standard	NM_022113		Approved	bA500C11.2	uc003ncg.4	Q9H1H9	OTTHUMG00000014313	ENST00000259711.6:c.1804G>A	chr6.hg19:g.17817447C>T	ENSP00000259711:p.Val602Ile	153.0	0.0	.		131.0	41.0	.	NM_001105567	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Missense_Mutation	SNP	ENST00000259711.6	hg19	CCDS47381.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.074673	0.76415	.	.	ENSG00000137177	ENST00000378814;ENST00000259711;ENST00000378826;ENST00000378843;ENST00000378816	T;T;T;T;T	0.71579	-0.58;-0.58;-0.58;-0.58;-0.58	5.92	5.92	0.95590	.	0.060329	0.64402	D	0.000003	T	0.43787	0.1263	L	0.27053	0.805	0.58432	D	0.99999	B;B;P;B;P	0.37731	0.112;0.094;0.48;0.112;0.607	B;B;B;B;B	0.34722	0.034;0.108;0.188;0.034;0.187	T	0.52064	-0.8625	10	0.08599	T	0.76	.	20.3248	0.98698	0.0:1.0:0.0:0.0	.	573;602;602;602;602	E7ER65;Q9H1H9-4;Q9H1H9-2;Q9H1H9;Q9H1H9-3	.;.;.;KI13A_HUMAN;.	I	602	ENSP00000368091:V602I;ENSP00000259711:V602I;ENSP00000368103:V602I;ENSP00000368120:V602I;ENSP00000368093:V602I	ENSP00000259711:V602I	V	-	1	0	KIF13A	17925426	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.432000	0.80349	2.818000	0.97014	0.655000	0.94253	GTT	.	.	.	none		0.532	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4		
UHRF1BP1	54887	hgsc.bcm.edu	37	6	34825520	34825520	+	Silent	SNP	C	C	T			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr6:34825520C>T	ENST00000192788.5	+	13	1764	c.1593C>T	c.(1591-1593)taC>taT	p.Y531Y	UHRF1BP1_ENST00000452449.2_Silent_p.Y531Y	NM_017754.3	NP_060224.3	Q6BDS2	URFB1_HUMAN	UHRF1 binding protein 1	531							histone deacetylase binding (GO:0042826)|identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(24)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	54						CTAATCTCTACATTCAGTTAA	0.398																																					p.Y531Y		Atlas-SNP	.											.	UHRF1BP1	102	.	0			c.C1593T						PASS	.						158.0	148.0	151.0					6																	34825520		1859	4088	5947	SO:0001819	synonymous_variant	54887	exon13			TCTCTACATTCAG	AB126777	CCDS43455.1	6p21.31	2008-10-28	2008-08-15	2007-11-27	ENSG00000065060	ENSG00000065060			21216	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 107"""	C6orf107			Standard	NM_017754		Approved	FLJ20302, dJ349A12.1, ICBP90	uc003oju.4	Q6BDS2	OTTHUMG00000014557	ENST00000192788.5:c.1593C>T	chr6.hg19:g.34825520C>T		174.0	0.0	.		144.0	9.0	.	NM_017754	Q9NXE0	Silent	SNP	ENST00000192788.5	hg19	CCDS43455.1																																																																																			.	.	.	none		0.398	UHRF1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040260.1	NM_017754	
COL12A1	1303	hgsc.bcm.edu	37	6	75861881	75861881	+	Silent	SNP	T	T	C			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr6:75861881T>C	ENST00000322507.8	-	19	4110	c.3801A>G	c.(3799-3801)gcA>gcG	p.A1267A	COL12A1_ENST00000483888.2_Silent_p.A1267A|COL12A1_ENST00000416123.2_Silent_p.A1267A|COL12A1_ENST00000345356.6_Silent_p.A103A	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	1267	VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						ACGGCAAGTTTGCCACAGCTT	0.473																																					p.A1267A		Atlas-SNP	.											.	COL12A1	385	.	0			c.A3801G						PASS	.						102.0	99.0	100.0					6																	75861881		1976	4162	6138	SO:0001819	synonymous_variant	1303	exon19			CAAGTTTGCCACA	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"", ""Fibronectin type III domain containing"""	2188	protein-coding gene	gene with protein product	"""collagen type XII proteoglycan"""	120320	"""collagen, type XII, alpha 1-like"""	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.3801A>G	chr6.hg19:g.75861881T>C		211.0	0.0	.		199.0	74.0	.	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Silent	SNP	ENST00000322507.8	hg19	CCDS43482.1	.	.	.	.	.	.	.	.	.	.	T	4.645	0.119852	0.08881	.	.	ENSG00000111799	ENST00000419671	.	.	.	5.94	-10.2	0.00374	.	.	.	.	.	T	0.24851	0.0603	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48570	-0.9024	4	.	.	.	.	5.2576	0.15555	0.078:0.3395:0.3536:0.2289	.	.	.	.	E	9	.	.	K	-	1	0	COL12A1	75918601	0.080000	0.21391	0.440000	0.26846	0.478000	0.33099	-0.719000	0.04974	-1.241000	0.02526	-1.293000	0.01348	AAA	.	.	.	none		0.473	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370	
TMEM30A	55754	hgsc.bcm.edu	37	6	75977367	75977367	+	Missense_Mutation	SNP	T	T	A			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr6:75977367T>A	ENST00000230461.6	-	2	664	c.335A>T	c.(334-336)aAg>aTg	p.K112M	TMEM30A_ENST00000475111.2_Intron|TMEM30A_ENST00000370050.5_De_novo_Start_InFrame	NM_018247.3	NP_060717.1	Q9NV96	CC50A_HUMAN	transmembrane protein 30A	112					drug transmembrane transport (GO:0006855)|phospholipid translocation (GO:0045332)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|protein localization to endosome (GO:0036010)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(1)|haematopoietic_and_lymphoid_tissue(8)|kidney(1)|large_intestine(4)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						CTCAAATGACTTTTCCAGTGT	0.363																																					p.K112M		Atlas-SNP	.											.	TMEM30A	40	.	0			c.A335T						PASS	.						130.0	135.0	133.0					6																	75977367		2203	4300	6503	SO:0001583	missense	55754	exon2			AATGACTTTTCCA	AK001718	CCDS4983.1, CCDS47453.1	6q14.1	2014-01-28	2004-06-17	2004-06-18	ENSG00000112697	ENSG00000112697			16667	protein-coding gene	gene with protein product		611028	"""chromosome 6 open reading frame 67"""	C6orf67		15375526	Standard	NM_001143958		Approved	FLJ10856, CDC50A	uc003phw.2	Q9NV96	OTTHUMG00000015050	ENST00000230461.6:c.335A>T	chr6.hg19:g.75977367T>A	ENSP00000230461:p.Lys112Met	41.0	0.0	.		44.0	18.0	.	NM_018247	A8K9V8|E1P539|Q658Z3|Q96H09|Q9NSL9	Missense_Mutation	SNP	ENST00000230461.6	hg19	CCDS4983.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.082970	0.76642	.	.	ENSG00000112697	ENST00000230461;ENST00000545449	.	.	.	5.28	5.28	0.74379	.	0.326351	0.37761	N	0.001944	T	0.77890	0.4198	M	0.84326	2.69	0.80722	D	1	B	0.27264	0.173	P	0.47251	0.542	T	0.80511	-0.1350	9	0.66056	D	0.02	.	14.8721	0.70465	0.0:0.0:0.0:1.0	.	112	Q9NV96	CC50A_HUMAN	M	112;96	.	ENSP00000230461:K112M	K	-	2	0	TMEM30A	76034087	1.000000	0.71417	0.998000	0.56505	0.886000	0.51366	7.596000	0.82721	1.997000	0.58415	0.454000	0.30748	AAG	.	.	.	none		0.363	TMEM30A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041248.2	NM_018247	
HDAC2	3066	hgsc.bcm.edu	37	6	114264645	114264645	+	Silent	SNP	A	A	C			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr6:114264645A>C	ENST00000519065.1	-	12	1624	c.1248T>G	c.(1246-1248)gcT>gcG	p.A416A	HDAC2_ENST00000519108.1_Silent_p.A386A|HDAC2_ENST00000398283.2_Silent_p.A510A|HDAC2_ENST00000368632.2_Silent_p.A386A			Q92769	HDAC2_HUMAN	histone deacetylase 2	416					ATP-dependent chromatin remodeling (GO:0043044)|blood coagulation (GO:0007596)|cardiac muscle cell development (GO:0055013)|chromatin remodeling (GO:0006338)|circadian regulation of gene expression (GO:0032922)|dendrite development (GO:0016358)|embryonic digit morphogenesis (GO:0042733)|epidermal cell differentiation (GO:0009913)|eyelid development in camera-type eye (GO:0061029)|fungiform papilla formation (GO:0061198)|hair follicle placode formation (GO:0060789)|hippocampus development (GO:0021766)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|maintenance of chromatin silencing (GO:0006344)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of cell cycle (GO:0045786)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of neuron projection development (GO:0010977)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell proliferation (GO:0008284)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of proteolysis (GO:0045862)|positive regulation of receptor biosynthetic process (GO:0010870)|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 protein deacetylation (GO:0090311)|regulation of protein kinase B signaling (GO:0051896)|regulation of sarcomere organization (GO:0060297)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|heterochromatin (GO:0000792)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)|replication fork (GO:0005657)|Sin3 complex (GO:0016580)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|deacetylase activity (GO:0019213)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|poly(A) RNA binding (GO:0044822)|protein deacetylase activity (GO:0033558)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			biliary_tract(1)|central_nervous_system(5)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)|skin(2)	27		all_cancers(87;0.000629)|all_epithelial(87;0.00274)|Colorectal(196;0.0317)|all_lung(197;0.24)		all cancers(137;0.00318)|OV - Ovarian serous cystadenocarcinoma(136;0.00569)|Epithelial(106;0.0112)|GBM - Glioblastoma multiforme(226;0.0832)	Aminophylline(DB01223)|Lovastatin(DB00227)|Oxtriphylline(DB01303)|Theophylline(DB00277)|Valproic Acid(DB00313)|Vorinostat(DB02546)	CTTCATCACAAGCTATCCGCT	0.363																																					p.A416A		Atlas-SNP	.											.	HDAC2	102	.	0			c.T1248G						PASS	.						126.0	110.0	115.0					6																	114264645		1841	4082	5923	SO:0001819	synonymous_variant	3066	exon12			ATCACAAGCTATC	U31814	CCDS43493.1, CCDS43493.2	6q21	2008-08-29			ENSG00000196591	ENSG00000196591			4853	protein-coding gene	gene with protein product		605164				9782097	Standard	NM_001527		Approved	RPD3, YAF1	uc003pwd.2	Q92769	OTTHUMG00000015411	ENST00000519065.1:c.1248T>G	chr6.hg19:g.114264645A>C		16.0	0.0	.		15.0	8.0	.	NM_001527	B3KRS5|B4DL58|E1P561|Q5SRI8|Q5SZ86|Q8NEH4	Silent	SNP	ENST00000519065.1	hg19	CCDS43493.2																																																																																			.	.	.	none		0.363	HDAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041909.2		
ELMO1	9844	hgsc.bcm.edu	37	7	37053037	37053037	+	Missense_Mutation	SNP	C	C	T			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr7:37053037C>T	ENST00000310758.4	-	16	1951	c.1304G>A	c.(1303-1305)aGt>aAt	p.S435N	ELMO1_ENST00000341056.3_Missense_Mutation_p.S137N|ELMO1-AS1_ENST00000419535.1_RNA|ELMO1_ENST00000448602.1_Missense_Mutation_p.S435N|ELMO1_ENST00000442504.1_Missense_Mutation_p.S435N	NM_001206480.1|NM_014800.10	NP_001193409.1|NP_055615.8	Q92556	ELMO1_HUMAN	engulfment and cell motility 1	435	ELMO. {ECO:0000255|PROSITE- ProRule:PRU00664}.				actin cytoskeleton organization (GO:0030036)|apoptotic process (GO:0006915)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|phagocytosis, engulfment (GO:0006911)|Rac protein signal transduction (GO:0016601)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(28)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	58						GCAGGTCTCACTAGCTGGAGG	0.458																																					p.S435N		Atlas-SNP	.											.	ELMO1	141	.	0			c.G1304A						PASS	.						79.0	75.0	76.0					7																	37053037		2203	4300	6503	SO:0001583	missense	9844	exon16			GTCTCACTAGCTG	AF398885	CCDS5449.1, CCDS5450.1	7p14.1	2012-07-10	2006-01-20		ENSG00000155849	ENSG00000155849		"""Engulfment and cell motility proteins"""	16286	protein-coding gene	gene with protein product		606420	"""engulfment and cell motility 1 (ced-12 homolog, C. elegans)"""			11595183	Standard	NM_001039459		Approved	KIAA0281, CED12, ELMO-1, CED-12	uc003tfk.2	Q92556	OTTHUMG00000023701	ENST00000310758.4:c.1304G>A	chr7.hg19:g.37053037C>T	ENSP00000312185:p.Ser435Asn	122.0	0.0	.		88.0	31.0	.	NM_014800	A4D1X6|Q29R79|Q6ZTJ0|Q96PB0|Q9H0I1	Missense_Mutation	SNP	ENST00000310758.4	hg19	CCDS5449.1	.	.	.	.	.	.	.	.	.	.	C	15.24	2.774299	0.49786	.	.	ENSG00000155849	ENST00000341056;ENST00000310758;ENST00000361912;ENST00000442504;ENST00000448602	T;T;T;T	0.30981	1.51;1.51;1.51;1.51	6.06	6.06	0.98353	Engulfment/cell motility, ELMO (2);	0.147484	0.64402	D	0.000020	T	0.21841	0.0526	N	0.12527	0.23	0.48571	D	0.999678	B	0.06786	0.001	B	0.12156	0.007	T	0.07366	-1.0776	10	0.22109	T	0.4	.	20.2348	0.98355	0.0:1.0:0.0:0.0	.	435	Q92556	ELMO1_HUMAN	N	137;435;339;435;435	ENSP00000342142:S137N;ENSP00000312185:S435N;ENSP00000406952:S435N;ENSP00000394458:S435N	ENSP00000312185:S435N	S	-	2	0	ELMO1	37019562	1.000000	0.71417	0.988000	0.46212	0.765000	0.43378	4.885000	0.63142	2.879000	0.98667	0.650000	0.86243	AGT	.	.	.	none		0.458	ELMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219830.4	NM_130442	
KMT2E	55904	hgsc.bcm.edu	37	7	104717538	104717538	+	Missense_Mutation	SNP	G	G	C			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr7:104717538G>C	ENST00000311117.3	+	10	1442	c.897G>C	c.(895-897)gaG>gaC	p.E299D	KMT2E_ENST00000257745.4_Missense_Mutation_p.E299D|KMT2E_ENST00000334877.4_Missense_Mutation_p.E299D|KMT2E_ENST00000476671.1_Missense_Mutation_p.E299D|KMT2E_ENST00000334914.7_5'UTR	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	299					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)										TTCAGAGGGAGGCACAAAGAA	0.393																																					p.E299D		Atlas-SNP	.											.	MLL5	173	.	0			c.G897C						PASS	.						125.0	115.0	118.0					7																	104717538		2203	4300	6503	SO:0001583	missense	55904	exon9			GAGGGAGGCACAA	AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	18541	protein-coding gene	gene with protein product		608444	"""myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"""	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.897G>C	chr7.hg19:g.104717538G>C	ENSP00000312379:p.Glu299Asp	180.0	0.0	.		166.0	19.0	.	NM_018682	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Missense_Mutation	SNP	ENST00000311117.3	hg19	CCDS34723.1	.	.	.	.	.	.	.	.	.	.	G	18.22	3.576129	0.65878	.	.	ENSG00000005483	ENST00000311117;ENST00000393656;ENST00000334877;ENST00000351043;ENST00000257745;ENST00000478990;ENST00000476671;ENST00000537308	D;D;D;D;D	0.95756	-2.92;-2.54;-2.92;-3.8;-3.28	6.07	4.28	0.50868	.	0.000000	0.64402	D	0.000001	D	0.94185	0.8134	L	0.44542	1.39	0.80722	D	1	D;P	0.67145	0.996;0.943	P;P	0.54499	0.754;0.576	D	0.91766	0.5424	10	0.14656	T	0.56	.	12.3705	0.55252	0.1346:0.0:0.8654:0.0	.	299;299	Q8IZD2;Q8IZD2-3	MLL5_HUMAN;.	D	299;299;299;299;299;157;299;233	ENSP00000312379:E299D;ENSP00000335599:E299D;ENSP00000257745:E299D;ENSP00000419883:E157D;ENSP00000417888:E299D	ENSP00000257745:E299D	E	+	3	2	MLL5	104504774	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.197000	0.72100	1.587000	0.49959	-0.136000	0.14681	GAG	.	.	.	none		0.393	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1		
MET	4233	hgsc.bcm.edu	37	7	116423474	116423474	+	Missense_Mutation	SNP	T	T	C	rs121913245		TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr7:116423474T>C	ENST00000318493.6	+	19	3990	c.3803T>C	c.(3802-3804)aTg>aCg	p.M1268T	MET_ENST00000539704.1_Missense_Mutation_p.M120T|MET_ENST00000397752.3_Missense_Mutation_p.M1250T			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)	p.M1268T(4)		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)			GTGAAGTGGATGGCTTTGGAA	0.393			Mis		"""papillary renal, head-neck squamous cell """	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.M1268T		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	MET,rectum,carcinoma,+1,5	MET	412	.	4	Substitution - Missense(4)	kidney(4)	c.T3803C	GRCh37	CM992181	MET	M	rs121913245	PASS	.						93.0	92.0	92.0					7																	116423474		1872	4102	5974	SO:0001583	missense	4233	exon19	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	AGTGGATGGCTTT	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.3803T>C	chr7.hg19:g.116423474T>C	ENSP00000317272:p.Met1268Thr	98.0	0.0	.		83.0	27.0	.	NM_001127500	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	hg19	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	T	18.99	3.740165	0.69304	.	.	ENSG00000105976	ENST00000397752;ENST00000318493;ENST00000539704	T;T;T	0.37752	1.18;1.18;1.18	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	0.61714	0.2369	M	0.75264	2.295	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.97110	1.0;1.0	T	0.65734	-0.6096	10	0.87932	D	0	.	16.2225	0.82267	0.0:0.0:0.0:1.0	.	1268;1250	P08581-2;P08581	.;MET_HUMAN	T	1250;1268;120	ENSP00000380860:M1250T;ENSP00000317272:M1268T;ENSP00000445020:M120T	ENSP00000317272:M1268T	M	+	2	0	MET	116210710	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.997000	0.88414	2.289000	0.77006	0.460000	0.39030	ATG	.	.	.	weak		0.393	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3		
GPR37	2861	hgsc.bcm.edu	37	7	124405027	124405027	+	Nonsense_Mutation	SNP	G	G	A			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr7:124405027G>A	ENST00000303921.2	-	1	654	c.4C>T	c.(4-6)Cga>Tga	p.R2*		NM_005302.3	NP_005293.1	O15354	GPR37_HUMAN	G protein-coupled receptor 37 (endothelin receptor type B-like)	2					dopamine biosynthetic process (GO:0042416)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotion involved in locomotory behavior (GO:0031987)|positive regulation of dopamine metabolic process (GO:0045964)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|ubiquitin ligase complex (GO:0000151)	G-protein coupled receptor activity (GO:0004930)|heat shock protein binding (GO:0031072)|Hsp70 protein binding (GO:0030544)|ubiquitin protein ligase binding (GO:0031625)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(11)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						CCCGGGGCTCGCATGGCTTGG	0.637																																					p.R2X		Atlas-SNP	.											.	GPR37	89	.	0			c.C4T						PASS	.						7.0	6.0	7.0					7																	124405027		2164	4249	6413	SO:0001587	stop_gained	2861	exon1			GGGCTCGCATGGC		CCDS5792.1	7q31	2012-08-21			ENSG00000170775	ENSG00000170775		"""GPCR / Class A : Orphans"""	4494	protein-coding gene	gene with protein product		602583				9339362	Standard	NM_005302		Approved	EDNRBL, hET(B)R-LP, PAELR	uc003vli.4	O15354	OTTHUMG00000157197	ENST00000303921.2:c.4C>T	chr7.hg19:g.124405027G>A	ENSP00000306449:p.Arg2*	4.0	0.0	.		6.0	4.0	.	NM_005302	A4D0Y6|O00348|O14768|Q8TD39	Nonsense_Mutation	SNP	ENST00000303921.2	hg19	CCDS5792.1	.	.	.	.	.	.	.	.	.	.	G	40	8.449312	0.98815	.	.	ENSG00000170775	ENST00000303921	.	.	.	5.31	3.45	0.39498	.	0.960325	0.08673	N	0.910555	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05436	T	0.98	-4.8252	6.6615	0.23016	0.0898:0.0:0.7349:0.1753	.	.	.	.	X	2	.	ENSP00000306449:R2X	R	-	1	2	GPR37	124192263	0.983000	0.35010	0.703000	0.30354	0.397000	0.30659	1.951000	0.40333	0.767000	0.33267	0.655000	0.94253	CGA	.	.	.	none		0.637	GPR37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347873.1	NM_005302	
