#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_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_ORegAnno_bin	i_TTotCov	i_TVarCov	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_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
GNB1	2782	hgsc.bcm.edu	37	1	1721974	1721974	+	Missense_Mutation	SNP	C	C	A			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr1:1721974C>A	ENST00000378609.4	-	9	890	c.559G>T	c.(559-561)Gtc>Ttc	p.V187F		NM_001282539.1|NM_002074.3	NP_001269468.1|NP_002065.1	P62873	GBB1_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 1	187					adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|blood coagulation (GO:0007596)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|energy reserve metabolic process (GO:0006112)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|GTP catabolic process (GO:0006184)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|Ras protein signal transduction (GO:0007265)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	GTPase activity (GO:0003924)|GTPase binding (GO:0051020)|protein complex binding (GO:0032403)|signal transducer activity (GO:0004871)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(3)|skin(1)	12	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.62e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;1.14e-35)|OV - Ovarian serous cystadenocarcinoma(86;7.31e-23)|GBM - Glioblastoma multiforme(42;3.1e-07)|COAD - Colon adenocarcinoma(227;0.000323)|Colorectal(212;0.000374)|Kidney(185;0.00392)|BRCA - Breast invasive adenocarcinoma(365;0.00573)|STAD - Stomach adenocarcinoma(132;0.0072)|KIRC - Kidney renal clear cell carcinoma(229;0.0482)|Lung(427;0.236)		AGGCTCATGACATCTCCAGTG	0.562																																					p.V187F		Atlas-SNP	.											.	GNB1	39	.	0			c.G559T						.						152.0	108.0	123.0					1																	1721974		2203	4300	6503	SO:0001583	missense	2782	exon9			TCATGACATCTCC	BC004186	CCDS34.1, CCDS72685.1	1p36.33	2013-01-10			ENSG00000078369	ENSG00000078369		"""WD repeat domain containing"""	4396	protein-coding gene	gene with protein product		139380					Standard	NM_002074		Approved		uc001aif.3	P62873	OTTHUMG00000000940	ENST00000378609.4:c.559G>T	chr1.hg19:g.1721974C>A	ENSP00000367872:p.Val187Phe	87.0	0.0		124.0	44.0	NM_002074	B1AJZ7|P04697|P04901|Q1RMY8	Missense_Mutation	SNP	ENST00000378609.4	hg19	CCDS34.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	35|35	5.452542|5.452542	0.96223|0.96223	.|.	.|.	ENSG00000078369|ENSG00000078369	ENST00000424622|ENST00000378609;ENST00000455156;ENST00000378606	.|T	.|0.73897	.|-0.79	5.43|5.43	5.43|5.43	0.79202|0.79202	.|WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	.|0.055920	.|0.64402	.|D	.|0.000001	D|D	0.91998|0.91998	0.7465|0.7465	H|H	0.98333|0.98333	4.205|4.205	0.80722|0.80722	D|D	1|1	.|D	.|0.76494	.|0.999	.|D	.|0.77004	.|0.989	D|D	0.94971|0.94971	0.8117|0.8117	5|10	.|0.87932	.|D	.|0	-13.3509|-13.3509	18.2284|18.2284	0.89926|0.89926	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|187	.|P62873	.|GBB1_HUMAN	I|F	44|187;87;187	.|ENSP00000367872:V187F	.|ENSP00000367869:V187F	M|V	-|-	3|1	0|0	GNB1|GNB1	1711834|1711834	1.000000|1.000000	0.71417|0.71417	0.954000|0.954000	0.39281|0.39281	0.983000|0.983000	0.72400|0.72400	7.586000|7.586000	0.82596|0.82596	2.538000|2.538000	0.85594|0.85594	0.655000|0.655000	0.94253|0.94253	ATG|GTC	.	.		0.562	GNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002762.3	NM_002074	
XKR8	55113	hgsc.bcm.edu	37	1	28293332	28293332	+	Missense_Mutation	SNP	A	A	G			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr1:28293332A>G	ENST00000373884.5	+	3	1417	c.809A>G	c.(808-810)tAt>tGt	p.Y270C		NM_018053.2	NP_060523.2	Q9H6D3	XKR8_HUMAN	XK, Kell blood group complex subunit-related family, member 8	270					engulfment of apoptotic cell (GO:0043652)|phosphatidylserine exposure on apoptotic cell surface (GO:0070782)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(2)|lung(1)	4		Colorectal(325;0.000147)|Renal(390;0.00357)|Lung NSC(340;0.00588)|all_lung(284;0.00645)|Breast(348;0.0174)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0545)|all_neural(195;0.0557)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;4.72e-24)|Colorectal(126;1.52e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00269)|STAD - Stomach adenocarcinoma(196;0.00303)|BRCA - Breast invasive adenocarcinoma(304;0.00572)|READ - Rectum adenocarcinoma(331;0.0526)		ACCATCCTCTATTTCTCCTGG	0.632																																					p.Y270C		Atlas-SNP	.											.	XKR8	15	.	0			c.A809G						.						23.0	24.0	23.0					1																	28293332		2203	4299	6502	SO:0001583	missense	55113	exon3			TCCTCTATTTCTC	AK091615	CCDS315.1	1p35.3	2008-02-05	2006-01-12		ENSG00000158156	ENSG00000158156			25508	protein-coding gene	gene with protein product			"""X Kell blood group precursor-related family, member 8"""			12477932	Standard	NM_018053		Approved	FLJ10307	uc001bph.1	Q9H6D3	OTTHUMG00000003912	ENST00000373884.5:c.809A>G	chr1.hg19:g.28293332A>G	ENSP00000362991:p.Tyr270Cys	78.0	0.0		110.0	50.0	NM_018053		Missense_Mutation	SNP	ENST00000373884.5	hg19	CCDS315.1	.	.	.	.	.	.	.	.	.	.	A	26.5	4.746479	0.89663	.	.	ENSG00000158156	ENST00000373884	T	0.64803	-0.12	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.74612	0.3739	M	0.76838	2.35	0.80722	D	1	D	0.54964	0.969	P	0.55965	0.788	T	0.75915	-0.3149	10	0.39692	T	0.17	.	15.2805	0.73781	1.0:0.0:0.0:0.0	.	270	Q9H6D3	XKR8_HUMAN	C	270	ENSP00000362991:Y270C	ENSP00000362991:Y270C	Y	+	2	0	XKR8	28165919	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.855000	0.92236	2.019000	0.59389	0.533000	0.62120	TAT	.	.		0.632	XKR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011175.1	NM_018053	
CACHD1	57685	hgsc.bcm.edu	37	1	65147714	65147714	+	Missense_Mutation	SNP	G	G	C			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr1:65147714G>C	ENST00000371073.2	+	26	3511	c.3511G>C	c.(3511-3513)Gtc>Ctc	p.V1171L	CACHD1_ENST00000495994.1_3'UTR|CACHD1_ENST00000290039.5_Missense_Mutation_p.V1120L			Q5VU97	CAHD1_HUMAN	cache domain containing 1	1171					calcium ion transport (GO:0006816)	integral component of membrane (GO:0016021)				breast(4)|endometrium(3)|kidney(3)|large_intestine(20)|lung(14)|ovary(2)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						TATAGCTGCGGTCATCGAACG	0.473																																					p.V1120L		Atlas-SNP	.											CACHD1,colon,carcinoma,0,1	CACHD1	125	.	0			c.G3358C						.						119.0	106.0	111.0					1																	65147714		2203	4300	6503	SO:0001583	missense	57685	exon26			GCTGCGGTCATCG	AB046793	CCDS628.2	1p31.3	2008-02-05	2005-10-11	2005-10-11	ENSG00000158966	ENSG00000158966			29314	protein-coding gene	gene with protein product			"""von Willebrand factor type A and cache domain containing 1"""	VWCD1		10997877	Standard	NM_020925		Approved	KIAA1573	uc001dbo.1	Q5VU97	OTTHUMG00000009030	ENST00000371073.2:c.3511G>C	chr1.hg19:g.65147714G>C	ENSP00000360113:p.Val1171Leu	244.0	0.0		310.0	132.0	NM_020925	Q49AE9|Q658T4|Q7Z3P2|Q9H7W4|Q9H9W3|Q9HCJ9	Missense_Mutation	SNP	ENST00000371073.2	hg19		.	.	.	.	.	.	.	.	.	.	G	16.83	3.232356	0.58777	.	.	ENSG00000158966	ENST00000371073;ENST00000290039	T;T	0.23950	1.88;1.89	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.28101	0.0693	N	0.22421	0.69	0.80722	D	1	P	0.44690	0.841	P	0.58820	0.846	T	0.02214	-1.1194	10	0.44086	T	0.13	-28.5069	20.2985	0.98592	0.0:0.0:1.0:0.0	.	1171	Q5VU97	CAHD1_HUMAN	L	1171;1120	ENSP00000360113:V1171L;ENSP00000290039:V1120L	ENSP00000290039:V1120L	V	+	1	0	CACHD1	64920302	1.000000	0.71417	0.964000	0.40570	0.754000	0.42855	9.374000	0.97172	2.793000	0.96121	0.655000	0.94253	GTC	.	.		0.473	CACHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_020925	
APOA1BP	128240	hgsc.bcm.edu	37	1	156562201	156562201	+	Silent	SNP	G	G	T			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr1:156562201G>T	ENST00000368235.3	+	3	379	c.336G>T	c.(334-336)ctG>ctT	p.L112L	APOA1BP_ENST00000368234.3_Silent_p.L112L|APOA1BP_ENST00000368233.3_Silent_p.L112L|APOA1BP_ENST00000467374.1_3'UTR	NM_144772.2	NP_658985.2			apolipoprotein A-I binding protein											central_nervous_system(1)|large_intestine(2)|lung(3)|prostate(2)|urinary_tract(1)	9	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CTACTGTCCTGGTCATCTGTG	0.582																																					p.L112L		Atlas-SNP	.											.	APOA1BP	16	.	0			c.G336T						.						100.0	101.0	101.0					1																	156562201		2203	4300	6503	SO:0001819	synonymous_variant	128240	exon3			TGTCCTGGTCATC	AJ315849	CCDS1145.1	1q21	2008-08-14			ENSG00000163382	ENSG00000163382			18453	protein-coding gene	gene with protein product	"""apoA-I binding protein"""	608862				11991719, 17533573	Standard	NM_144772		Approved	AIBP, MGC119143, MGC119144, MGC119145, YJEFN1	uc001fph.3	Q8NCW5	OTTHUMG00000033206	ENST00000368235.3:c.336G>T	chr1.hg19:g.156562201G>T		46.0	0.0		105.0	64.0	NM_144772		Silent	SNP	ENST00000368235.3	hg19	CCDS1145.1																																																																																			.	.		0.582	APOA1BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081044.1	NM_144772	
OLFML2B	25903	hgsc.bcm.edu	37	1	161989951	161989951	+	Missense_Mutation	SNP	C	C	T			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr1:161989951C>T	ENST00000294794.3	-	2	619	c.196G>A	c.(196-198)Gtc>Atc	p.V66I	OLFML2B_ENST00000367940.2_Missense_Mutation_p.V66I	NM_015441.1	NP_056256.1	Q68BL8	OLM2B_HUMAN	olfactomedin-like 2B	66					extracellular matrix organization (GO:0030198)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(22)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	48	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.0172)			ATAGCCTTGACCTTGTCATAG	0.567																																					p.V66I		Atlas-SNP	.											.	OLFML2B	114	.	0			c.G196A						.						69.0	67.0	68.0					1																	161989951		2203	4300	6503	SO:0001583	missense	25903	exon2			CCTTGACCTTGTC	BX648975	CCDS1236.1, CCDS72966.1	1q23.1	2008-02-05			ENSG00000162745	ENSG00000162745			24558	protein-coding gene	gene with protein product							Standard	XM_005245075		Approved	DKFZP586L151	uc001gbu.3	Q68BL8	OTTHUMG00000024047	ENST00000294794.3:c.196G>A	chr1.hg19:g.161989951C>T	ENSP00000294794:p.Val66Ile	58.0	0.0		92.0	38.0	NM_015441	B7ZA39|Q5VU96|Q6NX46|Q86X11|Q9Y3X6	Missense_Mutation	SNP	ENST00000294794.3	hg19	CCDS1236.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.738110	0.89573	.	.	ENSG00000162745	ENST00000294794;ENST00000367940	T;T	0.50277	0.75;0.75	4.33	4.33	0.51752	.	.	.	.	.	T	0.47967	0.1474	L	0.56199	1.76	0.35513	D	0.800825	D;D	0.62365	0.976;0.991	P;P	0.55222	0.609;0.771	T	0.55477	-0.8135	8	0.87932	D	0	.	14.7277	0.69357	0.0:1.0:0.0:0.0	.	66;66	F2Z3N3;Q68BL8	.;OLM2B_HUMAN	I	66	ENSP00000294794:V66I;ENSP00000356917:V66I	ENSP00000294794:V66I	V	-	1	0	OLFML2B	160256575	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	7.078000	0.76821	2.404000	0.81709	0.561000	0.74099	GTC	.	.		0.567	OLFML2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060552.2	NM_015441	
CPSF3	51692	hgsc.bcm.edu	37	2	9613123	9613123	+	Missense_Mutation	SNP	G	G	A			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr2:9613123G>A	ENST00000238112.3	+	18	2238	c.2032G>A	c.(2032-2034)Gag>Aag	p.E678K	IAH1_ENST00000545602.1_5'Flank|CPSF3_ENST00000460593.1_Missense_Mutation_p.E641K|IAH1_ENST00000470914.1_5'Flank|IAH1_ENST00000482918.1_5'Flank|IAH1_ENST00000497473.1_5'Flank|CPSF3_ENST00000489403.1_3'UTR	NM_016207.3	NP_057291.1	Q9UKF6	CPSF3_HUMAN	cleavage and polyadenylation specific factor 3, 73kDa	678					gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)|ribonucleoprotein complex (GO:0030529)	5'-3' exonuclease activity (GO:0008409)|endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)			NS(1)|breast(3)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;2.39e-25)|all_epithelial(98;8.75e-19)|Lung NSC(108;2.38e-06)|Ovarian(717;0.0308)		all cancers(51;2.2e-40)|Epithelial(75;6.71e-35)|OV - Ovarian serous cystadenocarcinoma(76;4.35e-21)|STAD - Stomach adenocarcinoma(1183;0.00644)		GAGACTGTACGAGGCCCTGAC	0.438																																					p.E678K	Colon(194;1259 2048 3845 5218 19985)	Atlas-SNP	.											.	CPSF3	63	.	0			c.G2032A						.						86.0	78.0	81.0					2																	9613123		2203	4300	6503	SO:0001583	missense	51692	exon18			CTGTACGAGGCCC	AF171877	CCDS1664.1	2p25.1	2009-01-06	2002-08-29		ENSG00000119203	ENSG00000119203			2326	protein-coding gene	gene with protein product		606029	"""cleavage and polyadenylation specific factor 3, 73kD subunit"""			8929409	Standard	NM_016207		Approved	CPSF-73, CPSF73, YSH1	uc002qzo.2	Q9UKF6	OTTHUMG00000090415	ENST00000238112.3:c.2032G>A	chr2.hg19:g.9613123G>A	ENSP00000238112:p.Glu678Lys	62.0	0.0		98.0	40.0	NM_016207	O14769|Q53RS2|Q96F36	Missense_Mutation	SNP	ENST00000238112.3	hg19	CCDS1664.1	.	.	.	.	.	.	.	.	.	.	G	12.01	1.808479	0.31961	.	.	ENSG00000119203	ENST00000238112;ENST00000540142;ENST00000460593	T;T	0.42513	0.97;0.97	5.24	5.24	0.73138	-end-processing endonuclease polyadenylation factor C-term (1);Pre-mRNA 3&apos (1);	0.171767	0.47852	D	0.000209	T	0.34716	0.0907	L	0.38175	1.15	0.58432	D	0.999991	B	0.20459	0.045	B	0.26416	0.069	T	0.19063	-1.0317	10	0.06236	T	0.91	-5.1796	18.8183	0.92086	0.0:0.0:1.0:0.0	.	678	Q9UKF6	CPSF3_HUMAN	K	678;400;641	ENSP00000238112:E678K;ENSP00000418957:E641K	ENSP00000238112:E678K	E	+	1	0	CPSF3	9530574	1.000000	0.71417	0.976000	0.42696	0.837000	0.47467	8.615000	0.90920	2.453000	0.82957	0.561000	0.74099	GAG	.	.		0.438	CPSF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206843.1	NM_016207	
KCNF1	3754	hgsc.bcm.edu	37	2	11052594	11052594	+	Silent	SNP	C	C	T			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr2:11052594C>T	ENST00000295082.1	+	1	532	c.42C>T	c.(40-42)agC>agT	p.S14S		NM_002236.4	NP_002227.2	Q9H3M0	KCNF1_HUMAN	potassium voltage-gated channel, subfamily F, member 1	14					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)	p.S14R(1)		NS(1)|endometrium(2)|large_intestine(2)|lung(10)|ovary(2)|skin(1)|urinary_tract(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.128)		AGCCGGGCAGCCAGAGCTCCG	0.746																																					p.S14S		Atlas-SNP	.											KCNF1,NS,carcinoma,0,1	KCNF1	70	.	1	Substitution - Missense(1)	lung(1)	c.C42T						.						7.0	8.0	8.0					2																	11052594		2165	4249	6414	SO:0001819	synonymous_variant	3754	exon1			GGGCAGCCAGAGC	AF033382	CCDS1676.1	2p25	2011-07-05			ENSG00000162975	ENSG00000162975		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6246	protein-coding gene	gene with protein product		603787		KCNF		9434767, 16382104	Standard	NM_002236		Approved	Kv5.1, kH1, IK8	uc002rax.3	Q9H3M0	OTTHUMG00000119054	ENST00000295082.1:c.42C>T	chr2.hg19:g.11052594C>T		25.0	0.0		38.0	18.0	NM_002236	O43527|Q585L3	Silent	SNP	ENST00000295082.1	hg19	CCDS1676.1																																																																																			.	.		0.746	KCNF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239265.1	NM_002236	
PFN4	375189	hgsc.bcm.edu	37	2	24342547	24342547	+	Silent	SNP	G	G	A			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr2:24342547G>A	ENST00000313213.4	-	4	632	c.261C>T	c.(259-261)aaC>aaT	p.N87N	PFN4_ENST00000465360.1_5'UTR	NM_199346.1	NP_955378.1	Q8NHR9	PROF4_HUMAN	profilin family, member 4	87					actin cytoskeleton organization (GO:0030036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	lipid binding (GO:0008289)			breast(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCACACCAGTGTTCTCCTGTA	0.453																																					p.N87N		Atlas-SNP	.											.	PFN4	16	.	0			c.C261T						.						85.0	80.0	82.0					2																	24342547		2203	4300	6503	SO:0001819	synonymous_variant	375189	exon4			ACCAGTGTTCTCC	BC029523	CCDS1709.1	2p24.1	2008-02-05			ENSG00000176732	ENSG00000176732			31103	protein-coding gene	gene with protein product							Standard	NM_199346		Approved		uc002rfa.1	Q8NHR9	OTTHUMG00000090816	ENST00000313213.4:c.261C>T	chr2.hg19:g.24342547G>A		41.0	0.0		39.0	16.0	NM_199346	Q53TL9	Silent	SNP	ENST00000313213.4	hg19	CCDS1709.1																																																																																			.	.		0.453	PFN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207617.2	NM_199346	