NRG1	3084	hgsc.bcm.edu	37	8	32616873	32616873	+	Missense_Mutation	SNP	A	A	T			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr8:32616873A>T	ENST00000405005.3	+	10	980	c.980A>T	c.(979-981)gAa>gTa	p.E327V	NRG1_ENST00000287842.3_Missense_Mutation_p.E324V|NRG1_ENST00000287845.5_Missense_Mutation_p.E298V|NRG1_ENST00000523079.1_Missense_Mutation_p.E324V|NRG1_ENST00000338921.4_Missense_Mutation_p.E335V|NRG1_ENST00000539990.1_Missense_Mutation_p.E170V|NRG1_ENST00000519301.1_Missense_Mutation_p.E277V|NRG1_ENST00000341377.5_3'UTR|NRG1_ENST00000356819.4_Missense_Mutation_p.E332V|NRG1_ENST00000521670.1_Missense_Mutation_p.E327V			Q02297	NRG1_HUMAN	neuregulin 1	327					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell myoblast differentiation (GO:0060379)|cell communication (GO:0007154)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cellular protein complex disassembly (GO:0043624)|embryo development (GO:0009790)|endocardial cell differentiation (GO:0060956)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell fate commitment (GO:0021781)|innate immune response (GO:0045087)|locomotory behavior (GO:0007626)|mammary gland development (GO:0030879)|MAPK cascade (GO:0000165)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of secretion (GO:0051048)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|neural crest cell development (GO:0014032)|neuron fate commitment (GO:0048663)|neurotransmitter receptor metabolic process (GO:0045213)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of striated muscle cell differentiation (GO:0051155)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|synapse assembly (GO:0007416)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular trabecula myocardium morphogenesis (GO:0003222)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)	cytokine activity (GO:0005125)|ErbB-3 class receptor binding (GO:0043125)|growth factor activity (GO:0008083)|protein tyrosine kinase activator activity (GO:0030296)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(1)|skin(1)	39		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		GTTGAGAGAGAAGCAGAGACA	0.408																																					p.E332V		Atlas-SNP	.											.	NRG1	260	.	0			c.A995T						PASS	.						201.0	169.0	180.0					8																	32616873		2203	4300	6503	SO:0001583	missense	3084	exon11			AGAGAGAAGCAGA	L12261	CCDS6084.1, CCDS6085.1, CCDS6086.1, CCDS6087.1, CCDS47836.1, CCDS55218.1, CCDS55219.1, CCDS75727.1	8p21-p12	2014-06-23			ENSG00000157168	ENSG00000157168		"""Immunoglobulin superfamily / I-set domain containing"""	7997	protein-coding gene	gene with protein product		142445	"""NRG1 intronic transcript 2 (non-protein coding)"""	HGL, NRG1-IT2		1350381, 8095334	Standard	NM_013962		Approved	HRG, NDF, GGF	uc003xiu.2	Q02297	OTTHUMG00000163918	ENST00000405005.3:c.980A>T	chr8.hg19:g.32616873A>T	ENSP00000384620:p.Glu327Val	157.0	0.0	.		145.0	41.0	.	NM_013956	A5YAK4|A5YAK5|A8K1L2|B7Z4Z3|E9PHH4|O14667|P98202|Q02298|Q02299|Q07110|Q07111|Q12779|Q12780|Q12781|Q12782|Q12783|Q12784|Q15491|Q7RTV9|Q7RTW0|Q7RTW1|Q7RTW2|Q8NFN1|Q8NFN2|Q8NFN3|Q9UPE3	Missense_Mutation	SNP	ENST00000405005.3	hg19	CCDS6085.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.300044	0.81136	.	.	ENSG00000157168	ENST00000518104;ENST00000519301;ENST00000523534;ENST00000523079;ENST00000338921;ENST00000356819;ENST00000287840;ENST00000287845;ENST00000287842;ENST00000405005;ENST00000521670;ENST00000539990	T;T;T;T;T;T;T;T;T;T;T;T	0.62364	0.03;0.03;0.03;0.03;0.03;0.03;0.03;0.03;0.03;0.03;0.03;0.03	6.16	6.16	0.99307	Neuregulin 1-related, C-terminal (1);	0.100274	0.64402	D	0.000002	T	0.70824	0.3268	L	0.41573	1.285	0.53688	D	0.999971	D;D;D;D;D;D;D;D;D;D;D	0.89917	0.996;1.0;1.0;1.0;1.0;1.0;0.983;0.999;0.999;1.0;1.0	D;D;D;D;D;D;P;D;D;D;D	0.97110	0.997;0.999;1.0;0.984;0.991;1.0;0.592;0.984;0.985;0.984;0.999	T	0.64694	-0.6347	10	0.14252	T	0.57	-8.3311	16.8061	0.85666	1.0:0.0:0.0:0.0	.	170;173;324;298;332;323;335;324;327;332;327	B7Z1E3;B7Z1D7;E9PHH4;F8W9E3;Q7RTW4;B0FYA9;Q02297-2;Q02297-7;Q02297;Q02297-6;Q02297-3	.;.;.;.;.;.;.;.;NRG1_HUMAN;.;.	V	294;277;400;324;335;332;327;298;324;327;327;170	ENSP00000430053:E294V;ENSP00000429582:E277V;ENSP00000429067:E400V;ENSP00000430120:E324V;ENSP00000343395:E335V;ENSP00000349275:E332V;ENSP00000287840:E327V;ENSP00000287845:E298V;ENSP00000287842:E324V;ENSP00000384620:E327V;ENSP00000428828:E327V;ENSP00000439276:E170V	ENSP00000287840:E327V	E	+	2	0	NRG1	32736415	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.312000	0.65792	2.367000	0.80283	0.528000	0.53228	GAA	.	.	.	none		0.408	NRG1-017	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472504.1		
NKX6-3	157848	hgsc.bcm.edu	37	8	41504065	41504065	+	Missense_Mutation	SNP	G	G	T			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr8:41504065G>T	ENST00000524115.2	-	2	314	c.311C>A	c.(310-312)cCg>cAg	p.P104Q		NM_152568.2	NP_689781.1	A6NJ46	NKX63_HUMAN	NK6 homeobox 3	234					cell fate determination (GO:0001709)|glandular epithelial cell differentiation (GO:0002067)|negative regulation of epithelial cell differentiation (GO:0030857)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			lung(1)	1	Ovarian(28;0.00541)|Colorectal(14;0.0202)|Lung SC(25;0.211)	all_lung(54;0.0131)|Lung NSC(58;0.0363)|Esophageal squamous(32;0.0844)|Hepatocellular(245;0.154)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			GGGGTCCAGCGGCTTGTTGTA	0.731																																					p.P104Q		Atlas-SNP	.											.	NKX6-3	10	.	0			c.C311A						PASS	.						43.0	38.0	39.0					8																	41504065		2201	4300	6501	SO:0001583	missense	157848	exon2			TCCAGCGGCTTGT	AK057898	CCDS6118.1	8p11.21	2014-08-12	2007-07-09		ENSG00000165066	ENSG00000165066		"""Homeoboxes / ANTP class : NKL subclass"""	26328	protein-coding gene	gene with protein product		610772	"""NK6 transcription factor related, locus 3 (Drosophila)"""			16326147	Standard	XM_005273422		Approved	FLJ25169	uc003xoa.2	A6NJ46	OTTHUMG00000164083	ENST00000524115.2:c.311C>A	chr8.hg19:g.41504065G>T	ENSP00000429553:p.Pro104Gln	32.0	0.0	.		24.0	15.0	.	NM_152568	Q96LR0	Missense_Mutation	SNP	ENST00000524115.2	hg19	CCDS6118.1	.	.	.	.	.	.	.	.	.	.	G	32	5.124514	0.94429	.	.	ENSG00000165066	ENST00000524115;ENST00000425142;ENST00000518699	T;T	0.57907	0.37;0.37	4.9	4.02	0.46733	.	0.000000	0.85682	D	0.000000	T	0.70718	0.3256	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	T	0.73170	-0.4067	9	0.56958	D	0.05	.	12.1998	0.54319	0.0832:0.0:0.9168:0.0	.	104	A6NJ46-2	.	Q	104;234;234	ENSP00000429553:P104Q;ENSP00000428361:P234Q	ENSP00000414183:P234Q	P	-	2	0	NKX6-3	41623222	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	7.856000	0.86956	1.066000	0.40716	0.491000	0.48974	CCG	.	.	.	none		0.731	NKX6-3-002	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000377166.2	NM_152568	
NCOA2	10499	hgsc.bcm.edu	37	8	71053580	71053580	+	Missense_Mutation	SNP	G	G	A			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr8:71053580G>A	ENST00000452400.2	-	14	3048	c.2867C>T	c.(2866-2868)cCg>cTg	p.P956L	NCOA2_ENST00000267974.4_Missense_Mutation_p.P44L	NM_006540.2	NP_006531.1	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	956					cellular lipid metabolic process (GO:0044255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucose metabolic process (GO:0010906)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|signal transducer activity (GO:0004871)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)		PAX3/NCOA2(4)|HEY1/NCOA2(10)	NS(1)|breast(4)|endometrium(7)|kidney(4)|large_intestine(10)|lung(25)|ovary(1)|pancreas(2)|prostate(2)|skin(4)	60	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)			CGAACTCTGCGGTGCCCATTC	0.532			T	"""RUNXBP2, HEY1"""	"""AML, Chondrosarcoma"""																																p.P956L		Atlas-SNP	.		Dom	yes		8	8q13.1	10499	nuclear receptor coactivator 2 (TIF2)		L	NCOA2,NS,carcinoma,0,1	NCOA2	147	.	0			c.C2867T						PASS	.						57.0	60.0	59.0					8																	71053580		2052	4211	6263	SO:0001583	missense	10499	exon14			CTCTGCGGTGCCC	X97674	CCDS47872.1	8q13.3	2011-07-01			ENSG00000140396	ENSG00000140396		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7669	protein-coding gene	gene with protein product		601993				9111344, 8670870	Standard	XM_005251128		Approved	TIF2, GRIP1, NCoA-2, KAT13C, bHLHe75	uc003xyn.1	Q15596	OTTHUMG00000164671	ENST00000452400.2:c.2867C>T	chr8.hg19:g.71053580G>A	ENSP00000399968:p.Pro956Leu	155.0	0.0	.		152.0	28.0	.	NM_006540	Q14CD2	Missense_Mutation	SNP	ENST00000452400.2	hg19	CCDS47872.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	1.585|1.585	-0.530666|-0.530666	0.04112|0.04112	.|.	.|.	ENSG00000140396|ENSG00000140396	ENST00000452400;ENST00000267974|ENST00000518363	T;T|.	0.06849|.	4.9;3.25|.	5.64|5.64	5.64|5.64	0.86602|0.86602	.|.	0.483437|.	0.22937|.	N|.	0.053835|.	T|T	0.28532|0.28532	0.0706|0.0706	N|N	0.04880|0.04880	-0.145|-0.145	0.09310|0.09310	N|N	0.999999|0.999999	P;B|.	0.35192|.	0.489;0.059|.	B;B|.	0.24974|.	0.057;0.01|.	T|T	0.19289|0.19289	-1.0310|-1.0310	10|5	0.02654|.	T|.	1|.	.|.	16.5528|16.5528	0.84476|0.84476	0.0:0.1389:0.8611:0.0|0.0:0.1389:0.8611:0.0	.|.	44;956|.	F8WAJ2;Q15596|.	.;NCOA2_HUMAN|.	L|C	956;44|57	ENSP00000399968:P956L;ENSP00000267974:P44L|.	ENSP00000267974:P44L|.	P|R	-|-	2|1	0|0	NCOA2|NCOA2	71216134|71216134	0.778000|0.778000	0.28640|0.28640	0.149000|0.149000	0.22428|0.22428	0.831000|0.831000	0.47069|0.47069	4.231000|4.231000	0.58639|0.58639	2.820000|2.820000	0.97059|0.97059	0.650000|0.650000	0.86243|0.86243	CCG|CGC	.	.	.	none		0.532	NCOA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379696.1		
CSMD3	114788	hgsc.bcm.edu	37	8	113316994	113316994	+	Missense_Mutation	SNP	G	G	A			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr8:113316994G>A	ENST00000297405.5	-	52	8466	c.8222C>T	c.(8221-8223)cCt>cTt	p.P2741L	CSMD3_ENST00000343508.3_Missense_Mutation_p.P2701L|CSMD3_ENST00000352409.3_Missense_Mutation_p.P2671L|CSMD3_ENST00000455883.2_Intron	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2741	Sushi 16. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						AGTACCATTAGGAAGACATTC	0.388										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.P2741L		Atlas-SNP	.											.	CSMD3	2325	.	0			c.C8222T						PASS	.						133.0	118.0	123.0					8																	113316994		2203	4300	6503	SO:0001583	missense	114788	exon52			CCATTAGGAAGAC	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.8222C>T	chr8.hg19:g.113316994G>A	ENSP00000297405:p.Pro2741Leu	151.0	0.0	.		136.0	53.0	.	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	G	15.64	2.891954	0.52014	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000352409	T;T;T;T	0.64085	-0.08;-0.08;-0.08;-0.08	4.9	4.9	0.64082	Complement control module (2);Sushi/SCR/CCP (3);	0.178361	0.34200	N	0.004165	T	0.48259	0.1490	N	0.13272	0.32	0.54753	D	0.99998	B;B	0.30211	0.273;0.006	B;B	0.30105	0.111;0.026	T	0.47849	-0.9085	10	0.38643	T	0.18	.	18.4479	0.90691	0.0:0.0:1.0:0.0	.	2741;2701	Q7Z407;Q7Z407-2	CSMD3_HUMAN;.	L	2701;2741;2011;2671	ENSP00000345799:P2701L;ENSP00000297405:P2741L;ENSP00000341558:P2011L;ENSP00000343124:P2671L	ENSP00000297405:P2741L	P	-	2	0	CSMD3	113386170	1.000000	0.71417	1.000000	0.80357	0.427000	0.31564	9.775000	0.98995	2.385000	0.81259	0.561000	0.74099	CCT	.	.	.	none		0.388	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
PHF20L1	51105	hgsc.bcm.edu	37	8	133806739	133806739	+	Missense_Mutation	SNP	A	A	G			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr8:133806739A>G	ENST00000395386.2	+	3	466	c.167A>G	c.(166-168)gAg>gGg	p.E56G	PHF20L1_ENST00000395390.2_Missense_Mutation_p.E56G|PHF20L1_ENST00000395376.1_Missense_Mutation_p.E56G|PHF20L1_ENST00000220847.7_5'UTR|PHF20L1_ENST00000395379.1_Missense_Mutation_p.E56G|PHF20L1_ENST00000337920.4_Missense_Mutation_p.E56G	NM_016018.4	NP_057102.4	A8MW92	P20L1_HUMAN	PHD finger protein 20-like 1	56	Tudor 1.						zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(1)|lung(10)|ovary(2)	15	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)			CGTTATGATGAGTGGATTTAC	0.408																																					p.E56G		Atlas-SNP	.											.	PHF20L1	129	.	0			c.A167G						PASS	.						134.0	122.0	126.0					8																	133806739		2203	4300	6503	SO:0001583	missense	51105	exon3			ATGATGAGTGGAT	AF230666	CCDS6367.2, CCDS6368.1, CCDS75791.1	8q24.22	2014-03-24			ENSG00000129292	ENSG00000129292		"""Tudor domain containing"", ""Zinc fingers, PHD-type"""	24280	protein-coding gene	gene with protein product	"""tudor domain containing 20B"""					10810093, 24492612	Standard	NM_016018		Approved	CGI-72, FLJ13649, MGC64923, FLJ21615, TDRD20B	uc003ytt.3	A8MW92	OTTHUMG00000148656	ENST00000395386.2:c.167A>G	chr8.hg19:g.133806739A>G	ENSP00000378784:p.Glu56Gly	130.0	0.0	.		140.0	48.0	.	NM_016018	A8MZC9|Q86U89|Q86W43|Q96BT0|Q9H702|Q9HBK3|Q9NYR3|Q9Y381	Missense_Mutation	SNP	ENST00000395386.2	hg19	CCDS6367.2	.	.	.	.	.	.	.	.	.	.	A	31	5.078557	0.94050	.	.	ENSG00000129292	ENST00000395383;ENST00000395379;ENST00000361997;ENST00000395386;ENST00000315808;ENST00000337920;ENST00000395376;ENST00000522580;ENST00000395390	T;T;T;T;T;T;T;T	0.56275	0.53;0.48;0.51;1.1;0.47;0.49;0.55;1.13	5.91	5.91	0.95273	Tudor-like, plant (1);Tudor domain (1);	0.000000	0.85682	D	0.000000	T	0.77942	0.4206	M	0.90759	3.145	0.80722	D	1	D;P;D;D;P	0.89917	1.0;0.735;1.0;1.0;0.714	D;P;D;D;P	0.91635	0.997;0.734;0.999;0.994;0.669	T	0.82833	-0.0262	10	0.87932	D	0	7.5356	15.5298	0.75948	1.0:0.0:0.0:0.0	.	56;56;56;56;56	F8W9L8;A8MW92;A8MW92-4;A8MW92-2;A8MUE8	.;P20L1_HUMAN;.;.;.	G	56;56;56;56;56;56;56;14;56	ENSP00000378781:E56G;ENSP00000378777:E56G;ENSP00000355301:E56G;ENSP00000378784:E56G;ENSP00000324519:E56G;ENSP00000338269:E56G;ENSP00000378775:E56G;ENSP00000378788:E56G	ENSP00000324519:E56G	E	+	2	0	PHF20L1	133875921	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.317000	0.96327	2.259000	0.74868	0.528000	0.53228	GAG	.	.	.	none		0.408	PHF20L1-008	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308949.3	NM_016018	
PALM2	114299	hgsc.bcm.edu	37	9	112705604	112705604	+	Missense_Mutation	SNP	A	A	G			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr9:112705604A>G	ENST00000374531.2	+	7	1113	c.1039A>G	c.(1039-1041)Aca>Gca	p.T347A	PALM2_ENST00000314527.4_Missense_Mutation_p.T379A|PALM2_ENST00000448454.2_Missense_Mutation_p.T381A|PALM2-AKAP2_ENST00000302798.7_Intron|PALM2-AKAP2_ENST00000374530.3_Intron|AKAP2_ENST00000510514.5_Intron|PALM2_ENST00000483909.1_Missense_Mutation_p.T345A|AKAP2_ENST00000555236.1_Intron	NM_001037293.2	NP_001032370.1	Q8IXS6	PALM2_HUMAN	paralemmin 2	347					regulation of cell shape (GO:0008360)	plasma membrane (GO:0005886)				breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(2)|pancreas(2)|skin(3)|upper_aerodigestive_tract(1)	18						CTCAGACACCACAGAGCCCTC	0.552																																					p.T379A		Atlas-SNP	.											.	PALM2	51	.	0			c.A1135G						PASS	.						113.0	110.0	111.0					9																	112705604		2203	4300	6503	SO:0001583	missense	114299	exon7			GACACCACAGAGC	AJ312216	CCDS35099.1, CCDS48002.1, CCDS48002.2	9q31.3	2009-10-16			ENSG00000243444	ENSG00000243444			15845	protein-coding gene	gene with protein product						11478809	Standard	NM_001037293		Approved			Q8IXS6	OTTHUMG00000020479	ENST00000374531.2:c.1039A>G	chr9.hg19:g.112705604A>G	ENSP00000363656:p.Thr347Ala	118.0	0.0	.		128.0	19.0	.	NM_053016	A9Z1X9|Q8N9D5|Q96DU1	Missense_Mutation	SNP	ENST00000374531.2	hg19	CCDS35099.1	.	.	.	.	.	.	.	.	.	.	A	15.03	2.711967	0.48517	.	.	ENSG00000243444;ENSG00000243444;ENSG00000243444;ENSG00000243444;ENSG00000157654	ENST00000374531;ENST00000448454;ENST00000483909;ENST00000314527;ENST00000413420	T;T;T;T;T	0.22945	2.36;2.36;2.36;2.36;1.93	5.86	5.86	0.93980	.	.	.	.	.	T	0.33498	0.0865	L	0.59436	1.845	0.80722	D	1	P;P	0.48503	0.788;0.911	P;P	0.51516	0.548;0.672	T	0.13710	-1.0499	9	0.05351	T	0.99	.	15.4456	0.75228	1.0:0.0:0.0:0.0	.	347;381	Q8IXS6;D3YTA4	PALM2_HUMAN;.	A	347;381;345;379;379	ENSP00000363656:T347A;ENSP00000400206:T381A;ENSP00000417525:T345A;ENSP00000323805:T379A;ENSP00000397839:T379A	ENSP00000397839:T379A	T	+	1	0	PALM2-AKAP2;PALM2	111745425	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	9.339000	0.96797	2.244000	0.73946	0.528000	0.53228	ACA	.	.	.	none		0.552	PALM2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053604.1	NM_001037293	
FAM102A	399665	hgsc.bcm.edu	37	9	130707096	130707096	+	Silent	SNP	G	G	A			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr9:130707096G>A	ENST00000373095.1	-	9	1374	c.999C>T	c.(997-999)atC>atT	p.I333I	FAM102A_ENST00000300434.3_5'UTR|FAM102A_ENST00000373084.4_Silent_p.I191I	NM_001035254.2	NP_001030331.1	Q5T9C2	F102A_HUMAN	family with sequence similarity 102, member A	333										breast(1)|cervix(1)|large_intestine(3)|lung(1)|ovary(4)	10						GGCTCTGCACGATCTTCTCCA	0.672																																					p.I333I		Atlas-SNP	.											.	FAM102A	32	.	0			c.C999T						PASS	.						89.0	64.0	72.0					9																	130707096		2203	4300	6503	SO:0001819	synonymous_variant	399665	exon9			CTGCACGATCTTC		CCDS6888.1, CCDS35150.1	9q34.11	2012-11-05	2005-11-17	2005-11-17	ENSG00000167106	ENSG00000167106			31419	protein-coding gene	gene with protein product	"""sym-3 homolog A (C. elegans)"""	610891	"""chromosome 9 open reading frame 132"""	C9orf132			Standard	NM_001035254		Approved	Eeig1, bA203J24.7, SYM-3A	uc004bsx.2	Q5T9C2	OTTHUMG00000020720	ENST00000373095.1:c.999C>T	chr9.hg19:g.130707096G>A		60.0	0.0	.		39.0	23.0	.	NM_001035254	A2A329|Q8TEL4	Silent	SNP	ENST00000373095.1	hg19	CCDS35150.1																																																																																			.	.	.	none		0.672	FAM102A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054298.2		
INS	3630	hgsc.bcm.edu	37	11	2181135	2181135	+	Missense_Mutation	SNP	G	G	T			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr11:2181135G>T	ENST00000397262.1	-	2	512	c.280C>A	c.(280-282)Caa>Aaa	p.Q94K	INS_ENST00000381330.4_Missense_Mutation_p.Q94K|INS_ENST00000512523.1_Missense_Mutation_p.Q82K|INS_ENST00000250971.3_Missense_Mutation_p.Q94K|INS-IGF2_ENST00000397270.1_Intron|INS-IGF2_ENST00000481781.1_5'Flank	NM_001185098.1	NP_001172027.1	P01308	INS_HUMAN	insulin	94					activation of protein kinase B activity (GO:0032148)|acute-phase response (GO:0006953)|alpha-beta T cell activation (GO:0046631)|cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|fatty acid homeostasis (GO:0055089)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|insulin receptor signaling pathway (GO:0008286)|MAPK cascade (GO:0000165)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of fatty acid metabolic process (GO:0045922)|negative regulation of feeding behavior (GO:2000252)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of glycogen catabolic process (GO:0045818)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of NAD(P)H oxidase activity (GO:0033861)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein oligomerization (GO:0032460)|negative regulation of protein secretion (GO:0050709)|negative regulation of proteolysis (GO:0045861)|negative regulation of respiratory burst involved in inflammatory response (GO:0060266)|negative regulation of vasodilation (GO:0045908)|positive regulation of brown fat cell differentiation (GO:0090336)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of DNA replication (GO:0045740)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of respiratory burst (GO:0060267)|positive regulation of vasodilation (GO:0045909)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of insulin secretion (GO:0050796)|regulation of protein localization (GO:0032880)|regulation of protein secretion (GO:0050708)|regulation of transcription, DNA-templated (GO:0006355)|regulation of transmembrane transporter activity (GO:0022898)|small molecule metabolic process (GO:0044281)|wound healing (GO:0042060)	endoplasmic reticulum lumen (GO:0005788)|endosome lumen (GO:0031904)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|secretory granule lumen (GO:0034774)	hormone activity (GO:0005179)|identical protein binding (GO:0042802)|insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|protease binding (GO:0002020)			haematopoietic_and_lymphoid_tissue(1)|lung(3)|prostate(1)	5		Lung NSC(207;8.94e-06)|all_epithelial(84;3.17e-05)|all_lung(207;3.67e-05)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)	Colorectal(5;0.00245)|COAD - Colon adenocarcinoma(6;0.0239)	BRCA - Breast invasive adenocarcinoma(625;0.0025)|LUSC - Lung squamous cell carcinoma(625;0.082)|Lung(200;0.14)		GTACAGCATTGTTCCACAATG	0.672																																					p.Q94K		Atlas-SNP	.											.	INS	10	.	0			c.C280A						PASS	.						63.0	53.0	57.0					11																	2181135		2187	4293	6480	SO:0001583	missense	3630	exon3			AGCATTGTTCCAC	X70508	CCDS7729.1	11p15.5	2014-02-03			ENSG00000254647	ENSG00000254647			6081	protein-coding gene	gene with protein product		176730	"""insulin-dependent diabetes mellitus 2"""	IDDM2, IDDM1		6243748, 7773291	Standard	NM_000207		Approved			P01308	OTTHUMG00000009558	ENST00000397262.1:c.280C>A	chr11.hg19:g.2181135G>T	ENSP00000380432:p.Gln94Lys	73.0	0.0	.		51.0	18.0	.	NM_001185097	Q5EEX2	Missense_Mutation	SNP	ENST00000397262.1	hg19	CCDS7729.1	.	.	.	.	.	.	.	.	.	.	G	14.14	2.445461	0.43429	.	.	ENSG00000254647	ENST00000397262;ENST00000250971;ENST00000381330;ENST00000512523	D;D;D;D	0.88431	-2.38;-2.38;-2.38;-2.38	3.68	2.73	0.32206	Insulin-like (4);	.	.	.	.	D	0.94466	0.8219	M	0.89534	3.04	0.52501	D	0.999953	D;B	0.60160	0.987;0.437	D;P	0.69307	0.963;0.511	D	0.94552	0.7754	9	0.72032	D	0.01	.	11.9365	0.52876	0.0:0.1778:0.8222:0.0	.	82;94	A6XGL2;P01308	.;INS_HUMAN	K	94;94;94;82	ENSP00000380432:Q94K;ENSP00000250971:Q94K;ENSP00000370731:Q94K;ENSP00000424008:Q82K	ENSP00000250971:Q94K	Q	-	1	0	INS	2137711	1.000000	0.71417	0.918000	0.36340	0.079000	0.17450	4.878000	0.63093	0.860000	0.35481	0.462000	0.41574	CAA	.	.	.	none		0.672	INS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026395.3	NM_000207	
PDE3B	5140	hgsc.bcm.edu	37	11	14808189	14808189	+	Missense_Mutation	SNP	A	A	T			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr11:14808189A>T	ENST00000282096.4	+	3	1589	c.1236A>T	c.(1234-1236)gaA>gaT	p.E412D	PDE3B_ENST00000455098.2_Intron	NM_000922.3	NP_000913.2	Q13370	PDE3B_HUMAN	phosphodiesterase 3B, cGMP-inhibited	412					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cellular response to insulin stimulus (GO:0032869)|endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|insulin receptor signaling pathway (GO:0008286)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of lipid catabolic process (GO:0050995)|regulation of insulin secretion (GO:0050796)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|guanyl-nucleotide exchange factor complex (GO:0032045)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)|protein kinase B binding (GO:0043422)			NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(15)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39					Caffeine(DB00201)	CCTGTTCTGAAATAGAGGACC	0.373																																					p.E412D		Atlas-SNP	.											.	PDE3B	98	.	0			c.A1236T						PASS	.						120.0	130.0	126.0					11																	14808189		2200	4294	6494	SO:0001583	missense	5140	exon3			TTCTGAAATAGAG	U38178	CCDS7817.1	11p15.2	2008-03-18			ENSG00000152270	ENSG00000152270	3.1.4.17	"""Phosphodiesterases"""	8779	protein-coding gene	gene with protein product		602047				8884271, 16395595	Standard	NM_000922		Approved	HcGIP1	uc001mln.3	Q13370	OTTHUMG00000165898	ENST00000282096.4:c.1236A>T	chr11.hg19:g.14808189A>T	ENSP00000282096:p.Glu412Asp	169.0	0.0	.		150.0	59.0	.	NM_000922	B7ZM37|O00639|Q14408|Q6SEI4	Missense_Mutation	SNP	ENST00000282096.4	hg19	CCDS7817.1	.	.	.	.	.	.	.	.	.	.	a	14.21	2.468783	0.43839	.	.	ENSG00000152270	ENST00000282096	T	0.34275	1.37	5.72	3.42	0.39159	.	0.151781	0.27749	U	0.018012	T	0.36552	0.0971	N	0.20986	0.625	0.80722	D	1	D	0.69078	0.997	D	0.72625	0.978	T	0.22312	-1.0220	10	0.05959	T	0.93	.	9.8395	0.40991	0.8619:0.0:0.1381:0.0	.	412	Q13370	PDE3B_HUMAN	D	412	ENSP00000282096:E412D	ENSP00000282096:E412D	E	+	3	2	PDE3B	14764765	1.000000	0.71417	0.992000	0.48379	0.978000	0.69477	3.979000	0.56888	0.452000	0.26830	0.456000	0.33151	GAA	.	.	.	none		0.373	PDE3B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386974.1	NM_000922	
CHRM1	1128	hgsc.bcm.edu	37	11	62677207	62677207	+	Missense_Mutation	SNP	G	G	A			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr11:62677207G>A	ENST00000306960.3	-	2	1907	c.1366C>T	c.(1366-1368)Ccc>Tcc	p.P456S	AP000438.2_ENST00000543624.1_RNA	NM_000738.2	NP_000729.2	P11229	ACM1_HUMAN	cholinergic receptor, muscarinic 1	456					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|cognition (GO:0050890)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|neuromuscular synaptic transmission (GO:0007274)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of ion transport (GO:0043270)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of locomotion (GO:0040012)|saliva secretion (GO:0046541)|signal transduction (GO:0007165)	asymmetric synapse (GO:0032279)|axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	drug binding (GO:0008144)|G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)			large_intestine(5)|lung(3)|stomach(1)	9					Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Benzatropine(DB00245)|Biperiden(DB00810)|Brompheniramine(DB00835)|Buclizine(DB00354)|Carbachol(DB00411)|Cevimeline(DB00185)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Citalopram(DB00215)|Clidinium(DB00771)|Clozapine(DB00363)|Cocaine(DB00907)|Cryptenamine(DB00785)|Cyclopentolate(DB00979)|Cycrimine(DB00942)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Dicyclomine(DB00804)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxepin(DB01142)|Doxylamine(DB00366)|Escitalopram(DB01175)|Ethopropazine(DB00392)|Fesoterodine(DB06702)|Flavoxate(DB01148)|Flupentixol(DB00875)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Mepenzolate(DB04843)|Methantheline(DB00940)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Metoclopramide(DB01233)|Minaprine(DB00805)|Molindone(DB01618)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Oxyphenonium(DB00219)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pirenzepine(DB00670)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propantheline(DB00782)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Trospium(DB00209)|Ziprasidone(DB00246)	TGGCGGGAGGGAGTGCGGTGC	0.667																																					p.P456S		Atlas-SNP	.											.	CHRM1	29	.	0			c.C1366T						PASS	.						72.0	79.0	77.0					11																	62677207		2201	4298	6499	SO:0001583	missense	1128	exon2			GGGAGGGAGTGCG	Y00508	CCDS8040.1	11q12-q13	2012-08-08				ENSG00000168539		"""Cholinergic receptors"", ""GPCR / Class A : Cholinergic receptors, muscarinic"""	1950	protein-coding gene	gene with protein product	"""acetylcholine receptor, muscarinic 1"""	118510					Standard	NM_000738		Approved		uc001nwi.3	P11229		ENST00000306960.3:c.1366C>T	chr11.hg19:g.62677207G>A	ENSP00000306490:p.Pro456Ser	86.0	0.0	.		70.0	15.0	.	NM_000738	Q96RH1	Missense_Mutation	SNP	ENST00000306960.3	hg19	CCDS8040.1	.	.	.	.	.	.	.	.	.	.	G	15.52	2.857391	0.51376	.	.	ENSG00000168539	ENST00000306960	T	0.57595	0.39	4.53	3.58	0.41010	.	0.211607	0.23760	N	0.044839	T	0.37892	0.1020	N	0.24115	0.695	0.35793	D	0.822568	B	0.12630	0.006	B	0.14578	0.011	T	0.40289	-0.9571	10	0.42905	T	0.14	-15.4337	11.7385	0.51780	0.0:0.2317:0.7683:0.0	.	456	P11229	ACM1_HUMAN	S	456	ENSP00000306490:P456S	ENSP00000306490:P456S	P	-	1	0	CHRM1	62433783	1.000000	0.71417	0.993000	0.49108	0.930000	0.56654	5.691000	0.68249	0.995000	0.38917	0.561000	0.74099	CCC	.	.	.	none		0.667	CHRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396178.1	NM_000738	
CHRM1	1128	hgsc.bcm.edu	37	11	62677510	62677510	+	Missense_Mutation	SNP	A	A	T			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr11:62677510A>T	ENST00000306960.3	-	2	1604	c.1063T>A	c.(1063-1065)Ttc>Atc	p.F355I	AP000438.2_ENST00000543624.1_RNA	NM_000738.2	NP_000729.2	P11229	ACM1_HUMAN	cholinergic receptor, muscarinic 1	355					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|cognition (GO:0050890)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|neuromuscular synaptic transmission (GO:0007274)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of ion transport (GO:0043270)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of locomotion (GO:0040012)|saliva secretion (GO:0046541)|signal transduction (GO:0007165)	asymmetric synapse (GO:0032279)|axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	drug binding (GO:0008144)|G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)			large_intestine(5)|lung(3)|stomach(1)	9					Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Benzatropine(DB00245)|Biperiden(DB00810)|Brompheniramine(DB00835)|Buclizine(DB00354)|Carbachol(DB00411)|Cevimeline(DB00185)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Citalopram(DB00215)|Clidinium(DB00771)|Clozapine(DB00363)|Cocaine(DB00907)|Cryptenamine(DB00785)|Cyclopentolate(DB00979)|Cycrimine(DB00942)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Dicyclomine(DB00804)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxepin(DB01142)|Doxylamine(DB00366)|Escitalopram(DB01175)|Ethopropazine(DB00392)|Fesoterodine(DB06702)|Flavoxate(DB01148)|Flupentixol(DB00875)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Mepenzolate(DB04843)|Methantheline(DB00940)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Metoclopramide(DB01233)|Minaprine(DB00805)|Molindone(DB01618)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Oxyphenonium(DB00219)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pirenzepine(DB00670)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propantheline(DB00782)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Trospium(DB00209)|Ziprasidone(DB00246)	ACCAGCGAGAAGGTCTTCCGC	0.592																																					p.F355I		Atlas-SNP	.											.	CHRM1	29	.	0			c.T1063A						PASS	.						55.0	53.0	54.0					11																	62677510		2201	4298	6499	SO:0001583	missense	1128	exon2			GCGAGAAGGTCTT	Y00508	CCDS8040.1	11q12-q13	2012-08-08				ENSG00000168539		"""Cholinergic receptors"", ""GPCR / Class A : Cholinergic receptors, muscarinic"""	1950	protein-coding gene	gene with protein product	"""acetylcholine receptor, muscarinic 1"""	118510					Standard	NM_000738		Approved		uc001nwi.3	P11229		ENST00000306960.3:c.1063T>A	chr11.hg19:g.62677510A>T	ENSP00000306490:p.Phe355Ile	78.0	0.0	.		59.0	25.0	.	NM_000738	Q96RH1	Missense_Mutation	SNP	ENST00000306960.3	hg19	CCDS8040.1	.	.	.	.	.	.	.	.	.	.	A	11.63	1.696730	0.30142	.	.	ENSG00000168539	ENST00000306960;ENST00000543973	T;T	0.72051	-0.62;-0.62	4.49	4.49	0.54785	GPCR, rhodopsin-like superfamily (1);	0.232532	0.26293	N	0.025212	T	0.43634	0.1256	N	0.04275	-0.24	0.36087	D	0.843175	B	0.14805	0.011	B	0.17098	0.017	T	0.45920	-0.9228	10	0.17369	T	0.5	-24.428	7.3553	0.26714	0.8052:0.0:0.0:0.1948	.	355	P11229	ACM1_HUMAN	I	355	ENSP00000306490:F355I;ENSP00000441188:F355I	ENSP00000306490:F355I	F	-	1	0	CHRM1	62434086	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.101000	0.31037	1.870000	0.54199	0.459000	0.35465	TTC	.	.	.	none		0.592	CHRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396178.1	NM_000738	
SYTL2	54843	hgsc.bcm.edu	37	11	85409045	85409045	+	Missense_Mutation	SNP	A	A	C	rs554484063		TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr11:85409045A>C	ENST00000528231.1	-	16	2707	c.2430T>G	c.(2428-2430)agT>agG	p.S810R	SYTL2_ENST00000354566.3_Missense_Mutation_p.S1148R|SYTL2_ENST00000529581.1_Missense_Mutation_p.S252R|SYTL2_ENST00000389960.4_Missense_Mutation_p.S786R|SYTL2_ENST00000524452.1_Missense_Mutation_p.S786R|SYTL2_ENST00000525702.1_Missense_Mutation_p.S252R|SYTL2_ENST00000527523.1_Missense_Mutation_p.S778R|SYTL2_ENST00000389958.3_Missense_Mutation_p.S241R|SYTL2_ENST00000359152.5_Missense_Mutation_p.S1656R|SYTL2_ENST00000533892.1_Missense_Mutation_p.S212R|SYTL2_ENST00000525423.1_Missense_Mutation_p.S1132R|SYTL2_ENST00000316356.4_Missense_Mutation_p.S811R	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2	810	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		AATTTAGATGACTTCCCCTTA	0.393																																					p.S1148R		Atlas-SNP	.											.	SYTL2	231	.	0			c.T3444G						PASS	.						96.0	87.0	90.0					11																	85409045		2203	4299	6502	SO:0001583	missense	54843	exon11			TAGATGACTTCCC	AJ303364	CCDS31649.1, CCDS31652.1, CCDS41698.1, CCDS53687.1, CCDS53688.1, CCDS53689.1	11q14.1	2014-06-13			ENSG00000137501	ENSG00000137501			15585	protein-coding gene	gene with protein product	"""chromosome 11 synaptotagmin"", ""breast cancer-associated antigen SGA-72M"", ""protein phosphatase 1, regulatory subunit 151"""	612880				10997877	Standard	XM_005274057		Approved	FLJ20163, FLJ21219, KIAA1597, exophilin-4, CHR11SYT, SLP2, SGA72M, MGC102768, PPP1R151	uc001pbb.3	Q9HCH5	OTTHUMG00000166977	ENST00000528231.1:c.2430T>G	chr11.hg19:g.85409045A>C	ENSP00000431701:p.Ser810Arg	52.0	0.0	.		50.0	7.0	.	NM_206927	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Missense_Mutation	SNP	ENST00000528231.1	hg19	CCDS53688.1	.	.	.	.	.	.	.	.	.	.	A	14.92	2.679575	0.47886	.	.	ENSG00000137501	ENST00000389960;ENST00000359152;ENST00000354566;ENST00000316356;ENST00000525702;ENST00000525423;ENST00000529581;ENST00000389958;ENST00000530351;ENST00000528231;ENST00000533892;ENST00000527523;ENST00000524452	T;T;T;T;T;T;T;T;T;T;T;T;T	0.08193	3.12;3.12;3.12;3.12;3.12;3.12;3.12;3.12;3.12;3.12;3.12;3.12;3.12	5.93	4.98	0.66077	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.357017	0.24240	N	0.040262	T	0.09335	0.0230	N	0.12637	0.245	0.30841	N	0.735693	B;B;B;B;B;D;P;D;B;B	0.54047	0.284;0.409;0.154;0.135;0.288;0.964;0.939;0.964;0.137;0.041	B;B;B;B;B;P;P;P;B;B	0.54346	0.091;0.091;0.148;0.091;0.091;0.749;0.681;0.749;0.091;0.023	T	0.10268	-1.0637	9	.	.	.	-1.3853	11.3673	0.49679	0.191:0.0:0.809:0.0	.	778;786;810;811;628;1108;1132;1148;241;212	Q9HCH5-14;Q9HCH5-6;Q9HCH5;Q9HCH5-13;Q9HCH5-15;Q9HCH5-11;Q9HCH5-7;Q9HCH5-8;Q9HCH5-9;Q9HCH5-4	.;.;SYTL2_HUMAN;.;.;.;.;.;.;.	R	786;1656;1148;811;252;1132;252;241;527;810;212;778;786	ENSP00000374610:S786R;ENSP00000352065:S1656R;ENSP00000346576:S1148R;ENSP00000318803:S811R;ENSP00000432996:S252R;ENSP00000432694:S1132R;ENSP00000435855:S252R;ENSP00000374608:S241R;ENSP00000435009:S527R;ENSP00000431701:S810R;ENSP00000432144:S212R;ENSP00000434010:S778R;ENSP00000435238:S786R	.	S	-	3	2	SYTL2	85086693	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.506000	0.45433	1.497000	0.48584	-0.177000	0.13119	AGT	.	.	.	none		0.393	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927	
NCAPD3	23310	hgsc.bcm.edu	37	11	134063948	134063948	+	Missense_Mutation	SNP	C	C	T			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr11:134063948C>T	ENST00000534548.2	-	15	1851	c.1787G>A	c.(1786-1788)cGg>cAg	p.R596Q		NM_015261.2	NP_056076.1	P42695	CNDD3_HUMAN	non-SMC condensin II complex, subunit D3	596					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	germinal vesicle (GO:0042585)|membrane (GO:0016020)|nuclear condensin complex (GO:0000799)|nuclear pericentric heterochromatin (GO:0031618)|nucleoplasm (GO:0005654)	methylated histone binding (GO:0035064)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_hematologic(175;0.127)	all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227)		GGCCTGCTTCCGGACAGACAC	0.443																																					p.R596Q		Atlas-SNP	.											.	NCAPD3	141	.	0			c.G1787A						PASS	.						70.0	67.0	68.0					11																	134063948		2201	4297	6498	SO:0001583	missense	23310	exon15			TGCTTCCGGACAG	AK124878	CCDS31723.1	11q25	2008-02-04			ENSG00000151503	ENSG00000151503			28952	protein-coding gene	gene with protein product		609276				7584044, 8619474, 14532007	Standard	NM_015261		Approved	hCAP-D3, CAP-D3, hHCP-6, KIAA0056, FLJ42888, hcp-6	uc001qhd.1	P42695	OTTHUMG00000167172	ENST00000534548.2:c.1787G>A	chr11.hg19:g.134063948C>T	ENSP00000433681:p.Arg596Gln	101.0	0.0	.		100.0	14.0	.	NM_015261	A6NFS2|Q4KMQ9	Missense_Mutation	SNP	ENST00000534548.2	hg19	CCDS31723.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.777630	0.90195	.	.	ENSG00000151503	ENST00000534548	T	0.75938	-0.98	5.55	5.55	0.83447	Armadillo-like helical (1);Armadillo-type fold (1);	0.110622	0.64402	D	0.000010	D	0.87795	0.6267	M	0.83118	2.625	0.80722	D	1	D	0.89917	1.0	D	0.74023	0.982	D	0.88588	0.3141	10	0.72032	D	0.01	-26.9521	19.8686	0.96842	0.0:1.0:0.0:0.0	.	596	P42695	CNDD3_HUMAN	Q	596	ENSP00000433681:R596Q	ENSP00000431612:R596Q	R	-	2	0	NCAPD3	133569158	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.278000	0.51662	2.768000	0.95171	0.655000	0.94253	CGG	.	.	.	none		0.443	NCAPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393575.2	NM_015261	