PLEKHH2	130271	hgsc.bcm.edu	37	2	43956801	43956801	+	Missense_Mutation	SNP	T	T	C			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr2:43956801T>C	ENST00000282406.4	+	18	2857	c.2747T>C	c.(2746-2748)gTt>gCt	p.V916A		NM_172069.3	NP_742066.2	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 2	916	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				negative regulation of actin filament depolymerization (GO:0030835)	cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	actin binding (GO:0003779)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(24)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	56		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				CATCTGACTGTTGCAGCTGGA	0.328																																					p.V916A		Atlas-SNP	.											.	PLEKHH2	156	.	0			c.T2747C						.						96.0	92.0	94.0					2																	43956801		2203	4300	6503	SO:0001583	missense	130271	exon18			TGACTGTTGCAGC	AB095948	CCDS1812.1	2p22	2013-01-10			ENSG00000152527	ENSG00000152527		"""Pleckstrin homology (PH) domain containing"""	30506	protein-coding gene	gene with protein product		612723					Standard	NM_172069		Approved	KIAA2028, PLEKHH1L	uc010yny.2	Q8IVE3	OTTHUMG00000128657	ENST00000282406.4:c.2747T>C	chr2.hg19:g.43956801T>C	ENSP00000282406:p.Val916Ala	75.0	0.0		113.0	44.0	NM_172069	Q5JPJ6|Q6P4Q1|Q8N3Q3	Missense_Mutation	SNP	ENST00000282406.4	hg19	CCDS1812.1	.	.	.	.	.	.	.	.	.	.	T	18.80	3.701077	0.68501	.	.	ENSG00000152527	ENST00000282406	T	0.21734	1.99	5.38	5.38	0.77491	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.065813	0.64402	D	0.000011	T	0.45736	0.1357	M	0.78801	2.425	0.58432	D	0.999998	P;P	0.51351	0.944;0.835	P;B	0.61201	0.885;0.352	T	0.44065	-0.9352	10	0.51188	T	0.08	-18.5117	15.3875	0.74714	0.0:0.0:0.0:1.0	.	916;353	Q8IVE3;Q8IVE3-2	PKHH2_HUMAN;.	A	916	ENSP00000282406:V916A	ENSP00000282406:V916A	V	+	2	0	PLEKHH2	43810305	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.572000	0.82409	2.019000	0.59389	0.528000	0.53228	GTT	.	.		0.328	PLEKHH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250537.1	NM_172069	
DYTN	391475	hgsc.bcm.edu	37	2	207572184	207572184	+	Silent	SNP	A	A	G			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr2:207572184A>G	ENST00000452335.2	-	3	254	c.138T>C	c.(136-138)cgT>cgC	p.R46R	DYTN_ENST00000477734.1_5'Flank	NM_001093730.1	NP_001087199.1	A2CJ06	DYTN_HUMAN	dystrotelin	46						plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(24)|ovary(1)|upper_aerodigestive_tract(1)	36				LUSC - Lung squamous cell carcinoma(261;0.082)|Epithelial(149;0.129)|Lung(261;0.153)		AGAAACTTGGACGCAGTAGGA	0.493																																					p.R46R		Atlas-SNP	.											.	DYTN	168	.	0			c.T138C						.						46.0	46.0	46.0					2																	207572184		1885	4119	6004	SO:0001819	synonymous_variant	391475	exon3			ACTTGGACGCAGT	ABF55377	CCDS46502.1	2q33.3	2007-01-22			ENSG00000232125	ENSG00000232125			23279	protein-coding gene	gene with protein product						17233888	Standard	NM_001093730		Approved		uc002vbr.1	A2CJ06	OTTHUMG00000154729	ENST00000452335.2:c.138T>C	chr2.hg19:g.207572184A>G		127.0	0.0		186.0	79.0	NM_001093730		Silent	SNP	ENST00000452335.2	hg19	CCDS46502.1																																																																																			.	.		0.493	DYTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336799.1		
FN1	2335	hgsc.bcm.edu	37	2	216299523	216299523	+	Missense_Mutation	SNP	T	T	C			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr2:216299523T>C	ENST00000359671.1	-	2	438	c.173A>G	c.(172-174)cAc>cGc	p.H58R	FN1_ENST00000421182.1_Missense_Mutation_p.H58R|AC012462.1_ENST00000412951.1_RNA|FN1_ENST00000446046.1_Missense_Mutation_p.H58R|FN1_ENST00000443816.1_Missense_Mutation_p.H58R|FN1_ENST00000356005.4_Missense_Mutation_p.H58R|FN1_ENST00000426059.1_Missense_Mutation_p.H58R|FN1_ENST00000354785.4_Missense_Mutation_p.H58R|FN1_ENST00000357009.2_Missense_Mutation_p.H58R|FN1_ENST00000323926.6_Missense_Mutation_p.H58R|FN1_ENST00000432072.2_Missense_Mutation_p.H58R|FN1_ENST00000345488.5_Missense_Mutation_p.H58R|FN1_ENST00000346544.3_Missense_Mutation_p.H58R|FN1_ENST00000336916.4_Missense_Mutation_p.H58R|FN1_ENST00000357867.4_Missense_Mutation_p.H58R			P02751	FINC_HUMAN	fibronectin 1	58	Fibrin- and heparin-binding 1.|Fibronectin type-I 1. {ECO:0000255|PROSITE-ProRule:PRU00478}.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	TATCTGATAGTGTTTTCCATT	0.393																																					p.H58R		Atlas-SNP	.											.	FN1	521	.	0			c.A173G						.						189.0	170.0	176.0					2																	216299523		2203	4300	6503	SO:0001583	missense	2335	exon2			TGATAGTGTTTTC		CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"""Fibronectin type III domain containing"", ""Endogenous ligands"""	3778	protein-coding gene	gene with protein product	"""migration-stimulating factor"", ""cold-insoluble globulin"""	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.173A>G	chr2.hg19:g.216299523T>C	ENSP00000352696:p.His58Arg	69.0	0.0		85.0	37.0	NM_212476	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Missense_Mutation	SNP	ENST00000359671.1	hg19		.	.	.	.	.	.	.	.	.	.	T	18.79	3.698852	0.68501	.	.	ENSG00000115414	ENST00000421182;ENST00000323926;ENST00000336916;ENST00000357867;ENST00000354785;ENST00000265313;ENST00000359671;ENST00000346544;ENST00000345488;ENST00000357009;ENST00000446046;ENST00000443816;ENST00000432072;ENST00000356005;ENST00000426059	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93	6.06	6.06	0.98353	.	0.083281	0.52532	D	0.000071	T	0.43634	0.1256	N	0.08118	0	0.38596	D	0.950543	P;D;B;P;P;P;P;P;P;P;P	0.61697	0.495;0.99;0.001;0.801;0.61;0.662;0.731;0.93;0.61;0.61;0.913	B;D;B;P;B;B;B;P;B;B;P	0.74348	0.356;0.983;0.004;0.569;0.154;0.239;0.395;0.596;0.154;0.154;0.519	T	0.48281	-0.9049	10	0.19147	T	0.46	.	16.6093	0.84858	0.0:0.0:0.0:1.0	.	58;58;58;58;58;58;58;58;58;58;58	E9PG29;P02751-13;P02751-7;P02751-10;P02751-8;E9PE77;P02751-3;E7ERA1;P02751-9;P02751-14;P02751-15	.;.;.;.;.;.;.;.;.;.;.	R	58	ENSP00000394423:H58R;ENSP00000323534:H58R;ENSP00000338200:H58R;ENSP00000350534:H58R;ENSP00000346839:H58R;ENSP00000352696:H58R;ENSP00000265312:H58R;ENSP00000273049:H58R;ENSP00000349509:H58R;ENSP00000410422:H58R;ENSP00000415018:H58R;ENSP00000399538:H58R;ENSP00000348285:H58R;ENSP00000398907:H58R	ENSP00000265313:H58R	H	-	2	0	FN1	216007768	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.843000	0.55865	2.324000	0.78689	0.533000	0.62120	CAC	.	.		0.393	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476	
RRP9	9136	hgsc.bcm.edu	37	3	51970364	51970364	+	Splice_Site	SNP	G	G	C			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr3:51970364G>C	ENST00000232888.6	-	8	717	c.644C>G	c.(643-645)gCc>gGc	p.A215G		NM_004704.3	NP_004695.1	O43818	U3IP2_HUMAN	ribosomal RNA processing 9, small subunit (SSU) processome component, homolog (yeast)	215					rRNA processing (GO:0006364)	nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(1)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|ovary(1)|skin(1)	21				BRCA - Breast invasive adenocarcinoma(193;8.04e-05)|Kidney(197;0.000553)|KIRC - Kidney renal clear cell carcinoma(197;0.000724)		GTCACCAGAGGCCTGCAGGGA	0.607																																					p.A215G		Atlas-SNP	.											.	RRP9	40	.	0			c.C644G						.						112.0	112.0	112.0					3																	51970364		2203	4300	6503	SO:0001630	splice_region_variant	9136	exon8			CCAGAGGCCTGCA	AJ001340	CCDS2837.1	3p21.31	2013-01-10	2008-02-26	2006-10-24	ENSG00000114767	ENSG00000114767		"""WD repeat domain containing"""	16829	protein-coding gene	gene with protein product			"""RNA, U3 small nucleolar interacting protein 2"""	RNU3IP2		9418896, 12032086	Standard	NM_004704		Approved	U3-55K	uc003dbw.2	O43818	OTTHUMG00000156930	ENST00000232888.6:c.643-1C>G	chr3.hg19:g.51970364G>C		106.0	0.0		154.0	65.0	NM_004704	B2R996|Q8IZ30	Missense_Mutation	SNP	ENST00000232888.6	hg19	CCDS2837.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.936879	0.73557	.	.	ENSG00000114767	ENST00000232888	T	0.70045	-0.45	5.3	5.3	0.74995	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	D	0.86083	0.5848	M	0.90922	3.16	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.89186	0.3547	10	0.87932	D	0	-19.0591	18.5692	0.91129	0.0:0.0:1.0:0.0	.	215	O43818	U3IP2_HUMAN	G	215	ENSP00000232888:A215G	ENSP00000232888:A215G	A	-	2	0	RRP9	51945404	1.000000	0.71417	1.000000	0.80357	0.290000	0.27261	7.342000	0.79310	2.494000	0.84150	0.655000	0.94253	GCC	.	.		0.607	RRP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346637.1	NM_004704	Missense_Mutation
MGLL	11343	hgsc.bcm.edu	37	3	127540605	127540605	+	Silent	SNP	G	G	T			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr3:127540605G>T	ENST00000434178.2	-	2	953	c.57C>A	c.(55-57)ctC>ctA	p.L19L	MGLL_ENST00000453507.2_Silent_p.L29L|MGLL_ENST00000265052.5_Silent_p.L29L|MGLL_ENST00000398104.1_Silent_p.L19L			Q99685	MGLL_HUMAN	monoglyceride lipase	19					acylglycerol acyl-chain remodeling (GO:0036155)|acylglycerol catabolic process (GO:0046464)|arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|fatty acid biosynthetic process (GO:0006633)|glycerophospholipid biosynthetic process (GO:0046474)|inflammatory response (GO:0006954)|lipid metabolic process (GO:0006629)|long term synaptic depression (GO:0060292)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|regulation of endocannabinoid signaling pathway (GO:2000124)|regulation of inflammatory response (GO:0050727)|regulation of sensory perception of pain (GO:0051930)|regulation of signal transduction (GO:0009966)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	endoplasmic reticulum membrane (GO:0005789)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acylglycerol lipase activity (GO:0047372)|lipid binding (GO:0008289)|lysophospholipase activity (GO:0004622)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	6						CCAGGTGAGGGAGGTCCTGGT	0.557																																					p.L29L		Atlas-SNP	.											MGLL,NS,carcinoma,0,1	MGLL	19	.	0			c.C87A						.						120.0	125.0	124.0					3																	127540605		1904	4111	6015	SO:0001819	synonymous_variant	11343	exon2			GTGAGGGAGGTCC	BC000551	CCDS43148.1, CCDS46902.1, CCDS58852.1	3p13-q13.33	2014-03-14			ENSG00000074416	ENSG00000074416	3.1.1.23		17038	protein-coding gene	gene with protein product		609699				9495531	Standard	NM_007283		Approved	HU-K5, MGL	uc003ejx.4	Q99685	OTTHUMG00000159641	ENST00000434178.2:c.57C>A	chr3.hg19:g.127540605G>T		78.0	0.0		126.0	51.0	NM_007283	B3KRC2|B7Z9D1|Q6IBG9|Q96AA5	Silent	SNP	ENST00000434178.2	hg19	CCDS43148.1																																																																																			.	.		0.557	MGLL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356637.2	NM_007283	
SLC25A36	55186	hgsc.bcm.edu	37	3	140660913	140660913	+	Missense_Mutation	SNP	C	C	T			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr3:140660913C>T	ENST00000324194.6	+	1	185	c.17C>T	c.(16-18)aCg>aTg	p.T6M	SLC25A36_ENST00000507429.1_Missense_Mutation_p.T6M|SLC25A36_ENST00000446041.2_Missense_Mutation_p.T6M|SLC25A36_ENST00000393015.4_3'UTR|SLC25A36_ENST00000453248.2_Missense_Mutation_p.T6M			Q96CQ1	S2536_HUMAN	solute carrier family 25 (pyrimidine nucleotide carrier ), member 36	6					response to estradiol (GO:0032355)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				endometrium(2)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	6						CAGAGGGACACGCTGGTGCAT	0.721																																					p.T6M		Atlas-SNP	.											.	SLC25A36	24	.	0			c.C17T						.						65.0	47.0	54.0					3																	140660913		1787	3423	5210	SO:0001583	missense	55186	exon1			GGGACACGCTGGT	AK001480	CCDS3114.1, CCDS46927.1	3q23	2013-05-22	2012-03-29		ENSG00000114120	ENSG00000114120		"""Solute carriers"""	25554	protein-coding gene	gene with protein product			"""solute carrier family 25, member 36"""				Standard	NM_001104647		Approved	FLJ10618, PNC2	uc003etr.2	Q96CQ1	OTTHUMG00000160260	ENST00000324194.6:c.17C>T	chr3.hg19:g.140660913C>T	ENSP00000320688:p.Thr6Met	128.0	0.0		178.0	89.0	NM_018155	A8MYF7|Q05CY1|Q9H0G8|Q9NVN5	Missense_Mutation	SNP	ENST00000324194.6	hg19	CCDS46927.1	.	.	.	.	.	.	.	.	.	.	C	15.56	2.870636	0.51588	.	.	ENSG00000114120	ENST00000446041;ENST00000507429;ENST00000324194;ENST00000453248	T;T;T;T	0.78924	-1.22;-1.22;-1.22;-1.22	4.88	4.0	0.46444	Mitochondrial carrier domain (2);	0.259837	0.43919	D	0.000513	T	0.72716	0.3495	L	0.47190	1.495	0.52099	D	0.999942	P;B;P;P	0.46952	0.535;0.291;0.887;0.48	B;B;B;B	0.44085	0.228;0.146;0.44;0.146	T	0.74185	-0.3747	10	0.56958	D	0.05	-7.9419	10.9965	0.47580	0.0:0.8116:0.1884:0.0	.	6;6;6;6	B4DL01;Q96CQ1-3;Q96CQ1;F6SDC8	.;.;S2536_HUMAN;.	M	6	ENSP00000401938:T6M;ENSP00000421470:T6M;ENSP00000320688:T6M;ENSP00000391521:T6M	ENSP00000320688:T6M	T	+	2	0	SLC25A36	142143603	1.000000	0.71417	1.000000	0.80357	0.693000	0.40251	2.019000	0.41001	1.248000	0.43934	0.561000	0.74099	ACG	.	.		0.721	SLC25A36-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359929.1	NM_018155	
EVC2	132884	hgsc.bcm.edu	37	4	5624510	5624510	+	Missense_Mutation	SNP	C	C	T	rs139717271		TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr4:5624510C>T	ENST00000344408.5	-	14	2308	c.2255G>A	c.(2254-2256)cGg>cAg	p.R752Q	EVC2_ENST00000310917.2_Missense_Mutation_p.R672Q|EVC2_ENST00000344938.1_Missense_Mutation_p.R752Q	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	752					smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						CTGCAGGCGCCGCAGCTCGTC	0.647																																					p.R752Q		Atlas-SNP	.											EVC2,colon,carcinoma,-1,1	EVC2	202	.	0			c.G2255A						.	C	GLN/ARG,GLN/ARG	2,4404	4.2+/-10.8	0,2,2201	50.0	47.0	48.0		2015,2255	4.5	1.0	4	dbSNP_134	48	0,8600		0,0,4300	no	missense,missense	EVC2	NM_001166136.1,NM_147127.4	43,43	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	probably-damaging,probably-damaging	672/1229,752/1309	5624510	2,13004	2203	4300	6503	SO:0001583	missense	132884	exon14			AGGCGCCGCAGCT	AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.2255G>A	chr4.hg19:g.5624510C>T	ENSP00000342144:p.Arg752Gln	116.0	0.0		143.0	61.0	NM_147127	Q86YT3|Q86YT4|Q8NG49	Missense_Mutation	SNP	ENST00000344408.5	hg19	CCDS3382.2	.	.	.	.	.	.	.	.	.	.	C	22.4	4.278417	0.80692	4.54E-4	0.0	ENSG00000173040	ENST00000344938;ENST00000310917;ENST00000344408	T;T;T	0.74315	-0.83;-0.82;-0.82	5.32	4.48	0.54585	.	0.235349	0.34291	N	0.004084	T	0.72938	0.3523	L	0.54323	1.7	0.27599	N	0.949033	D	0.71674	0.998	P	0.51895	0.683	T	0.64019	-0.6505	10	0.18710	T	0.47	-27.5673	9.3644	0.38215	0.0:0.819:0.0:0.181	.	752	Q86UK5	LBN_HUMAN	Q	752;672;752	ENSP00000339954:R752Q;ENSP00000311683:R672Q;ENSP00000342144:R752Q	ENSP00000311683:R672Q	R	-	2	0	EVC2	5675411	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	2.807000	0.47955	1.245000	0.43885	0.462000	0.41574	CGG	.	C|1.000;T|0.000		0.647	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127	
SLIT2	9353	hgsc.bcm.edu	37	4	20535222	20535222	+	Silent	SNP	T	T	C			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr4:20535222T>C	ENST00000504154.1	+	18	1968	c.1716T>C	c.(1714-1716)gaT>gaC	p.D572D	SLIT2_ENST00000503823.1_Silent_p.D564D|SLIT2_ENST00000503837.1_Silent_p.D568D|SLIT2_ENST00000273739.5_Silent_p.D576D	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	572					apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)			NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						AGATCACAGATATTGAGGAGG	0.328																																					p.D572D		Atlas-SNP	.											.	SLIT2	290	.	0			c.T1716C						.						93.0	94.0	94.0					4																	20535222		2203	4300	6503	SO:0001819	synonymous_variant	9353	exon18			CACAGATATTGAG	AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"""slit (Drosophila) homolog 2"""	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	ENST00000504154.1:c.1716T>C	chr4.hg19:g.20535222T>C		587.0	0.0		634.0	274.0	NM_004787	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Silent	SNP	ENST00000504154.1	hg19	CCDS3426.1																																																																																			.	.		0.328	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2		
WDFY3	23001	hgsc.bcm.edu	37	4	85758098	85758098	+	Missense_Mutation	SNP	T	T	A			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr4:85758098T>A	ENST00000295888.4	-	7	967	c.560A>T	c.(559-561)cAg>cTg	p.Q187L	WDFY3_ENST00000322366.6_Missense_Mutation_p.Q187L	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	187					aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		AAAAACTTTCTGGAGTAGTCC	0.408																																					p.Q187L		Atlas-SNP	.											.	WDFY3	314	.	0			c.A560T						.						92.0	79.0	84.0					4																	85758098		2203	4300	6503	SO:0001583	missense	23001	exon7			ACTTTCTGGAGTA	AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"""Zinc fingers, FYVE domain containing"", ""WD repeat domain containing"""	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.560A>T	chr4.hg19:g.85758098T>A	ENSP00000295888:p.Gln187Leu	343.0	1.0		464.0	173.0	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Missense_Mutation	SNP	ENST00000295888.4	hg19	CCDS3609.1	.	.	.	.	.	.	.	.	.	.	T	27.5	4.837935	0.91117	.	.	ENSG00000163625	ENST00000322366;ENST00000295888	T;T	0.68025	-0.29;-0.3	5.76	5.76	0.90799	.	0.054736	0.85682	D	0.000000	T	0.81211	0.4775	M	0.71581	2.175	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.87578	0.998;0.996	T	0.82835	-0.0261	10	0.62326	D	0.03	.	16.0697	0.80914	0.0:0.0:0.0:1.0	.	187;187	E2QRK8;Q8IZQ1	.;WDFY3_HUMAN	L	187	ENSP00000318466:Q187L;ENSP00000295888:Q187L	ENSP00000295888:Q187L	Q	-	2	0	WDFY3	85977122	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.542000	0.82095	2.190000	0.69967	0.374000	0.22700	CAG	.	.		0.408	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991	