FAM186A	121006	hgsc.bcm.edu	37	12	50745132	50745132	+	Missense_Mutation	SNP	G	G	T			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr12:50745132G>T	ENST00000327337.5	-	4	5482	c.5483C>A	c.(5482-5484)tCt>tAt	p.S1828Y	FAM186A_ENST00000543096.1_5'Flank|FAM186A_ENST00000543111.1_Missense_Mutation_p.S1828Y	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	1828	Pro-rich.																AGGGGCCCGAGATATTGGGAG	0.612																																					p.S1828Y	NSCLC(138;1796 1887 12511 19463 37884)	Atlas-SNP	.											FAM186A_ENST00000327337,caecum,carcinoma,0,1	FAM186A	181	.	0			c.C5483A						PASS	.						16.0	19.0	18.0					12																	50745132		692	1591	2283	SO:0001583	missense	121006	exon4			GCCCGAGATATTG		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.5483C>A	chr12.hg19:g.50745132G>T	ENSP00000329995:p.Ser1828Tyr	89.0	0.0	.		72.0	33.0	.	NM_001145475		Missense_Mutation	SNP	ENST00000327337.5	hg19	CCDS44878.1	.	.	.	.	.	.	.	.	.	.	G	9.695	1.152884	0.21371	.	.	ENSG00000185958	ENST00000543111;ENST00000327337	T;T	0.17528	2.27;2.27	5.01	0.755	0.18415	.	.	.	.	.	T	0.08268	0.0206	N	0.08118	0	0.09310	N	1	B;B	0.33171	0.4;0.4	B;B	0.33690	0.168;0.168	T	0.36359	-0.9751	9	0.33141	T	0.24	.	7.4753	0.27371	0.2556:0.1227:0.6216:0.0	.	1828;1828	F5GYN0;A6NE01	.;F186A_HUMAN	Y	1828	ENSP00000441337:S1828Y;ENSP00000329995:S1828Y	ENSP00000329995:S1828Y	S	-	2	0	FAM186A	49031399	0.001000	0.12720	0.000000	0.03702	0.027000	0.11550	0.914000	0.28624	-0.269000	0.09298	-1.164000	0.01763	TCT	.	.	.	none		0.612	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1	XM_001718353	
GALNT6	11226	hgsc.bcm.edu	37	12	51758021	51758021	+	Silent	SNP	G	G	C			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr12:51758021G>C	ENST00000543196.2	-	5	1138	c.933C>G	c.(931-933)ccC>ccG	p.P311P	GALNT6_ENST00000356317.3_Silent_p.P311P			Q8NCL4	GALT6_HUMAN	polypeptide N-acetylgalactosaminyltransferase 6	311					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			endometrium(2)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						CCCTCTGGACGGGCTTGGCGA	0.577																																					p.P311P		Atlas-SNP	.											GALNT6,NS,carcinoma,0,1	GALNT6	63	.	0			c.C933G						PASS	.						97.0	90.0	92.0					12																	51758021		2203	4300	6503	SO:0001819	synonymous_variant	11226	exon6			CTGGACGGGCTTG	Y08565	CCDS8813.1	12q13	2014-03-13	2014-03-13		ENSG00000139629	ENSG00000139629		"""Glycosyltransferase family 2 domain containing"""	4128	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 6"""	605148	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6 (GalNAc-T6)"""			10464263	Standard	NM_007210		Approved	GalNAc-T6	uc001ryl.1	Q8NCL4		ENST00000543196.2:c.933C>G	chr12.hg19:g.51758021G>C		291.0	0.0	.		270.0	97.0	.	NM_007210	Q8IYH4|Q9H6G2|Q9UIV5	Silent	SNP	ENST00000543196.2	hg19	CCDS8813.1																																																																																			.	.	.	none		0.577	GALNT6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469735.1	NM_007210	
GCN1L1	10985	hgsc.bcm.edu	37	12	120569801	120569801	+	Missense_Mutation	SNP	C	C	T			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr12:120569801C>T	ENST00000300648.6	-	54	7355	c.7343G>A	c.(7342-7344)gGg>gAg	p.G2448E		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	2448					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CCCTAGGCACCCGGCTGAGGA	0.567																																					p.G2448E		Atlas-SNP	.											.	GCN1L1	207	.	0			c.G7343A						PASS	.						58.0	60.0	60.0					12																	120569801		2016	4171	6187	SO:0001583	missense	10985	exon54			AGGCACCCGGCTG	U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"""GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"""			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.7343G>A	chr12.hg19:g.120569801C>T	ENSP00000300648:p.Gly2448Glu	221.0	0.0	.		173.0	25.0	.	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Missense_Mutation	SNP	ENST00000300648.6	hg19	CCDS41847.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.379586	0.82682	.	.	ENSG00000089154	ENST00000300648	T	0.61040	0.14	4.19	4.19	0.49359	Armadillo-like helical (1);Armadillo-type fold (1);	0.124142	0.53938	D	0.000052	T	0.75184	0.3815	M	0.77103	2.36	0.80722	D	1	D	0.71674	0.998	D	0.70935	0.971	T	0.76462	-0.2950	10	0.39692	T	0.17	-19.3318	17.0673	0.86562	0.0:1.0:0.0:0.0	.	2448	Q92616	GCN1L_HUMAN	E	2448	ENSP00000300648:G2448E	ENSP00000300648:G2448E	G	-	2	0	GCN1L1	119054184	1.000000	0.71417	0.969000	0.41365	0.975000	0.68041	6.918000	0.75788	2.330000	0.79161	0.655000	0.94253	GGG	.	.	.	none		0.567	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1		
ATP11A	23250	hgsc.bcm.edu	37	13	113526110	113526110	+	Missense_Mutation	SNP	T	T	C			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr13:113526110T>C	ENST00000487903.1	+	26	3141	c.3053T>C	c.(3052-3054)cTa>cCa	p.L1018P	ATP11A_ENST00000283558.8_Missense_Mutation_p.L1018P|ATP11A_ENST00000375630.2_Missense_Mutation_p.L1018P|ATP11A_ENST00000375645.3_Missense_Mutation_p.L1018P			P98196	AT11A_HUMAN	ATPase, class VI, type 11A	1018					phospholipid translocation (GO:0045332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(12)|lung(17)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	51	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.134)|all_epithelial(44;0.141)				ACAGTTACACTAAAGGTAAGT	0.483																																					p.L1018P		Atlas-SNP	.											.	ATP11A	225	.	0			c.T3053C						PASS	.						159.0	151.0	154.0					13																	113526110		2203	4300	6503	SO:0001583	missense	23250	exon26			TTACACTAAAGGT	AB028944	CCDS32011.1	13q34	2010-04-20	2007-09-19		ENSG00000068650	ENSG00000068650	3.6.3.1	"""ATPases / P-type"""	13552	protein-coding gene	gene with protein product	"""potential phospholipid-transporting ATPase IH"", ""phospholipid-translocating ATPase"""	605868	"""ATPase, Class VI, type 11A"""			11015572	Standard	NM_032189		Approved	ATPIH, ATPIS, KIAA1021	uc001vsj.4	P98196	OTTHUMG00000017371	ENST00000487903.1:c.3053T>C	chr13.hg19:g.113526110T>C	ENSP00000420387:p.Leu1018Pro	99.0	0.0	.		77.0	33.0	.	NM_032189	Q5VXT2	Missense_Mutation	SNP	ENST00000487903.1	hg19	CCDS32011.1	.	.	.	.	.	.	.	.	.	.	T	16.06	3.016751	0.54468	.	.	ENSG00000068650	ENST00000487903;ENST00000375630;ENST00000375645;ENST00000283558;ENST00000419631	T;T;T;T;T	0.51325	0.71;0.71;0.71;0.71;0.71	4.15	4.15	0.48705	.	0.410679	0.24585	N	0.037266	T	0.75191	0.3816	H	0.96175	3.78	0.80722	D	1	D;D	0.67145	0.996;0.978	P;P	0.62014	0.897;0.841	D	0.83543	0.0097	10	0.66056	D	0.02	.	13.4786	0.61322	0.0:0.0:0.0:1.0	.	1018;1018	E9PEJ6;P98196	.;AT11A_HUMAN	P	1018;1018;1018;1018;10	ENSP00000420387:L1018P;ENSP00000364781:L1018P;ENSP00000364796:L1018P;ENSP00000283558:L1018P;ENSP00000410824:L10P	ENSP00000283558:L1018P	L	+	2	0	ATP11A	112574111	0.962000	0.33011	0.392000	0.26245	0.244000	0.25665	7.271000	0.78506	1.628000	0.50416	0.379000	0.24179	CTA	.	.	.	none		0.483	ATP11A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045834.3	NM_015205	
GPHN	10243	hgsc.bcm.edu	37	14	67291218	67291218	+	Missense_Mutation	SNP	A	A	C			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr14:67291218A>C	ENST00000315266.5	+	4	1349	c.228A>C	c.(226-228)gaA>gaC	p.E76D	GPHN_ENST00000543237.1_Missense_Mutation_p.E76D|GPHN_ENST00000478722.1_Missense_Mutation_p.E76D|GPHN_ENST00000305960.9_Intron|GPHN_ENST00000544752.2_3'UTR|GPHN_ENST00000459628.1_Intron	NM_001024218.1	NP_001019389.1	Q9NQX3	GEPH_HUMAN	gephyrin	76	MPT Mo-transferase.				establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycine receptor clustering (GO:0072579)|Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|molybdopterin cofactor biosynthetic process (GO:0032324)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|inhibitory synapse (GO:0060077)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|molybdopterin adenylyltransferase activity (GO:0061598)|molybdopterin molybdotransferase activity (GO:0061599)|transferase activity (GO:0016740)			large_intestine(8)|liver(1)|ovary(2)|stomach(1)	12		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)		GGTGTGATGAAAAGGAACTTA	0.393			T	MLL	AL																																p.E76D		Atlas-SNP	.		Dom	yes		14	14q24	10243	gephyrin (GPH)		L	.	GPHN	79	.	0			c.A228C						PASS	.						97.0	92.0	94.0					14																	67291218		2203	4300	6503	SO:0001583	missense	10243	exon4			TGATGAAAAGGAA	AB037806	CCDS9777.1, CCDS32103.1	14q23.3	2008-04-22			ENSG00000171723	ENSG00000171723			15465	protein-coding gene	gene with protein product		603930				1319186, 10325225, 18403029	Standard	XM_005267250		Approved	KIAA1385	uc001xix.3	Q9NQX3	OTTHUMG00000029785	ENST00000315266.5:c.228A>C	chr14.hg19:g.67291218A>C	ENSP00000312771:p.Glu76Asp	94.0	0.0	.		70.0	19.0	.	NM_001024218	Q9H4E9|Q9P2G2	Missense_Mutation	SNP	ENST00000315266.5	hg19	CCDS32103.1	.	.	.	.	.	.	.	.	.	.	A	11.85	1.761655	0.31228	.	.	ENSG00000171723	ENST00000315266;ENST00000478722;ENST00000543237;ENST00000555456	T;T;T;T	0.77877	-1.13;-1.13;-1.13;-1.13	5.48	4.33	0.51752	Molybdenum cofactor synthesis (1);Molybdopterin binding (4);	0.046743	0.85682	D	0.000000	T	0.56572	0.1994	N	0.10664	0.02	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.0;0.001	T	0.46721	-0.9171	10	0.16896	T	0.51	-9.6865	11.3654	0.49668	0.9283:0.0:0.0717:0.0	.	76;76;76	F5H039;Q9NQX3;Q9NQX3-2	.;GEPH_HUMAN;.	D	76;76;76;9	ENSP00000312771:E76D;ENSP00000417901:E76D;ENSP00000438404:E76D;ENSP00000450706:E9D	ENSP00000312771:E76D	E	+	3	2	GPHN	66360971	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	1.444000	0.35068	0.910000	0.36722	0.254000	0.18369	GAA	.	.	.	none		0.393	GPHN-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000074299.2	NM_020806	
VPS13C	54832	hgsc.bcm.edu	37	15	62211634	62211634	+	Missense_Mutation	SNP	T	T	C			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr15:62211634T>C	ENST00000261517.5	-	58	7565	c.7492A>G	c.(7492-7494)Aca>Gca	p.T2498A	VPS13C_ENST00000395898.3_Missense_Mutation_p.T2455A|VPS13C_ENST00000395896.4_Missense_Mutation_p.T2498A|VPS13C_ENST00000249837.3_Missense_Mutation_p.T2455A	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)											NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						GCAACTTCTGTATATCCATGA	0.378																																					p.T2498A		Atlas-SNP	.											.	VPS13C	506	.	0			c.A7492G						PASS	.						127.0	126.0	126.0					15																	62211634		2203	4299	6502	SO:0001583	missense	54832	exon58			CTTCTGTATATCC	AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"""vacuolar protein sorting 13C (yeast)"""				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.7492A>G	chr15.hg19:g.62211634T>C	ENSP00000261517:p.Thr2498Ala	83.0	0.0	.		103.0	42.0	.	NM_020821		Missense_Mutation	SNP	ENST00000261517.5	hg19	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	T	16.21	3.059562	0.55325	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.44881	0.92;0.91;1.09	5.08	5.08	0.68730	.	0.343050	0.31071	N	0.008307	T	0.38585	0.1046	M	0.69823	2.125	0.36345	D	0.85969	B;B;B;P	0.35745	0.257;0.171;0.257;0.518	B;B;B;B	0.30316	0.089;0.089;0.089;0.114	T	0.49753	-0.8906	10	0.30078	T	0.28	.	11.1995	0.48733	0.0:0.0745:0.0:0.9255	.	2455;2498;2455;2498	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	A	2455;2498;2498;2498	ENSP00000249837:T2455A;ENSP00000261517:T2498A;ENSP00000379233:T2498A	ENSP00000249837:T2455A	T	-	1	0	VPS13C	59998926	1.000000	0.71417	0.996000	0.52242	0.988000	0.76386	2.093000	0.41710	2.023000	0.59567	0.533000	0.62120	ACA	.	.	.	none		0.378	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684	
RPL3L	6123	hgsc.bcm.edu	37	16	1995508	1995508	+	Missense_Mutation	SNP	C	C	A			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr16:1995508C>A	ENST00000268661.7	-	9	1253	c.1159G>T	c.(1159-1161)Gcc>Tcc	p.A387S	MSRB1_ENST00000564908.1_5'Flank|MSRB1_ENST00000361871.3_5'Flank|MSRB1_ENST00000399753.2_5'Flank	NM_005061.2	NP_005052.1	Q92901	RL3L_HUMAN	ribosomal protein L3-like	387					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|membrane (GO:0016020)|ribosome (GO:0005840)	RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	17						ACCATGAAGGCCCTCTTCTCT	0.597																																					p.A387S		Atlas-SNP	.											.	RPL3L	42	.	0			c.G1159T						PASS	.						55.0	46.0	50.0					16																	1995508		2199	4300	6499	SO:0001583	missense	6123	exon9			TGAAGGCCCTCTT	U65581	CCDS10450.1	16p13.3	2008-02-05			ENSG00000140986	ENSG00000140986		"""L ribosomal proteins"""	10351	protein-coding gene	gene with protein product						8921388	Standard	NM_005061		Approved		uc002cnh.3	Q92901	OTTHUMG00000128685	ENST00000268661.7:c.1159G>T	chr16.hg19:g.1995508C>A	ENSP00000268661:p.Ala387Ser	89.0	0.0	.		66.0	27.0	.	NM_005061		Missense_Mutation	SNP	ENST00000268661.7	hg19	CCDS10450.1	.	.	.	.	.	.	.	.	.	.	C	10.72	1.430672	0.25726	.	.	ENSG00000140986	ENST00000268661	T	0.32753	1.44	3.92	3.92	0.45320	.	0.259903	0.37178	N	0.002207	T	0.39384	0.1076	M	0.69248	2.105	0.50632	D	0.999888	P	0.44139	0.827	P	0.45856	0.495	T	0.40553	-0.9557	10	0.46703	T	0.11	-1.9802	15.4739	0.75461	0.0:1.0:0.0:0.0	.	387	Q92901	RL3L_HUMAN	S	387	ENSP00000268661:A387S	ENSP00000268661:A387S	A	-	1	0	RPL3L	1935509	1.000000	0.71417	0.999000	0.59377	0.185000	0.23345	4.700000	0.61803	2.185000	0.69588	0.563000	0.77884	GCC	.	.	.	none		0.597	RPL3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250582.2	NM_005061	
SCNN1B	6338	hgsc.bcm.edu	37	16	23360139	23360139	+	Silent	SNP	C	C	G			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr16:23360139C>G	ENST00000343070.2	+	2	395	c.219C>G	c.(217-219)acC>acG	p.T73T	SCNN1B_ENST00000568085.1_Silent_p.T73T|SCNN1B_ENST00000307331.5_Silent_p.T118T|SCNN1B_ENST00000569789.1_3'UTR|SCNN1B_ENST00000568923.1_Silent_p.T73T	NM_000336.2	NP_000327.2	P51168	SCNNB_HUMAN	sodium channel, non-voltage-gated 1, beta subunit	73					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|WW domain binding (GO:0050699)			breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	32				GBM - Glioblastoma multiforme(48;0.0465)	Amiloride(DB00594)|Triamterene(DB00384)	TCATCAGGACCTACTTGAGCT	0.587																																					p.T73T		Atlas-SNP	.											.	SCNN1B	81	.	0			c.C219G						PASS	.						84.0	69.0	74.0					16																	23360139		2197	4300	6497	SO:0001819	synonymous_variant	6338	exon2			CAGGACCTACTTG	X87159	CCDS10609.1	16p12.2-p12.1	2012-02-28	2012-02-28		ENSG00000168447	ENSG00000168447		"""Ion channels / Sodium channel, nonvoltage-gated"", ""Sodium channels"""	10600	protein-coding gene	gene with protein product	"""Liddle syndrome"""	600760	"""sodium channel, nonvoltage-gated 1, beta"", ""sodium channel, non-voltage-gated 1, beta"""				Standard	NM_000336		Approved	ENaCbeta	uc002dln.3	P51168	OTTHUMG00000131608	ENST00000343070.2:c.219C>G	chr16.hg19:g.23360139C>G		289.0	0.0	.		227.0	102.0	.	NM_000336	C5HTZ2|O60891|Q96KG2|Q9UJ32|Q9UMU5	Silent	SNP	ENST00000343070.2	hg19	CCDS10609.1																																																																																			.	.	.	none		0.587	SCNN1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254495.2		
MYLK3	91807	hgsc.bcm.edu	37	16	46781755	46781755	+	Missense_Mutation	SNP	C	C	A			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr16:46781755C>A	ENST00000394809.4	-	1	466	c.351G>T	c.(349-351)atG>atT	p.M117I	MYLK3_ENST00000536476.1_Intron	NM_182493.2	NP_872299.2	Q32MK0	MYLK3_HUMAN	myosin light chain kinase 3	117					cardiac myofibril assembly (GO:0055003)|cellular response to interleukin-1 (GO:0071347)|positive regulation of sarcomere organization (GO:0060298)|protein phosphorylation (GO:0006468)|regulation of vascular permeability involved in acute inflammatory response (GO:0002528)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|myosin light chain kinase activity (GO:0004687)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(3)|skin(5)|stomach(3)	37		all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				CCGCAGCCACCATCCTGAAGA	0.657																																					p.M117I		Atlas-SNP	.											.	MYLK3	82	.	0			c.G351T						PASS	.						45.0	40.0	42.0					16																	46781755		2203	4300	6503	SO:0001583	missense	91807	exon1			AGCCACCATCCTG	AJ247087	CCDS10723.2	16q11.2	2008-10-23			ENSG00000140795	ENSG00000140795			29826	protein-coding gene	gene with protein product	"""MLC kinase"""	612147				17885681	Standard	NM_182493		Approved	caMLCK, MLCK	uc002eei.4	Q32MK0	OTTHUMG00000132543	ENST00000394809.4:c.351G>T	chr16.hg19:g.46781755C>A	ENSP00000378288:p.Met117Ile	146.0	0.0	.		93.0	48.0	.	NM_182493	B5BUL9|B7Z5U8|Q32MK1|Q96DV1	Missense_Mutation	SNP	ENST00000394809.4	hg19	CCDS10723.2	.	.	.	.	.	.	.	.	.	.	C	14.42	2.530435	0.45073	.	.	ENSG00000140795	ENST00000394809	T	0.69435	-0.4	4.87	4.87	0.63330	.	0.000000	0.43260	D	0.000583	T	0.65101	0.2659	M	0.67953	2.075	0.80722	D	1	P	0.38922	0.651	B	0.33521	0.165	T	0.69942	-0.5008	10	0.46703	T	0.11	.	18.3666	0.90392	0.0:1.0:0.0:0.0	.	117	Q32MK0	MYLK3_HUMAN	I	117	ENSP00000378288:M117I	ENSP00000378288:M117I	M	-	3	0	MYLK3	45339256	1.000000	0.71417	1.000000	0.80357	0.273000	0.26683	2.195000	0.42677	2.394000	0.81467	0.491000	0.48974	ATG	.	.	.	none		0.657	MYLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255743.2	NM_182493	