GLRA3	8001	hgsc.bcm.edu	37	4	175636670	175636670	+	Silent	SNP	A	A	G			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr4:175636670A>G	ENST00000274093.3	-	5	1045	c.543T>C	c.(541-543)gaT>gaC	p.D181D	GLRA3_ENST00000340217.5_Silent_p.D181D	NM_006529.2	NP_006520.2	O75311	GLRA3_HUMAN	glycine receptor, alpha 3	181					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glycine-gated chloride channel activity (GO:0016934)|glycine binding (GO:0016594)|transmitter-gated ion channel activity (GO:0022824)			endometrium(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(3)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	35		Prostate(90;0.00601)|Breast(14;0.0091)|Melanoma(52;0.00959)|Renal(120;0.0183)|all_neural(102;0.0891)|all_hematologic(60;0.107)		all cancers(43;4.99e-18)|Epithelial(43;1.18e-16)|OV - Ovarian serous cystadenocarcinoma(60;5.88e-09)|STAD - Stomach adenocarcinoma(60;0.00442)|GBM - Glioblastoma multiforme(59;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0421)	Glycine(DB00145)|Ivermectin(DB00602)|Lindane(DB00431)	ATGTTTGTACATCCATGGGAA	0.274																																					p.D181D		Atlas-SNP	.											.	GLRA3	76	.	0			c.T543C						.						79.0	82.0	81.0					4																	175636670		2203	4295	6498	SO:0001819	synonymous_variant	8001	exon5			TTGTACATCCATG	AF017724	CCDS3822.1, CCDS43283.1	4q34.1	2012-02-07			ENSG00000145451	ENSG00000145451		"""Ligand-gated ion channels / Glycine receptors"""	4328	protein-coding gene	gene with protein product		600421				9677400	Standard	NM_001042543		Approved		uc003ity.1	O75311	OTTHUMG00000149816	ENST00000274093.3:c.543T>C	chr4.hg19:g.175636670A>G		389.0	1.0		555.0	230.0	NM_001042543	D3DP44|O75816|Q5D0E3	Silent	SNP	ENST00000274093.3	hg19	CCDS3822.1																																																																																			.	.		0.274	GLRA3-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313427.1		
SLC6A19	340024	hgsc.bcm.edu	37	5	1219158	1219158	+	Silent	SNP	C	C	T	rs141604151		TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr5:1219158C>T	ENST00000304460.10	+	9	1370	c.1314C>T	c.(1312-1314)ggC>ggT	p.G438G		NM_001003841.2	NP_001003841.1	Q695T7	S6A19_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 19	438					amino acid transport (GO:0006865)|ion transport (GO:0006811)|response to nutrient (GO:0007584)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)|neutral amino acid transmembrane transporter activity (GO:0015175)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(25)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	44	all_cancers(3;3.55e-15)|Lung NSC(6;2.89e-14)|all_lung(6;2.2e-13)|all_epithelial(6;3.75e-10)		Epithelial(17;0.000356)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			ACATGGAGGGCGTCGTTGTGC	0.587																																					p.G438G		Atlas-SNP	.											.	SLC6A19	99	.	0			c.C1314T						.	C		0,4406		0,0,2203	318.0	250.0	273.0		1314	-8.6	0.4	5	dbSNP_134	273	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	SLC6A19	NM_001003841.2		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		438/635	1219158	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	340024	exon9			GGAGGGCGTCGTT	AK096054	CCDS34130.1	5p15	2013-07-19			ENSG00000174358	ENSG00000174358		"""Solute carriers"""	27960	protein-coding gene	gene with protein product	"""Hartnup disease"""	608893					Standard	NM_001003841		Approved		uc003jbw.4	Q695T7	OTTHUMG00000161636	ENST00000304460.10:c.1314C>T	chr5.hg19:g.1219158C>T		62.0	0.0		139.0	39.0	NM_001003841	A8K446	Silent	SNP	ENST00000304460.10	hg19	CCDS34130.1																																																																																			.	C|1.000;T|0.000		0.587	SLC6A19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365557.1	XM_291120	
C5orf42	65250	hgsc.bcm.edu	37	5	37170312	37170312	+	Nonsense_Mutation	SNP	G	G	C			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr5:37170312G>C	ENST00000508244.1	-	32	6386	c.6293C>G	c.(6292-6294)tCa>tGa	p.S2098*	C5orf42_ENST00000274258.7_Nonsense_Mutation_p.S978*|C5orf42_ENST00000425232.2_Nonsense_Mutation_p.S2098*			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	2098						integral component of membrane (GO:0016021)				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			TCTTAGGTTTGATTCTTGGCT	0.413																																					p.S2098X		Atlas-SNP	.											.	C5orf42	422	.	0			c.C6293G						.						186.0	181.0	183.0					5																	37170312		2203	4300	6503	SO:0001587	stop_gained	65250	exon33			AGGTTTGATTCTT		CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.6293C>G	chr5.hg19:g.37170312G>C	ENSP00000421690:p.Ser2098*	102.0	0.0		152.0	67.0	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Nonsense_Mutation	SNP	ENST00000508244.1	hg19	CCDS34146.2	.	.	.	.	.	.	.	.	.	.	G	58	32.101669	0.99979	.	.	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429;ENST00000388739	.	.	.	5.79	3.57	0.40892	.	1.506760	0.04150	N	0.321100	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.32370	T	0.25	.	9.2163	0.37348	0.3276:0.0:0.6724:0.0	.	.	.	.	X	2098;2098;978;1146;978	.	ENSP00000274258:S978X	S	-	2	0	C5orf42	37206069	0.000000	0.05858	0.001000	0.08648	0.744000	0.42396	0.174000	0.16743	0.509000	0.28195	0.555000	0.69702	TCA	.	.		0.413	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073	
RBM22	55696	hgsc.bcm.edu	37	5	150071321	150071321	+	Missense_Mutation	SNP	T	T	G			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr5:150071321T>G	ENST00000199814.4	-	11	1376	c.1255A>C	c.(1255-1257)Agc>Cgc	p.S419R	RBM22_ENST00000447771.2_Missense_Mutation_p.S370R|RBM22_ENST00000540000.1_Missense_Mutation_p.S370R	NM_018047.2	NP_060517.1	Q9NW64	RBM22_HUMAN	RNA binding motif protein 22	419					cellular response to drug (GO:0035690)|mRNA cis splicing, via spliceosome (GO:0045292)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of RNA splicing (GO:0033120)|protein import into nucleus, translocation (GO:0000060)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium-dependent protein binding (GO:0048306)|metal ion binding (GO:0046872)|nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|pre-mRNA binding (GO:0036002)|snRNA binding (GO:0017069)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(4)|ovary(1)	17		Medulloblastoma(196;0.167)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGCTAGGGGCTGCTGTGTTTT	0.512																																					p.S419R		Atlas-SNP	.											.	RBM22	33	.	0			c.A1255C						.						105.0	107.0	107.0					5																	150071321		2203	4300	6503	SO:0001583	missense	55696	exon11			AGGGGCTGCTGTG	AL136933	CCDS34278.1	5q33.1	2013-02-12			ENSG00000086589	ENSG00000086589		"""Zinc fingers, CCCH-type domain containing"", ""RNA binding motif (RRM) containing"""	25503	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 47"""	612430				20013661, 19133299	Standard	NM_018047		Approved	FLJ10290, ZC3H16, fSAP47, Cwc2	uc031slu.1	Q9NW64	OTTHUMG00000163589	ENST00000199814.4:c.1255A>C	chr5.hg19:g.150071321T>G	ENSP00000199814:p.Ser419Arg	57.0	0.0		79.0	27.0	NM_018047	A6NDM5|B4DLI9|O95607	Missense_Mutation	SNP	ENST00000199814.4	hg19	CCDS34278.1	.	.	.	.	.	.	.	.	.	.	T	13.99	2.401385	0.42613	.	.	ENSG00000086589	ENST00000199814;ENST00000540000;ENST00000447771	.	.	.	6.02	6.02	0.97574	.	0.122178	0.85682	D	0.000000	T	0.43523	0.1251	N	0.08118	0	0.46701	D	0.999168	B	0.31910	0.346	B	0.35655	0.207	T	0.49744	-0.8907	9	0.59425	D	0.04	-28.0363	16.5446	0.84426	0.0:0.0:0.0:1.0	.	419	Q9NW64	RBM22_HUMAN	R	419;370;370	.	ENSP00000199814:S419R	S	-	1	0	RBM22	150051514	1.000000	0.71417	1.000000	0.80357	0.629000	0.37895	4.573000	0.60893	2.311000	0.77944	0.533000	0.62120	AGC	.	.		0.512	RBM22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374431.2	NM_018047	
BOD1	91272	hgsc.bcm.edu	37	5	173036375	173036375	+	Missense_Mutation	SNP	T	T	C			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr5:173036375T>C	ENST00000311086.4	-	3	648	c.425A>G	c.(424-426)aAc>aGc	p.N142S	BOD1_ENST00000285908.5_Intron|BOD1_ENST00000480951.1_Intron|BOD1_ENST00000471339.1_5'Flank	NM_138369.2	NP_612378.1	Q96IK1	BOD1_HUMAN	biorientation of chromosomes in cell division 1	142					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|kinetochore (GO:0000776)				endometrium(1)|large_intestine(2)|lung(2)|ovary(2)	7						GAAGATGTGGTTAAGTTTTGG	0.493																																					p.N142S		Atlas-SNP	.											.	BOD1	15	.	0			c.A425G						.						157.0	141.0	146.0					5																	173036375		2203	4300	6503	SO:0001583	missense	91272	exon3			ATGTGGTTAAGTT	AY303777	CCDS4389.1, CCDS54951.1	5q35.2	2013-10-11	2009-03-04	2009-03-04	ENSG00000145919	ENSG00000145919			25114	protein-coding gene	gene with protein product	"""biorientation defective 1"""		"""family with sequence similarity 44, member B"""	FAM44B		17938248	Standard	NM_138369		Approved		uc003mcq.2	Q96IK1	OTTHUMG00000130540	ENST00000311086.4:c.425A>G	chr5.hg19:g.173036375T>C	ENSP00000309644:p.Asn142Ser	65.0	0.0		109.0	44.0	NM_138369	B4DXH8|Q9BTW1	Missense_Mutation	SNP	ENST00000311086.4	hg19	CCDS4389.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.099105	0.76983	.	.	ENSG00000145919	ENST00000311086;ENST00000462674	.	.	.	5.65	5.65	0.86999	.	0.085313	0.85682	D	0.000000	T	0.54935	0.1889	L	0.34521	1.04	0.80722	D	1	P	0.41498	0.752	P	0.46479	0.518	T	0.51450	-0.8704	9	0.28530	T	0.3	-38.5526	15.8715	0.79122	0.0:0.0:0.0:1.0	.	142	Q96IK1	BOD1_HUMAN	S	142;37	.	ENSP00000309644:N142S	N	-	2	0	BOD1	172968981	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	7.684000	0.84104	2.155000	0.67459	0.533000	0.62120	AAC	.	.		0.493	BOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252963.1	NM_138369	
HIST1H4C	8364	hgsc.bcm.edu	37	6	26104293	26104293	+	Missense_Mutation	SNP	C	C	G			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr6:26104293C>G	ENST00000377803.2	+	1	190	c.118C>G	c.(118-120)Cgg>Ggg	p.R40G		NM_003542.3	NP_003533.1	P62805	H4_HUMAN	histone cluster 1, H4c	40					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of megakaryocyte differentiation (GO:0045653)|nucleosome assembly (GO:0006334)|telomere maintenance (GO:0000723)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|histone demethylase activity (H4-K20 specific) (GO:0035575)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|skin(1)	7						CCGTTTGGCTCGGCGCGGTGG	0.542																																					p.R40G		Atlas-SNP	.											.	HIST1H4C	14	.	0			c.C118G						.						62.0	62.0	62.0					6																	26104293		2203	4300	6503	SO:0001583	missense	8364	exon1			TTGGCTCGGCGCG	X60486	CCDS4583.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000197061	ENSG00000197061		"""Histones / Replication-dependent"""	4787	protein-coding gene	gene with protein product		602827	"""H4 histone family, member G"", ""histone 1, H4c"""	H4FG		9119399, 12408966	Standard	NM_003542		Approved	H4/g, dJ221C16.1	uc003ngi.3	P62805	OTTHUMG00000014429	ENST00000377803.2:c.118C>G	chr6.hg19:g.26104293C>G	ENSP00000367034:p.Arg40Gly	96.0	0.0		146.0	7.0	NM_003542	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Missense_Mutation	SNP	ENST00000377803.2	hg19	CCDS4583.1	.	.	.	.	.	.	.	.	.	.	.	17.58	3.424850	0.62733	.	.	ENSG00000197061	ENST00000377803	T	0.77620	-1.11	4.57	4.57	0.56435	.	0.000000	0.85682	D	0.000000	D	0.83695	0.5310	.	.	.	0.80722	D	1	.	.	.	.	.	.	D	0.85878	0.1420	7	0.87932	D	0	.	16.8752	0.86050	0.0:1.0:0.0:0.0	.	.	.	.	G	40	ENSP00000367034:R40G	ENSP00000367034:R40G	R	+	1	2	HIST1H4C	26212272	1.000000	0.71417	0.734000	0.30879	0.009000	0.06853	7.642000	0.83385	2.538000	0.85594	0.561000	0.74099	CGG	.	.		0.542	HIST1H4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040092.2	NM_003542	
FAM83B	222584	hgsc.bcm.edu	37	6	54805688	54805688	+	Missense_Mutation	SNP	A	A	G	rs239798	byFrequency	TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr6:54805688A>G	ENST00000306858.7	+	5	2035	c.1919A>G	c.(1918-1920)aAa>aGa	p.K640R	RP3-523K23.2_ENST00000562834.1_RNA	NM_001010872.1	NP_001010872.1	Q5T0W9	FA83B_HUMAN	family with sequence similarity 83, member B	640			K -> T (in dbSNP:rs239798). {ECO:0000269|PubMed:15489334}.					p.K640T(1)		autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(28)|ovary(6)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	71	Lung NSC(77;0.0178)|Renal(3;0.122)					TATATATATAAAACCTTGGGT	0.373																																					p.K640R		Atlas-SNP	.											FAM83B,NS,carcinoma,0,1	FAM83B	186	.	1	Substitution - Missense(1)	prostate(1)	c.A1919G						.						41.0	43.0	42.0					6																	54805688		2198	4297	6495	SO:0001583	missense	222584	exon5			TATATAAAACCTT	AK055204	CCDS34479.1	6p12.1	2014-03-13	2006-03-23	2006-03-23	ENSG00000168143	ENSG00000168143			21357	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 143"""	C6orf143		22886302	Standard	NM_001010872		Approved	FLJ30642	uc003pck.4	Q5T0W9	OTTHUMG00000014899	ENST00000306858.7:c.1919A>G	chr6.hg19:g.54805688A>G	ENSP00000304078:p.Lys640Arg	218.0	1.0		266.0	113.0	NM_001010872	Q2M1P3|Q96DQ2	Missense_Mutation	SNP	ENST00000306858.7	hg19	CCDS34479.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.022864	0.75275	.	.	ENSG00000168143	ENST00000306858	T	0.30182	1.54	5.55	4.66	0.58398	.	0.865524	0.10264	N	0.695617	T	0.08492	0.0211	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.16012	-1.0417	9	0.45353	T	0.12	-7.5696	15.0301	0.71698	0.2604:0.7396:0.0:0.0	.	640	Q5T0W9	FA83B_HUMAN	R	640	ENSP00000304078:K640R	ENSP00000304078:K640R	K	+	2	0	FAM83B	54913647	0.528000	0.26314	0.067000	0.19924	0.901000	0.52897	4.107000	0.57811	0.801000	0.34066	-0.121000	0.15023	AAA	.	A|0.690;C|0.310		0.373	FAM83B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040994.1	XM_294139	
PRDM13	59336	hgsc.bcm.edu	37	6	100061789	100061789	+	Silent	SNP	G	G	T			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr6:100061789G>T	ENST00000369215.4	+	4	1583	c.1278G>T	c.(1276-1278)gcG>gcT	p.A426A		NM_021620.3	NP_067633.2	Q9H4Q3	PRD13_HUMAN	PR domain containing 13	426					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurogenesis (GO:0022008)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(9)|prostate(1)	17		all_cancers(76;1.64e-05)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0128)|Colorectal(196;0.069)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.0598)		TGCCCCCTGCGCCGGGGTTGC	0.756																																					p.A426A		Atlas-SNP	.											.	PRDM13	65	.	0			c.G1278T						.						8.0	9.0	9.0					6																	100061789		1499	3370	4869	SO:0001819	synonymous_variant	59336	exon4			CCCTGCGCCGGGG	AY004253	CCDS43487.1	6q16.2	2012-03-28			ENSG00000112238	ENSG00000112238			13998	protein-coding gene	gene with protein product							Standard	NM_021620		Approved		uc003pqg.1	Q9H4Q3	OTTHUMG00000015269	ENST00000369215.4:c.1278G>T	chr6.hg19:g.100061789G>T		36.0	0.0		55.0	18.0	NM_021620	Q5TGC1|Q5TGC2	Silent	SNP	ENST00000369215.4	hg19	CCDS43487.1																																																																																			.	.		0.756	PRDM13-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041619.2		
NR2E1	7101	hgsc.bcm.edu	37	6	108502144	108502144	+	Silent	SNP	C	C	A	rs368041869		TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr6:108502144C>A	ENST00000368986.4	+	7	1581	c.873C>A	c.(871-873)atC>atA	p.I291I	NR2E1_ENST00000368983.3_Silent_p.I328I	NM_003269.3	NP_003260.1	Q9Y466	NR2E1_HUMAN	nuclear receptor subfamily 2, group E, member 1	291	Ligand-binding. {ECO:0000250}.				aggressive behavior (GO:0002118)|amygdala development (GO:0021764)|anterior commissure morphogenesis (GO:0021960)|behavioral fear response (GO:0001662)|cell fate commitment (GO:0045165)|cerebral cortex neuron differentiation (GO:0021895)|dentate gyrus development (GO:0021542)|extracellular matrix organization (GO:0030198)|forebrain generation of neurons (GO:0021872)|gene expression (GO:0010467)|glial cell migration (GO:0008347)|layer formation in cerebral cortex (GO:0021819)|long-term synaptic potentiation (GO:0060291)|negative regulation of apoptotic process (GO:0043066)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron differentiation (GO:0045665)|nervous system development (GO:0007399)|olfactory bulb development (GO:0021772)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle (GO:0045787)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of stem cell proliferation (GO:2000648)|regulation of cell migration involved in sprouting angiogenesis (GO:0090049)|regulation of dendrite morphogenesis (GO:0048814)|regulation of timing of neuron differentiation (GO:0060164)|retina development in camera-type eye (GO:0060041)|social behavior (GO:0035176)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|visual perception (GO:0007601)	nucleoplasm (GO:0005654)	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)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.I291I(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(4)|liver(1)|lung(16)|prostate(1)|skin(3)	30		all_cancers(87;8.13e-05)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00866)|Colorectal(196;0.0637)		BRCA - Breast invasive adenocarcinoma(108;0.013)|Epithelial(106;0.0521)|all cancers(137;0.068)|OV - Ovarian serous cystadenocarcinoma(136;0.0689)		TAAAATGCATCGTCACTTTCA	0.458																																					p.I291I		Atlas-SNP	.											NR2E1,NS,carcinoma,0,1	NR2E1	57	.	1	Substitution - coding silent(1)	endometrium(1)	c.C873A						.						160.0	157.0	158.0					6																	108502144		2203	4300	6503	SO:0001819	synonymous_variant	7101	exon7			ATGCATCGTCACT	Y13276	CCDS5063.1, CCDS69165.1	6q21	2013-01-16			ENSG00000112333	ENSG00000112333		"""Nuclear hormone receptors"""	7973	protein-coding gene	gene with protein product		603849		TLX		9628820	Standard	NM_003269		Approved	TLL, XTLL	uc003psg.3	Q9Y466	OTTHUMG00000015319	ENST00000368986.4:c.873C>A	chr6.hg19:g.108502144C>A		112.0	0.0		154.0	70.0	NM_003269	Q6ZMP8	Silent	SNP	ENST00000368986.4	hg19	CCDS5063.1																																																																																			.	.		0.458	NR2E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041712.2		
COL10A1	1300	hgsc.bcm.edu	37	6	116442516	116442516	+	Missense_Mutation	SNP	G	G	T			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr6:116442516G>T	ENST00000327673.4	-	2	1170	c.763C>A	c.(763-765)Cct>Act	p.P255T	AL121963.1_ENST00000430695.1_Missense_Mutation_p.G57V|COL10A1_ENST00000243222.4_Missense_Mutation_p.P255T|NT5DC1_ENST00000319550.4_Intron			Q03692	COAA1_HUMAN	collagen, type X, alpha 1	255	Triple-helical region.				cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	cell cortex (GO:0005938)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|lung(6)|skin(3)|upper_aerodigestive_tract(1)	13		all_cancers(87;0.0176)|all_epithelial(87;0.0263)|Colorectal(196;0.234)		all cancers(137;0.0157)|OV - Ovarian serous cystadenocarcinoma(136;0.0325)|GBM - Glioblastoma multiforme(226;0.0446)|Epithelial(106;0.0711)		CGTTCCCCAGGAGGGCCTTGG	0.597																																					p.P255T		Atlas-SNP	.											.	COL10A1	51	.	0			c.C763A						.						43.0	48.0	47.0					6																	116442516		2203	4299	6502	SO:0001583	missense	1300	exon3			CCCCAGGAGGGCC		CCDS5105.1	6q21-q22	2013-01-16	2008-07-29		ENSG00000123500	ENSG00000123500		"""Collagens"""	2185	protein-coding gene	gene with protein product	"""Schmid metaphyseal chondrodysplasia"""	120110				2037056	Standard	XM_006715332		Approved		uc003pwm.3	Q03692	OTTHUMG00000015426	ENST00000327673.4:c.763C>A	chr6.hg19:g.116442516G>T	ENSP00000327368:p.Pro255Thr	57.0	0.0		88.0	41.0	NM_000493	A1L4P2	Missense_Mutation	SNP	ENST00000327673.4	hg19	CCDS5105.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.06|10.06	1.246837|1.246837	0.22796|0.22796	.|.	.|.	ENSG00000234188|ENSG00000123500	ENST00000430695|ENST00000243222;ENST00000327673	.|D;D	.|0.96651	.|-4.08;-4.08	5.65|5.65	5.65|5.65	0.86999|0.86999	.|.	.|0.224117	.|0.46442	.|D	.|0.000285	D|D	0.90830|0.90830	0.7120|0.7120	L|L	0.39898|0.39898	1.24|1.24	0.40748|0.40748	D|D	0.982893|0.982893	.|B	.|0.17465	.|0.022	.|B	.|0.15052	.|0.012	D|D	0.87037|0.87037	0.2138|0.2138	6|10	0.34782|0.42905	T|T	0.22|0.14	.|.	13.3219|13.3219	0.60438|0.60438	0.0724:0.0:0.9276:0.0|0.0724:0.0:0.9276:0.0	.|.	.|255	.|Q03692	.|COAA1_HUMAN	V|T	57|255	.|ENSP00000243222:P255T;ENSP00000327368:P255T	ENSP00000415795:G57V|ENSP00000243222:P255T	G|P	+|-	2|1	0|0	AL121963.1|COL10A1	116549209|116549209	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.458000|0.458000	0.32498|0.32498	3.491000|3.491000	0.53252|0.53252	2.825000|2.825000	0.97269|0.97269	0.655000|0.655000	0.94253|0.94253	GGA|CCT	.	.		0.597	COL10A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041926.1		
COL28A1	340267	hgsc.bcm.edu	37	7	7421217	7421217	+	Silent	SNP	T	T	A			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr7:7421217T>A	ENST00000399429.3	-	28	2303	c.2163A>T	c.(2161-2163)ccA>ccT	p.P721P		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	721					cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		CCTTTGGGCCTGGGAAGCCTT	0.473																																					p.P721P		Atlas-SNP	.											.	COL28A1	113	.	0			c.A2163T						.						196.0	194.0	195.0					7																	7421217		1871	4104	5975	SO:0001819	synonymous_variant	340267	exon28			TGGGCCTGGGAAG	AJ890451	CCDS43553.1	7p21.3	2013-01-16			ENSG00000215018	ENSG00000215018		"""Collagens"""	22442	protein-coding gene	gene with protein product		609996				16330543	Standard	NM_001037763		Approved		uc003src.1	Q2UY09	OTTHUMG00000150034	ENST00000399429.3:c.2163A>T	chr7.hg19:g.7421217T>A		126.0	0.0		136.0	50.0	NM_001037763	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Silent	SNP	ENST00000399429.3	hg19	CCDS43553.1																																																																																			.	.		0.473	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763	
GTF2I	2969	hgsc.bcm.edu	37	7	74114719	74114719	+	Missense_Mutation	SNP	G	G	T			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr7:74114719G>T	ENST00000324896.4	+	5	905	c.516G>T	c.(514-516)tgG>tgT	p.W172C	AC083884.8_ENST00000450426.2_RNA|GTF2I_ENST00000346152.4_Missense_Mutation_p.W172C|GTF2I_ENST00000353920.4_Missense_Mutation_p.W172C|GTF2I_ENST00000416070.1_Missense_Mutation_p.W172C|AC083884.8_ENST00000594967.1_RNA|AC083884.8_ENST00000434256.1_RNA|GTF2I_ENST00000443166.1_Missense_Mutation_p.W172C	NM_032999.2	NP_127492.1	P78347	GTF2I_HUMAN	general transcription factor IIi	172					negative regulation of angiogenesis (GO:0016525)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(7)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	19						CCCTGAAATGGATTTTGGAGA	0.438																																					p.W172C		Atlas-SNP	.											.	GTF2I	40	.	0			c.G516T						.						107.0	109.0	108.0					7																	74114719		2203	4300	6503	SO:0001583	missense	2969	exon5			GAAATGGATTTTG	U77948	CCDS5573.1, CCDS5574.1, CCDS5575.1, CCDS47614.1, CCDS64680.1	7q11.23	2011-05-25	2009-07-23			ENSG00000263001		"""General transcription factors"""	4659	protein-coding gene	gene with protein product		601679	"""general transcription factor II, i"""	WBSCR6		9334314, 9012831	Standard	NM_032999		Approved	TFII-I, BAP-135, SPIN, BTKAP1, DIWS, IB291	uc003uau.3	P78347		ENST00000324896.4:c.516G>T	chr7.hg19:g.74114719G>T	ENSP00000322542:p.Trp172Cys	168.0	0.0		252.0	116.0	NM_032999	O14743|O15359|O43546|O43588|O43589|Q75M85|Q75M86|Q75M87|Q75M88|Q86U51|Q9BSZ4	Missense_Mutation	SNP	ENST00000324896.4	hg19	CCDS5573.1	.	.	.	.	.	.	.	.	.	.	G	15.62	2.888334	0.52014	.	.	ENSG00000077809	ENST00000324896;ENST00000539339;ENST00000353920;ENST00000346152;ENST00000416070;ENST00000443166	T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97	5.51	5.51	0.81932	.	0.287858	0.30869	N	0.008717	T	0.64972	0.2647	M	0.68317	2.08	0.80722	D	1	D;B;D;D;D;B	0.89917	0.992;0.168;1.0;0.99;1.0;0.127	D;B;D;D;D;B	0.91635	0.95;0.085;0.998;0.917;0.999;0.189	T	0.66854	-0.5818	10	0.72032	D	0.01	-6.6822	18.3968	0.90502	0.0:0.0:1.0:0.0	.	172;172;172;172;172;172	Q499G6;P78347-2;P78347-3;P78347-4;P78347;Q86U51	.;.;.;.;GTF2I_HUMAN;.	C	172;167;172;172;172;172	ENSP00000322542:W172C;ENSP00000322671:W172C;ENSP00000322599:W172C;ENSP00000387651:W172C;ENSP00000404240:W172C	ENSP00000322542:W172C	W	+	3	0	GTF2I	73752655	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.517000	0.60503	2.594000	0.87642	0.484000	0.47621	TGG	.	.		0.438	GTF2I-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252708.1	NM_032999	
TUSC3	7991	hgsc.bcm.edu	37	8	15480625	15480625	+	Missense_Mutation	SNP	T	T	C			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr8:15480625T>C	ENST00000503731.1	+	2	323	c.175T>C	c.(175-177)Tgg>Cgg	p.W59R	TUSC3_ENST00000506802.1_Missense_Mutation_p.W59R|TUSC3_ENST00000382020.4_Missense_Mutation_p.W59R|TUSC3_ENST00000509380.1_Missense_Mutation_p.W59R|TUSC3_ENST00000503191.1_3'UTR	NM_006765.3	NP_006756.2	Q13454	TUSC3_HUMAN	tumor suppressor candidate 3	59	Thioredoxin.				cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|cognition (GO:0050890)|magnesium ion transport (GO:0015693)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|oligosaccharyltransferase complex (GO:0008250)	magnesium ion transmembrane transporter activity (GO:0015095)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(10)|ovary(2)	28				Colorectal(111;0.113)		GCTGATGGAATGGAGTTCCAG	0.348																																					p.W59R		Atlas-SNP	.											.	TUSC3	98	.	0			c.T175C						.						66.0	66.0	66.0					8																	15480625		2203	4300	6503	SO:0001583	missense	7991	exon2			ATGGAATGGAGTT	AK026149	CCDS5993.1, CCDS5994.1	8p22	2010-10-22			ENSG00000104723	ENSG00000104723			30242	protein-coding gene	gene with protein product	"""oligosaccharyltransferase 3 homolog A (S. cerevisiae)"""	601385				8661104, 10097140	Standard	NM_178234		Approved	MGC13453, N33, OST3A, MRT7	uc003wwt.3	Q13454	OTTHUMG00000094803	ENST00000503731.1:c.175T>C	chr8.hg19:g.15480625T>C	ENSP00000424544:p.Trp59Arg	79.0	0.0		64.0	47.0	NM_178234	A8MSM0|D3DSP2|Q14911|Q14912|Q96FW0	Missense_Mutation	SNP	ENST00000503731.1	hg19	CCDS5994.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.433993	0.83776	.	.	ENSG00000104723	ENST00000382020;ENST00000506802;ENST00000509380;ENST00000503731	T;T;T;T	0.44482	0.94;0.92;0.94;0.94	5.59	5.59	0.84812	Thioredoxin-like fold (1);	0.104887	0.64402	D	0.000001	T	0.54175	0.1842	L	0.39245	1.2	0.58432	D	0.999997	D;D;D;D;D;D	0.76494	0.992;0.992;0.994;0.984;0.999;0.999	D;D;D;P;D;D	0.83275	0.946;0.938;0.991;0.823;0.984;0.996	T	0.45745	-0.9240	10	0.22706	T	0.39	-11.8531	15.2531	0.73564	0.0:0.0:0.0:1.0	.	59;59;59;59;59;59	D6RDV0;D6RIY7;Q13454-2;Q13454;D6RA37;A8MSM0	.;.;.;TUSC3_HUMAN;.;.	R	59	ENSP00000371450:W59R;ENSP00000425777:W59R;ENSP00000423426:W59R;ENSP00000424544:W59R	ENSP00000221167:W59R	W	+	1	0	TUSC3	15524996	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.698000	0.84413	2.263000	0.75096	0.528000	0.53228	TGG	.	.		0.348	TUSC3-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365367.1	NM_006765	
FAM135B	51059	hgsc.bcm.edu	37	8	139263216	139263216	+	Missense_Mutation	SNP	G	G	T			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr8:139263216G>T	ENST00000395297.1	-	6	580	c.410C>A	c.(409-411)aCg>aAg	p.T137K		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	137										NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			CAGGCCAAGCGTTCGGCTGCT	0.592										HNSCC(54;0.14)																											p.T137K		Atlas-SNP	.											LOC51059,colon,carcinoma,0,2	FAM135B	423	.	0			c.C410A						.						108.0	122.0	117.0					8																	139263216		2159	4243	6402	SO:0001583	missense	51059	exon6			CCAAGCGTTCGGC	AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.410C>A	chr8.hg19:g.139263216G>T	ENSP00000378710:p.Thr137Lys	104.0	0.0		130.0	56.0	NM_015912	B5MDB3|O95879|Q2WGJ7|Q3KP46	Missense_Mutation	SNP	ENST00000395297.1	hg19	CCDS6375.2	.	.	.	.	.	.	.	.	.	.	G	18.96	3.734272	0.69189	.	.	ENSG00000147724	ENST00000395297;ENST00000160713	T	0.15834	2.39	5.61	4.74	0.60224	.	0.060370	0.64402	D	0.000004	T	0.32852	0.0843	M	0.77820	2.39	0.51767	D	0.999931	P	0.49559	0.925	P	0.50896	0.653	T	0.16958	-1.0385	10	0.62326	D	0.03	-1.1655	13.6346	0.62215	0.0744:0.0:0.9256:0.0	.	137	Q49AJ0	F135B_HUMAN	K	137	ENSP00000378710:T137K	ENSP00000160713:T137K	T	-	2	0	FAM135B	139332398	1.000000	0.71417	0.246000	0.24233	0.118000	0.20060	5.802000	0.69122	1.390000	0.46547	0.655000	0.94253	ACG	.	.		0.592	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912	
RMI1	80010	hgsc.bcm.edu	37	9	86616608	86616608	+	Missense_Mutation	SNP	T	T	G			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr9:86616608T>G	ENST00000325875.3	+	3	1039	c.707T>G	c.(706-708)cTa>cGa	p.L236R		NM_024945.2	NP_079221.2	Q9H9A7	RMI1_HUMAN	RecQ mediated genome instability 1	236					DNA replication (GO:0006260)|glucose homeostasis (GO:0042593)|multicellular organism growth (GO:0035264)|reduction of food intake in response to dietary excess (GO:0002023)|response to glucose (GO:0009749)	nucleus (GO:0005634)				biliary_tract(1)|central_nervous_system(1)|kidney(2)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	18						ACAGATGTTCTAGATCCTGCA	0.378																																					p.L236R		Atlas-SNP	.											.	RMI1	50	.	0			c.T707G						.						107.0	106.0	106.0					9																	86616608		2203	4299	6502	SO:0001583	missense	80010	exon3			ATGTTCTAGATCC	AK022950	CCDS6669.1	9q22.1	2013-06-10	2013-06-10	2006-06-12	ENSG00000178966	ENSG00000178966			25764	protein-coding gene	gene with protein product	"""BLM-Associated Polypeptide, 75 kDa"""	610404	"""chromosome 9 open reading frame 76"", ""RMI1, RecQ mediated genome instability 1, homolog (S. cerevisiae)"""	C9orf76		15775963, 20826341	Standard	NM_024945		Approved	FLJ12888, BLAP75	uc004anq.4	Q9H9A7	OTTHUMG00000020113	ENST00000325875.3:c.707T>G	chr9.hg19:g.86616608T>G	ENSP00000317039:p.Leu236Arg	96.0	0.0		135.0	64.0	NM_024945	Q05BX1|Q05CW3|Q5SQG8|Q5SQG9|Q6P1Q4|Q6PI89|Q7Z6L6	Missense_Mutation	SNP	ENST00000325875.3	hg19	CCDS6669.1	.	.	.	.	.	.	.	.	.	.	T	13.24	2.178430	0.38511	.	.	ENSG00000178966	ENST00000445877;ENST00000325875	T;T	0.51071	0.72;1.31	5.62	2.04	0.26737	.	0.227208	0.28088	N	0.016646	T	0.57169	0.2035	M	0.66939	2.045	0.22127	N	0.99934	D	0.71674	0.998	P	0.60789	0.879	T	0.47156	-0.9139	10	0.34782	T	0.22	-10.1409	9.0664	0.36467	0.0:0.2095:0.0:0.7905	.	236	Q9H9A7	RMI1_HUMAN	R	236	ENSP00000402433:L236R;ENSP00000317039:L236R	ENSP00000317039:L236R	L	+	2	0	RMI1	85806428	0.179000	0.23135	0.094000	0.20943	0.940000	0.58332	1.847000	0.39299	0.499000	0.27970	0.533000	0.62120	CTA	.	.		0.378	RMI1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052870.1	NM_024945	
RAD23B	5887	hgsc.bcm.edu	37	9	110091936	110091936	+	Nonstop_Mutation	SNP	G	G	T			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr9:110091936G>T	ENST00000358015.3	+	10	1580	c.1229G>T	c.(1228-1230)tGa>tTa	p.*410L	RAD23B_ENST00000416373.2_Nonstop_Mutation_p.*338L	NM_001244713.1|NM_002874.4	NP_001231642.1|NP_002865.1	P54727	RD23B_HUMAN	RAD23 homolog B (S. cerevisiae)	0					DNA repair (GO:0006281)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage recognition (GO:0000715)|nucleotide-excision repair, DNA damage removal (GO:0000718)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|XPC complex (GO:0071942)	damaged DNA binding (GO:0003684)|polyubiquitin binding (GO:0031593)|single-stranded DNA binding (GO:0003697)			breast(3)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14						GATGAAGATTGAAAGGGACTT	0.398								Direct reversal of damage;Nucleotide excision repair (NER)																													p.X410L		Atlas-SNP	.											.	RAD23B	31	.	0			c.G1229T						.						65.0	65.0	65.0					9																	110091936		2203	4299	6502	SO:0001578	stop_lost	5887	exon10			AAGATTGAAAGGG		CCDS6769.1, CCDS59138.1	9q31.2	2008-07-21	2001-11-28		ENSG00000119318	ENSG00000119318			9813	protein-coding gene	gene with protein product	"""XP-C repair complementing protein"", ""XP-C repair complementing complex 58 kDa"""	600062	"""RAD23 (S. cerevisiae) homolog B"""			7851894, 8168482	Standard	NM_002874		Approved	HHR23B, P58, HR23B	uc004bde.3	P54727	OTTHUMG00000020446	ENST00000358015.3:c.1229G>T	chr9.hg19:g.110091936G>T	ENSP00000350708:p.*410Leuext*62	45.0	0.0		51.0	22.0	NM_002874	B3KWK8|G5E9P0|Q7Z5K8|Q8WUB0	Missense_Mutation	SNP	ENST00000358015.3	hg19	CCDS6769.1	.	.	.	.	.	.	.	.	.	.	G	12.85	2.060214	0.36373	.	.	ENSG00000119318	ENST00000358015;ENST00000416373	.	.	.	4.34	3.43	0.39272	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.2193	0.54425	0.0849:0.0:0.9151:0.0	.	.	.	.	L	410;338	.	.	X	+	2	2	RAD23B	109131757	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.737000	0.47393	0.930000	0.37217	0.563000	0.77884	TGA	.	.		0.398	RAD23B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053548.1	NM_002874	
PCDH15	65217	hgsc.bcm.edu	37	10	55849778	55849778	+	Nonsense_Mutation	SNP	C	C	A			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr10:55849778C>A	ENST00000320301.6	-	16	2357	c.1963G>T	c.(1963-1965)Gga>Tga	p.G655*	PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000437009.1_Intron|PCDH15_ENST00000395432.2_Nonsense_Mutation_p.G618*|PCDH15_ENST00000373957.3_Nonsense_Mutation_p.G633*|PCDH15_ENST00000395446.1_Nonsense_Mutation_p.G655*|PCDH15_ENST00000395430.1_Nonsense_Mutation_p.G655*|PCDH15_ENST00000409834.1_Nonsense_Mutation_p.G266*|PCDH15_ENST00000373955.1_Nonsense_Mutation_p.G655*|PCDH15_ENST00000373965.2_Nonsense_Mutation_p.G662*|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000414778.1_Nonsense_Mutation_p.G660*|PCDH15_ENST00000361849.3_Nonsense_Mutation_p.G655*|PCDH15_ENST00000395438.1_Nonsense_Mutation_p.G655*|PCDH15_ENST00000395433.1_Nonsense_Mutation_p.G633*|PCDH15_ENST00000395445.1_Nonsense_Mutation_p.G662*	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	655	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				TGAGGATCTCCATTCTCAATG	0.348										HNSCC(58;0.16)																											p.G660X		Atlas-SNP	.											.	PCDH15	1715	.	0			c.G1978T						.						67.0	68.0	67.0					10																	55849778		2203	4300	6503	SO:0001587	stop_gained	65217	exon17			GATCTCCATTCTC	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"""Cadherins / Cadherin-related"""	14674	protein-coding gene	gene with protein product	"""cadherin-related family member 15"""	605514	"""deafness, autosomal recessive 23"", ""protocadherin 15"""	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.1963G>T	chr10.hg19:g.55849778C>A	ENSP00000322604:p.Gly655*	86.0	0.0		106.0	43.0	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Nonsense_Mutation	SNP	ENST00000320301.6	hg19	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	C	44	10.563949	0.99428	.	.	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000409834;ENST00000395445;ENST00000395446;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000373957;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000373955	.	.	.	6.16	6.16	0.99307	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	18.6329	0.91366	0.0:1.0:0.0:0.0	.	.	.	.	X	662;660;655;655;266;662;655;618;655;633;633;655;655;660;655	.	ENSP00000322604:G655X	G	-	1	0	PCDH15	55519784	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.099000	0.64554	2.937000	0.99478	0.650000	0.86243	GGA	.	.		0.348	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056	