EDC4	23644	hgsc.bcm.edu	37	16	67910858	67910858	+	Missense_Mutation	SNP	T	T	G			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr16:67910858T>G	ENST00000358933.5	+	4	673	c.434T>G	c.(433-435)tTg>tGg	p.L145W	EDC4_ENST00000574770.1_3'UTR|AC040162.1_ENST00000408599.1_RNA	NM_014329.4	NP_055144.3	Q6P2E9	EDC4_HUMAN	enhancer of mRNA decapping 4	145					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(4)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	41		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)		AACTCCTTCTTGGCCTATGCC	0.507																																					p.L145W		Atlas-SNP	.											.	EDC4	101	.	0			c.T434G						PASS	.						136.0	130.0	132.0					16																	67910858		2198	4300	6498	SO:0001583	missense	23644	exon4			CCTTCTTGGCCTA	U17474	CCDS10849.1	16q22.1	2008-02-05			ENSG00000038358	ENSG00000038358			17157	protein-coding gene	gene with protein product		606030				9067524	Standard	NM_014329		Approved	RCD-8, Ge-1, HEDLS	uc002eur.3	Q6P2E9	OTTHUMG00000137543	ENST00000358933.5:c.434T>G	chr16.hg19:g.67910858T>G	ENSP00000351811:p.Leu145Trp	173.0	0.0	.		123.0	50.0	.	NM_014329	A6NGM1|A8K4T4|Q13025|Q13826|Q6ZR12|Q7Z6H7	Missense_Mutation	SNP	ENST00000358933.5	hg19	CCDS10849.1	.	.	.	.	.	.	.	.	.	.	T	28.6	4.935710	0.92458	.	.	ENSG00000038358	ENST00000358933;ENST00000536072	T	0.42131	0.98	5.83	5.83	0.93111	WD40 repeat-like-containing domain (1);	0.081121	0.51477	D	0.000086	T	0.62901	0.2466	M	0.69823	2.125	0.58432	D	0.999996	D;D	0.71674	0.998;0.997	D;P	0.65140	0.932;0.903	T	0.66740	-0.5847	10	0.87932	D	0	-7.7554	15.8624	0.79035	0.0:0.0:0.0:1.0	.	77;145	B7Z7V8;Q6P2E9	.;EDC4_HUMAN	W	145;77	ENSP00000351811:L145W	ENSP00000351811:L145W	L	+	2	0	EDC4	66468359	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.997000	0.88414	2.235000	0.73313	0.533000	0.62120	TTG	.	.	.	none		0.507	EDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268874.2	NM_014329	
MYO15A	51168	hgsc.bcm.edu	37	17	18057182	18057182	+	Missense_Mutation	SNP	C	C	G			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr17:18057182C>G	ENST00000205890.5	+	43	8398	c.8060C>G	c.(8059-8061)gCc>gGc	p.A2687G	MYO15A_ENST00000585180.1_5'Flank|MYO15A_ENST00000418233.3_5'UTR	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	2687	Tail.				inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					TATCAGGACGCCCCCTGGAAG	0.657																																					p.A2687G		Atlas-SNP	.											.	MYO15A	268	.	0			c.C8060G						PASS	.						45.0	46.0	46.0					17																	18057182		1888	4114	6002	SO:0001583	missense	51168	exon42			AGGACGCCCCCTG	AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"""Myosins / Myosin superfamily : Class XV"""	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.8060C>G	chr17.hg19:g.18057182C>G	ENSP00000205890:p.Ala2687Gly	272.0	0.0	.		294.0	70.0	.	NM_016239	B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	hg19	CCDS42271.1	.	.	.	.	.	.	.	.	.	.	C	18.05	3.536404	0.65085	.	.	ENSG00000091536	ENST00000205890	D	0.88586	-2.4	5.07	2.79	0.32731	.	.	.	.	.	T	0.82263	0.4999	M	0.64997	1.995	0.80722	D	1	P	0.35433	0.501	B	0.27608	0.081	T	0.80400	-0.1398	9	0.87932	D	0	.	2.5033	0.04638	0.222:0.4596:0.0:0.3183	.	2687	Q9UKN7	MYO15_HUMAN	G	2687	ENSP00000205890:A2687G	ENSP00000205890:A2687G	A	+	2	0	MYO15A	17997907	1.000000	0.71417	0.800000	0.32199	0.904000	0.53231	2.694000	0.47035	1.107000	0.41642	0.563000	0.77884	GCC	.	.	.	none		0.657	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239	
ITGA2B	3674	hgsc.bcm.edu	37	17	42449792	42449792	+	Splice_Site	SNP	C	C	T			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr17:42449792C>T	ENST00000262407.5	-	30	3092		c.e30-1		ITGA2B_ENST00000353281.4_Splice_Site	NM_000419.3	NP_000410.2	P08514	ITA2B_HUMAN	integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41)						axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of leukocyte migration (GO:0002687)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)	extracellular matrix binding (GO:0050840)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			biliary_tract(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(8)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.191)	Abciximab(DB00054)|Tirofiban(DB00775)	AGAAGCCGACCTGGGGGTACA	0.577																																					.		Atlas-SNP	.											.	ITGA2B	88	.	0			c.3061-1G>A						PASS	.						58.0	44.0	49.0					17																	42449792		2203	4300	6503	SO:0001630	splice_region_variant	3674	exon31			GCCGACCTGGGGG		CCDS32665.1	17q21.32	2014-09-17	2006-02-22			ENSG00000005961		"""CD molecules"", ""Integrins"""	6138	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 93"""	607759	"""integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41B)"""	GP2B			Standard	NM_000419		Approved	CD41B, CD41, PPP1R93	uc002igt.1	P08514		ENST00000262407.5:c.3061-1G>A	chr17.hg19:g.42449792C>T		84.0	0.0	.		97.0	22.0	.	NM_000419	B2RCY8|O95366|Q14443|Q17R67	Splice_Site	SNP	ENST00000262407.5	hg19	CCDS32665.1	.	.	.	.	.	.	.	.	.	.	C	17.11	3.306424	0.60305	.	.	ENSG00000005961	ENST00000262407;ENST00000353281	.	.	.	4.54	4.54	0.55810	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8074	0.69968	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ITGA2B	39805318	0.993000	0.37304	0.275000	0.24674	0.303000	0.27691	4.088000	0.57678	2.357000	0.79964	0.561000	0.74099	.	.	.	.	none		0.577	ITGA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439823.1		Intron
C17orf104	284071	hgsc.bcm.edu	37	17	42744196	42744196	+	Missense_Mutation	SNP	A	A	T			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr17:42744196A>T	ENST00000409122.2	+	5	1059	c.917A>T	c.(916-918)cAa>cTa	p.Q306L	C17orf104_ENST00000359945.3_Missense_Mutation_p.Q306L|C17orf104_ENST00000409464.1_Missense_Mutation_p.Q140L	NM_001145080.2	NP_001138552.2	A2RUB1	CQ104_HUMAN	chromosome 17 open reading frame 104	306										autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|pancreas(1)|skin(1)	24						CCACTACAGCAAAAAAGGGCA	0.348																																					p.Q306L		Atlas-SNP	.											.	C17orf104	75	.	0			c.A917T						PASS	.						27.0	28.0	28.0					17																	42744196		2202	4298	6500	SO:0001583	missense	284071	exon5			TACAGCAAAAAAG		CCDS45703.1, CCDS45703.2	17q21.31	2009-09-08			ENSG00000180336	ENSG00000180336			26670	protein-coding gene	gene with protein product							Standard	NM_001145080		Approved	FLJ35848	uc002iha.3	A2RUB1	OTTHUMG00000153039	ENST00000409122.2:c.917A>T	chr17.hg19:g.42744196A>T	ENSP00000386452:p.Gln306Leu	43.0	0.0	.		40.0	14.0	.	NM_001145080	B4DXJ2|B5MD93|B9EGQ6|C4AM97|Q4G0Y1|Q8IVZ7|Q8NA45	Missense_Mutation	SNP	ENST00000409122.2	hg19	CCDS45703.2	.	.	.	.	.	.	.	.	.	.	A	1.742	-0.491410	0.04322	.	.	ENSG00000180336	ENST00000359945;ENST00000409122;ENST00000432494;ENST00000409464	T;T;T;T	0.35421	1.31;1.31;1.37;1.31	5.45	4.38	0.52667	.	0.063895	0.64402	D	0.000008	T	0.25975	0.0633	N	0.24115	0.695	0.24874	N	0.992265	B;B;B	0.31548	0.328;0.161;0.161	B;B;B	0.35413	0.202;0.202;0.202	T	0.19257	-1.0311	10	0.59425	D	0.04	-14.3041	8.5529	0.33462	0.8008:0.1303:0.0689:0.0	.	306;306;140	A2RUB1-5;A2RUB1;A2RUB1-1	.;CQ104_HUMAN;.	L	306;306;140;140	ENSP00000353028:Q306L;ENSP00000386452:Q306L;ENSP00000399809:Q140L;ENSP00000386586:Q140L	ENSP00000353028:Q306L	Q	+	2	0	C17orf104	40099722	1.000000	0.71417	0.998000	0.56505	0.014000	0.08584	4.646000	0.61411	1.017000	0.39495	-0.388000	0.06559	CAA	.	.	.	none		0.348	C17orf104-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329171.2	NM_001145080	
SPAG9	9043	hgsc.bcm.edu	37	17	49067112	49067112	+	Silent	SNP	G	G	T			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr17:49067112G>T	ENST00000262013.7	-	21	2947	c.2739C>A	c.(2737-2739)gtC>gtA	p.V913V	SPAG9_ENST00000505279.1_Silent_p.V903V|SPAG9_ENST00000357122.4_Silent_p.V899V|SPAG9_ENST00000510283.1_Silent_p.V756V	NM_001130528.2	NP_001124000.1	O60271	JIP4_HUMAN	sperm associated antigen 9	913					activation of JUN kinase activity (GO:0007257)|muscle cell differentiation (GO:0042692)|negative regulation of protein homodimerization activity (GO:0090074)|positive regulation of cell migration (GO:0030335)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron differentiation (GO:0045666)|protein homooligomerization (GO:0051260)|retrograde transport, endosome to Golgi (GO:0042147)|spermatogenesis (GO:0007283)|striated muscle cell differentiation (GO:0051146)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)				NS(1)|breast(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)			GCTCTGTGTAGACGCCAGTTT	0.473																																					p.V913V		Atlas-SNP	.											.	SPAG9	151	.	0			c.C2739A						PASS	.						165.0	133.0	144.0					17																	49067112		2203	4300	6503	SO:0001819	synonymous_variant	9043	exon21			TGTGTAGACGCCA	AB011088	CCDS11577.1, CCDS45740.1, CCDS58577.1, CCDS58578.1	17q21.33	2013-09-23			ENSG00000008294	ENSG00000008294			14524	protein-coding gene	gene with protein product	"""sperm surface protein"", ""JNK/SAPK-associated protein"", ""JNK interacting protein"", ""sperm specific protein"", ""c-Jun NH2-terminal kinase-associated leucine zipper protein"", ""Max-binding protein"", ""JNK-associated leucine-zipper protein"", ""HLC-4 protein"", ""lung cancer oncogene 4"", ""proliferation-inducing gene 6"", ""cancer/testis antigen 89"""	605430				9480848, 11106729	Standard	NM_003971		Approved	HSS, SYD1, KIAA0516, MGC14967, MGC74461, MGC117291, JLP, PHET, HLC4, PIG6, FLJ13450, FLJ14006, FLJ26141, FLJ34602, CT89	uc002itc.3	O60271	OTTHUMG00000162316	ENST00000262013.7:c.2739C>A	chr17.hg19:g.49067112G>T		221.0	0.0	.		259.0	56.0	.	NM_001130528	A6H8U5|A8MSX0|B4DHH2|O60905|Q3KQU8|Q3MKM7|Q86WC7|Q86WC8|Q8IZX7|Q96II0|Q9H811	Silent	SNP	ENST00000262013.7	hg19	CCDS45740.1	.	.	.	.	.	.	.	.	.	.	G	9.197	1.027489	0.19512	.	.	ENSG00000008294	ENST00000513906	.	.	.	5.77	0.0229	0.14135	.	.	.	.	.	T	0.41627	0.1167	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.24548	-1.0157	4	.	.	.	-12.8707	1.4604	0.02394	0.2848:0.2293:0.3304:0.1555	.	.	.	.	Y	157	.	.	S	-	2	0	SPAG9	46422111	0.969000	0.33509	0.999000	0.59377	0.960000	0.62799	0.071000	0.14594	0.094000	0.17404	-1.467000	0.01014	TCT	.	.	.	none		0.473	SPAG9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368543.2	NM_003971	
METTL23	124512	hgsc.bcm.edu	37	17	74729098	74729098	+	Silent	SNP	C	C	A			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr17:74729098C>A	ENST00000341249.6	+	3	455	c.123C>A	c.(121-123)gcC>gcA	p.A41A	METTL23_ENST00000588822.1_5'UTR|MFSD11_ENST00000586622.1_5'Flank|METTL23_ENST00000590964.1_5'UTR|METTL23_ENST00000588302.1_5'UTR|RP11-318A15.7_ENST00000587459.1_Silent_p.A13A|METTL23_ENST00000586752.1_5'UTR|METTL23_ENST00000586200.1_Intron|METTL23_ENST00000588783.1_Silent_p.A41A|METTL23_ENST00000591571.1_5'UTR|METTL23_ENST00000586738.1_Silent_p.A41A|METTL23_ENST00000589977.1_Silent_p.A41A	NM_001206984.1	NP_001193913.1	Q86XA0	MET23_HUMAN	methyltransferase like 23	41						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	methyltransferase activity (GO:0008168)			large_intestine(2)|lung(1)	3						TTTTGGCTGCCAAATGTGGTG	0.438																																					p.A41A		Atlas-SNP	.											.	METTL23	19	.	0			c.C123A						PASS	.						26.0	24.0	25.0					17																	74729098		1915	4132	6047	SO:0001819	synonymous_variant	124512	exon3			GGCTGCCAAATGT		CCDS45787.1, CCDS59298.1	17q25.2	2011-03-03	2011-03-03	2011-03-03	ENSG00000181038	ENSG00000181038			26988	protein-coding gene	gene with protein product		615262	"""chromosome 17 open reading frame 95"""	C17orf95		12477932	Standard	NM_001080510		Approved	LOC124512	uc021udl.1	Q86XA0		ENST00000341249.6:c.123C>A	chr17.hg19:g.74729098C>A		74.0	0.0	.		80.0	13.0	.	NM_001206984	H9ZYJ0|K7EK32	Silent	SNP	ENST00000341249.6	hg19	CCDS45787.1																																																																																			.	.	.	none		0.438	METTL23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451002.1	NM_001080510	
AATK	9625	hgsc.bcm.edu	37	17	79095314	79095314	+	Missense_Mutation	SNP	G	G	T			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr17:79095314G>T	ENST00000326724.4	-	11	2446	c.2422C>A	c.(2422-2424)Cca>Aca	p.P808T	AATK_ENST00000417379.1_Missense_Mutation_p.P705T	NM_001080395.2	NP_001073864.2	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase	808	Pro-rich.				brain development (GO:0007420)|negative regulation of axon extension (GO:0030517)|neuron apoptotic process (GO:0051402)|peptidyl-tyrosine autophosphorylation (GO:0038083)|Rab protein signal transduction (GO:0032482)	axonal growth cone (GO:0044295)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			endometrium(2)|kidney(2)|lung(8)|ovary(3)|prostate(1)|stomach(4)|upper_aerodigestive_tract(1)	21	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			GAGGGAAGTGGGGCTCCCTCC	0.701																																					p.P808T		Atlas-SNP	.											.	AATK	102	.	0			c.C2422A						PASS	.						16.0	21.0	19.0					17																	79095314		2062	4182	6244	SO:0001583	missense	9625	exon11			GAAGTGGGGCTCC	AB014541	CCDS45807.1, CCDS58607.1	17q25.3	2014-06-12			ENSG00000181409	ENSG00000181409			21	protein-coding gene	gene with protein product	"""lemur tyrosine kinase 1"", ""protein phosphatase 1, regulatory subunit 77"""	605276				9734811, 10083745	Standard	NM_001080395		Approved	AATYK, KIAA0641, LMTK1, LMR1, AATYK1, PPP1R77	uc010dia.3	Q6ZMQ8	OTTHUMG00000132717	ENST00000326724.4:c.2422C>A	chr17.hg19:g.79095314G>T	ENSP00000324196:p.Pro808Thr	69.0	0.0	.		60.0	15.0	.	NM_001080395	O75136|Q6ZN31|Q86X28	Missense_Mutation	SNP	ENST00000326724.4	hg19	CCDS45807.1	.	.	.	.	.	.	.	.	.	.	G	7.050	0.564179	0.13498	.	.	ENSG00000181409	ENST00000326724;ENST00000374792	T;T	0.78246	-1.06;-1.16	4.36	2.21	0.28008	.	0.938651	0.08819	U	0.889000	T	0.66366	0.2782	L	0.43152	1.355	0.19575	N	0.999966	B	0.15141	0.012	B	0.09377	0.004	T	0.50276	-0.8847	10	0.22706	T	0.39	.	5.0003	0.14261	0.1085:0.0:0.552:0.3395	.	808	Q6ZMQ8	LMTK1_HUMAN	T	808;772	ENSP00000324196:P808T;ENSP00000363924:P772T	ENSP00000324196:P808T	P	-	1	0	AATK	76709909	0.000000	0.05858	0.647000	0.29507	0.154000	0.21943	0.726000	0.25984	0.801000	0.34066	0.561000	0.74099	CCA	.	.	.	none		0.701	AATK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256055.1	NM_004920	
MALT1	10892	hgsc.bcm.edu	37	18	56400802	56400802	+	Missense_Mutation	SNP	A	A	G			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr18:56400802A>G	ENST00000348428.3	+	11	1654	c.1396A>G	c.(1396-1398)Aaa>Gaa	p.K466E	MALT1_ENST00000345724.3_Missense_Mutation_p.K455E|RP11-126O1.4_ENST00000588835.1_RNA	NM_006785.2|NM_173844.1	NP_006776.1|NP_776216.1	Q9UDY8	MALT1_HUMAN	mucosa associated lymphoid tissue lymphoma translocation gene 1	466	Caspase-like.				activation of NF-kappaB-inducing kinase activity (GO:0007250)|B-1 B cell differentiation (GO:0001923)|defense response (GO:0006952)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|nuclear export (GO:0051168)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|protein oligomerization (GO:0051259)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of T cell receptor signaling pathway (GO:0050856)|response to fungus (GO:0009620)|response to molecule of bacterial origin (GO:0002237)|T cell proliferation (GO:0042098)|T cell receptor signaling pathway (GO:0050852)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	cysteine-type endopeptidase activity (GO:0004197)|peptidase activity (GO:0008233)|protein self-association (GO:0043621)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(1)|large_intestine(7)|lung(1)|ovary(2)|skin(1)	12						TATGTGTAGGAAAAGGTAAGT	0.313			T	BIRC3	MALT																																p.K466E		Atlas-SNP	.		Dom	yes		18	18q21	10892	mucosa associated lymphoid tissue lymphoma translocation gene 1		L	.	MALT1	55	.	0			c.A1396G						PASS	.						59.0	66.0	64.0					18																	56400802		2203	4299	6502	SO:0001583	missense	10892	exon11			TGTAGGAAAAGGT		CCDS11967.1, CCDS11968.1	18q21	2013-01-11			ENSG00000172175	ENSG00000172175		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6819	protein-coding gene	gene with protein product	"""paracaspase"""	604860		MLT		10339464, 10406266, 10523859	Standard	NM_006785		Approved		uc002lhm.1	Q9UDY8	OTTHUMG00000132761	ENST00000348428.3:c.1396A>G	chr18.hg19:g.56400802A>G	ENSP00000319279:p.Lys466Glu	59.0	0.0	.		66.0	5.0	.	NM_006785	Q9NTB7|Q9ULX4	Missense_Mutation	SNP	ENST00000348428.3	hg19	CCDS11967.1	.	.	.	.	.	.	.	.	.	.	A	25.1	4.599615	0.87055	.	.	ENSG00000172175	ENST00000348428;ENST00000345724	T;T	0.41400	1.0;1.0	5.52	5.52	0.82312	Peptidase C14, caspase catalytic (1);	0.000000	0.85682	D	0.000000	T	0.63390	0.2507	M	0.65975	2.015	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	T	0.66767	-0.5840	10	0.72032	D	0.01	.	15.304	0.73979	1.0:0.0:0.0:0.0	.	455;466	Q9UDY8-2;Q9UDY8	.;MALT1_HUMAN	E	466;455	ENSP00000319279:K466E;ENSP00000304161:K455E	ENSP00000304161:K455E	K	+	1	0	MALT1	54551782	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.153000	0.77428	2.106000	0.64143	0.528000	0.53228	AAA	.	.	.	none		0.313	MALT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256132.2		
ZNF799	90576	hgsc.bcm.edu	37	19	12502161	12502161	+	Missense_Mutation	SNP	A	A	T	rs541416821		TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr19:12502161A>T	ENST00000430385.3	-	4	1251	c.1051T>A	c.(1051-1053)Tca>Aca	p.S351T	CTD-3105H18.14_ENST00000435033.1_Intron|ZNF799_ENST00000419318.1_Missense_Mutation_p.S319T	NM_001080821.2	NP_001074290.1	Q96GE5	ZN799_HUMAN	zinc finger protein 799	351					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S351T(1)|p.S138T(1)		breast(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|prostate(2)|skin(2)	19						CTTTTCAGTGAACTAGGACAA	0.413																																					p.S351T		Atlas-SNP	.											ZNF799_ENST00000430385,NS,carcinoma,0,2	ZNF799	111	.	2	Substitution - Missense(2)	kidney(2)	c.T1051A						PASS	.						161.0	157.0	158.0					19																	12502161		2203	4300	6503	SO:0001583	missense	90576	exon4			TCAGTGAACTAGG	BC009517	CCDS45989.1	19p13.2	2013-01-08			ENSG00000196466	ENSG00000196466		"""Zinc fingers, C2H2-type"", ""-"""	28071	protein-coding gene	gene with protein product			"""zinc finger protein 842"""	ZNF842			Standard	NM_001080821		Approved	HIT-40, MGC71805	uc002mts.4	Q96GE5	OTTHUMG00000156408	ENST00000430385.3:c.1051T>A	chr19.hg19:g.12502161A>T	ENSP00000411084:p.Ser351Thr	100.0	1.0	.		81.0	5.0	.	NM_001080821		Missense_Mutation	SNP	ENST00000430385.3	hg19	CCDS45989.1	.	.	.	.	.	.	.	.	.	.	A	11.22	1.574140	0.28092	.	.	ENSG00000196466	ENST00000419318;ENST00000430385	T;T	0.07567	3.18;3.18	1.31	1.31	0.21738	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09949	0.0244	N	0.16478	0.41	0.09310	N	1	D	0.60575	0.988	P	0.60173	0.87	T	0.34378	-0.9831	9	0.30078	T	0.28	.	6.6913	0.23174	1.0:0.0:0.0:0.0	.	351	Q96GE5	ZN799_HUMAN	T	319;351	ENSP00000415278:S319T;ENSP00000411084:S351T	ENSP00000415278:S319T	S	-	1	0	ZNF799	12363161	0.000000	0.05858	0.005000	0.12908	0.140000	0.21249	0.679000	0.25291	0.846000	0.35142	0.352000	0.21897	TCA	.	.	.	none		0.413	ZNF799-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344099.2	NM_001080821	
SYDE1	85360	hgsc.bcm.edu	37	19	15220001	15220001	+	Missense_Mutation	SNP	A	A	T			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr19:15220001A>T	ENST00000342784.2	+	2	254	c.223A>T	c.(223-225)Agc>Tgc	p.S75C	SYDE1_ENST00000600252.1_5'UTR|SYDE1_ENST00000600440.1_Intron	NM_033025.4	NP_149014.3	Q6ZW31	SYDE1_HUMAN	synapse defective 1, Rho GTPase, homolog 1 (C. elegans)	75	Pro-rich.				activation of Rho GTPase activity (GO:0032862)|positive regulation of synaptic transmission (GO:0050806)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptonemal complex assembly (GO:0007130)	cerebellar mossy fiber (GO:0044300)|cytosol (GO:0005829)|synaptic membrane (GO:0097060)	Rho GTPase activator activity (GO:0005100)			endometrium(4)|kidney(1)|large_intestine(7)|lung(2)|ovary(1)|pancreas(1)|skin(1)	17						CTACCTGCAAAGCCTGGAGCC	0.706																																					p.S75C		Atlas-SNP	.											.	SYDE1	44	.	0			c.A223T						PASS	.						13.0	13.0	13.0					19																	15220001		2148	4200	6348	SO:0001583	missense	85360	exon2			CTGCAAAGCCTGG	BC029926	CCDS12324.1, CCDS74299.1	19p13.12	2008-02-05				ENSG00000105137			25824	protein-coding gene	gene with protein product						12477932	Standard	XM_005260126		Approved	7h3, FLJ13511	uc002nah.1	Q6ZW31		ENST00000342784.2:c.223A>T	chr19.hg19:g.15220001A>T	ENSP00000341489:p.Ser75Cys	51.0	0.0	.		37.0	13.0	.	NM_033025	Q7L2I8|Q8N6J2|Q9H8K4	Missense_Mutation	SNP	ENST00000342784.2	hg19	CCDS12324.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.951011	0.73787	.	.	ENSG00000105137	ENST00000342784	T	0.13778	2.56	4.32	4.32	0.51571	.	0.000000	0.85682	D	0.000000	T	0.26484	0.0647	L	0.47716	1.5	0.27009	N	0.964736	D	0.76494	0.999	D	0.80764	0.994	T	0.02781	-1.1111	10	0.87932	D	0	.	8.0008	0.30295	0.7926:0.2074:0.0:0.0	.	75	Q6ZW31	SYDE1_HUMAN	C	75	ENSP00000341489:S75C	ENSP00000341489:S75C	S	+	1	0	SYDE1	15081001	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	4.770000	0.62309	1.598000	0.50083	0.533000	0.62120	AGC	.	.	.	none		0.706	SYDE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465666.1	NM_033025	
WDR87	83889	hgsc.bcm.edu	37	19	38385244	38385244	+	Missense_Mutation	SNP	G	G	T			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr19:38385244G>T	ENST00000303868.5	-	4	1206	c.982C>A	c.(982-984)Cag>Aag	p.Q328K	WDR87_ENST00000447313.2_Missense_Mutation_p.Q367K	NM_031951.3	NP_114157.3	Q6ZQQ6	WDR87_HUMAN	WD repeat domain 87	328										NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|prostate(1)|skin(3)|stomach(1)	36						CGACGCAACTGCTGGGGAGCA	0.532																																					p.Q328K		Atlas-SNP	.											.	WDR87	191	.	0			c.C982A						PASS	.						40.0	44.0	43.0					19																	38385244		692	1591	2283	SO:0001583	missense	83889	exon4			GCAACTGCTGGGG	AK128826	CCDS46063.1, CCDS74356.1	19q13.13	2013-01-09			ENSG00000171804	ENSG00000171804		"""WD repeat domain containing"""	29934	protein-coding gene	gene with protein product							Standard	XM_005259304		Approved	NYD-SP11	uc010efu.2	Q6ZQQ6	OTTHUMG00000048187	ENST00000303868.5:c.982C>A	chr19.hg19:g.38385244G>T	ENSP00000368025:p.Gln328Lys	332.0	0.0	.		285.0	26.0	.	NM_031951	Q9BWV9	Missense_Mutation	SNP	ENST00000303868.5	hg19	CCDS46063.1	.	.	.	.	.	.	.	.	.	.	G	9.397	1.077065	0.20227	.	.	ENSG00000171804	ENST00000447313;ENST00000303868	T;T	0.08807	3.05;3.61	6.06	2.62	0.31277	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.250921	0.28659	N	0.014578	T	0.05593	0.0147	L	0.48642	1.525	0.09310	N	1	P;P	0.39480	0.675;0.675	B;B	0.31442	0.13;0.13	T	0.32771	-0.9894	10	0.23302	T	0.38	-11.2696	5.4761	0.16695	0.0794:0.1424:0.6311:0.1472	.	328;367	Q6ZQQ6;E7ESW6	WDR87_HUMAN;.	K	367;328	ENSP00000405012:Q367K;ENSP00000368025:Q328K	ENSP00000368025:Q328K	Q	-	1	0	WDR87	43077084	0.045000	0.20229	0.992000	0.48379	0.739000	0.42172	0.957000	0.29215	1.562000	0.49601	0.643000	0.83706	CAG	.	.	.	none		0.532	WDR87-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314628.2	XM_940478	
PLTP	5360	hgsc.bcm.edu	37	20	44539886	44539886	+	Silent	SNP	C	C	T			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr20:44539886C>T	ENST00000477313.1	-	2	699	c.105G>A	c.(103-105)aaG>aaA	p.K35K	PLTP_ENST00000372420.1_5'Flank|PLTP_ENST00000354050.4_Silent_p.K35K|PLTP_ENST00000542937.1_Silent_p.K55K|PLTP_ENST00000372431.3_Silent_p.K35K|PLTP_ENST00000420868.2_Silent_p.K35K			P55058	PLTP_HUMAN	phospholipid transfer protein	35					lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|sperm motility (GO:0030317)|vitamin E biosynthetic process (GO:0010189)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	lipid binding (GO:0008289)			endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)	21		Myeloproliferative disorder(115;0.0122)				GCCCCTCCTGCTTCACTGAAG	0.602																																					p.K35K		Atlas-SNP	.											.	PLTP	49	.	0			c.G105A						PASS	.						70.0	71.0	71.0					20																	44539886		2203	4300	6503	SO:0001819	synonymous_variant	5360	exon3			CTCCTGCTTCACT	L26232	CCDS13386.1, CCDS13387.1, CCDS56196.1, CCDS56197.1	20q13.12	2011-08-16			ENSG00000100979	ENSG00000100979		"""BPI fold containing"""	9093	protein-coding gene	gene with protein product	"""BPI fold containing family E"""	172425					Standard	NM_006227		Approved	BPIFE	uc002xqn.2	P55058	OTTHUMG00000033047	ENST00000477313.1:c.105G>A	chr20.hg19:g.44539886C>T		124.0	0.0	.		91.0	32.0	.	NM_182676	A8K006|B4DDD5|B4DRB4|E1P5N8|E7EV16|Q8WTT1|Q9BR07|Q9BSH8	Silent	SNP	ENST00000477313.1	hg19	CCDS13386.1																																																																																			.	.	.	none		0.602	PLTP-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354633.1	NM_006227	
SAMSN1	64092	hgsc.bcm.edu	37	21	15889252	15889252	+	Missense_Mutation	SNP	T	T	A			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr21:15889252T>A	ENST00000400566.1	-	3	321	c.240A>T	c.(238-240)aaA>aaT	p.K80N	SAMSN1_ENST00000285670.2_Missense_Mutation_p.K148N|SAMSN1_ENST00000400564.1_Intron	NM_022136.4	NP_071419.3	Q9NSI8	SAMN1_HUMAN	SAM domain, SH3 domain and nuclear localization signals 1	80					negative regulation of adaptive immune response (GO:0002820)|negative regulation of B cell activation (GO:0050869)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)	cell projection (GO:0042995)|cytosol (GO:0005829)|nucleus (GO:0005634)	phosphotyrosine binding (GO:0001784)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	24				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.00118)|Colorectal(24;0.00961)|Lung(58;0.164)		TTTTACCCACTTTTTTCTTCA	0.328																																					p.K148N		Atlas-SNP	.											.	SAMSN1	112	.	0			c.A444T						PASS	.						124.0	109.0	114.0					21																	15889252		1797	4068	5865	SO:0001583	missense	64092	exon4			ACCCACTTTTTTC	AF222927	CCDS42906.1, CCDS58786.1, CCDS74774.1	21q11	2013-01-10	2006-12-13		ENSG00000155307	ENSG00000155307		"""SAM and SH3 domain containing"", ""Sterile alpha motif (SAM) domain containing"""	10528	protein-coding gene	gene with protein product	"""nuclear localization signals, SAM and SH3 domain containing 1"", ""SAM and SH3 domain containing 2"", ""hematopoietic adapter-containing SH3 and sterile &#945;-motif (SAM) domains 1"", ""Src homology domain 3 (SH3)-containing adapter protein SH3 lymphocyte protein 2"""	607978				11536050, 11594764	Standard	NM_022136		Approved	NASH1, SASH2, SH3D6B, HACS1, SLy2	uc002yjv.1	Q9NSI8	OTTHUMG00000074317	ENST00000400566.1:c.240A>T	chr21.hg19:g.15889252T>A	ENSP00000383411:p.Lys80Asn	47.0	0.0	.		51.0	21.0	.	NM_001256370	B3KWJ3|F8WAA1|Q8NFF7|Q9C041	Missense_Mutation	SNP	ENST00000400566.1	hg19	CCDS42906.1	.	.	.	.	.	.	.	.	.	.	T	14.39	2.520541	0.44866	.	.	ENSG00000155307	ENST00000285670;ENST00000400566	T;T	0.57752	0.38;0.38	5.35	5.35	0.76521	.	0.100854	0.64402	D	0.000003	T	0.66076	0.2753	M	0.83953	2.67	0.43750	D	0.996253	D;D	0.56746	0.977;0.962	P;P	0.55923	0.787;0.688	T	0.71500	-0.4574	10	0.87932	D	0	-16.1663	7.6865	0.28544	0.0:0.1638:0.0:0.8362	.	148;80	F8WAA1;Q9NSI8	.;SAMN1_HUMAN	N	148;80	ENSP00000285670:K148N;ENSP00000383411:K80N	ENSP00000285670:K148N	K	-	3	2	SAMSN1	14811123	1.000000	0.71417	0.880000	0.34516	0.214000	0.24535	2.251000	0.43187	2.033000	0.60031	0.533000	0.62120	AAA	.	.	.	none		0.328	SAMSN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157914.1		
TRPM2	7226	hgsc.bcm.edu	37	21	45825794	45825794	+	Silent	SNP	C	C	T			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr21:45825794C>T	ENST00000397928.1	+	18	3109	c.2664C>T	c.(2662-2664)atC>atT	p.I888I	TRPM2_ENST00000300482.5_Silent_p.I888I|TRPM2_ENST00000300481.9_Silent_p.I868I|TRPM2_ENST00000498430.1_3'UTR|TRPM2_ENST00000397932.2_Silent_p.I888I	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	888					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|response to hydroperoxide (GO:0033194)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ADP-ribose diphosphatase activity (GO:0047631)|calcium channel activity (GO:0005262)|manganese ion transmembrane transporter activity (GO:0005384)|sodium channel activity (GO:0005272)			breast(3)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(15)|lung(29)|ovary(3)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	76						CCAGGCTCATCCCGGCGACGC	0.642																																					p.I888I		Atlas-SNP	.											.	TRPM2	196	.	0			c.C2664T						PASS	.						67.0	71.0	70.0					21																	45825794		2203	4297	6500	SO:0001819	synonymous_variant	7226	exon18			GCTCATCCCGGCG	AB001535	CCDS13710.1	21q22.3	2011-12-14		2002-01-18	ENSG00000142185	ENSG00000142185		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Nudix motif containing"""	12339	protein-coding gene	gene with protein product		603749		TRPC7		9806837, 11385575, 16382100	Standard	NR_038257		Approved	KNP3, LTRPC2, NUDT9L1, NUDT9H, EREG1	uc002zew.1	O94759	OTTHUMG00000040840	ENST00000397928.1:c.2664C>T	chr21.hg19:g.45825794C>T		18.0	0.0	.		19.0	10.0	.	NM_003307	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Silent	SNP	ENST00000397928.1	hg19	CCDS13710.1																																																																																			.	.	.	none		0.642	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307	
ADORA2A	135	hgsc.bcm.edu	37	22	24836558	24836558	+	Missense_Mutation	SNP	G	G	T			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr22:24836558G>T	ENST00000337539.7	+	3	799	c.340G>T	c.(340-342)Ggc>Tgc	p.G114C	ADORA2A-AS1_ENST00000427813.2_RNA|SPECC1L-ADORA2A_ENST00000358654.2_3'UTR|ADORA2A-AS1_ENST00000543438.1_RNA|ADORA2A-AS1_ENST00000326341.4_RNA|ADORA2A_ENST00000496497.1_3'UTR	NM_000675.4|NM_001278497.1|NM_001278498.1|NM_001278499.1|NM_001278500.1	NP_000666.2|NP_001265426.1|NP_001265427.1|NP_001265428.1|NP_001265429.1	P29274	AA2AR_HUMAN	adenosine A2a receptor	114					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|apoptotic process (GO:0006915)|blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cAMP biosynthetic process (GO:0006171)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|central nervous system development (GO:0007417)|inflammatory response (GO:0006954)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phagocytosis (GO:0006909)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|sensory perception (GO:0007600)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|G-protein coupled adenosine receptor activity (GO:0001609)|identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(1)|lung(7)|skin(1)	21	Colorectal(2;0.196)				Adenosine(DB00640)|Caffeine(DB00201)|Defibrotide(DB04932)|Dyphylline(DB00651)|Enprofylline(DB00824)|Mefloquine(DB00358)|Oxtriphylline(DB01303)|Pentoxifylline(DB00806)|Regadenoson(DB06213)|Theobromine(DB01412)|Theophylline(DB00277)	CAGGTACAATGGCTTGGTGAC	0.567																																					p.G114C		Atlas-SNP	.											.	ADORA2A	44	.	0			c.G340T						PASS	.						107.0	101.0	103.0					22																	24836558		2203	4300	6503	SO:0001583	missense	135	exon3			TACAATGGCTTGG	X68486	CCDS13826.1	22q11.23	2012-08-08			ENSG00000128271	ENSG00000128271		"""GPCR / Class A : Adenosine receptors"""	263	protein-coding gene	gene with protein product		102776		ADORA2		1662665, 2541503	Standard	NM_001278497		Approved	RDC8	uc002zzy.4	P29274	OTTHUMG00000150761	ENST00000337539.7:c.340G>T	chr22.hg19:g.24836558G>T	ENSP00000336630:p.Gly114Cys	155.0	0.0	.		129.0	50.0	.	NM_000675	B2R7E0	Missense_Mutation	SNP	ENST00000337539.7	hg19	CCDS13826.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.71|15.71	2.914051|2.914051	0.52546|0.52546	.|.	.|.	ENSG00000128271|ENSG00000258555	ENST00000444262;ENST00000541988;ENST00000337539;ENST00000417596|ENST00000493440	T;T|.	0.20332|.	2.08;2.08|.	4.97|4.97	3.95|3.95	0.45737|0.45737	GPCR, rhodopsin-like superfamily (1);|.	0.205313|.	0.49305|.	D|.	0.000152|.	T|T	0.56217|0.56217	0.1970|0.1970	L|L	0.45470|0.45470	1.425|1.425	0.43814|0.43814	D|D	0.996375|0.996375	D|.	0.65815|.	0.995|.	P|.	0.62014|.	0.897|.	T|T	0.51872|0.51872	-0.8650|-0.8650	10|5	0.59425|.	D|.	0.04|.	-27.3119|-27.3119	9.0177|9.0177	0.36179|0.36179	0.1684:0.0:0.8316:0.0|0.1684:0.0:0.8316:0.0	.|.	114|.	P29274|.	AA2AR_HUMAN|.	C|I	114|46	ENSP00000414802:G114C;ENSP00000336630:G114C|.	ENSP00000336630:G114C|.	G|M	+|+	1|3	0|0	ADORA2A|KB-1896H10.1	23166558|23166558	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.973000|0.973000	0.67179|0.67179	3.477000|3.477000	0.53151|0.53151	1.213000|1.213000	0.43380|0.43380	0.563000|0.563000	0.77884|0.77884	GGC|ATG	.	.	.	none		0.567	ADORA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319971.2	NM_000675	
SMC1A	8243	hgsc.bcm.edu	37	X	53440302	53440302	+	Silent	SNP	C	C	G			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chrX:53440302C>G	ENST00000322213.4	-	4	622	c.495G>C	c.(493-495)gcG>gcC	p.A165A	SMC1A_ENST00000375340.6_Intron	NM_006306.2	NP_006297.2	Q14683	SMC1A_HUMAN	structural maintenance of chromosomes 1A	165					DNA repair (GO:0006281)|gene expression (GO:0010467)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic sister chromatid cohesion (GO:0007064)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle organization (GO:0007052)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of DNA endoreduplication (GO:0032876)|response to radiation (GO:0009314)|RNA splicing (GO:0008380)|signal transduction in response to DNA damage (GO:0042770)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin core heterodimer (GO:0008280)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|meiotic cohesin complex (GO:0030893)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)	p.A165A(1)		NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(8)|ovary(5)|upper_aerodigestive_tract(2)	49						CATACTCCTGCGCCAGCTCCC	0.463																																					p.A165A		Atlas-SNP	.											.	SMC1A	112	.	1	Substitution - coding silent(1)	lung(1)	c.G495C						PASS	.						138.0	124.0	129.0					X																	53440302		2203	4300	6503	SO:0001819	synonymous_variant	8243	exon4			CTCCTGCGCCAGC	S78271	CCDS14352.1, CCDS75985.1	Xp11.22-p11.21	2014-09-17	2006-07-06	2006-07-06	ENSG00000072501	ENSG00000072501		"""Structural maintenance of chromosomes proteins"""	11111	protein-coding gene	gene with protein product		300040	"""SMC1 (structural maintenance of chromosomes 1, yeast)-like 1"", ""SMC1 structural maintenance of chromosomes 1-like 1 (yeast)"""	SMC1L1		7757074	Standard	NM_006306		Approved	DXS423E, KIAA0178, SB1.8, Smcb	uc004dsg.3	Q14683	OTTHUMG00000021614	ENST00000322213.4:c.495G>C	chrX.hg19:g.53440302C>G		102.0	0.0	.		50.0	40.0	.	NM_006306	O14995|Q16351|Q2M228	Silent	SNP	ENST00000322213.4	hg19	CCDS14352.1	.	.	.	.	.	.	.	.	.	.	C	5.699	0.313435	0.10789	.	.	ENSG00000072501	ENST00000428014	.	.	.	4.63	0.543	0.17179	.	.	.	.	.	T	0.41971	0.1182	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.20773	-1.0265	4	.	.	.	.	1.4228	0.02316	0.1701:0.1318:0.2791:0.419	.	.	.	.	P	170	.	.	R	-	2	0	SMC1A	53457027	0.002000	0.14202	0.996000	0.52242	0.942000	0.58702	-1.093000	0.03362	-0.226000	0.09899	-1.768000	0.00664	CGC	.	.	.	none		0.463	SMC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056756.2	NM_006306	
GLRA4	441509	hgsc.bcm.edu	37	X	102973934	102973934	+	Intron	SNP	T	T	A			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chrX:102973934T>A	ENST00000372617.4	-	7	1354				GLRA4_ENST00000469567.1_5'Flank	NM_001024452.2	NP_001019623.2	Q5JXX5	GLRA4_HUMAN	glycine receptor, alpha 4							cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|glycine binding (GO:0016594)|transmitter-gated ion channel activity (GO:0022824)			cervix(1)|endometrium(2)|large_intestine(2)|lung(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	21						TTGGGATGAATGGGAAATGGG	0.522																																					p.P328P		Atlas-SNP	.											.	GLRA4	86	.	0			c.A984T						PASS	.						30.0	32.0	31.0					X																	102973934		2194	4293	6487	SO:0001627	intron_variant	441509	exon7			GATGAATGGGAAA	Z93848	CCDS43980.2	Xq22.2	2012-01-16			ENSG00000188828	ENSG00000188828		"""Ligand-gated ion channels / Glycine receptors"""	31715	protein-coding gene	gene with protein product							Standard	NM_001024452		Approved		uc011mse.2	Q5JXX5	OTTHUMG00000022110	ENST00000372617.4:c.933+50A>T	chrX.hg19:g.102973934T>A		100.0	0.0	.		86.0	22.0	.	NM_001172285		Silent	SNP	ENST00000372617.4	hg19	CCDS43980.2																																																																																			.	.	.	none		0.522	GLRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057742.2	NM_001024452	