SLC6A5	9152	hgsc.bcm.edu	37	11	20660007	20660007	+	Silent	SNP	T	T	C			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr11:20660007T>C	ENST00000525748.1	+	13	2145	c.1872T>C	c.(1870-1872)ggT>ggC	p.G624G	SLC6A5_ENST00000528440.1_3'UTR	NM_004211.3	NP_004202.2	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 5	624					glycine import (GO:0036233)|synaptic transmission (GO:0007268)|synaptic transmission, glycinergic (GO:0060012)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine:sodium symporter activity (GO:0015375)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(34)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	63					Glycine(DB00145)	CCTGTTAGGGTGGAATTTACA	0.453																																					p.G624G		Atlas-SNP	.											.	SLC6A5	151	.	0			c.T1872C						.						368.0	274.0	306.0					11																	20660007		2203	4300	6503	SO:0001819	synonymous_variant	9152	exon13			TTAGGGTGGAATT	AF085412	CCDS7854.1	11p15.1	2013-07-19	2013-07-19		ENSG00000165970	ENSG00000165970		"""Solute carriers"""	11051	protein-coding gene	gene with protein product	"""glycine transporter 2"""	604159	"""solute carrier family 6 (neurotransmitter transporter, glycine), member 5"""	NET1		9845349	Standard	NM_004211		Approved	GLYT2	uc001mqd.3	Q9Y345	OTTHUMG00000166024	ENST00000525748.1:c.1872T>C	chr11.hg19:g.20660007T>C		32.0	0.0		71.0	27.0	NM_004211	O95288|Q4VAM7|Q9BX77	Silent	SNP	ENST00000525748.1	hg19	CCDS7854.1																																																																																			.	.		0.453	SLC6A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387497.2	NM_004211	
PPFIA1	8500	hgsc.bcm.edu	37	11	70194365	70194365	+	Missense_Mutation	SNP	A	A	C			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr11:70194365A>C	ENST00000253925.7	+	16	2217	c.2002A>C	c.(2002-2004)Agt>Cgt	p.S668R	PPFIA1_ENST00000389547.3_Missense_Mutation_p.S668R|AP000487.6_ENST00000528607.1_RNA	NM_003626.3	NP_003617.1	Q13136	LIPA1_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1	668					cell-matrix adhesion (GO:0007160)|negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of stress fiber assembly (GO:0051497)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|presynaptic active zone (GO:0048786)	signal transducer activity (GO:0004871)			breast(3)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	65			BRCA - Breast invasive adenocarcinoma(2;1.04e-44)|LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)			TGGCAGTGGAAGTCTAGACAA	0.502																																					p.S668R		Atlas-SNP	.											.	PPFIA1	114	.	0			c.A2002C						.						211.0	171.0	185.0					11																	70194365		2200	4294	6494	SO:0001583	missense	8500	exon16			AGTGGAAGTCTAG	U22816	CCDS31627.1, CCDS31628.1	11q13.3	2013-01-10			ENSG00000131626	ENSG00000131626		"""Sterile alpha motif (SAM) domain containing"""	9245	protein-coding gene	gene with protein product	"""Liprin-alpha1"""	611054				7796809, 9624153	Standard	NM_003626		Approved	LIP.1, LIPRIN	uc001opo.3	Q13136	OTTHUMG00000167266	ENST00000253925.7:c.2002A>C	chr11.hg19:g.70194365A>C	ENSP00000253925:p.Ser668Arg	98.0	0.0		105.0	44.0	NM_177423	A6NLE3|Q13135|Q14567|Q8N4I2	Missense_Mutation	SNP	ENST00000253925.7	hg19	CCDS31627.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.33|10.33	1.319566|1.319566	0.23994|0.23994	.|.	.|.	ENSG00000131626|ENSG00000131626	ENST00000528750|ENST00000253925;ENST00000389547;ENST00000544950	.|T;T	.|0.49139	.|0.79;0.79	5.65|5.65	4.51|4.51	0.55191|0.55191	.|.	.|0.089199	.|0.46442	.|D	.|0.000286	T|T	0.45357|0.45357	0.1338|0.1338	L|L	0.60455|0.60455	1.87|1.87	0.37560|0.37560	D|D	0.919014|0.919014	.|P;B	.|0.40834	.|0.73;0.264	.|B;B	.|0.39027	.|0.288;0.078	T|T	0.54248|0.54248	-0.8322|-0.8322	5|10	.|0.66056	.|D	.|0.02	.|.	12.1312|12.1312	0.53944|0.53944	0.8715:0.0:0.0:0.1285|0.8715:0.0:0.0:0.1285	.|.	.|668;668	.|Q13136;Q13136-2	.|LIPA1_HUMAN;.	D|R	71|668;668;155	.|ENSP00000253925:S668R;ENSP00000374198:S668R	.|ENSP00000253925:S668R	E|S	+|+	3|1	2|0	PPFIA1|PPFIA1	69872013|69872013	1.000000|1.000000	0.71417|0.71417	0.003000|0.003000	0.11579|0.11579	0.114000|0.114000	0.19823|0.19823	7.277000|7.277000	0.78572|0.78572	0.947000|0.947000	0.37659|0.37659	0.533000|0.533000	0.62120|0.62120	GAA|AGT	.	.		0.502	PPFIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393905.1	NM_003626	
KIAA1377	57562	hgsc.bcm.edu	37	11	101849150	101849150	+	Missense_Mutation	SNP	A	A	G			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr11:101849150A>G	ENST00000263468.8	+	7	3188	c.2918A>G	c.(2917-2919)aAc>aGc	p.N973S	KIAA1377_ENST00000537689.1_Missense_Mutation_p.N774S	NM_020802.2	NP_065853.2	Q9P2H0	K1377_HUMAN	KIAA1377	973										breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(18)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	53	all_epithelial(12;0.0104)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00931)		BRCA - Breast invasive adenocarcinoma(274;0.038)		AAAAGACAAAACCCTGGATCT	0.328																																					p.N973S		Atlas-SNP	.											.	KIAA1377	111	.	0			c.A2918G						.						136.0	147.0	144.0					11																	101849150		2203	4299	6502	SO:0001583	missense	57562	exon7			GACAAAACCCTGG	AK095004	CCDS31658.1	11q22.2	2006-02-03			ENSG00000110318	ENSG00000110318			29264	protein-coding gene	gene with protein product		614634				10718198	Standard	XM_005271627		Approved		uc001pgm.3	Q9P2H0	OTTHUMG00000167319	ENST00000263468.8:c.2918A>G	chr11.hg19:g.101849150A>G	ENSP00000263468:p.Asn973Ser	184.0	0.0		163.0	8.0	NM_020802	Q4G0U6	Missense_Mutation	SNP	ENST00000263468.8	hg19	CCDS31658.1	.	.	.	.	.	.	.	.	.	.	A	11.95	1.790827	0.31685	.	.	ENSG00000110318	ENST00000263468;ENST00000537689	T;T	0.07021	3.23;3.23	5.09	-0.895	0.10560	.	0.555420	0.17103	N	0.186932	T	0.07999	0.0200	L	0.57536	1.79	0.09310	N	1	B	0.24426	0.103	B	0.28011	0.085	T	0.29427	-1.0012	10	0.32370	T	0.25	-2.271	5.225	0.15389	0.2348:0.3499:0.0:0.4153	.	973	Q9P2H0	K1377_HUMAN	S	973;774	ENSP00000263468:N973S;ENSP00000443184:N774S	ENSP00000263468:N973S	N	+	2	0	KIAA1377	101354360	0.025000	0.19082	0.523000	0.27875	0.908000	0.53690	0.058000	0.14301	0.193000	0.20303	0.455000	0.32223	AAC	.	.		0.328	KIAA1377-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394140.1	NM_020802	
TECTA	7007	hgsc.bcm.edu	37	11	121037416	121037416	+	Missense_Mutation	SNP	C	C	A			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr11:121037416C>A	ENST00000392793.1	+	18	5784	c.5513C>A	c.(5512-5514)aCc>aAc	p.T1838N	TECTA_ENST00000264037.2_Missense_Mutation_p.T1838N			O75443	TECTA_HUMAN	tectorin alpha	1838	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)			TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		AGACAGTGCACCGGCATCGAG	0.493																																					p.T1838N		Atlas-SNP	.											.	TECTA	329	.	0			c.C5513A						.						140.0	123.0	129.0					11																	121037416		2203	4299	6502	SO:0001583	missense	7007	exon17			AGTGCACCGGCAT	AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.5513C>A	chr11.hg19:g.121037416C>A	ENSP00000376543:p.Thr1838Asn	62.0	0.0		104.0	12.0	NM_005422		Missense_Mutation	SNP	ENST00000392793.1	hg19	CCDS8434.1	.	.	.	.	.	.	.	.	.	.	C	7.831	0.719814	0.15372	.	.	ENSG00000109927	ENST00000392793;ENST00000264037	D;D	0.81908	-1.55;-1.55	6.05	4.1	0.47936	Zona pellucida sperm-binding protein (3);	0.813870	0.11699	N	0.538141	T	0.65801	0.2726	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.16722	0.016	T	0.48352	-0.9043	10	0.10377	T	0.69	.	10.8388	0.46702	0.1311:0.8018:0.0:0.0671	.	1838	O75443	TECTA_HUMAN	N	1838	ENSP00000376543:T1838N;ENSP00000264037:T1838N	ENSP00000264037:T1838N	T	+	2	0	TECTA	120542626	0.000000	0.05858	0.128000	0.21923	0.945000	0.59286	1.072000	0.30678	1.568000	0.49683	0.650000	0.86243	ACC	.	.		0.493	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422	
VSIG2	23584	hgsc.bcm.edu	37	11	124618542	124618542	+	Missense_Mutation	SNP	G	G	C	rs560008973	byFrequency	TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr11:124618542G>C	ENST00000326621.5	-	5	804	c.704C>G	c.(703-705)aCc>aGc	p.T235S	RP11-677M14.2_ENST00000531241.1_RNA|VSIG2_ENST00000403470.1_Missense_Mutation_p.T235S	NM_014312.3	NP_055127.2	Q96IQ7	VSIG2_HUMAN	V-set and immunoglobulin domain containing 2	235						integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(5)	19	all_hematologic(175;0.215)	Breast(109;0.00663)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0215)		ATCCCTACCGGTCACAGAGAG	0.622																																					p.T235S		Atlas-SNP	.											.	VSIG2	38	.	0			c.C704G						.						92.0	81.0	85.0					11																	124618542		2201	4299	6500	SO:0001583	missense	23584	exon5			CTACCGGTCACAG	AF061022	CCDS8452.1	11q24	2013-01-11			ENSG00000019102	ENSG00000019102		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"""	17149	protein-coding gene	gene with protein product		606011				9862345	Standard	NM_014312		Approved	CTXL, CTH	uc001qas.3	Q96IQ7	OTTHUMG00000150357	ENST00000326621.5:c.704C>G	chr11.hg19:g.124618542G>C	ENSP00000318684:p.Thr235Ser	71.0	0.0		94.0	43.0	NM_014312	O95791|Q9NX42	Missense_Mutation	SNP	ENST00000326621.5	hg19	CCDS8452.1	.	.	.	.	.	.	.	.	.	.	G	10.63	1.402838	0.25291	.	.	ENSG00000019102	ENST00000326621;ENST00000403470	T;T	0.12984	2.63;2.63	5.65	5.65	0.86999	Immunoglobulin-like fold (1);	0.088528	0.47852	D	0.000220	T	0.15349	0.0370	L	0.60455	1.87	0.35212	D	0.775236	B	0.23540	0.087	B	0.20577	0.03	T	0.10613	-1.0622	10	0.15066	T	0.55	.	15.093	0.72211	0.0:0.0:1.0:0.0	.	235	Q96IQ7	VSIG2_HUMAN	S	235	ENSP00000318684:T235S;ENSP00000385013:T235S	ENSP00000318684:T235S	T	-	2	0	VSIG2	124123752	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.361000	0.44160	2.941000	0.99782	0.655000	0.94253	ACC	.	.		0.622	VSIG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317785.1	NM_014312	
SETD1B	23067	hgsc.bcm.edu	37	12	122261155	122261155	+	Missense_Mutation	SNP	A	A	T			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr12:122261155A>T	ENST00000604567.1	+	12	4738	c.4670A>T	c.(4669-4671)cAg>cTg	p.Q1557L	SETD1B_ENST00000542440.1_Missense_Mutation_p.Q1514L|SETD1B_ENST00000267197.5_Missense_Mutation_p.Q1514L			Q9UPS6	SET1B_HUMAN	SET domain containing 1B	1557	Pro-rich.				histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone-lysine N-methyltransferase activity (GO:0018024)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|endometrium(6)|kidney(2)|prostate(2)	11						GGCCAGCCACAGACCCCCGTC	0.692																																					p.Q1514L		Atlas-SNP	.											.	SETD1B	105	.	0			c.A4541T						.						5.0	10.0	9.0					12																	122261155		626	1496	2122	SO:0001583	missense	23067	exon12			AGCCACAGACCCC	AB028999	CCDS53838.1	12q24.31	2013-02-12			ENSG00000139718	ENSG00000139718		"""Chromatin-modifying enzymes / K-methyltransferases"", ""RNA binding motif (RRM) containing"""	29187	protein-coding gene	gene with protein product		611055				10470851, 17355966	Standard	NM_015048		Approved	KIAA1076, Set1B, KMT2G	uc001ubi.3	Q9UPS6	OTTHUMG00000169080	ENST00000604567.1:c.4670A>T	chr12.hg19:g.122261155A>T	ENSP00000474253:p.Gln1557Leu	88.0	0.0		96.0	34.0	NM_015048	F6MFW1	Missense_Mutation	SNP	ENST00000604567.1	hg19		.	.	.	.	.	.	.	.	.	.	A	6.524	0.464921	0.12402	.	.	ENSG00000139718	ENST00000542440;ENST00000267197	D;D	0.94537	-3.45;-3.45	4.36	1.6	0.23607	.	0.440470	0.19851	U	0.104638	D	0.89636	0.6772	L	0.43152	1.355	0.20638	N	0.999871	B	0.23058	0.079	B	0.26614	0.071	T	0.74405	-0.3676	10	0.10636	T	0.68	.	11.1239	0.48306	0.6919:0.3081:0.0:0.0	.	1514	Q9UPS6	SET1B_HUMAN	L	1514	ENSP00000442924:Q1514L;ENSP00000267197:Q1514L	ENSP00000267197:Q1514L	Q	+	2	0	SETD1B	120745538	0.998000	0.40836	0.962000	0.40283	0.364000	0.29643	2.067000	0.41461	0.501000	0.28013	0.374000	0.22700	CAG	.	.		0.692	SETD1B-002	PUTATIVE	non_canonical_U12|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000468264.1	XM_037523	
NID2	22795	hgsc.bcm.edu	37	14	52481919	52481919	+	Missense_Mutation	SNP	G	G	A			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr14:52481919G>A	ENST00000216286.5	-	15	3102	c.3103C>T	c.(3103-3105)Cgg>Tgg	p.R1035W	NID2_ENST00000541773.1_Missense_Mutation_p.R934W	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	1035	Thyroglobulin type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00500}.				basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)			NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87	Breast(41;0.0639)|all_epithelial(31;0.123)					TGGTCATCCCGGGGGGTGCCA	0.622																																					p.R1035W		Atlas-SNP	.											.	NID2	201	.	0			c.C3103T						.						50.0	47.0	48.0					14																	52481919		2203	4300	6503	SO:0001583	missense	22795	exon15			CATCCCGGGGGGT	AB009799	CCDS9706.1	14q22.1	2008-05-14			ENSG00000087303	ENSG00000087303			13389	protein-coding gene	gene with protein product		605399				9733643	Standard	NM_007361		Approved		uc001wzo.3	Q14112	OTTHUMG00000140298	ENST00000216286.5:c.3103C>T	chr14.hg19:g.52481919G>A	ENSP00000216286:p.Arg1035Trp	106.0	0.0		145.0	64.0	NM_007361	A8K6I7|B4DU19|O43710	Missense_Mutation	SNP	ENST00000216286.5	hg19	CCDS9706.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.48|15.48	2.847145|2.847145	0.51164|0.51164	.|.	.|.	ENSG00000087303|ENSG00000087303	ENST00000556572|ENST00000216286;ENST00000316204;ENST00000541773;ENST00000395707	T|T;T	0.62364|0.63913	0.03|-0.07;-0.07	5.67|5.67	-0.0259|-0.0259	0.13933|0.13933	.|Thyroglobulin type-1 (4);	.|0.527175	.|0.23090	.|N	.|0.052051	T|T	0.68513|0.68513	0.3009|0.3009	L|L	0.49640|0.49640	1.575|1.575	0.09310|0.09310	N|N	0.999995|0.999995	.|D;D;D;D	.|0.89917	.|0.999;0.999;1.0;0.999	.|D;P;D;D	.|0.68765	.|0.932;0.9;0.96;0.957	T|T	0.61792|0.61792	-0.6990|-0.6990	6|10	.|0.72032	.|D	.|0.01	.|.	9.7544|9.7544	0.40494|0.40494	0.0:0.1675:0.3884:0.444|0.0:0.1675:0.3884:0.444	.|.	.|629;934;1037;1035	.|E7EPP3;Q14112-2;Q5CZI2;Q14112	.|.;.;.;NID2_HUMAN	L|W	303|1035;629;934;1037	ENSP00000452190:P303L|ENSP00000216286:R1035W;ENSP00000443730:R934W	.|ENSP00000216286:R1035W	P|R	-|-	2|1	0|2	NID2|NID2	51551669|51551669	0.000000|0.000000	0.05858|0.05858	0.066000|0.066000	0.19879|0.19879	0.477000|0.477000	0.33069|0.33069	0.144000|0.144000	0.16135|0.16135	-0.324000|-0.324000	0.08589|0.08589	-0.169000|-0.169000	0.13324|0.13324	CCG|CGG	.	.		0.622	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1		
HCN4	10021	hgsc.bcm.edu	37	15	73635902	73635902	+	Missense_Mutation	SNP	C	C	A			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr15:73635902C>A	ENST00000261917.3	-	2	2026	c.1033G>T	c.(1033-1035)Gat>Tat	p.D345Y	RP11-272D12.1_ENST00000558742.1_RNA|RP11-272D12.1_ENST00000557981.1_RNA	NM_005477.2	NP_005468.1	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 4	345					blood circulation (GO:0008015)|cation transport (GO:0006812)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)	cAMP binding (GO:0030552)|cation channel activity (GO:0005261)|identical protein binding (GO:0042802)|intracellular cAMP activated cation channel activity (GO:0005222)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(13)|liver(1)|lung(18)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				COAD - Colon adenocarcinoma(1;0.142)		GAAATGAAATCTACCATGAAC	0.537																																					p.D345Y		Atlas-SNP	.											.	HCN4	150	.	0			c.G1033T						.						112.0	97.0	102.0					15																	73635902		2198	4297	6495	SO:0001583	missense	10021	exon2			TGAAATCTACCAT	AJ132429	CCDS10248.1	15q24.1	2011-07-05			ENSG00000138622	ENSG00000138622		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	16882	protein-coding gene	gene with protein product		605206				10228147, 10430953, 16382102	Standard	NM_005477		Approved		uc002avp.3	Q9Y3Q4	OTTHUMG00000137563	ENST00000261917.3:c.1033G>T	chr15.hg19:g.73635902C>A	ENSP00000261917:p.Asp345Tyr	99.0	0.0		162.0	58.0	NM_005477	Q9UMQ7	Missense_Mutation	SNP	ENST00000261917.3	hg19	CCDS10248.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.587899	0.86851	.	.	ENSG00000138622	ENST00000261917	D	0.99399	-5.83	5.34	5.34	0.76211	Ion transport (1);	.	.	.	.	D	0.99708	0.9888	H	0.95365	3.66	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97514	1.0068	9	0.87932	D	0	.	19.4036	0.94640	0.0:1.0:0.0:0.0	.	345	Q9Y3Q4	HCN4_HUMAN	Y	345	ENSP00000261917:D345Y	ENSP00000261917:D345Y	D	-	1	0	HCN4	71422955	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.671000	0.83941	2.657000	0.90304	0.655000	0.94253	GAT	.	.		0.537	HCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268900.2	NM_005477	
IGF1R	3480	hgsc.bcm.edu	37	15	99482513	99482513	+	Missense_Mutation	SNP	C	C	A			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr15:99482513C>A	ENST00000268035.6	+	18	3992	c.3381C>A	c.(3379-3381)aaC>aaA	p.N1127K	IGF1R_ENST00000558762.1_Missense_Mutation_p.N1126K	NM_000875.3	NP_000866.1	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	1127	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		"""""""Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"""	CATACCTCAACGCCAATAAGT	0.488																																					p.N1127K		Atlas-SNP	.											.	IGF1R	147	.	0			c.C3381A						.						163.0	151.0	155.0					15																	99482513		2197	4297	6494	SO:0001583	missense	3480	exon18			CCTCAACGCCAAT	M69229	CCDS10378.1, CCDS73785.1	15q26.3	2013-02-11			ENSG00000140443	ENSG00000140443		"""CD molecules"", ""Fibronectin type III domain containing"""	5465	protein-coding gene	gene with protein product		147370				1316909	Standard	XM_006720486		Approved	JTK13, CD221, IGFIR, MGC18216, IGFR	uc002bul.3	P08069	OTTHUMG00000149851	ENST00000268035.6:c.3381C>A	chr15.hg19:g.99482513C>A	ENSP00000268035:p.Asn1127Lys	99.0	0.0		167.0	75.0	NM_000875	B1B5Y2|Q14CV2|Q9UCC0	Missense_Mutation	SNP	ENST00000268035.6	hg19	CCDS10378.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.201698	0.79015	.	.	ENSG00000140443	ENST00000268035	D	0.88975	-2.45	5.9	-4.89	0.03103	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000008	D	0.88081	0.6341	N	0.22421	0.69	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.77557	0.99;0.972	D	0.85675	0.1297	10	0.66056	D	0.02	.	15.7659	0.78126	0.0:0.2581:0.0:0.7419	.	1126;1127	C9J5X1;P08069	.;IGF1R_HUMAN	K	1127	ENSP00000268035:N1127K	ENSP00000268035:N1127K	N	+	3	2	IGF1R	97300036	0.036000	0.19791	0.936000	0.37596	0.976000	0.68499	-0.646000	0.05403	-0.764000	0.04651	-0.768000	0.03414	AAC	.	.		0.488	IGF1R-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313537.2	NM_000875	
C17orf96	100170841	hgsc.bcm.edu	37	17	36830528	36830528	+	Missense_Mutation	SNP	T	T	A			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr17:36830528T>A	ENST00000325814.5	-	1	659	c.221A>T	c.(220-222)cAg>cTg	p.Q74L		NM_001130677.1	NP_001124149.1	A6NHQ4	CQ096_HUMAN	chromosome 17 open reading frame 96	74	Pro-rich.				neuron fate commitment (GO:0048663)												CAGGGGGGCCTGAGGGCCCCG	0.781																																					p.Q74L		Atlas-SNP	.											.	.	.	.	0			c.A221T						.						1.0	2.0	2.0					17																	36830528		298	908	1206	SO:0001583	missense	100170841	exon1			GGGGCCTGAGGGC		CCDS45661.1	17q12	2014-04-17			ENSG00000179294	ENSG00000273604			34493	protein-coding gene	gene with protein product	"""proline rich 28"""					24550272	Standard	NM_001130677		Approved	LOC100170841, PRR28	uc010wdq.2	A6NHQ4	OTTHUMG00000188495	ENST00000325814.5:c.221A>T	chr17.hg19:g.36830528T>A	ENSP00000317905:p.Gln74Leu	17.0	0.0		54.0	28.0	NM_001130677		Missense_Mutation	SNP	ENST00000325814.5	hg19	CCDS45661.1	.	.	.	.	.	.	.	.	.	.	T	13.88	2.370085	0.42003	.	.	ENSG00000179294	ENST00000325814	.	.	.	3.28	-4.28	0.03732	.	.	.	.	.	T	0.14614	0.0353	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.18840	-1.0324	8	0.35671	T	0.21	.	4.6753	0.12708	0.0:0.441:0.1567:0.4023	.	74	A6NHQ4	CQ096_HUMAN	L	74	.	ENSP00000317905:Q74L	Q	-	2	0	C17orf96	34084054	0.000000	0.05858	0.292000	0.24919	0.563000	0.35712	-0.476000	0.06591	-0.758000	0.04690	-0.464000	0.05259	CAG	.	.		0.781	C17orf96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255465.2	NM_001130677	
CERS4	79603	hgsc.bcm.edu	37	19	8326959	8326959	+	Missense_Mutation	SNP	G	G	A			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr19:8326959G>A	ENST00000251363.5	+	12	1451	c.1151G>A	c.(1150-1152)gGg>gAg	p.G384E	CERS4_ENST00000559450.1_Missense_Mutation_p.G384E|CERS4_ENST00000558331.1_Missense_Mutation_p.G333E|CERS4_ENST00000559336.1_Missense_Mutation_p.G296E|CERS4_ENST00000595722.1_3'UTR	NM_024552.2	NP_078828.2	Q9HA82	CERS4_HUMAN	ceramide synthase 4	384					ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										CGGGTGGCCGGGCGTCTGACC	0.692																																					p.G384E		Atlas-SNP	.											.	.	.	.	0			c.G1151A						.						6.0	8.0	8.0					19																	8326959		2146	4215	6361	SO:0001583	missense	79603	exon12			TGGCCGGGCGTCT		CCDS12197.1	19p13.2	2014-09-11	2011-07-08	2011-07-08	ENSG00000090661	ENSG00000090661		"""Homeoboxes / CERS class"""	23747	protein-coding gene	gene with protein product		615334	"""LAG1 longevity assurance homolog 4 (S. cerevisiae)"", ""LAG1 homolog, ceramide synthase 4"""	LASS4			Standard	NM_024552		Approved	FLJ12089, Trh1	uc002mjg.3	Q9HA82	OTTHUMG00000172570	ENST00000251363.5:c.1151G>A	chr19.hg19:g.8326959G>A	ENSP00000251363:p.Gly384Glu	63.0	0.0		66.0	32.0	NM_024552	D6W665	Missense_Mutation	SNP	ENST00000251363.5	hg19	CCDS12197.1	.	.	.	.	.	.	.	.	.	.	G	12.11	1.838467	0.32513	.	.	ENSG00000090661	ENST00000251363	T	0.05513	3.43	4.94	2.71	0.32032	.	7.123110	0.00166	N	0.000005	T	0.09335	0.0230	M	0.65498	2.005	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.52223	-0.8604	10	0.08179	T	0.78	-10.1263	6.599	0.22691	0.1002:0.182:0.7178:0.0	.	384;384	Q53HF9;Q9HA82	.;CERS4_HUMAN	E	384	ENSP00000251363:G384E	ENSP00000251363:G384E	G	+	2	0	CERS4	8232959	0.006000	0.16342	0.002000	0.10522	0.006000	0.05464	1.672000	0.37523	0.443000	0.26582	0.491000	0.48974	GGG	.	.		0.692	CERS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419200.1	NM_024552	
KEAP1	9817	hgsc.bcm.edu	37	19	10610154	10610154	+	Missense_Mutation	SNP	C	C	T			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr19:10610154C>T	ENST00000171111.5	-	2	1103	c.556G>A	c.(556-558)Ggc>Agc	p.G186S	KEAP1_ENST00000588024.1_5'UTR|KEAP1_ENST00000393623.2_Missense_Mutation_p.G186S	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	186	BACK.				cellular response to interleukin-4 (GO:0071353)|in utero embryonic development (GO:0001701)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)|regulation of epidermal cell differentiation (GO:0045604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)				breast(3)|endometrium(2)|kidney(4)|large_intestine(4)|liver(2)|lung(69)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	92			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)		Dimethyl fumarate(DB08908)	TTGGCGATGCCGATGGCATTG	0.592																																					p.G186S		Atlas-SNP	.											.	KEAP1	182	.	0			c.G556A						.						105.0	85.0	92.0					19																	10610154		2203	4300	6503	SO:0001583	missense	9817	exon2			CGATGCCGATGGC	AF361886	CCDS12239.1	19p13.2	2013-01-30				ENSG00000079999		"""Kelch-like"", ""BTB/POZ domain containing"""	23177	protein-coding gene	gene with protein product	"""kelch-like family member 19"""	606016					Standard	NM_012289		Approved	KIAA0132, MGC10630, MGC1114, MGC20887, MGC4407, MGC9454, INrf2, KLHL19	uc002mor.1	Q14145		ENST00000171111.5:c.556G>A	chr19.hg19:g.10610154C>T	ENSP00000171111:p.Gly186Ser	55.0	0.0		42.0	31.0	NM_012289	B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	Missense_Mutation	SNP	ENST00000171111.5	hg19	CCDS12239.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.990571	0.93106	.	.	ENSG00000079999	ENST00000171111;ENST00000393623	T;T	0.70282	-0.47;-0.47	4.81	4.81	0.61882	BTB/Kelch-associated (2);	0.000000	0.85682	D	0.000000	D	0.82912	0.5140	M	0.71296	2.17	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85287	0.1065	10	0.87932	D	0	.	15.3825	0.74669	0.0:1.0:0.0:0.0	.	186	Q14145	KEAP1_HUMAN	S	186	ENSP00000171111:G186S;ENSP00000377245:G186S	ENSP00000171111:G186S	G	-	1	0	KEAP1	10471154	1.000000	0.71417	0.996000	0.52242	0.916000	0.54674	5.912000	0.69948	2.232000	0.73038	0.561000	0.74099	GGC	.	.		0.592	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1	NM_012289	
DOCK6	57572	hgsc.bcm.edu	37	19	11339628	11339628	+	Missense_Mutation	SNP	G	G	C			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr19:11339628G>C	ENST00000294618.7	-	23	2813	c.2802C>G	c.(2800-2802)ttC>ttG	p.F934L	DOCK6_ENST00000319867.7_Missense_Mutation_p.F273L	NM_020812.3	NP_065863.2	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	934					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(1)|endometrium(11)|large_intestine(8)|liver(2)|lung(9)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	39						TGAGCTGGAAGAAGAACCAGG	0.627																																					p.F934L		Atlas-SNP	.											.	DOCK6	104	.	0			c.C2802G						.						39.0	44.0	42.0					19																	11339628		2119	4237	6356	SO:0001583	missense	57572	exon23			CTGGAAGAAGAAC		CCDS45975.1	19p13.2	2011-08-04			ENSG00000130158	ENSG00000130158			19189	protein-coding gene	gene with protein product		614194				12432077	Standard	NM_020812		Approved	KIAA1395, ZIR1	uc002mqs.5	Q96HP0		ENST00000294618.7:c.2802C>G	chr19.hg19:g.11339628G>C	ENSP00000294618:p.Phe934Leu	93.0	0.0		57.0	44.0	NM_020812	A6H8X5|Q7Z7P4|Q9P2F2	Missense_Mutation	SNP	ENST00000294618.7	hg19	CCDS45975.1	.	.	.	.	.	.	.	.	.	.	G	12.78	2.041759	0.35989	.	.	ENSG00000130158	ENST00000294618;ENST00000319867	T;T	0.28666	1.6;1.6	4.4	2.24	0.28232	.	0.060416	0.64402	N	0.000002	T	0.34221	0.0890	L	0.43152	1.355	0.52099	D	0.99994	P;D	0.65815	0.538;0.995	B;P	0.60886	0.217;0.88	T	0.13415	-1.0510	10	0.30078	T	0.28	-22.689	3.6724	0.08279	0.2711:0.0:0.5517:0.1773	.	273;934	C9IZV6;Q96HP0	.;DOCK6_HUMAN	L	934;273	ENSP00000294618:F934L;ENSP00000321556:F273L	ENSP00000294618:F934L	F	-	3	2	DOCK6	11200628	1.000000	0.71417	1.000000	0.80357	0.845000	0.48019	4.387000	0.59626	0.402000	0.25451	-0.372000	0.07161	TTC	.	.		0.627	DOCK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453155.1	NM_020812	
MAST1	22983	hgsc.bcm.edu	37	19	12977547	12977547	+	Missense_Mutation	SNP	T	T	C			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr19:12977547T>C	ENST00000251472.4	+	18	2149	c.2110T>C	c.(2110-2112)Ttc>Ctc	p.F704L		NM_014975.2	NP_055790.1			microtubule associated serine/threonine kinase 1											NS(1)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(20)|ovary(5)|prostate(5)|skin(3)	56						AATCCGCCAGTTCTCTTCCTG	0.617																																					p.F704L		Atlas-SNP	.											.	MAST1	214	.	0			c.T2110C						.						84.0	55.0	65.0					19																	12977547		2203	4300	6503	SO:0001583	missense	22983	exon18			CGCCAGTTCTCTT	AB023190	CCDS32921.1	19p13.2	2008-02-05				ENSG00000105613			19034	protein-coding gene	gene with protein product		612256					Standard	NM_014975		Approved	SAST, KIAA0973	uc002mvm.3	Q9Y2H9		ENST00000251472.4:c.2110T>C	chr19.hg19:g.12977547T>C	ENSP00000251472:p.Phe704Leu	54.0	0.0		63.0	48.0	NM_014975		Missense_Mutation	SNP	ENST00000251472.4	hg19	CCDS32921.1	.	.	.	.	.	.	.	.	.	.	T	35	5.526622	0.96431	.	.	ENSG00000105613	ENST00000251472;ENST00000542153	T	0.22945	1.93	4.84	4.84	0.62591	AGC-kinase, C-terminal (2);Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.53433	0.1796	M	0.89287	3.02	0.58432	D	0.999999	D	0.61697	0.99	D	0.63283	0.913	T	0.63229	-0.6684	10	0.87932	D	0	-29.8221	12.6644	0.56833	0.0:0.0:0.0:1.0	.	704	Q9Y2H9	MAST1_HUMAN	L	704	ENSP00000251472:F704L	ENSP00000251472:F704L	F	+	1	0	MAST1	12838547	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.967000	0.87967	1.947000	0.56498	0.455000	0.32223	TTC	.	.		0.617	MAST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451733.2	NM_014975	
CYP2A6	1548	hgsc.bcm.edu	37	19	41352896	41352896	+	Missense_Mutation	SNP	G	G	C	rs138978736	byFrequency	TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr19:41352896G>C	ENST00000301141.5	-	5	735	c.715C>G	c.(715-717)Cag>Gag	p.Q239E	CTC-490E21.12_ENST00000601627.1_Intron	NM_000762.5	NP_000753	P11509	CP2A6_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 6	239					coumarin catabolic process (GO:0046226)|coumarin metabolic process (GO:0009804)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum membrane (GO:0005789)	coumarin 7-hydroxylase activity (GO:0008389)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)	p.Q239K(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(2)	37			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Acetaminophen(DB00316)|Amiodarone(DB01118)|Amlodipine(DB00381)|Amobarbital(DB01351)|Amphetamine(DB00182)|Antipyrine(DB01435)|Arformoterol(DB01274)|Azelastine(DB00972)|Azithromycin(DB00207)|Buprenorphine(DB00921)|Bupropion(DB01156)|Chlorzoxazone(DB00356)|Cinnarizine(DB00568)|Cisapride(DB00604)|Clofibrate(DB00636)|Clomifene(DB00882)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cyclophosphamide(DB00531)|Dapagliflozin(DB06292)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Diethylstilbestrol(DB00255)|Dronabinol(DB00470)|Eletriptan(DB00216)|Ezogabine(DB04953)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Flurazepam(DB00690)|Fomepizole(DB01213)|Formoterol(DB00983)|Halothane(DB01159)|Ifosfamide(DB01181)|Isoniazid(DB00951)|Ketoconazole(DB01026)|Letrozole(DB01006)|Lidocaine(DB00281)|Lorcaserin(DB04871)|Memantine(DB01043)|Menadione(DB00170)|Methimazole(DB00763)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Metyrapone(DB01011)|Miconazole(DB01110)|Montelukast(DB00471)|Nevirapine(DB00238)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Norfloxacin(DB01059)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Pilocarpine(DB01085)|Prednisolone(DB00860)|Progesterone(DB00396)|Propofol(DB00818)|Rifampicin(DB01045)|Rosiglitazone(DB00412)|Selegiline(DB01037)|Sevoflurane(DB01236)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tranylcypromine(DB00752)|Tretinoin(DB00755)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Zidovudine(DB00495)	TGCAGCAACTGAAAGGCCTGT	0.547																																					p.Q239E		Atlas-SNP	.											CYP2A6,NS,carcinoma,0,1	CYP2A6	69	.	1	Substitution - Missense(1)	prostate(1)	c.C715G						.						131.0	100.0	110.0					19																	41352896		2203	4300	6503	SO:0001583	missense	1548	exon5			GCAACTGAAAGGC	AF182275	CCDS12568.1	19q13.2	2013-11-11	2003-01-14		ENSG00000255974	ENSG00000255974		"""Cytochrome P450s"""	2610	protein-coding gene	gene with protein product		122720	"""cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 6"""	CYP2A3		7668294, 2748347	Standard	NM_000762		Approved	CPA6, CYP2A	uc002opl.4	P11509	OTTHUMG00000182713	ENST00000301141.5:c.715C>G	chr19.hg19:g.41352896G>C	ENSP00000301141:p.Gln239Glu	116.0	0.0		130.0	49.0	NM_000762	A7YAE5|B2R7F6|P00190|P10890|Q16803|Q4VAT9|Q4VAU0|Q4VAU1|Q9H1Z7|Q9UCU0|Q9UK48	Missense_Mutation	SNP	ENST00000301141.5	hg19	CCDS12568.1	.	.	.	.	.	.	.	.	.	.	-	7.281	0.609113	0.14066	.	.	ENSG00000255974	ENST00000301141	T	0.67345	-0.26	2.37	2.37	0.29283	.	0.270324	0.36066	N	0.002815	T	0.43366	0.1244	N	0.10809	0.05	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.32693	-0.9897	10	0.52906	T	0.07	.	7.7566	0.28927	0.0:0.0:0.4111:0.5889	.	239;239	Q13120;P11509	.;CP2A6_HUMAN	E	239	ENSP00000301141:Q239E	ENSP00000301141:Q239E	Q	-	1	0	CYP2A6	46044736	0.000000	0.05858	0.022000	0.16811	0.818000	0.46254	0.131000	0.15870	0.174000	0.19809	-0.874000	0.02982	CAG	.	.		0.547	CYP2A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463259.1	NM_000762	
ZNF816	125893	hgsc.bcm.edu	37	19	53454513	53454513	+	Missense_Mutation	SNP	G	G	T			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr19:53454513G>T	ENST00000357666.4	-	5	815	c.515C>A	c.(514-516)aCt>aAt	p.T172N	ZNF816_ENST00000434371.2_Intron|ZNF816_ENST00000444460.2_Missense_Mutation_p.T172N|ZNF321P_ENST00000391777.3_Intron	NM_001031665.2	NP_001026835.1	Q0VGE8	ZN816_HUMAN	zinc finger protein 816	172					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(10)|lung(9)|stomach(1)|urinary_tract(2)	27						TTTCCCTTTAGTCTGAAACAT	0.403																																					p.T172N		Atlas-SNP	.											.	ZNF816	73	.	0			c.C515A						.						133.0	146.0	142.0					19																	53454513		2203	4300	6503	SO:0001583	missense	125893	exon4			CCTTTAGTCTGAA	BC063805	CCDS33096.1	19q13.41	2013-01-08	2010-07-23	2010-07-23		ENSG00000180257		"""Zinc fingers, C2H2-type"", ""-"""	26995	protein-coding gene	gene with protein product			"""zinc finger protein 816A"""	ZNF816A			Standard	NM_001031665		Approved		uc002qam.2	Q0VGE8		ENST00000357666.4:c.515C>A	chr19.hg19:g.53454513G>T	ENSP00000350295:p.Thr172Asn	110.0	0.0		107.0	47.0	NM_001202457	A8K7H5|Q3KR39|Q659B3	Missense_Mutation	SNP	ENST00000357666.4	hg19	CCDS33096.1	.	.	.	.	.	.	.	.	.	.	N	8.663	0.901000	0.17760	.	.	ENSG00000180257	ENST00000357666;ENST00000444460	T;T	0.05717	3.4;3.4	1.77	1.77	0.24775	.	.	.	.	.	T	0.08935	0.0221	M	0.80028	2.48	0.80722	D	1	B	0.29432	0.244	B	0.21917	0.037	T	0.05801	-1.0863	9	0.52906	T	0.07	.	6.8841	0.24189	0.0:0.0:1.0:0.0	.	172	Q0VGE8	ZN816_HUMAN	N	172	ENSP00000350295:T172N;ENSP00000403266:T172N	ENSP00000350295:T172N	T	-	2	0	ZNF816	58146325	.	.	0.006000	0.13384	0.014000	0.08584	.	.	0.955000	0.37878	0.185000	0.17295	ACT	.	.		0.403	ZNF816-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396132.1	NM_001031665	