UPF3B	65109	hgsc.bcm.edu	37	X	118985467	118985467	+	Missense_Mutation	SNP	C	C	G			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chrX:118985467C>G	ENST00000276201.2	-	3	430	c.361G>C	c.(361-363)Gac>Cac	p.D121H	UPF3B_ENST00000345865.2_Missense_Mutation_p.D121H	NM_080632.2	NP_542199.1	Q9BZI7	REN3B_HUMAN	UPF3 regulator of nonsense transcripts homolog B (yeast)	121	Necessary for interaction with UPF2.|Sufficient for association with EJC core.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(12)|ovary(2)|prostate(1)	30						CCTTTATTGTCAAGGAATACA	0.363																																					p.D121H		Atlas-SNP	.											.	UPF3B	74	.	0			c.G361C						PASS	.						104.0	86.0	92.0					X																	118985467		2203	4300	6503	SO:0001583	missense	65109	exon3			TATTGTCAAGGAA	AF318576	CCDS14587.1, CCDS14588.1	Xq25-q26	2014-01-31			ENSG00000125351	ENSG00000125351			20439	protein-coding gene	gene with protein product		300298	"""mental retardation, X-linked 62"""	MRX62		11113196, 11163187, 19238151	Standard	NM_023010		Approved	RENT3B, UPF3X, HUPF3B	uc004erz.2	Q9BZI7	OTTHUMG00000022282	ENST00000276201.2:c.361G>C	chrX.hg19:g.118985467C>G	ENSP00000276201:p.Asp121His	214.0	1.0	.		159.0	121.0	.	NM_023010	D3DWI3|D3DWI4|Q0VAK8|Q9H1J0	Missense_Mutation	SNP	ENST00000276201.2	hg19	CCDS14588.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.031576	0.75504	.	.	ENSG00000125351	ENST00000276201;ENST00000345865;ENST00000439808	T;T	0.74526	-0.85;-0.85	5.1	5.1	0.69264	Regulator of nonsense-mediated decay, UPF3 (1);Nucleotide-binding, alpha-beta plait (1);	0.000000	0.85682	D	0.000000	D	0.90246	0.6950	H	0.95079	3.62	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.93290	0.6667	10	0.87932	D	0	.	16.142	0.81534	0.0:1.0:0.0:0.0	.	121;121	Q9BZI7-2;Q9BZI7	.;REN3B_HUMAN	H	121	ENSP00000276201:D121H;ENSP00000245418:D121H	ENSP00000276201:D121H	D	-	1	0	UPF3B	118869495	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.226000	0.78060	2.111000	0.64477	0.600000	0.82982	GAC	.	.	.	none		0.363	UPF3B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058068.1		
CENPL	91687	hgsc.bcm.edu	37	1	173772297	173772298	+	Frame_Shift_Ins	INS	-	-	T	rs139873333	byFrequency	TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:173772297_173772298insT	ENST00000345664.6	-	4	979_980	c.766_767insA	c.(766-768)atafs	p.I256fs	CENPL_ENST00000356198.2_Frame_Shift_Ins_p.I302fs|CENPL_ENST00000367710.3_Frame_Shift_Ins_p.I256fs	NM_001171182.1	NP_001164653.1	Q8N0S6	CENPL_HUMAN	centromere protein L	256					mitotic cell cycle (GO:0000278)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(3)	11						CTCTGGATGTATTGCGAAAGAA	0.45																																					p.I302fs		Atlas-INDEL	.											.	CENPL	26	.	0			c.905_906insA						PASS	.																																			SO:0001589	frameshift_variant	91687	exon6			.	BC033154, BC019022, AK055606	CCDS30938.1, CCDS44277.1	1q25.1	2013-11-05	2006-06-15	2006-06-15	ENSG00000120334	ENSG00000120334			17879	protein-coding gene	gene with protein product		611503	"""chromosome 1 open reading frame 155"""	C1orf155		16622420, 16622419	Standard	NM_033319		Approved	dJ383J4.3, FLJ31044	uc001gje.4	Q8N0S6	OTTHUMG00000034802	ENST00000345664.6:c.767dupA	chr1.hg19:g.173772299_173772299dupT	ENSP00000323543:p.Ile256fs	123.0	0.0	0		74.0	18.0	0.243243	NM_001127181	Q5TEL5|Q96ND4	Frame_Shift_Ins	INS	ENST00000345664.6	hg19	CCDS30938.1																																																																																			.	.	.	none		0.450	CENPL-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084213.1	NM_033319	
LAMB4	22798	hgsc.bcm.edu	37	7	107732109	107732120	+	In_Frame_Del	DEL	CCTCGTAGAGAT	CCTCGTAGAGAT	-			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	CCTCGTAGAGAT	CCTCGTAGAGAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr7:107732109_107732120delCCTCGTAGAGAT	ENST00000388781.3	-	14	1735_1746	c.1652_1663delATCTCTACGAGG	c.(1651-1665)tatctctacgaggca>tca	p.551_555YLYEA>S	LAMB4_ENST00000418464.1_In_Frame_Del_p.551_555YLYEA>S|LAMB4_ENST00000205386.4_In_Frame_Del_p.551_555YLYEA>S|LAMB4_ENST00000388780.3_In_Frame_Del_p.551_555YLYEA>S|LAMB4_ENST00000414450.2_In_Frame_Del_p.551_555YLYEA>S	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	551	Laminin EGF-like 5; truncated. {ECO:0000255|PROSITE-ProRule:PRU00460}.|Laminin IV type B. {ECO:0000255|PROSITE- ProRule:PRU00462}.				cell adhesion (GO:0007155)	basement membrane (GO:0005604)		p.Y553D(1)		NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						GCTTCCTCTGCCTCGTAGAGATAGAAATTCAA	0.491																																					p.551_555del		Atlas-Indel,Pindel	.											.	LAMB4	253	.	1	Substitution - Missense(1)	prostate(1)	c.1653_1664del						PASS	.																																			SO:0001651	inframe_deletion	22798	exon14			.	AF028816	CCDS34732.1	7q31	2013-03-01			ENSG00000091128	ENSG00000091128		"""Laminins"""	6491	protein-coding gene	gene with protein product							Standard	NM_007356		Approved		uc010ljo.1	A4D0S4	OTTHUMG00000154874	ENST00000388781.3:c.1652_1663delATCTCTACGAGG	chr7.hg19:g.107732109_107732120delCCTCGTAGAGAT	ENSP00000373433:p.Tyr551_Ala555delinsSer	174.0	0.0	0		119.0	23.0	0.193277	NM_007356	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	In_Frame_Del	DEL	ENST00000388781.3	hg19	CCDS34732.1																																																																																			.	.	.	none		0.491	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857	
FBXW7	55294	hgsc.bcm.edu	37	4	153250883	153250883	+	Frame_Shift_Del	DEL	G	G	-			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr4:153250883delG	ENST00000281708.4	-	8	2406	c.1177delC	c.(1177-1179)cgafs	p.R393fs	FBXW7_ENST00000393956.3_Frame_Shift_Del_p.R217fs|FBXW7_ENST00000603548.1_Frame_Shift_Del_p.R393fs|FBXW7_ENST00000263981.5_Frame_Shift_Del_p.R313fs|FBXW7_ENST00000296555.5_Frame_Shift_Del_p.R275fs|FBXW7_ENST00000603841.1_Frame_Shift_Del_p.R393fs	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	393					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.R393*(7)|p.R313*(1)|p.R154*(1)|p.?(1)|p.R275*(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)				CTAACTATTCGGTTACCACAA	0.343			"""Mis, N, D, F"""		"""colorectal, endometrial, T-ALL"""																																p.R393fs		Atlas-Indel,Pindel	.		Rec	yes		4	4q31.3	55294	"""F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"""		"""E, L"""	FBXW7_NM_018315_2,NS,carcinoma,-1,5	FBXW7	2157	.	11	Substitution - Nonsense(10)|Unknown(1)	endometrium(5)|large_intestine(4)|haematopoietic_and_lymphoid_tissue(1)|stomach(1)	c.1178delG						PASS	.						118.0	107.0	111.0					4																	153250883		2203	4300	6503	SO:0001589	frameshift_variant	55294	exon8			.	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.1177delC	chr4.hg19:g.153250883delG	ENSP00000281708:p.Arg393fs	89.0	0.0	0		98.0	35.0	0.357143	NM_033632	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Frame_Shift_Del	DEL	ENST00000281708.4	hg19	CCDS3777.1																																																																																			.	.	.	none		0.343	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1		
PDCD5	9141	hgsc.bcm.edu	37	19	33077794	33077794	+	Frame_Shift_Del	DEL	A	A	-			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr19:33077794delA	ENST00000590247.2	+	5	483	c.289delA	c.(289-291)aaafs	p.K98fs	PDCD5_ENST00000379316.3_Intron|PDCD5_ENST00000592786.1_Stop_Codon_Del|PDCD5_ENST00000419343.3_3'UTR|PDCD5_ENST00000586035.1_Frame_Shift_Del_p.K60fs	NM_004708.3	NP_004699.1	O14737	PDCD5_HUMAN	programmed cell death 5	98					apoptotic process (GO:0006915)|positive regulation of apoptotic process (GO:0043065)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|large_intestine(2)|lung(1)|ovary(1)	5	Esophageal squamous(110;0.137)					AGAAATCCTTAAAAAAGTAAG	0.323																																					p.L96fs		Atlas-Indel,Pindel	.											.	PDCD5	18	.	0			c.288delT						PASS	.						81.0	87.0	85.0					19																	33077794		2203	4300	6503	SO:0001589	frameshift_variant	9141	exon5			.	AF014955	CCDS12423.1	19q13.11	2012-10-15			ENSG00000105185	ENSG00000105185			8764	protein-coding gene	gene with protein product	"""TFAR19 novel apoptosis-related"", ""TF1 cell apoptosis-related gene 19"""	604583				9920759	Standard	NM_004708		Approved	TFAR19, MGC9294	uc002ntm.3	O14737	OTTHUMG00000180224	ENST00000590247.2:c.289delA	chr19.hg19:g.33077794delA	ENSP00000466214:p.Lys98fs	144.0	0.0	0		124.0	43.0	0.346774	NM_004708	B4DE64|Q53YC9|Q6IB70	Frame_Shift_Del	DEL	ENST00000590247.2	hg19	CCDS12423.1																																																																																			.	.	.	none		0.323	PDCD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450320.2	NM_004708	
MAP3K7	6885	hgsc.bcm.edu	37	6	91226399	91226400	+	Splice_Site	DEL	GC	GC	-			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr6:91226399_91226400delGC	ENST00000369329.3	-	17	1802_1803	c.1641_1642delGC	c.(1639-1644)aagcaa>aaaa	p.Q548fs	MAP3K7_ENST00000479630.1_5'UTR|MAP3K7_ENST00000369332.3_Splice_Site_p.Q521fs|MAP3K7_ENST00000369320.1_Splice_Site_p.Q202fs|MAP3K7_ENST00000369327.3_Splice_Site_p.A482fs|MAP3K7_ENST00000369325.3_Splice_Site_p.A509fs	NM_145331.2	NP_663304.1	O43318	M3K7_HUMAN	mitogen-activated protein kinase kinase kinase 7	548					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|Fc-epsilon receptor signaling pathway (GO:0038095)|histone H3 acetylation (GO:0043966)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of ripoptosome assembly involved in necroptotic process (GO:1902443)|neural tube formation (GO:0001841)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|regulation of reactive oxygen species metabolic process (GO:2000377)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase activity (GO:0004708)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|scaffold protein binding (GO:0097110)			endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	28		all_cancers(76;6.4e-08)|Acute lymphoblastic leukemia(125;1.43e-09)|Prostate(29;9.32e-09)|all_hematologic(105;3.69e-06)|all_epithelial(107;0.000187)|Ovarian(999;0.0164)		OV - Ovarian serous cystadenocarcinoma(136;2.05e-11)|all cancers(137;3.25e-11)|GBM - Glioblastoma multiforme(226;0.0416)|BRCA - Breast invasive adenocarcinoma(108;0.0429)		ACTAGTTCTTGCCTACAAACAA	0.351																																					p.548_548del		Atlas-INDEL	.											.	MAP3K7	100	.	0			c.1642_1643del						PASS	.																																			SO:0001630	splice_region_variant	6885	exon17			.	AB009356	CCDS5027.1, CCDS5028.1, CCDS5029.1, CCDS5030.1	6q15	2011-06-09			ENSG00000135341	ENSG00000135341		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6859	protein-coding gene	gene with protein product		602614		TAK1		9466656	Standard	NM_003188		Approved	MEKK7	uc003pnz.2	O43318	OTTHUMG00000015217	ENST00000369329.3:c.1641-1GC>-	chr6.hg19:g.91226399_91226400delGC		76.0	0.0	0		66.0	20.0	0.30303	NM_145331	B2RE27|E1P523|O43317|O43319|Q5TDN2|Q5TDN3|Q5TDT7|Q9NTR3|Q9NZ70	Frame_Shift_Del	DEL	ENST00000369329.3	hg19	CCDS5028.1																																																																																			.	.	.	none		0.351	MAP3K7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041530.1	NM_145331	Frame_Shift_Del
YARS2	51067	hgsc.bcm.edu	37	12	32908454	32908454	+	Frame_Shift_Del	DEL	G	G	-			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr12:32908454delG	ENST00000324868.8	-	1	382	c.355delC	c.(355-357)ctgfs	p.L119fs		NM_001040436.2	NP_001035526.1	Q9Y2Z4	SYYM_HUMAN	tyrosyl-tRNA synthetase 2, mitochondrial	119					gene expression (GO:0010467)|mitochondrial tyrosyl-tRNA aminoacylation (GO:0070184)|translation (GO:0006412)|tRNA aminoacylation (GO:0043039)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tRNA binding (GO:0000049)|tyrosine binding (GO:0072545)|tyrosine-tRNA ligase activity (GO:0004831)			endometrium(1)|large_intestine(4)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	16	Lung NSC(5;2.43e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)				L-Tyrosine(DB00135)	GGGTCTCCCAGGCGCGCCGTG	0.682											OREG0021729	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L119fs		Atlas-INDEL	.											YARS2,larynx,carcinoma,0,1	YARS2	33	.	0			c.356delT						PASS	.						14.0	16.0	16.0					12																	32908454		2196	4290	6486	SO:0001589	frameshift_variant	51067	exon1			.	AF132939	CCDS31770.1	12p11.21	2014-03-19	2007-02-23		ENSG00000139131	ENSG00000139131	6.1.1.1	"""Aminoacyl tRNA synthetases / Class I"""	24249	protein-coding gene	gene with protein product	"""tyrosine tRNA ligase 2, mitochondrial"""	610957				15779907, 15840810	Standard	NM_001040436		Approved	FLJ13995, CGI-04, mt-TyrRS	uc001rli.3	Q9Y2Z4	OTTHUMG00000169454	ENST00000324868.8:c.355delC	chr12.hg19:g.32908454delG	ENSP00000320658:p.Leu119fs	29.0	0.0	0	836	47.0	18.0	0.382979	NM_001040436	D3DUW8|Q9H817	Frame_Shift_Del	DEL	ENST00000324868.8	hg19	CCDS31770.1																																																																																			.	.	.	none		0.682	YARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404153.1	NM_015936	
AKR1C2	1646	hgsc.bcm.edu	37	10	5038014	5038014	+	Frame_Shift_Del	DEL	A	A	-			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr10:5038014delA	ENST00000380753.4	-	6	801	c.614delT	c.(613-615)ttcfs	p.F205fs	RP11-499O7.7_ENST00000451575.2_RNA|AKR1C2_ENST00000407674.1_Frame_Shift_Del_p.F205fs|AKR1C2_ENST00000421196.3_Frame_Shift_Del_p.F179fs|RP11-499O7.7_ENST00000440414.1_RNA	NM_205845.2	NP_995317.1	P52895	AK1C2_HUMAN	aldo-keto reductase family 1, member C2	205					cellular response to jasmonic acid stimulus (GO:0071395)|daunorubicin metabolic process (GO:0044597)|digestion (GO:0007586)|doxorubicin metabolic process (GO:0044598)|epithelial cell differentiation (GO:0030855)|G-protein coupled receptor signaling pathway (GO:0007186)|oxidation-reduction process (GO:0055114)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein kinase B signaling (GO:0051897)|progesterone metabolic process (GO:0042448)|prostaglandin metabolic process (GO:0006693)|response to prostaglandin (GO:0034694)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)	alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|bile acid binding (GO:0032052)|carboxylic acid binding (GO:0031406)|ketosteroid monooxygenase activity (GO:0047086)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|phenanthrene 9,10-monooxygenase activity (GO:0018636)|prostaglandin F receptor activity (GO:0004958)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			breast(1)|large_intestine(5)|lung(3)|skin(1)	10					Ursodeoxycholic acid(DB01586)	TGACTTGCAGAAATCCAGCAG	0.393																																					p.F205fs		Atlas-Indel,Pindel	.											.	AKR1C2	68	.	0			c.615delC						PASS	.						62.0	57.0	59.0					10																	5038014		2203	4296	6499	SO:0001589	frameshift_variant	1646	exon8			.	L32592	CCDS7062.1, CCDS44350.1	10p15-p14	2014-01-29	2012-12-04		ENSG00000151632	ENSG00000151632	1.3.1.20, 1.1.1.213	"""Aldo-keto reductases"""	385	protein-coding gene	gene with protein product	"""dihydrodiol dehydrogenase 2; bile acid binding protein; 3-alpha hydroxysteroid dehydrogenase, type III"""	600450	"""aldo-keto reductase family 1, member C2 (dihydrodiol dehydrogenase 2; bile acid binding protein; 3-alpha hydroxysteroid dehydrogenase, type III)"", ""testicular 17,20-desmolase deficiency"""	DDH2, TDD		9716498, 21802064	Standard	NM_001354		Approved	DD, BABP, DD2, HAKRD, MCDR2	uc001iht.3	P52895	OTTHUMG00000017584	ENST00000380753.4:c.614delT	chr10.hg19:g.5038014delA	ENSP00000370129:p.Phe205fs	706.0	0.0	0		638.0	51.0	0.0799373	NM_001354	A8K2N9|B4DKR9|Q14133|Q5SR16|Q7M4N1|Q96A71	Frame_Shift_Del	DEL	ENST00000380753.4	hg19	CCDS7062.1																																																																																			.	.	.	none		0.393	AKR1C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046531.1	NM_001354	
PTPN3	5774	hgsc.bcm.edu	37	9	112219466	112219466	+	Frame_Shift_Del	DEL	C	C	-			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr9:112219466delC	ENST00000374541.2	-	4	380	c.276delG	c.(274-276)aggfs	p.R92fs	PTPN3_ENST00000262539.3_Frame_Shift_Del_p.E10fs	NM_001145368.1|NM_002829.3	NP_001138840.1|NP_002820.3	P26045	PTN3_HUMAN	protein tyrosine phosphatase, non-receptor type 3	92	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				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						TTAACTGCTTCCTGATGGCTT	0.413																																					p.K93fs		Atlas-Indel,Pindel	.											.	PTPN3	106	.	0			c.277delA						PASS	.						197.0	168.0	177.0					9																	112219466		2203	4300	6503	SO:0001589	frameshift_variant	5774	exon4			.		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.276delG	chr9.hg19:g.112219466delC	ENSP00000363667:p.Arg92fs	167.0	0.0	0		113.0	32.0	0.283186	NM_001145368	A0AUW9|E7EN99|E9PGU7	Frame_Shift_Del	DEL	ENST00000374541.2	hg19	CCDS6776.1																																																																																			.	.	.	none		0.413	PTPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053598.4		
CEP350	9857	hgsc.bcm.edu	37	1	179959644	179959645	+	Frame_Shift_Del	DEL	GA	GA	-			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	GA	GA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:179959644_179959645delGA	ENST00000367607.3	+	4	541_542	c.123_124delGA	c.(121-126)ctgagafs	p.R42fs		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	42					microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						AACTTTAGCTGAGACACATTGA	0.337																																					p.41_41del		Atlas-Indel,Pindel	.											.	CEP350	418	.	0			c.122_123del						PASS	.																																			SO:0001589	frameshift_variant	9857	exon4			.	AF287356	CCDS1336.1	1q25.2	2014-02-20			ENSG00000135837	ENSG00000135837			24238	protein-coding gene	gene with protein product	"""centrosome associated protein 350"""					16314388, 15615782	Standard	NM_014810		Approved	KIAA0480, CAP350	uc001gnt.3	Q5VT06	OTTHUMG00000035269	ENST00000367607.3:c.123_124delGA	chr1.hg19:g.179959646_179959647delGA	ENSP00000356579:p.Arg42fs	67.0	0.0	0		66.0	14.0	0.212121	NM_014810	O75068|Q8TDK3|Q8WY20	Frame_Shift_Del	DEL	ENST00000367607.3	hg19	CCDS1336.1																																																																																			.	.	.	none		0.337	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810	
GRIK2	2898	hgsc.bcm.edu	37	6	102513771	102513771	+	Intron	DEL	T	T	-			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr6:102513771delT	ENST00000421544.1	+	16	3052				GRIK2_ENST00000369134.4_Intron|GRIK2_ENST00000369138.1_Frame_Shift_Del_p.L888fs|GRIK2_ENST00000369137.3_Intron|GRIK2_ENST00000413795.1_Intron	NM_021956.4	NP_068775.1	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2						behavioral fear response (GO:0001662)|cellular calcium ion homeostasis (GO:0006874)|glutamate receptor signaling pathway (GO:0007215)|intracellular protein transport (GO:0006886)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuronal action potential (GO:0019228)|positive regulation of synaptic transmission (GO:0050806)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission (GO:0050804)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	ttcatcatcattatcatcatG	0.363																																					p.S887fs		Atlas-Indel,Pindel	.											.	GRIK2	487	.	0			c.2661delA						PASS	.						287.0	228.0	246.0					6																	102513771		692	1590	2282	SO:0001627	intron_variant	2898	exon16			.		CCDS5048.1, CCDS5049.1, CCDS55045.1	6q16.3	2012-08-29			ENSG00000164418	ENSG00000164418		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4580	protein-coding gene	gene with protein product		138244		GLUR6		8034316	Standard	NM_021956		Approved	GluK2, MRT6	uc003pqp.4	Q13002	OTTHUMG00000016328	ENST00000421544.1:c.2563-2451T>-	chr6.hg19:g.102513771delT		96.0	0.0	0		80.0	37.0	0.4625	NM_001166247	A6NMY9|B5MCV0|D7RWZ3|D7RWZ4|D7RWZ5|D7RWZ6|D7RWZ7|Q8WWS1|Q96KS6|Q96KS7|Q96KS8	Frame_Shift_Del	DEL	ENST00000421544.1	hg19	CCDS5048.1																																																																																			.	.	.	none		0.363	GRIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043718.1		
NEFH	4744	hgsc.bcm.edu	37	22	29885591	29885592	+	In_Frame_Ins	INS	-	-	CCTGAGAAGGCCAAGTCC	rs200984527|rs267607533		TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr22:29885591_29885592insCCTGAGAAGGCCAAGTCC	ENST00000310624.6	+	4	1995_1996	c.1962_1963insCCTGAGAAGGCCAAGTCC	c.(1963-1965)cca>CCTGAGAAGGCCAAGTCCcca	p.655_655P>PEKAKSP		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	661	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						AGGCCAAGTCCCCAGAGAAGGA	0.559																																					p.S654delinsSPEKAKS		Atlas-INDEL	.											.,2	NEFH	178	.	0			c.1962_1963insCCTGAGAAGGCCAAGTCC						PASS	.																																			SO:0001652	inframe_insertion	4744	exon4			.		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.1945_1962dupCCTGAGAAGGCCAAGTCC	chr22.hg19:g.29885591_29885592insCCTGAGAAGGCCAAGTCC	ENSP00000311997:p.GluLysAlaLysSerPro655dup	329.0	0.0	0		226.0	59.0	0.261062	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	In_Frame_Ins	INS	ENST00000310624.6	hg19	CCDS13858.1																																																																																			.	.	.	none		0.559	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
SCN10A	6336	hgsc.bcm.edu	37	3	38740022	38740022	+	Frame_Shift_Del	DEL	A	A	-			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr3:38740022delA	ENST00000449082.2	-	27	4688	c.4689delT	c.(4687-4689)cttfs	p.L1563fs		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	1563					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	AGTAACTTTGAAGTGACTTAA	0.478																																					p.Q1564fs		Atlas-INDEL	.											.	SCN10A	359	.	0			c.4690delC						PASS	.						58.0	59.0	59.0					3																	38740022		2203	4300	6503	SO:0001589	frameshift_variant	6336	exon27			.	AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10582	protein-coding gene	gene with protein product		604427	"""sodium channel, voltage-gated, type X, alpha polypeptide"""			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.4689delT	chr3.hg19:g.38740022delA	ENSP00000390600:p.Leu1563fs	158.0	0.0	0		107.0	18.0	0.168224	NM_006514	A6NDQ1	Frame_Shift_Del	DEL	ENST00000449082.2	hg19	CCDS33736.1																																																																																			.	.	.	none		0.478	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514	
ZNF792	126375	hgsc.bcm.edu	37	19	35450211	35450211	+	Frame_Shift_Del	DEL	T	T	-			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr19:35450211delT	ENST00000404801.1	-	4	934	c.548delA	c.(547-549)aacfs	p.N183fs	ZNF792_ENST00000605484.1_Frame_Shift_Del_p.N116fs	NM_175872.4	NP_787068.3	Q3KQV3	ZN792_HUMAN	zinc finger protein 792	183					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(5)	12	all_lung(56;4.18e-08)|Lung NSC(56;6.62e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			GTTGTGTACGTTCTGCTGCAC	0.542																																					p.N183fs	GBM(1;7 183 21053 22581 22847)	Atlas-Indel,Pindel	.											.	ZNF792	46	.	0			c.549delC						PASS	.						256.0	248.0	251.0					19																	35450211		2203	4300	6503	SO:0001589	frameshift_variant	126375	exon4			.	AK095770	CCDS12440.2	19q13.11	2013-01-08			ENSG00000180884	ENSG00000180884		"""Zinc fingers, C2H2-type"", ""-"""	24751	protein-coding gene	gene with protein product						8889548	Standard	NM_175872		Approved	FLJ38451	uc002nxh.1	Q3KQV3	OTTHUMG00000150339	ENST00000404801.1:c.548delA	chr19.hg19:g.35450211delT	ENSP00000385099:p.Asn183fs	348.0	0.0	0		273.0	101.0	0.369963	NM_175872	B4E333|Q495L1|Q495L3|Q8N932	Frame_Shift_Del	DEL	ENST00000404801.1	hg19	CCDS12440.2																																																																																			.	.	.	none		0.542	ZNF792-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317673.1	NM_175872	
PPIP5K1	9677	hgsc.bcm.edu	37	15	43863609	43863609	+	Splice_Site	DEL	C	C	-			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr15:43863609delC	ENST00000396923.3	-	24	3089		c.e24+1		PPIP5K1_ENST00000432870.3_Splice_Site|PPIP5K1_ENST00000348806.6_Splice_Site|PPIP5K1_ENST00000360135.4_Splice_Site|PPIP5K1_ENST00000360301.4_Splice_Site|PPIP5K1_ENST00000381885.1_Splice_Site|PPIP5K1_ENST00000381879.4_Splice_Site|PPIP5K1_ENST00000420765.1_Splice_Site|PPIP5K1_ENST00000334933.4_Splice_Site			Q6PFW1	VIP1_HUMAN	diphosphoinositol pentakisphosphate kinase 1						inositol metabolic process (GO:0006020)|inositol phosphate metabolic process (GO:0043647)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	acid phosphatase activity (GO:0003993)|ATP binding (GO:0005524)|diphosphoinositol-pentakisphosphate kinase activity (GO:0033857)|inositol hexakisphosphate 1-kinase activity (GO:0052723)|inositol hexakisphosphate 3-kinase activity (GO:0052724)|inositol hexakisphosphate 5-kinase activity (GO:0000832)|inositol-1,3,4,5,6-pentakisphosphate kinase activity (GO:0000827)			large_intestine(1)	1						CCTCTCATTACCTCCATGGAA	0.557																																					.		Atlas-INDEL	.											.	PPIP5K1	34	.	0			c.2955+2G>-						PASS	.																																			SO:0001630	splice_region_variant	9677	exon25			.	AF502586	CCDS32215.1, CCDS45252.1, CCDS53937.1	15q15.3	2010-01-27	2010-01-26	2010-01-26	ENSG00000168781	ENSG00000168781	2.7.4.24		29023	protein-coding gene	gene with protein product		610979	"""histidine acid phosphatase domain containing 2A"""	HISPPD2A		17412958, 17690096, 18981179	Standard	NM_001190214		Approved	KIAA0377, IPS1, VIP1	uc001zrw.3	Q6PFW1	OTTHUMG00000059758	ENST00000396923.3:c.2967+1G>-	chr15.hg19:g.43863609delC		106.0	0.0	0		91.0	18.0	0.197802	NM_014659	O15082|Q5HYF8|Q7Z3A7|Q86TE7|Q86UV3|Q86UV4|Q86XW8|Q8IZN0	Splice_Site	DEL	ENST00000396923.3	hg19	CCDS45252.1																																																																																			.	.	.	none		0.557	PPIP5K1-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000132907.1	NM_014659	Intron
MTG1	92170	hgsc.bcm.edu	37	10	135209749	135209750	+	Frame_Shift_Ins	INS	-	-	GC			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr10:135209749_135209750insGC	ENST00000317502.6	+	3	310_311	c.260_261insGC	c.(259-264)ttggcgfs	p.A88fs	RP11-108K14.8_ENST00000468317.2_Frame_Shift_Ins_p.A93fs|MTG1_ENST00000477902.2_Frame_Shift_Ins_p.A47fs	NM_138384.2	NP_612393.2	Q9BT17	MTG1_HUMAN	mitochondrial ribosome-associated GTPase 1	88	CP-type G. {ECO:0000255|PROSITE- ProRule:PRU01058}.				GTP catabolic process (GO:0006184)|regulation of mitochondrial translation (GO:0070129)|regulation of respiratory system process (GO:0044065)|ribosome biogenesis (GO:0042254)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial ribosome (GO:0005761)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(5)|lung(5)|ovary(2)|skin(1)|urinary_tract(1)	15		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;1.21e-06)|all cancers(32;1.69e-06)|Epithelial(32;1.94e-06)		AAGATGGACTTGGCGGATCTTA	0.515																																					p.L87fs		Atlas-Indel,Pindel	.											.	MTG1	38	.	0			c.260_261insGC						PASS	.																																			SO:0001589	frameshift_variant	92170	exon3			.		CCDS31320.1	10q26.3	2013-05-24	2013-05-24	2006-01-09	ENSG00000148824	ENSG00000148824			32159	protein-coding gene	gene with protein product			"""GTP-binding protein 7"", ""GTP-binding protein 7 (putative)"", ""mitochondrial GTPase 1 homolog (S. cerevisiae)"""	GTPBP7		12808030, 23396448	Standard	NM_138384		Approved		uc001lnd.3	Q9BT17	OTTHUMG00000166564	Exception_encountered	chr10.hg19:g.135209749_135209750insGC	ENSP00000323047:p.Ala88fs	139.0	0.0	0		108.0	42.0	0.388889	NM_138384	Q5VWX8|Q6PIY9|Q8IYJ4|Q8NC48|Q9BVU8	Frame_Shift_Ins	INS	ENST00000317502.6	hg19	CCDS31320.1																																																																																			.	.	.	none		0.515	MTG1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051166.1	NM_138384	
ZNF831	128611	hgsc.bcm.edu	37	20	57782069	57782069	+	Frame_Shift_Del	DEL	A	A	-			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr20:57782069delA	ENST00000371030.2	+	3	3985	c.3985delA	c.(3985-3987)aagfs	p.K1329fs		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	1329							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					TGAGGGACTGAAGCCATGCAG	0.577																																					p.L1328fs		Atlas-Indel,Pindel	.											.	ZNF831	287	.	0			c.3984delG						PASS	.						68.0	73.0	71.0					20																	57782069		1968	4144	6112	SO:0001589	frameshift_variant	128611	exon3			.	AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 174"""	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.3985delA	chr20.hg19:g.57782069delA	ENSP00000360069:p.Lys1329fs	108.0	0.0	0		104.0	43.0	0.413462	NM_178457	Q5TDR4|Q8TCP0	Frame_Shift_Del	DEL	ENST00000371030.2	hg19	CCDS42894.1																																																																																			.	.	.	none		0.577	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457	
SCN10A	6336	hgsc.bcm.edu	37	3	38740016	38740018	+	In_Frame_Del	DEL	ACT	ACT	-	rs200063383	byFrequency	TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	ACT	ACT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr3:38740016_38740018delACT	ENST00000449082.2	-	27	4692_4694	c.4693_4695delAGT	c.(4693-4695)agtdel	p.S1565del		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	1565					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	GGGAGAAGTAACTTTGAAGTGAC	0.478																																					p.1565_1566del		Atlas-INDEL	.											.	SCN10A	359	.	0			c.4694_4696del						PASS	.																																			SO:0001651	inframe_deletion	6336	exon27			.	AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10582	protein-coding gene	gene with protein product		604427	"""sodium channel, voltage-gated, type X, alpha polypeptide"""			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.4693_4695delAGT	chr3.hg19:g.38740016_38740018delACT	ENSP00000390600:p.Ser1565del	164.0	0.0	0		118.0	18.0	0.152542	NM_006514	A6NDQ1	In_Frame_Del	DEL	ENST00000449082.2	hg19	CCDS33736.1																																																																																			.	.	.	none		0.478	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514	
MAP3K7	6885	hgsc.bcm.edu	37	6	91226399	91226401	+	Splice_Site	DEL	GCC	GCC	-			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	GCC	GCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr6:91226399_91226401delGCC	ENST00000369329.3	-	17	1802_1803	c.1641_1642delGGC	c.(1639-1644)aaggca>aaca	p.547_548KA>N	MAP3K7_ENST00000479630.1_5'UTR|MAP3K7_ENST00000369332.3_Splice_Site_p.520_521KA>N|MAP3K7_ENST00000369320.1_Splice_Site_p.201_202KA>N|MAP3K7_ENST00000369327.3_Splice_Site_p.G482del|MAP3K7_ENST00000369325.3_Splice_Site_p.G509del	NM_145331.2	NP_663304.1	O43318	M3K7_HUMAN	mitogen-activated protein kinase kinase kinase 7	547					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|Fc-epsilon receptor signaling pathway (GO:0038095)|histone H3 acetylation (GO:0043966)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of ripoptosome assembly involved in necroptotic process (GO:1902443)|neural tube formation (GO:0001841)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|regulation of reactive oxygen species metabolic process (GO:2000377)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase activity (GO:0004708)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|scaffold protein binding (GO:0097110)			endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	28		all_cancers(76;6.4e-08)|Acute lymphoblastic leukemia(125;1.43e-09)|Prostate(29;9.32e-09)|all_hematologic(105;3.69e-06)|all_epithelial(107;0.000187)|Ovarian(999;0.0164)		OV - Ovarian serous cystadenocarcinoma(136;2.05e-11)|all cancers(137;3.25e-11)|GBM - Glioblastoma multiforme(226;0.0416)|BRCA - Breast invasive adenocarcinoma(108;0.0429)		ACTAGTTCTTGCCTACAAACAAA	0.35																																					p.547_548del		Pindel	.											.	MAP3K7	100	.	0			c.1641_1643del						PASS	.																																			SO:0001630	splice_region_variant	6885	exon17			.	AB009356	CCDS5027.1, CCDS5028.1, CCDS5029.1, CCDS5030.1	6q15	2011-06-09			ENSG00000135341	ENSG00000135341		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6859	protein-coding gene	gene with protein product		602614		TAK1		9466656	Standard	NM_003188		Approved	MEKK7	uc003pnz.2	O43318	OTTHUMG00000015217	ENST00000369329.3:c.1641-1GGC>-	chr6.hg19:g.91226399_91226401delGCC		77.0	0.0	.		67.0	13.0	0.194	NM_145331	B2RE27|E1P523|O43317|O43319|Q5TDN2|Q5TDN3|Q5TDT7|Q9NTR3|Q9NZ70	In_Frame_Del	DEL	ENST00000369329.3	hg19	CCDS5028.1																																																																																			.	.	.	none		0.350	MAP3K7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041530.1	NM_145331	In_Frame_Del
ABCA4	24	hgsc.bcm.edu	37	1	94522320	94522320	+	Frame_Shift_Del	DEL	A	A	-			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:94522320delA	ENST00000370225.3	-	15	2305	c.2219delT	c.(2218-2220)ttcfs	p.F740fs	ABCA4_ENST00000535735.1_Intron	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	740					phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		GGCAGTGGAGAAAGCCAACAA	0.517																																					p.F740fs		Pindel	.											.	ABCA4	275	.	0			c.2220delC						PASS	.						111.0	98.0	102.0					1																	94522320		2203	4300	6503	SO:0001589	frameshift_variant	24	exon15			.	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"""ATP binding cassette transporters / subfamily A"""	34	protein-coding gene	gene with protein product	"""Stargardt disease"""	601691	"""ATP-binding cassette transporter, retinal-specific"""	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.2219delT	chr1.hg19:g.94522320delA	ENSP00000359245:p.Phe740fs	322.0	0.0	.		231.0	60.0	0.260	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Frame_Shift_Del	DEL	ENST00000370225.3	hg19	CCDS747.1																																																																																			.	.	.	none		0.517	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350	
ZNF256	10172	hgsc.bcm.edu	37	19	58452565	58452565	+	Frame_Shift_Del	DEL	A	A	-			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr19:58452565delA	ENST00000282308.3	-	3	1807	c.1611delT	c.(1609-1611)catfs	p.H537fs	ZNF256_ENST00000598928.1_3'UTR	NM_005773.2	NP_005764.2	Q9Y2P7	ZN256_HUMAN	zinc finger protein 256	537					multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|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(1)|kidney(3)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0155)		GACTTCTCCTATGTCTAATGA	0.468																																					p.R538fs	NSCLC(55;1313 1552 8040 11996)	Pindel	.											.	ZNF256	117	.	0			c.1612delA						PASS	.						66.0	58.0	61.0					19																	58452565		2203	4300	6503	SO:0001589	frameshift_variant	10172	exon3			.	AF067165	CCDS12966.1	19q13	2013-01-08				ENSG00000152454		"""Zinc fingers, C2H2-type"", ""-"""	13049	protein-coding gene	gene with protein product		606956					Standard	NM_005773		Approved	BMZF-3	uc002qqu.3	Q9Y2P7		ENST00000282308.3:c.1611delT	chr19.hg19:g.58452565delA	ENSP00000282308:p.His537fs	129.0	0.0	.		98.0	19.0	0.194	NM_005773	B2RA92|Q53Y85|Q9BV71	Frame_Shift_Del	DEL	ENST00000282308.3	hg19	CCDS12966.1																																																																																			.	.	.	none		0.468	ZNF256-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466702.1		
SCN10A	6336	hgsc.bcm.edu	37	3	38740016	38740023	+	Frame_Shift_Del	DEL	ACTTTGAA	ACTTTGAA	-	rs200063383	byFrequency	TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	ACTTTGAA	ACTTTGAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr3:38740016_38740023delACTTTGAA	ENST00000449082.2	-	27	4687_4694	c.4688_4695delTTCAAAGT	c.(4687-4695)cttcaaagtfs	p.LQS1563fs		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	1563					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	GGGAGAAGTAACTTTGAAGTGACTTAAG	0.476																																					p.1563_1566del		Pindel	.											.	SCN10A	359	.	0			c.4689_4696del						PASS	.																																			SO:0001589	frameshift_variant	6336	exon27			.	AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10582	protein-coding gene	gene with protein product		604427	"""sodium channel, voltage-gated, type X, alpha polypeptide"""			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.4688_4695delTTCAAAGT	chr3.hg19:g.38740016_38740023delACTTTGAA	ENSP00000390600:p.Leu1563fs	162.0	0.0	.		119.0	15.0	0.126	NM_006514	A6NDQ1	Frame_Shift_Del	DEL	ENST00000449082.2	hg19	CCDS33736.1																																																																																			.	.	.	none		0.476	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514	