LILRA3	11026	hgsc.bcm.edu	37	19	54802753	54802753	+	Missense_Mutation	SNP	C	C	A			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr19:54802753C>A	ENST00000251390.3	-	5	779	c.688G>T	c.(688-690)Gtg>Ttg	p.V230L	LILRA3_ENST00000391745.1_Missense_Mutation_p.V247L|LILRA3_ENST00000391744.3_Missense_Mutation_p.V166L	NM_006865.3	NP_006856.3	Q8N6C8	LIRA3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (without TM domain), member 3	230	Ig-like C2-type 3.				defense response (GO:0006952)|immune system process (GO:0002376)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			NS(3)|breast(1)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		CCCGGCTGCACTGAGAGTGAT	0.592																																					p.V230L		Atlas-SNP	.											.	LILRA3	65	.	0			c.G688T						.						57.0	54.0	55.0					19																	54802753		2193	4168	6361	SO:0001583	missense	11026	exon5			GCTGCACTGAGAG	U91926		19q13.4	2013-01-11						"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6604	protein-coding gene	gene with protein product		604818				9278324, 9548455	Standard	XM_006710242		Approved	LIR-4, HM43, ILT6, HM31, LIR4, CD85e		Q8N6C8		ENST00000251390.3:c.688G>T	chr19.hg19:g.54802753C>A	ENSP00000251390:p.Val230Leu	88.0	0.0		102.0	86.0	NM_006865	J3KPM2|O15469|O15470|O75016|Q8N151|Q8N154|Q8NHJ1|Q8NHJ2|Q8NHJ3|Q8NHJ4	Missense_Mutation	SNP	ENST00000251390.3	hg19	CCDS12887.1	.	.	.	.	.	.	.	.	.	.	C	9.074	0.997727	0.19043	.	.	ENSG00000170866	ENST00000251390;ENST00000391744;ENST00000391745	T;T;T	0.00724	5.78;5.78;5.78	2.11	-0.771	0.11002	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.991840	0.02621	N	0.103220	T	0.03053	0.0090	M	0.86740	2.835	0.09310	N	1	P;B	0.40834	0.73;0.221	P;B	0.49226	0.603;0.285	T	0.35525	-0.9785	10	0.87932	D	0	.	4.9791	0.14155	0.0:0.4595:0.0:0.5405	.	230;230	E7EU74;Q8N6C8	.;LIRA3_HUMAN	L	230;166;247	ENSP00000251390:V230L;ENSP00000375624:V166L;ENSP00000375625:V247L	ENSP00000251390:V230L	V	-	1	0	LILRA3	59494565	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.760000	0.00786	-0.204000	0.10235	-0.232000	0.12228	GTG	.	.		0.592	LILRA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140236.1		
LILRA5	353514	hgsc.bcm.edu	37	19	54822850	54822850	+	Silent	SNP	G	G	A			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr19:54822850G>A	ENST00000301219.3	-	5	665	c.546C>T	c.(544-546)tcC>tcT	p.S182S	LILRA5_ENST00000446712.3_Silent_p.S170S|LILRA5_ENST00000432233.3_Silent_p.S182S|AC008984.2_ENST00000507363.1_RNA|LILRA5_ENST00000346508.3_Silent_p.S170S	NM_021250.2	NP_067073.1	A6NI73	LIRA5_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 5	182	Ig-like C2-type 2.				innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	20	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		CCAAGGTCCAGGAGAGCTTGT	0.597																																					p.S182S		Atlas-SNP	.											.	LILRA5	49	.	0			c.C546T						.						58.0	58.0	58.0					19																	54822850		2203	4300	6503	SO:0001819	synonymous_variant	353514	exon5			GGTCCAGGAGAGC	AF212842	CCDS12888.1, CCDS12889.1	19q13.4	2013-01-11	2005-05-13	2005-05-13	ENSG00000187116	ENSG00000187116		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	16309	protein-coding gene	gene with protein product		606047		LILRB7		10941842	Standard	NM_181986		Approved	ILT11, LIR9, CD85, CD85f	uc002qfe.3	A6NI73	OTTHUMG00000065357	ENST00000301219.3:c.546C>T	chr19.hg19:g.54822850G>A		98.0	0.0		157.0	82.0	NM_181879	A6NHI3	Silent	SNP	ENST00000301219.3	hg19	CCDS12888.1																																																																																			.	.		0.597	LILRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140231.1	NM_181985	
EPN1	29924	hgsc.bcm.edu	37	19	56196948	56196948	+	Missense_Mutation	SNP	C	C	T	rs369409343		TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr19:56196948C>T	ENST00000270460.6	+	3	726	c.415C>T	c.(415-417)Cgg>Tgg	p.R139W	AC010525.2_ENST00000390145.1_RNA|EPN1_ENST00000411543.2_Missense_Mutation_p.R250W|EPN1_ENST00000591743.1_3'UTR|EPN1_ENST00000085079.7_Missense_Mutation_p.R139W	NM_001130072.1	NP_001123544.1	Q9Y6I3	EPN1_HUMAN	epsin 1	139	ENTH. {ECO:0000255|PROSITE- ProRule:PRU00243}.				embryonic organ development (GO:0048568)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|female pregnancy (GO:0007565)|in utero embryonic development (GO:0001701)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|Notch signaling pathway (GO:0007219)	coated pit (GO:0005905)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			endometrium(5)|kidney(1)|large_intestine(2)|lung(8)|skin(1)	17		Colorectal(82;0.00244)|Ovarian(87;0.133)		GBM - Glioblastoma multiforme(193;0.112)		CGACGAGGACCGGCTGCGGGA	0.667																																					p.R250W		Atlas-SNP	.											.	EPN1	98	.	0			c.C748T						.	C	TRP/ARG,TRP/ARG,TRP/ARG	0,4390		0,0,2195	34.0	38.0	37.0		748,415,415	2.6	1.0	19		37	1,8597		0,1,4298	no	missense,missense,missense	EPN1	NM_001130071.1,NM_001130072.1,NM_013333.3	101,101,101	0,1,6493	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging	250/663,139/577,139/551	56196948	1,12987	2195	4299	6494	SO:0001583	missense	29924	exon4			GAGGACCGGCTGC	AF073727	CCDS46198.1, CCDS46199.1, CCDS46200.1	19q13.42	2014-08-12			ENSG00000063245	ENSG00000063245			21604	protein-coding gene	gene with protein product		607262				9723620, 10557078	Standard	NM_001130072		Approved		uc002qlx.3	Q9Y6I3	OTTHUMG00000180911	ENST00000270460.6:c.415C>T	chr19.hg19:g.56196948C>T	ENSP00000270460:p.Arg139Trp	66.0	0.0		118.0	47.0	NM_001130071	Q86ST3|Q9HA18	Missense_Mutation	SNP	ENST00000270460.6	hg19	CCDS46199.1	.	.	.	.	.	.	.	.	.	.	C	16.59	3.165868	0.57476	0.0	1.16E-4	ENSG00000063245	ENST00000270460;ENST00000085079;ENST00000544375;ENST00000411543	T;T;T	0.48836	0.8;0.8;0.8	4.74	2.63	0.31362	Epsin domain, N-terminal (1);ENTH/VHS (2);Epsin-like, N-terminal (2);	0.054891	0.64402	D	0.000002	T	0.73032	0.3535	H	0.96430	3.82	0.80722	D	1	D;P;D;B	0.89917	1.0;0.709;1.0;0.249	D;B;D;B	0.87578	0.998;0.055;0.998;0.022	T	0.75147	-0.3420	10	0.87932	D	0	-26.7111	5.7931	0.18371	0.1592:0.6664:0.0:0.1744	.	100;250;139;139	B4DU91;Q9Y6I3-1;Q9Y6I3;Q9Y6I3-3	.;.;EPN1_HUMAN;.	W	139;139;100;250	ENSP00000270460:R139W;ENSP00000085079:R139W;ENSP00000406209:R250W	ENSP00000085079:R139W	R	+	1	2	EPN1	60888760	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.744000	0.38268	1.377000	0.46286	0.555000	0.69702	CGG	.	.		0.667	EPN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453610.1	NM_013333	
MCM5	4174	hgsc.bcm.edu	37	22	35802596	35802596	+	Silent	SNP	C	C	T			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr22:35802596C>T	ENST00000216122.4	+	5	628	c.474C>T	c.(472-474)gcC>gcT	p.A158A	MCM5_ENST00000382011.5_Silent_p.A115A	NM_006739.3	NP_006730.2	P33992	MCM5_HUMAN	minichromosome maintenance complex component 5	158					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	29						TCATCGCGGCCTCTGCGGTCC	0.602																																					p.A158A		Atlas-SNP	.											.	MCM5	54	.	0			c.C474T						.						86.0	65.0	72.0					22																	35802596		2203	4300	6503	SO:0001819	synonymous_variant	4174	exon5			CGCGGCCTCTGCG		CCDS13915.1	22q13.1-q13.2	2007-04-04	2007-04-04		ENSG00000100297	ENSG00000100297			6948	protein-coding gene	gene with protein product		602696	"""minichromosome maintenance deficient (S. cerevisiae) 5 (cell division cycle 46)"", ""MCM5 minichromosome maintenance deficient 5, cell division cycle 46 (S. cerevisiae)"""	CDC46		8751386, 10591208	Standard	NM_006739		Approved		uc003anu.4	P33992	OTTHUMG00000150961	ENST00000216122.4:c.474C>T	chr22.hg19:g.35802596C>T		33.0	0.0		55.0	25.0	NM_006739	O60785|Q14578|Q9BTJ4|Q9BWL8	Silent	SNP	ENST00000216122.4	hg19	CCDS13915.1																																																																																			.	.		0.602	MCM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320661.3		
MAOB	4129	hgsc.bcm.edu	37	X	43698229	43698229	+	Missense_Mutation	SNP	T	T	A			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chrX:43698229T>A	ENST00000378069.4	-	3	311	c.164A>T	c.(163-165)gAc>gTc	p.D55V	MAOB_ENST00000487544.1_5'UTR|MAOB_ENST00000538942.1_Missense_Mutation_p.D39V|MAOB_ENST00000536181.1_Missense_Mutation_p.D39V	NM_000898.4	NP_000889.3	P27338	AOFB_HUMAN	monoamine oxidase B	55					negative regulation of serotonin secretion (GO:0014063)|positive regulation of dopamine metabolic process (GO:0045964)|response to aluminum ion (GO:0010044)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial envelope (GO:0005740)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|primary amine oxidase activity (GO:0008131)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(2)|skin(5)	21					Amantadine(DB00915)|Amphetamine(DB00182)|Dopamine(DB00988)|Ephedra(DB01363)|Flavin adenine dinucleotide(DB03147)|Furazolidone(DB00614)|Isocarboxazid(DB01247)|Linezolid(DB00601)|Methamphetamine(DB01577)|Moclobemide(DB01171)|Nandrolone decanoate(DB08804)|Nicotine(DB00184)|Pargyline(DB01626)|Phenelzine(DB00780)|Phentermine(DB00191)|Procaine(DB00721)|Rasagiline(DB01367)|Selegiline(DB01037)|Sertraline(DB01104)|Tranylcypromine(DB00752)|Zonisamide(DB00909)	TCCTCCAAGGTCCACATATTT	0.363																																					p.D55V		Atlas-SNP	.											.	MAOB	52	.	0			c.A164T						.						113.0	97.0	103.0					X																	43698229		2203	4300	6503	SO:0001583	missense	4129	exon3			CCAAGGTCCACAT		CCDS14261.1	Xp11.4-p11.3	2008-02-05			ENSG00000069535	ENSG00000069535	1.4.3.4		6834	protein-coding gene	gene with protein product		309860					Standard	NM_000898		Approved		uc004dfz.4	P27338	OTTHUMG00000021388	ENST00000378069.4:c.164A>T	chrX.hg19:g.43698229T>A	ENSP00000367309:p.Asp55Val	102.0	0.0		70.0	51.0	NM_000898	B2R6R3|B7Z5H3|D3DWC3|Q7Z6S2	Missense_Mutation	SNP	ENST00000378069.4	hg19	CCDS14261.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.027345	0.75390	.	.	ENSG00000069535	ENST00000378069;ENST00000536181;ENST00000538942	T;T;T	0.20881	2.04;2.04;2.04	5.3	5.3	0.74995	Amine oxidase (1);	0.000000	0.85682	D	0.000000	T	0.59197	0.2176	H	0.95539	3.685	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.72956	-0.4134	10	0.87932	D	0	-26.0184	14.4948	0.67680	0.0:0.0:0.0:1.0	.	39;55;55	B7Z5H3;Q8TBI1;P27338	.;.;AOFB_HUMAN	V	55;39;39	ENSP00000367309:D55V;ENSP00000441613:D39V;ENSP00000442240:D39V	ENSP00000367309:D55V	D	-	2	0	MAOB	43583173	1.000000	0.71417	1.000000	0.80357	0.832000	0.47134	5.767000	0.68850	1.871000	0.54225	0.417000	0.27973	GAC	.	.		0.363	MAOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056303.1	NM_000898	
MT-ND5	4540	hgsc.bcm.edu	37	M	13608	13608	+	Silent	SNP	T	T	C			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chrM:13608T>C	ENST00000361567.2	+	1	1272	c.1272T>C	c.(1270-1272)acT>acC	p.T424T	MT-TE_ENST00000387459.1_RNA|MT-TT_ENST00000387460.2_RNA|MT-TP_ENST00000387461.2_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TH_ENST00000387441.1_RNA|MT-CYB_ENST00000361789.2_5'Flank			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	424					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						GCCTATAGCACTCGAATAATT	0.463																																					p.T424T		Atlas-SNP	.											.	.	.	.	0			c.T1272C						.																																			SO:0001819	synonymous_variant	0	exon1			TAGCACTCGAATA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.1272T>C	chrM.hg19:g.13608T>C		25.0	0.0		31.0	6.0	ENST00000361567	Q34773|Q8WCY3	Silent	SNP	ENST00000361567.2	hg19																																																																																				.	.		0.463	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
RYR3	6263	hgsc.bcm.edu	37	15	33990117	33990117	+	Frame_Shift_Del	DEL	C	C	-			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr15:33990117delC	ENST00000389232.4	+	40	6239	c.6169delC	c.(6169-6171)cccfs	p.P2057fs	RYR3_ENST00000415757.3_Frame_Shift_Del_p.P2057fs	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	2057	4 X approximate repeats.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		TTACCAGCATCCCAACCTCAT	0.448																																					p.H2056fs		Atlas-Indel,Pindel	.											.	RYR3	760	.	0			c.6168delT						.						172.0	164.0	167.0					15																	33990117		2040	4221	6261	SO:0001589	frameshift_variant	6263	exon40			.		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.6169delC	chr15.hg19:g.33990117delC	ENSP00000373884:p.Pro2057fs	147.0	0.0		221.0	90.0	NM_001243996	O15175|Q15412	Frame_Shift_Del	DEL	ENST00000389232.4	hg19	CCDS45210.1																																																																																			.	.		0.448	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
SYNPO2	171024	hgsc.bcm.edu	37	4	119951193	119951193	+	Frame_Shift_Del	DEL	G	G	-			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr4:119951193delG	ENST00000429713.2	+	4	1445	c.1263delG	c.(1261-1263)gcgfs	p.A421fs	SYNPO2_ENST00000434046.2_Frame_Shift_Del_p.A421fs|SYNPO2_ENST00000448416.2_Intron|SYNPO2_ENST00000307142.4_Frame_Shift_Del_p.A421fs	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	421						actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|Z disc (GO:0030018)	14-3-3 protein binding (GO:0071889)|muscle alpha-actinin binding (GO:0051371)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(18)|ovary(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						AGCGAGAGGCGGACGAGGAGG	0.517																																					p.A421fs		Atlas-Indel,Pindel	.											SYNPO2_ENST00000434046,NS,carcinoma,0,3	SYNPO2	353	.	0			c.1262delC						.						162.0	155.0	158.0					4																	119951193		2203	4300	6503	SO:0001589	frameshift_variant	171024	exon4			.	AJ010482	CCDS34054.1, CCDS47128.1, CCDS47129.1, CCDS75185.1, CCDS75186.1	4q26	2008-08-29			ENSG00000172403	ENSG00000172403			17732	protein-coding gene	gene with protein product						11673475, 17828378	Standard	NM_133477		Approved	MYOPODIN	uc010inb.3	Q9UMS6	OTTHUMG00000161165	ENST00000429713.2:c.1263delG	chr4.hg19:g.119951193delG	ENSP00000395143:p.Ala421fs	194.0	0.0		246.0	123.0	NM_001128934	B2RWP6|B2Y8J9|Q9UK89|S5XAM4	Frame_Shift_Del	DEL	ENST00000429713.2	hg19	CCDS47129.1																																																																																			.	.		0.517	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1		
WDR36	134430	hgsc.bcm.edu	37	5	110445911	110445911	+	Frame_Shift_Del	DEL	A	A	-			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr5:110445911delA	ENST00000513710.2	+	13	1522	c.1518delA	c.(1516-1518)ggafs	p.G506fs	WDR36_ENST00000506538.2_Frame_Shift_Del_p.G506fs|WDR36_ENST00000505303.1_Frame_Shift_Del_p.G450fs			Q8NI36	WDR36_HUMAN	WD repeat domain 36	506					regulation of axon extension (GO:0030516)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|rRNA processing (GO:0006364)|visual perception (GO:0007601)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(9)|kidney(4)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_cancers(142;2.72e-05)|all_epithelial(76;4.4e-07)|Prostate(80;0.00955)|Lung NSC(167;0.0418)|Ovarian(225;0.0443)|Colorectal(57;0.0465)|all_lung(232;0.0508)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;1.39e-08)|Epithelial(69;1.82e-07)|all cancers(49;2.04e-05)|COAD - Colon adenocarcinoma(37;0.111)		CTTCTTGTGGAAACTTTGCTG	0.348																																					p.G506fs		Atlas-Indel,Pindel	.											.	WDR36	111	.	0			c.1517delG						.						160.0	160.0	160.0					5																	110445911		2202	4300	6502	SO:0001589	frameshift_variant	134430	exon13			.	AF385437	CCDS4102.1	5q22.2	2013-01-09			ENSG00000134987	ENSG00000134987		"""WD repeat domain containing"""	30696	protein-coding gene	gene with protein product		609669	"""glaucoma 1, open angle, G"""	GLC1G		15590835, 15677485	Standard	NM_139281		Approved	TA-WDRP, UTP21	uc003kpd.3	Q8NI36	OTTHUMG00000128790	ENST00000513710.2:c.1518delA	chr5.hg19:g.110445911delA	ENSP00000424628:p.Gly506fs	94.0	0.0		97.0	40.0	NM_139281	A2RUS4|Q68E02|Q8N1Q2	Frame_Shift_Del	DEL	ENST00000513710.2	hg19	CCDS4102.1																																																																																			.	.		0.348	WDR36-008	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000373504.3	NM_139281	
ALB	213	hgsc.bcm.edu	37	4	74284021	74284024	+	Frame_Shift_Del	DEL	AAAC	AAAC	-	rs142299078	byFrequency	TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	AAAC	AAAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr4:74284021_74284024delAAAC	ENST00000503124.1	+	10	1402_1405	c.1195_1198delAAAC	c.(1195-1200)aaacaafs	p.KQ399fs	ALB_ENST00000509063.1_Frame_Shift_Del_p.KQ549fs|ALB_ENST00000505649.1_3'UTR|ALB_ENST00000401494.3_Frame_Shift_Del_p.KQ434fs|ALB_ENST00000415165.2_Frame_Shift_Del_p.KQ357fs|ALB_ENST00000295897.4_Frame_Shift_Del_p.KQ549fs			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			ACAAATCAAGAAACAAACGTGAGG	0.368																																					p.548_549del		Atlas-Indel,Pindel	.											.	ALB	132	.	0			c.1644_1647del						.																																			SO:0001589	frameshift_variant	213	exon12			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.1195_1198delAAAC	chr4.hg19:g.74284025_74284028delAAAC	ENSP00000421027:p.Lys399fs	36.0	0.0		41.0	17.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Frame_Shift_Del	DEL	ENST00000503124.1	hg19																																																																																				.	.		0.368	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477	
KIAA1377	57562	hgsc.bcm.edu	37	11	101833550	101833550	+	Frame_Shift_Del	DEL	T	T	-			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr11:101833550delT	ENST00000263468.8	+	6	2054	c.1784delT	c.(1783-1785)atafs	p.I595fs	KIAA1377_ENST00000537689.1_Frame_Shift_Del_p.I396fs	NM_020802.2	NP_065853.2	Q9P2H0	K1377_HUMAN	KIAA1377	595										breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(18)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	53	all_epithelial(12;0.0104)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00931)		BRCA - Breast invasive adenocarcinoma(274;0.038)		GCATTAATTATAAATCAGAGC	0.289																																					p.I595X		Atlas-Indel,Pindel	.											.	KIAA1377	111	.	0			c.1783delA						.						33.0	39.0	37.0					11																	101833550		2195	4275	6470	SO:0001589	frameshift_variant	57562	exon6			.	AK095004	CCDS31658.1	11q22.2	2006-02-03			ENSG00000110318	ENSG00000110318			29264	protein-coding gene	gene with protein product		614634				10718198	Standard	XM_005271627		Approved		uc001pgm.3	Q9P2H0	OTTHUMG00000167319	ENST00000263468.8:c.1784delT	chr11.hg19:g.101833550delT	ENSP00000263468:p.Ile595fs	115.0	0.0		160.0	62.0	NM_020802	Q4G0U6	Frame_Shift_Del	DEL	ENST00000263468.8	hg19	CCDS31658.1																																																																																			.	.		0.289	KIAA1377-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394140.1	NM_020802	
HECTD3	79654	hgsc.bcm.edu	37	1	45474271	45474271	+	Frame_Shift_Del	DEL	C	C	-			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr1:45474271delC	ENST00000372172.4	-	8	1246	c.1175delG	c.(1174-1176)cgafs	p.R392fs	HECTD3_ENST00000372168.3_5'Flank	NM_024602.5	NP_078878.3	Q5T447	HECD3_HUMAN	HECT domain containing E3 ubiquitin protein ligase 3	392	DOC. {ECO:0000255|PROSITE- ProRule:PRU00614}.				proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|stomach(1)	28	Acute lymphoblastic leukemia(166;0.155)					GCGTGGATATCGCACCAGACT	0.562																																					p.R392fs		Atlas-Indel,Pindel	.											.	HECTD3	158	.	0			c.1176delA						.						179.0	174.0	175.0					1																	45474271		2069	4204	6273	SO:0001589	frameshift_variant	79654	exon8			.	BC019105	CCDS41318.1	1p34.1	2012-02-23	2012-02-23		ENSG00000126107	ENSG00000126107			26117	protein-coding gene	gene with protein product			"""HECT domain containing 3"""			12477932	Standard	NM_024602		Approved	FLJ21156	uc009vxk.3	Q5T447	OTTHUMG00000008587	ENST00000372172.4:c.1175delG	chr1.hg19:g.45474271delC	ENSP00000361245:p.Arg392fs	80.0	0.0		118.0	39.0	NM_024602	B3KPV7|B3KRH4|Q5T448|Q9H783	Frame_Shift_Del	DEL	ENST00000372172.4	hg19	CCDS41318.1																																																																																			.	.		0.562	HECTD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023734.1	NM_024602	
UBE2D3	7323	hgsc.bcm.edu	37	4	103730836	103730837	+	Frame_Shift_Ins	INS	-	-	T			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr4:103730836_103730837insT	ENST00000453744.2	-	4	625_626	c.112_113insA	c.(112-114)atgfs	p.M38fs	UBE2D3_ENST00000350435.7_Frame_Shift_Ins_p.M32fs|UBE2D3_ENST00000394801.4_Frame_Shift_Ins_p.M38fs|UBE2D3_ENST00000394804.2_Frame_Shift_Ins_p.M38fs|UBE2D3_ENST00000513098.1_5'UTR|UBE2D3_ENST00000507845.1_Frame_Shift_Ins_p.M9fs|UBE2D3_ENST00000394803.5_Frame_Shift_Ins_p.M38fs|UBE2D3_ENST00000502404.1_Frame_Shift_Ins_p.M9fs|UBE2D3_ENST00000343106.5_Frame_Shift_Ins_p.M38fs|UBE2D3_ENST00000338145.3_Frame_Shift_Ins_p.M38fs|UBE2D3_ENST00000321805.7_Frame_Shift_Ins_p.M38fs|UBE2D3_ENST00000504211.1_Frame_Shift_Ins_p.M9fs|UBE2D3_ENST00000357194.6_Frame_Shift_Ins_p.M40fs|UBE2D3_ENST00000349311.8_Frame_Shift_Ins_p.M38fs|UBE2D3_ENST00000505207.1_Frame_Shift_Ins_p.M9fs	NM_181891.1	NP_871620.1	P61077	UB2D3_HUMAN	ubiquitin-conjugating enzyme E2D 3	38					apoptotic process (GO:0006915)|BMP signaling pathway (GO:0030509)|cellular protein modification process (GO:0006464)|cellular response to hypoxia (GO:0071456)|DNA repair (GO:0006281)|gene expression (GO:0010467)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of type I interferon production (GO:0032480)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K11-linked ubiquitination (GO:0070979)|protein K48-linked ubiquitination (GO:0070936)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)			kidney(1)|lung(3)|skin(1)	5		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.13e-08)		TACAGGTCCCATAATTGTGGCT	0.277																																					p.M40fs		Pindel	.											.	UBE2D3	25	.	0			c.119_120insA						.																																			SO:0001589	frameshift_variant	7323	exon3			.	U39318	CCDS3659.1, CCDS3660.1, CCDS3661.1, CCDS75172.1	4q24	2011-05-19	2011-05-19		ENSG00000109332	ENSG00000109332		"""Ubiquitin-conjugating enzymes E2"""	12476	protein-coding gene	gene with protein product		602963	"""ubiquitin-conjugating enzyme E2D 3 (homologous to yeast UBC4/5)"", ""ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast)"""			8530467	Standard	NM_181886		Approved	UbcH5C	uc003hwl.3	P61077	OTTHUMG00000131119	ENST00000453744.2:c.113dupA	chr4.hg19:g.103730837_103730837dupT	ENSP00000396901:p.Met38fs	489.0	0.0		615.0	120.0	NM_181893	A6NJ93|A6NJB1|A6NM99|P47986|Q6IB88|Q6NXS4|Q8N924	Frame_Shift_Ins	INS	ENST00000453744.2	hg19	CCDS3660.1																																																																																			.	.		0.277	UBE2D3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253791.2	NM_181893	
ADCY5	111	hgsc.bcm.edu	37	3	123003495	123003495	+	Frame_Shift_Del	DEL	A	A	-			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr3:123003495delA	ENST00000462833.1	-	21	4958	c.3746delT	c.(3745-3747)atgfs	p.M1250fs	ADCY5_ENST00000491190.1_Frame_Shift_Del_p.M908fs|RP11-797D24.4_ENST00000608436.1_RNA|ADCY5_ENST00000309879.5_Frame_Shift_Del_p.M900fs	NM_183357.2	NP_899200.1	O95622	ADCY5_HUMAN	adenylate cyclase 5	1250					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenosine receptor signaling pathway (GO:0001973)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			breast(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(22)|ovary(5)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(114;0.0342)		GTAGGTCATCATCTCGCCTTT	0.607																																					p.M1249fs		Pindel	.											.	ADCY5	169	.	0			c.3747delG						.						184.0	163.0	170.0					3																	123003495		2203	4300	6503	SO:0001589	frameshift_variant	111	exon21			.	U65473	CCDS3022.1, CCDS56274.1	3q21.1	2013-02-04			ENSG00000173175	ENSG00000173175	4.6.1.1	"""Adenylate cyclases"""	236	protein-coding gene	gene with protein product		600293				10481931	Standard	NM_183357		Approved	AC5	uc003egh.2	O95622	OTTHUMG00000159517	ENST00000462833.1:c.3746delT	chr3.hg19:g.123003495delA	ENSP00000419361:p.Met1250fs	51.0	0.0		81.0	27.0	NM_183357	B7Z8A6|Q7RTV7|Q8NFM3	Frame_Shift_Del	DEL	ENST00000462833.1	hg19	CCDS3022.1																																																																																			.	.		0.607	ADCY5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355889.4	XM_171048	
TYRO3	7301	hgsc.bcm.edu	37	15	41865504	41865699	+	Splice_Site	DEL	GTACGAATTCTGGAGGACTCGAGGGTGGGAGACAGCAGCAGGTGCCAAGAGGAGCTAGCTGATGGTCGGCTCCTGCCTGGGACAGTATCTGCTATGCATGGGGGTAGCTTGGGAGCAAAGATGCAAAGATGTCCTGGCTCTTGTGGGCCTGTGAGCATGGCAGAAGGCTGACTCTCTCCCTCAATGCCCCTTGTAG	GTACGAATTCTGGAGGACTCGAGGGTGGGAGACAGCAGCAGGTGCCAAGAGGAGCTAGCTGATGGTCGGCTCCTGCCTGGGACAGTATCTGCTATGCATGGGGGTAGCTTGGGAGCAAAGATGCAAAGATGTCCTGGCTCTTGTGGGCCTGTGAGCATGGCAGAAGGCTGACTCTCTCCCTCAATGCCCCTTGTAG	-	rs77680822|rs62001448|rs370070955|rs367718441|rs370573528|rs529826589|rs140748026|rs150084536|rs377334532|rs142510731|rs202087157|rs116540200	byFrequency	TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	GTACGAATTCTGGAGGACTCGAGGGTGGGAGACAGCAGCAGGTGCCAAGAGGAGCTAGCTGATGGTCGGCTCCTGCCTGGGACAGTATCTGCTATGCATGGGGGTAGCTTGGGAGCAAAGATGCAAAGATGTCCTGGCTCTTGTGGGCCTGTGAGCATGGCAGAAGGCTGACTCTCTCCCTCAATGCCCCTTGTAG	GTACGAATTCTGGAGGACTCGAGGGTGGGAGACAGCAGCAGGTGCCAAGAGGAGCTAGCTGATGGTCGGCTCCTGCCTGGGACAGTATCTGCTATGCATGGGGGTAGCTTGGGAGCAAAGATGCAAAGATGTCCTGGCTCTTGTGGGCCTGTGAGCATGGCAGAAGGCTGACTCTCTCCCTCAATGCCCCTTGTAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr15:41865504_41865699delGTACGAATTCTGGAGGACTCGAGGGTGGGAGACAGCAGCAGGTGCCAAGAGGAGCTAGCTGATGGTCGGCTCCTGCCTGGGACAGTATCTGCTATGCATGGGGGTAGCTTGGGAGCAAAGATGCAAAGATGTCCTGGCTCTTGTGGGCCTGTGAGCATGGCAGAAGGCTGACTCTCTCCCTCAATGCCCCTTGTAG	ENST00000263798.3	+	17	2209_2369	c.1985_2145delGTACGAATTCTGGAGGACTCGAGGGTGGGAGACAGCAGCAGGTGCCAAGAGGAGCTAGCTGATGGTCGGCTCCTGCCTGGGACAGTATCTGCTATGCATGGGGGTAGCTTGGGAGCAAAGATGCAAAGATGTCCTGGCTCTTGTGGGCCTGTGAGCATGGCAGAAGGCTGACTCTCTCCCTCAATGCCCCTTGTAG	c.(1984-2145)agtacgaattctggaggactcgagggtgggagacagcagcaggtgccaagaggagctagctgatggtcggctcctgcctgggacagtatctgctatgcatgggggtagcttgggagcaaagatgcaaagatgtcctggctcttgtgggcctgtgagcatggc>a	p.STNSGGLEGGRQQQVPRGAS*WSAPAWDSICYAWG*LGSKDAKMSWLLWACEHG662fs	TYRO3_ENST00000559066.1_Splice_Site_p.STNSGGLEGGRQQQVPRGAS*WSAPAWDSICYAWG*LGSKDAKMSWLLWACEHG617fs	NM_006293.3	NP_006284.2	Q06418	TYRO3_HUMAN	TYRO3 protein tyrosine kinase	662	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic cell clearance (GO:0043277)|cell adhesion (GO:0007155)|forebrain cell migration (GO:0021885)|natural killer cell differentiation (GO:0001779)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of lymphocyte activation (GO:0051250)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|neuron cellular homeostasis (GO:0070050)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein autophosphorylation (GO:0046777)|protein kinase B signaling (GO:0043491)|secretion by cell (GO:0032940)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.?(2)|p.R670R(1)|p.L686L(1)|p.G675R(1)|p.R678R(1)|p.L694L(1)		central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(26)|ovary(3)|prostate(1)	43		all_cancers(109;7.33e-15)|all_epithelial(112;2.8e-12)|Lung NSC(122;3.48e-08)|all_lung(180;1.71e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.31e-18)|GBM - Glioblastoma multiforme(113;9.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.117)		TGCCCCTTGTAGGCTGGCAGAGGACATGACAGTGTGTGTGGCTGACTTCGGACTCTCCCGGAAGATCTACAGTGGGGACTACTATCGTCAAGGCTGTGCCTCCAAACTGCCTGTCAAGTGGCTGGCCCTGGAGAGCCTGGCCGACAACCTGTATACTGTGCAGAGTGACGTGGTGAGCAGGGTGGCCCGTGAAGCTTGGTGGGGACGAGTGTGAGA	0.581																																					p.662_662del		Pindel	.											.	TYRO3	169	.	7	Substitution - coding silent(4)|Unknown(2)|Substitution - Missense(1)	lung(6)|stomach(1)	c.1985_1985del						.																																			SO:0001630	splice_region_variant	7301	exon16			.	D50479	CCDS10080.1	15q15.1-q21.1	2013-02-11			ENSG00000092445	ENSG00000092445	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12446	protein-coding gene	gene with protein product		600341		RSE		7851890	Standard	NM_006293		Approved	Dtk, Brt, Tif, Sky	uc001zof.2	Q06418	OTTHUMG00000130341	ENST00000263798.3:c.2145+1GTACGAATTCTGGAGGACTCGAGGGTGGGAGACAGCAGCAGGTGCCAAGAGGAGCTAGCTGATGGTCGGCTCCTGCCTGGGACAGTATCTGCTATGCATGGGGGTAGCTTGGGAGCAAAGATGCAAAGATGTCCTGGCTCTTGTGGGCCTGTGAGCATGGCAGAAGGCTGACTCTCTCCCTCAATGCCCCTTGTAG>-	chr15.hg19:g.41865504_41865699delGTACGAATTCTGGAGGACTCGAGGGTGGGAGACAGCAGCAGGTGCCAAGAGGAGCTAGCTGATGGTCGGCTCCTGCCTGGGACAGTATCTGCTATGCATGGGGGTAGCTTGGGAGCAAAGATGCAAAGATGTCCTGGCTCTTGTGGGCCTGTGAGCATGGCAGAAGGCTGACTCTCTCCCTCAATGCCCCTTGTAG		78.0	0.0		86.0	12.0	NM_006293	O14953|Q86VR3	Frame_Shift_Del	DEL	ENST00000263798.3	hg19	CCDS10080.1																																																																																			.	.		0.581	TYRO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252693.2		Frame_Shift_Del
FMN2	56776	hgsc.bcm.edu	37	1	240371023	240371055	+	In_Frame_Del	DEL	CCCGGAGCAGGAATACCTCCTCCACCCCCTCTA	CCCGGAGCAGGAATACCTCCTCCACCCCCTCTA	-	rs150102515|rs138468405|rs369734693|rs376697094|rs201199944|rs140720010|rs150843940|rs200418654|rs150923193|rs149715160|rs199853440	byFrequency	TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	CCCGGAGCAGGAATACCTCCTCCACCCCCTCTA	CCCGGAGCAGGAATACCTCCTCCACCCCCTCTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr1:240371023_240371055delCCCGGAGCAGGAATACCTCCTCCACCCCCTCTA	ENST00000319653.9	+	5	3141_3173	c.2911_2943delCCCGGAGCAGGAATACCTCCTCCACCCCCTCTA	c.(2911-2943)cccggagcaggaatacctcctccaccccctctadel	p.PGAGIPPPPPL1092del		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1092	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)	p.P1121T(1)|p.P1119T(1)		NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			TCCCCCTCTTCCCGGAGCAGGAATACCTCCTCCACCCCCTCTACCCGGAGCGG	0.708																																					p.970_981del		Pindel	.											.	FMN2	451	.	2	Substitution - Missense(2)	lung(2)	c.2910_2942del						.			222,4036		2,218,1909						-7.6	0.0			22	197,8037		5,187,3925	no	coding	FMN2	NM_020066.4		7,405,5834	A1A1,A1R,RR		2.3925,5.2137,3.3541				419,12073				SO:0001651	inframe_deletion	56776	exon5			.	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.2911_2943delCCCGGAGCAGGAATACCTCCTCCACCCCCTCTA	chr1.hg19:g.240371023_240371055delCCCGGAGCAGGAATACCTCCTCCACCCCCTCTA	ENSP00000318884:p.Pro1092_Leu1102del	84.0	0.0		94.0	13.0	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	In_Frame_Del	DEL	ENST00000319653.9	hg19	CCDS31069.2																																																																																			.	.		0.708	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
TP53	7157	hgsc.bcm.edu	37	17	7577589	7577594	+	In_Frame_Del	DEL	GTGGTA	GTGGTA	-			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	GTGGTA	GTGGTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr17:7577589_7577594delGTGGTA	ENST00000269305.4	-	7	876_881	c.687_692delTACCAC	c.(685-693)tgtaccacc>tgc	p.TT230del	TP53_ENST00000413465.2_In_Frame_Del_p.TT230del|TP53_ENST00000574684.1_5'UTR|TP53_ENST00000455263.2_In_Frame_Del_p.TT230del|TP53_ENST00000445888.2_In_Frame_Del_p.TT230del|TP53_ENST00000359597.4_In_Frame_Del_p.TT230del|TP53_ENST00000420246.2_In_Frame_Del_p.TT230del	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	230	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		T -> A (in sporadic cancers; somatic mutation).|T -> I (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:9450901}.|T -> N (in sporadic cancers; somatic mutation).|T -> P (in sporadic cancers; somatic mutation).|T -> S (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.C229fs*10(9)|p.T230I(9)|p.0?(8)|p.?(5)|p.C229*(3)|p.T231S(3)|p.T231A(2)|p.T231I(2)|p.C229_H233delCTTIH(2)|p.T231fs*16(2)|p.T230fs*6(2)|p.T230N(2)|p.T230P(2)|p.T230S(2)|p.T230fs*17(2)|p.V225fs*23(1)|p.C136fs*10(1)|p.T231del(1)|p.T231N(1)|p.T230fs*9(1)|p.C229_T230insX(1)|p.D228fs*12(1)|p.C229_I232del(1)|p.S227_I232delSDCTTI(1)|p.T230_Y234delTTIHY(1)|p.C229fs*1(1)|p.T230A(1)|p.T230T(1)|p.C229C(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GTAGTGGATGGTGGTACAGTCAGAGC	0.534		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.230_231del	Pancreas(47;798 1329 9957 10801)	Pindel	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	TP53_ENST00000545858,colon,carcinoma,-1,16	TP53	33396	.	69	Substitution - Missense(24)|Deletion - Frameshift(19)|Whole gene deletion(8)|Deletion - In frame(6)|Unknown(5)|Substitution - Nonsense(3)|Substitution - coding silent(2)|Insertion - In frame(1)|Complex - frameshift(1)	breast(9)|biliary_tract(8)|ovary(7)|upper_aerodigestive_tract(6)|oesophagus(6)|central_nervous_system(5)|large_intestine(5)|bone(4)|haematopoietic_and_lymphoid_tissue(3)|skin(3)|lung(3)|stomach(2)|urinary_tract(2)|thyroid(1)|soft_tissue(1)|thymus(1)|pancreas(1)|prostate(1)|liver(1)	c.688_693del	GRCh37	CD076915	TP53	D		.																																			SO:0001651	inframe_deletion	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	.	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.687_692delTACCAC	chr17.hg19:g.7577589_7577594delGTGGTA	ENSP00000269305:p.Thr230_Thr231del	68.0	0.0		47.0	20.0	NM_001126112	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	In_Frame_Del	DEL	ENST00000269305.4	hg19	CCDS11118.1																																																																																			.	.		0.534	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
PDE5A	8654	hgsc.bcm.edu	37	4	120481478	120481478	+	Frame_Shift_Del	DEL	A	A	-			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr4:120481478delA	ENST00000354960.3	-	7	1491	c.1172delT	c.(1171-1173)ttafs	p.L391fs	PDE5A_ENST00000394439.1_Frame_Shift_Del_p.L339fs|PDE5A_ENST00000264805.5_Frame_Shift_Del_p.L349fs	NM_001083.3	NP_001074.2	O76074	PDE5A_HUMAN	phosphodiesterase 5A, cGMP-specific	391	GAF 2.				blood coagulation (GO:0007596)|cGMP catabolic process (GO:0046069)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of oocyte development (GO:0060282)|relaxation of cardiac muscle (GO:0055119)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			breast(4)|endometrium(2)|kidney(3)|large_intestine(8)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	27					Avanafil(DB06237)|Caffeine(DB00201)|Dipyridamole(DB00975)|Pentoxifylline(DB00806)|Sildenafil(DB00203)|Tadalafil(DB00820)|Theophylline(DB00277)|Udenafil(DB06267)|Vardenafil(DB00862)	TGATTTTTCTAATTCCTCACA	0.318																																					p.L391fs		Pindel	.											.	PDE5A	83	.	0			c.1173delA						.						94.0	88.0	90.0					4																	120481478		2203	4298	6501	SO:0001589	frameshift_variant	8654	exon7			.	D89094	CCDS3713.1, CCDS34055.1	4q27	2008-05-15			ENSG00000138735	ENSG00000138735	3.1.4.17	"""Phosphodiesterases"""	8784	protein-coding gene	gene with protein product		603310				9714779, 9642111	Standard	NM_033437		Approved		uc003idh.3	O76074	OTTHUMG00000132971	ENST00000354960.3:c.1172delT	chr4.hg19:g.120481478delA	ENSP00000347046:p.Leu391fs	150.0	0.0		214.0	62.0	NM_001083	A0AV69|A8K2C4|O75026|O75887|Q86UI0|Q86V66|Q9Y6Z6	Frame_Shift_Del	DEL	ENST00000354960.3	hg19	CCDS3713.1																																																																																			.	.		0.318	PDE5A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256529.1	NM_001083	
